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License Information
All resources and application files in ChemBioOffice, ChemOffice, BioOffice, ChemBioDraw,
ChemDraw, BioDraw, ChemBio3D, Chem3D, ChemFinder, BioViz, Inventory, E-Notebook, BioAs-
say, ChemINDEX, ChemFinder, and ChemInfo programs, all resources in the ChemOffice,
ChemDraw, Chem3D, ChemFinder, and ChemInfo application files, and this manual are Copyright
© 1986-2009 by CambridgeSoft Corporation (“CS”) with all rights reserved worldwide. MOPAC
2002 is Copyright © 1993-2006 by Fujitsu Limited with all rights reserved.
Information in this document is subject to change without notice and does not represent a commit-
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Use of these materials is licensed by CS under the terms of a software license agreement; they may
be used only as provided for in said agreement.
ChemBioOffice, ChemOffice BioOffice, ChemBioDraw, ChemDraw, BioDraw, ChemBio3D,
Chem3D, CS MOPAC, ChemFinder, BioViz, Inventory, E-Notebook, and BioAssay, and ChemInfo
are not supplied with copy protection. Do not duplicate any of the copyrighted materials except for
your personal backups without written permission from CS. To do so would be in violation of federal
and international law, and may result in criminal as well as civil penalties. You may use ChemBioOf-
fice, ChemOffice BioOffice, ChemBioDraw, ChemDraw, BioDraw, ChemBio3D, Chem3D, CS
MOPAC, ChemFinder, BioViz, Inventory, E-Notebook, and BioAssay ChemOffice, ChemDraw,
Chem3D, CS MOPAC, ChemFinder, Inventory, E-Notebook, BioAssay, and ChemInfo on any com-
puter owned by you; however, extra copies may not be made for that purpose. Consult the CS
License Agreement for Software and Database Products for further details.
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Chem3D, ChemINDEX, ChemFinder, ChemInfo and ChemACX are registered trademarks of
CambridgeSoft Corporation (Cambridge Scientific Computing, Inc.).
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InChI™ is a trademark of the International Union of Pure and Applied Chemistry.
Jaguar is a trademark of Schrödinger, LLC.
THE MERCK INDEX® is a trademark of Merck & Company Incorporated, Whitehouse Station,
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Oracle® is a registered trademark of Oracle Corporation and/or its affiliates. Other names may be
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All other trademarks are the property of their respective holders. Any use of the marks in connection
with the sale, offering for sale, distribution or advertising of any goods and services, including any
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strictly prohibited.
Copyright Notice
The materials contained in CambridgeSoft Database Products, including but not limited to, Che-
mACX, ChemIndex, and The Merck Index, are protected by copyright laws and international copy-
right treaties, as well as other intellectual property laws and treaties. Copyright in the materials
contained on the CD and internet subscription products, including, but not limited to, the textual
material, chemical structures representations, artwork, photographs, computer software, audio and
visual elements, is owned or controlled separately by CS.
CS is a distributor (and not a publisher) of information supplied by third parties. Accordingly, CS has
no editorial control over such information. Database Suppliers (“Supplier”) individually own all
right, title, and interest, including copyright, in their database—and retain all such rights in providing
information to Customers.
The materials contained in The Merck Index are protected by copyright laws and international copy-
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visual elements, is owned or controlled separately by Merck & Co., Inc., (“Merck”) and
CambridgeSoft Corporation (“CS”).
The ChemReact68, ChemSynth, ChemReact500, and ChemSelect Reaction Database is copyrighted
© by InfoChem GmbH 1997.
AspTear is copyrighted © by Softwing.
InChI™ is a trademark of the International Union of Pure and Applied Chemistry. InChI™ Material
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CambridgeSoft End-User License Agreement for Software Products
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1. Copyright Notice. The materials contained in CambridgeSoft Database Products, including but
not limited to, ChemACX, ChemIndex, and The Merck Index, are protected by copyright laws and
international copyright treaties, as well as other intellectual property laws and treaties. Copyright in
the materials contained on the CD and internet subscription products, including, but not limited to,
the textual material, chemical structures representations, artwork, photographs, computer software,
audio and visual elements, is owned or controlled separately by CambridgeSoft Corporation (“CS”).
CS is a distributor (and not a publisher) of information supplied by third parties. Accordingly, CS has
no editorial control over such information. Database Suppliers (“Supplier”) individually own all
right, title, and interest, including copyright, in their database—and retain all such rights in providing
information to Customers.
The materials contained in The Merck Index are protected by copyright laws and international copy-
right treaties, as well as other intellectual property laws and treaties. Copyright in the materials con-
tained on the CD and internet subscription products, including, but not limited to, the textual
visual elements, is owned or controlled separately by the Merck & Co., Inc., (“Merck”) and
CambridgeSoft Corporation (“CS”).
2. Limitations on Use. Except as expressly provided by copyright law, copying, redistribution, or
publication, whether for commercial or non-commercial purposes, must be with the express permis-
sion of CS and/or Merck. In any copying, redistribution, or publication of copyrighted material, any
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computer (other than a network server), you may also use the Software on a portable or home com-
puter, provided that you use the software on only one computer at a time. You may not (a) electroni-
cally transfer the Software from one computer to another, (b) distribute copies of the Software to
others, or (c) modify or translate the Software without the prior written consent of CambridgeSoft,
(d) place the software on a server so that it is accessible via a public network such as the Internet, (e)
sublicense, rent, lease or lend any portion of the Software or Documentation, or (f) modify or adapt
the Software or merge it into another program. The Software may be placed on a file or disk server
connected to a network, provided that a license has been purchased for every computer with access to
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as permitted by this agreement, or are for purposes of backup and archival records; all copies shall
bear CambridgeSoft’s copyright and proprietary notices. You may not make copies of any accompa-
nying written materials.
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Software or any part thereof. You may transfer on a permanent basis the rights granted under this
license provided you transfer this Agreement and all copies of the Software, including prior versions,
and all accompanying materials. The recipient must agree to the terms of this Agreement in full and
register this transfer in writing with CambridgeSoft.
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Services; and, the Subscriber and any third party, to any other applicable civil or criminal penalties
under copyright or other laws. In the case of an authorized site license, a Subscriber shall cause any
employee, agent or other third party which the Subscriber allows to use the Paid Subscription Service
materials to abide by all of the terms and conditions of this Agreement. In all other cases, only the
Subscriber is permitted to access the Paid Subscription Service materials. Should CambridgeSoft
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The Subscriber shall have 90 days from date of notice to correct such violation before any action will
be taken.
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advertising of any goods and services, including any other Web site, which is likely to cause confu-
sion, to cause mistake or to deceive, is strictly prohibited.
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modify, suspend or discontinue any or all parts of any Paid Subscription Services and databases at
any time.
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other Supplier harmless from any damages, expenses and costs (including reasonable attorneys’ fees)
arising out of any breach or alleged breach of these Terms and Conditions, representations and/or
warranties herein, by the User or any third party to whom User shares her/his password or otherwise
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brought against CambridgeSoft, Merck, and/or other Database Suppliers.
In no event shall CS, Merck, and/or other Supplier be liable for any indirect, special, or consequential
damages, such as, but not limited to, loss of anticipated profits or other economic loss in connection
with or arising out of the use of the software by you or the services provided for in this agreement,
even if CS, Merck, and/or other Supplier has been advised of the possibility of such damages. CS
and/or Merck’s entire liability and your exclusive remedy shall be, at CS’s discretion a return of any
pro-rata portion of the subscription fee.
The failure of either party to assert a right hereunder or to insist upon compliance with any term or
condition of this
Agreement shall not constitute a waiver of that right or excuse a similar subsequent failure to per-
form any such term or condition by the other party.
This Agreement shall be construed according to the laws of the Commonwealth of Massachusetts,
United States of America.
: IS IT OK TO COPY MY COLLEAGUE’S Q: So I'm never allowed to copy software for any other
Q SOFTWARE?
NO, it’s not okay to copy your colleague’s
software. Software is protected by federal copyright law,
reason?
A: That’s correct. Other than copying the software you

which says that you can't make such additional copies purchase onto a single computer and making another
without the permission of the copyright holder. By copy “for archival purposes only” or “purposes only of
maintenance or repair,” the copyright law prohibits
protecting the investment of computer software
you from making additional copies of the software for
companies in software development, the copyright law any other reason unless you obtain the permission of
serves the cause of promoting broad public availability of the software company.
new, creative, and innovative products. These companies
devote large portions of their earnings to the creation of Q: At my company, we pass disks around all the time.
new software products and they deserve a fair return on We all assume that this must be okay since it was
their investment. The creative teams who develop the the company that purchased the software in the
software–programmers, writers, graphic artists and first place.
others–also deserve fair compensation for their efforts.
Without the protection given by our copyright laws, they A: Many employees don’t realize that corporations are
would be unable to produce the valuable programs that bound by the copyright laws, just like everyone else.
have become so important to our daily lives: educational Such conduct exposes the company (and possibly the
persons involved) to liability for copyright
software that teaches us much needed skills; business
infringement. Consequently, more and more
software that allows us to save time, effort and money; corporations concerned about their liability have
and entertainment and personal productivity software written policies against such “softlifting”. Employees
that enhances leisure time. may face disciplinary action if they make extra copies
of the company’s software for use at home or on
Q: That makes sense, but what do I get out of additional computers within the office. A good rule to
purchasing my own software? remember is that there must be one authorized copy
of a software product for every computer upon which
A: When you purchase authorized copies of software it is run
programs, you receive user guides and tutorials, quick
reference cards, the opportunity to purchase Q: Can I take a piece of software owned by my
upgrades, and technical support from the software company and install it on my personal computer at
home if instructed by my supervisor?
publishers. For most software programs, you can read
about user benefits in the registration brochure or A: A good rule of thumb to follow is one software
upgrade flyer in the product box. package per computer, unless the terms of the license
agreement allow for multiple use of the program. But
Q: What exactly does the law say about copying some software publishers’ licenses allow for “remote”
software? or “home” use of their software. If you travel or
telecommute, you may be permitted to copy your
A: The law says that anyone who purchases a copy of software onto a second machine for use when you are
software has the right to load that copy onto a single not at your office computer. Check the license care-
computer and to make another copy “for archival fully to see if you are allowed to do this.
purposes only” or, in limited circumstances, for
“purposes only of maintenance or repair.” It is illegal Q: What should I do if become aware of a company
that is not compliant with the copyright law or its
to use that software on more than one computer or to
software licenses?
make or distribute copies of that software for any
other purpose unless specific permission has been A: Cases of retail, corporate and Internet piracy or non-
obtained from the copyright owner. If you pirate compliance with software licenses can be reported on
software, you may face not only a civil suit for the Internet at http://www.siia.net/piracy/report.asp
damages and other relief, but criminal liability as well, or by calling the Anti-Piracy Hotline:
including fines and jail terms of up to one year (800) 388-7478.
Q: Do the same rules apply to bulletin boards and user SIIA also offers a number of other materials designed to
groups? I always thought that the reason they got help you comply with the Federal Copyright Law. These
together was to share software. materials include:
A: Yes. Bulletin boards and user groups are bound by the

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copyright law just as individuals and corporations.
This 12–minute video, available $10, has helped over
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A Guide to CambridgeSoft Manuals
Manuals: Chem & Bio Draw Chem & Bio Office Chem & Bio Office
Chem & Bio Desktop Software Workgroup Solutions
Drawing Standard ChemBio 3D and Databases
Includes: Finder & BioViz Including E-Notebook
Chem & Bio Draw ■
Chem & Bio 3D ■

Software
Chem & Bio Finder ■
BioAssay Desktop ■
BioViz Desktop ■
Inventory Desktop ■
E-Notebook Desktop ■
ChemDraw/Excel ■
Desktop Applications
Struct = Name ■
ChemNMR ■
CombiChem/Excel ■
ChemFinder/Office ■
MOPAC, GAMESS, MM2 ■
CS Gaussian, Jaguar Interface ■

Workgroup Solutions
CombiChem/E-Notebook ■
BioAssay Workgroup ■
BioSAR Enterprise ■
Inventory Workgroup ■
Formulations & Mixtures ■
Compliant SDMS ■
The Merck Index ■
R&D Insight/Chemists ■
ChemINDEX Database, NCI, AIDS & Cancer ■

Databases
Traditional Chinese Medicines ■
Drugs: Synonyms & Properties ■
Nanogens Index; Medicinal Chemistry ■
ChemACX, ChemMSDS Database ■
Sigma-Aldrich MSDS ■
ChemReact500, ChemReact68 & ChemSynth ■

Contents
What’s New ..............................................1 The Info Window ......................................10
Periodic Table..........................................10
Character Map.........................................11
Chapter 1
Introduction..............................................3
Chapter 3
The ChemDraw Series............................... 3
The BioDraw Series .................................. 3 Basic Drawings....................................... 13
About This Manual .................................4 Bonds .................................................... 13
Conventions for this guide......................... 4 Fixed Bonds..............................................13
Additional Information.............................. 4 Bond Types...............................................14
Editing Bonds...........................................15
Learning Chem & Bio Draw...................5
Chemical structures in Excel..................... 5 Captions and Atom labels ..................... 16
Converting Structures to Names ............... 5 Formatting captions and labels ...............17
About ChemNMR....................................... 5 Hotkeys and Nicknames ...........................18
Expanding Nicknames..............................19
Annotations ..............................................20
Chapter 2 Setting Preferences ..................................20
Getting Started .........................................7 Rings ..................................................... 21
Installing Chem & Bio Draw ..................7 Spiro and sprout rings..............................21
System Requirements................................. 7 Aromatic Structures .................................22
Site License Networks................................ 7 Acyclic Chains...................................... 22
The Work Area .......................................7 Arrows and Shapes ............................... 23
Toolbars ..................................................8 Arrows......................................................23
The Main Toolbar...................................... 8 Drawing Elements....................................25
Tearing Off Toolbars................................. 8 The Bracket Tools palette ........................26
Docking and Floating................................ 9 Framing Objects ......................................27
BioDraw Toolbar ...................................... 9 Pen Tools..................................................27
Documents ..............................................9 Selecting Objects......................................27
Creating Documents.................................. 9 Resizing Objects.......................................29
Opening Documents .................................. 9 Rotating Objects.......................................29
Discarding Changes.................................. 9 Moving Objects ........................................30
Undo, Redo, and Repeat............................ 9 Copying Objects.......................................30
Saving Documents ................................... 10 Deleting Objects.......................................30
Selecting an open document.................... 10 Joining Objects ........................................31
Grouping Objects.....................................31
Windows ...............................................10 Scaling Objects ........................................32
Chem & Bio Draw 12.0 i

User Guide
Centering Objects.................................... 32 Coloring objects.................................... 59
Aligning Objects...................................... 32 Coloring groups .......................................60
Distributing Objects ................................ 32
Labels.................................................... 60
Check Structure.....................................32 Expanding Labels.....................................60
Checking copied structures ..................... 33 Contracting Labels...................................61
Chemical Warnings...............................33 Multiple atoms..........................................61
Disabling chemical warnings.................. 33 Clean Up Structure ............................... 62
Warning Preferences............................... 33 Attachment Points................................. 63
Multi-Center Bonds..................................63
Chapter 4 Variable Attachment Points .....................64
BioDraw ..................................................35 Viewing Attachment Points ......................64
BioDraw Tools......................................35 Atom Numbering .................................. 64
BioDraw Templates................................. 35 Showing Atom Numbers ...........................64
Customizable Objects.............................. 36 Hiding atom numbers...............................64
Editing Atom Numbers .............................65
Drawing sequences ...............................40
Positioning Atom Numbers ......................65
Nonlinear sequences ............................... 41
Structure Perspective ............................ 65
Bonding from sequences.......................... 42
IUPAC codes ........................................... 42 Flatten Command.....................................66
Peptides ................................................... 43 Mass Fragmentation.............................. 66
Disulfide Bridges..................................... 43 Synthesis and Retrosynthesis ...................67
Drawing Reactions................................ 67
Chapter 5 The Reaction Interpreter..........................70
Tutorials..................................................45 Drawing an Intermediate ...................... 70
Overview...............................................45 Templates.............................................. 73
Tutorial 1: Drawing a Structure ............45 Selecting a template .................................73
Tutorial 2: Using Rings.........................46 New Drawings..........................................73
Fusing a Template....................................74
Tutorial 3: Fischer Projections..............48 Customizing Templates ............................74
Tutorial 4: Perspective Drawings .........51 Defining Nicknames ............................. 75
Tutorial 5: Newman Projections ...........54 Attachment points.....................................75
Tutorial 6: Stereochemistry ..................56 Deleting Nicknames .................................76
Tutorial 7: Templates............................57 Troubleshooting Nicknames.....................76
3D Viewing........................................... 77
Chapter 6 3D Model..................................................77
Chem & Bio 3D Preview options.............77
Advanced Drawing Techniques ............59
ChemScript ........................................... 78
Mirror Images .......................................59
ii Contents
Chapter 7 Setting Up ChemDraw/Excel ............. 103
Naming Structures .................................79 Importing Tables................................. 103
Struct=Name ........................................79 Converting Worksheets ...................... 104
Unsupported structures ........................... 79 Upgrading Workbooks ...........................104
Supported Structures ............................... 79 Importing Hit Lists ............................. 104
Auto Update............................................. 81 Error Messages ......................................104
Name=Struct .........................................82 Exporting Tables................................. 104
Converting Names to Structures ............. 82 Adding Structures ............................... 105
Adding a Structure From a File.............105
Chapter 8 SMILES Strings ......................................105
Chemistry Features................................85 Adding Structures by Name....................105
Chemical Analysis ................................85 Saving Structures ................................ 106
ChemBioFinder HotLink ......................86 Searching ............................................ 106
Using the ChemBioFinder HotLink......... 86 Opening a database ...............................106
Normal Searches ....................................106
Stereochemistry ....................................86
Similarity Searches ................................106
Displaying Stereochemistry Indicators ... 86
R-Group Analysis ............................... 107
Relative Stereochemistry ......................... 88
Interpreting Analysis Results .................107
Chemical Annotations...........................89
Working with Structures..................... 107
Orbitals.................................................... 89
Chemical Symbols ................................... 90 Naming Structures..................................107
Using the Clipboard...............................108
Chemical Properties .............................91
Displaying Structures.............................108
Viewing Chemical Properties.................. 92
ChemDraw/Excel Functions ............... 108
Stoichiometry Grid ..............................92
TLC .......................................................93
Chapter 10
Rf Display ................................................ 95
Resizing Spots.......................................... 95 Query Structures ................................. 119
Custom Spots .......................................... 95 Search limitations ..................................119
ChemNMR............................................95 Generic Nicknames............................. 119
NMR Shifts............................................... 95 Generic Nickname Hotkeys....................120
Assigning Structures to Spectra .............. 96 Defining Generic Nicknames .................120
Viewing Spectral Assignments ................ 96 Atom Properties .................................. 120
Removing Spectral Assignments.............. 97 Assigning atom properties .....................121
Custom Shift Correction Data................. 97 Query Indicators ....................................121
Removing Atom Properties ....................122
Chapter 9 Atom Property Options ..........................122
ChemDraw/Excel .................................103 Bond Properties .................................. 127
Chem & Bio Draw 12.0 iii

User Guide
Assigning Bond Properties.................... 127 Transferring Across Platforms............ 154
Viewing Bond Properties ...................... 128 Macintosh to Windows ...........................155
Removing Bond Properties.................... 128 Windows to Macintosh ...........................155
Bond Property Options.......................... 128
Element Lists ......................................130
Appendix A
Element Not-Lists .................................. 130
Preferences and Settings ..................... 157
Polymers .............................................131
Theme Options.................................... 157
Setting Bracket Properties .................... 131
Bracket Usage ....................................... 132 I/Draw ................................................. 157
Repeat Pattern....................................... 133 Setting Preferences ............................. 157
Link Nodes..........................................134 Setting the Default Tool .........................158
Flip Type ............................................... 134 Autosave ................................................158
New Lines and Closing Text Boxes ........158
Alternative Groups..............................134
Highlight Box Tolerance........................159
Multiple Attachment Points................... 136 The ChemDraw Items Folder.................159
Attachment Rank Indicators ...............137 Accessing Documents Quickly ...............159
Attachment Point Numbering ................ 137 Customizing Toolbars......................... 159
Anonymous Alternative Groups .........138 The toolbar schema................................159
Expand Generic Structures .................138 The toolbar XML files ............................160
R-Logic Queries .................................... 139 Editing the XML files .............................160
Editing toolbar icons..............................160
Atom-to-Atom Mapping .....................140
Document and Object Settings ........... 160
Stereochemical Symbols.....................142
Default Styles .........................................160
3D Properties ......................................142 Saving Customized Styles.......................161
Export Compatibility ..........................144 Settings From Other Documents............161
Drawing Settings....................................161
Chapter 11 Analysis and Properties ...................... 163
Sharing Information ............................147 Formatting Captions ........................... 163
The Clipboard .....................................147 Setting Font parameters.........................163
Text Line Notation................................. 147 Setting the Baseline Style .......................163
Drag-and-Drop ..................................... 149 Style Indicators ......................................164
Specifying Line Spacing .........................164
Transferring Objects ...........................149 Aligning Text ..........................................164
Embedding Objects (Windows) ..........150 Changing the Default Format ................165
Exporting ............................................151 Customizing Hotkeys.......................... 167
Importing ............................................152 Working with Color ............................ 168
ISIS™ compatibility .............................. 153 What you can color ................................169
Graphics export border preference....... 153 Changing colors.....................................169
File Formats.......................................... 153
iv Contents
The Color palette................................... 169 H-Dot/H-Dash........................................194
Removing Colors ................................... 170 Complexes ..............................................194
Templates and Color ............................. 171 Multi-center Attachments.......................194
Saving Color palette Settings ................ 171 Cahn-Ingold-Prelog ...............................194
Printing Background Color................... 171 Stereochemical Flags.............................195
Document Settings ..............................172 Polymer Representations .......................196
Publishing Documents........................... 173 Analysis Messages..................................197
Appendix B Appendix D
Page Layout ..........................................183 Property Calculations.......................... 201
LogP .......................................................201
The Drawing Area...............................183
Henry’s Law...........................................201
Setting up Pages..................................183 Molar Refractivity ..................................202
Paged Document Setup ......................... 183 CLogP and CMR....................................202
Poster Documents Setup........................ 184 Topological Polar Surface Area ............202
Headers and Footers............................. 184 Other Properties ....................................202
Page Setup............................................. 184
Printing................................................184 Appendix E
Print Options ......................................... 185
ChemNMR............................................ 203
Scaling................................................... 185
ChemNMR Limitations...........................203
Saving Page Setup Settings.................185
NMR References.....................................204
35mm Slide Boundary Guides ............185
Viewing Drawings ..............................186
Appendix F
Magnification ........................................ 186
Technical Support................................ 205
The Magnification Control.................... 187
Rulers .................................................... 187 Locating your serial number..................205
The Crosshair........................................ 187
Appendix G
Appendix C Shortcuts and Hotkeys ........................ 207
Chemical Interpretation......................189 Atom Keys .......................................... 207
Chemical Intelligence .........................189 Bond Hotkeys ..................................... 208
Database Conventions.........................189 Function Hotkeys................................ 208
Bond Conventions ................................. 190 Shortcuts ............................................. 209
Atom Labels........................................... 191 File .........................................................209
Chemically Significant Text .................. 192 Edit .........................................................209
Charges ................................................. 192 View........................................................209
Isotopes and Elements........................... 193 Object .....................................................209
Radicals................................................. 193 Structure.................................................210
Chem & Bio Draw 12.0 v

User Guide
Text ........................................................ 210 Suppliers on ACX.com ...........................216
Drawing................................................. 210 ACX Structures and Numbers ................216
Nicknames ..........................................212 Chem & Bio 3D ActiveX Control...........216
SciStore.com...........................................216
CambridgeSoft.com ...............................216
Appendix H Using the ChemOffice SDK....................217
The CambridgeSoft Web Site .............215
Registering Online................................. 215 Index .......................................... 219
User’s Guide ......................................... 215
Technical Support ................................. 215
vi Contents
What’s New
Chem & Bio Draw has long been the preferred complex ring assemblies, fused ring systems,
tool for illustrating chemical concepts. Chem and bridged fused ring systems than was possi-
& Bio Draw 12.0 introduces a variety of ble with earlier versions of Chem & Bio Draw:
improvements and new features not found in
• Struct>Name supports ring assemblies that
earlier versions. The new features in this latest
consist of two or more rings or ring sys-
version of Chem & Bio Draw are briefly
tems.
described below. You can find more informa-
tion on these and other features throughout the • Struct>Name in earlier versions of the
manual and online Help. Chem & Bio Draw supported fused ring
systems that consisted of only 2-3 rings. In
Disulfide Bridges. When you create a disul- Chem & Bio Draw 12.0, Struct>Name has
fide bond between cysteine residues, Chem & been enhanced to recognize much more
Bio Draw 12.0 will create the disulfide bridge complex systems.
for you. For information, see “Disulfide
Bridges” on page 43. • Struct>Name supports bridged fused ring
systems in Chem & Bio Draw 12.0.
Bonding from Sequence Atoms. In Chem &
Bio Draw 12.0, you can create bonds from spe- For information on Struct>Name, see
cific atoms in DNA, RNA, and protein “Struct=Name” on page 79.
sequences. The bonds are retained even if you Name>Struct Improvements. Name>Struct in
expand or collapse the sequence labels. See Chem & Bio Draw 12.0 reports whether a
“Bonding from sequences” on page 42. chemical name is ambiguous. For example, if
Rotation Centers. Using Chem & Bio Draw
you enter “dichloronaphthalene”, Chem & Bio
12.0, you can rotate your drawing around an Draw 12.0 displays an isomer of the structure
atom, an arbitrary center, or any other location but also report that the name is ambiguous.
on screen. See “Rotating Objects” on page 29. This new feature is quite useful in an auto-
mated environment (such as with ChemScript)
Export to SVG. In Chem & Bio Draw 12.0, where many names are converted at the same
you can export your drawings in the Scalable time.
Vector Graphics (SVG) format. SVG is an
Enhanced Color Palette. Chem & Bio Draw
XML-based format often used to describe two-
dimensional vector graphics. To save a draw- 12.0 supports 16 million colors.
ing as an SVG file, go to File>Save As. Advanced BioDraw Templates. BioDraw and
Struct>Name Improvements. Ring structure
ChemBioDraw Ultra include a set of high-
recognition has been greatly improved in the color templates for creating publication-quality
Struct>Name feature for Chem & Bio 12.0. illustrations of biological systems. To open the
You can now apply Struct>Name to more Advanced BioDraw and other templates, go to
Chem & Bio Draw 12.0 1

User Guide
File>Open Templates>Advanced BioDraw or go For more on drawing biological structures, see
to View>Templates. “BioDraw” on page 35.
More Versatile Nicknames. Nicknames have
long been a useful feature in Chem & Bio
Draw. With new enhancements for version
12.0, the nickname library includes structures
that can have an unlimited number of connec-
tion points or no connection points at all.
ChemScript Support. You can now execute
ChemScript scripts in ChemBioDraw Ultra
12.0. Use any of the sample scripts that are
provide or create your own. See “ChemScript”
on page 78.
Customize NMR Data. Chem & Bio Draw
12.0 lets you supplement the ChemNMR data
for proton found in Chem & Bio Draw 12.0
with your own data.
Just a few of the BioDraw templates that are new in

Chem & Bio Draw 12.0.
2 What’s New
1
Introduction
Designed for scientists, students, and scientific If you need an advanced drawing application
authors, Chem & Bio Draw 12.0 is a powerful that also includes the ability to draw biological
yet easy-to use tool for producing a nearly structures and pathways, you will want to refer
unlimited variety of biological and chemical to ChemBioDraw Ultra 12.0. ChemBioDraw
drawings. You can create your own drawings Ultra 12.0 includes all features that are avail-
or use those provided in the vast library of able in the Chem & Bio Draw 12.0 Series and
available templates. Having completed a draw- BioDraw Series.
ing, you can export it to a desktop publishing For more information on Chem & Bio Draw
program, post it on a Web page, or store it in a 12.0, see www.cambridgesoft.com.
database.
You can use Chem & Bio Draw 12.0 with The BioDraw Series
other CambridgeSoft products: Designed to complement the Chem & Bio
• ChemBioFinder & BioViz 12.0 Draw 12.0 Series, the BioDraw series of appli-
cations has been developed specifically for the
• Chem & Bio 3D 12.0 biology and biochemistry communities of
• Chem & Bio Draw 12.0/Excel users. The BioDraw series includes:
• Chem & Bio Office 2009 • BioDraw Pro 12.0
The ChemDraw Series • BioDraw Ultra 12.0
CambridgeSoft is proud to offer ChemDraw, a • ChemBioDraw Ultra 12.0 (also part of the
series of applications designed to help you cre- Chem & Bio Draw 12.0 series)
ate high-quality chemical drawings. The In addition to all the standard chemical draw-
ChemDraw series includes ChemBioDraw ing tools, the BioDraw series also includes
Ultra 12.0, ChemDraw Ultra 12.0, ChemDraw tools specifically designed to illustrate biologi-
Pro 12.0, and ChemDraw Standard 12.0. cal pathway and biochemical structure. For
ChemDraw Standard 12.0 is designed for users example, use the BioDraw tools to describe
who only need a fundamental method for binding sites for enzyme inhibitors, illustrate a
drawing structures. However, if you need a tRNA structure, or create virtually any other
more powerful application, one that is biological drawing. Then, just as in the Chem
designed for creating advanced chemical struc- & Bio Draw 12.0 series, you can export your
tures and analysis, you may consider BioDraw series drawings to your presenta-
ChemDraw Pro 12.0 or ChemDraw Ultra 12.0. tions, grant proposals, and publications.

User Guide
About This Manual TEXT
The manual also uses formatting for different
This manual describes all the drawing features types of information:
in Chem & Bio Draw 12.0 and how to use
them. The chapters are organized by task are
intended to help you familiarize yourself with NOTE: Notes such as this highlight important
Chem & Bio Draw so that you can start using it information.
as quickly as possible.
If you are a new user, you may want to first
read “Getting Started” on page 7. Then, con- TIP: Tips supply useful, “nice to know”, infor-
tinue with “Tutorials” on page 45. This section mation supplemental to the main text.
demonstrates most of the features of Chem &
Bio Draw 12.0.
Some of the material in this manual describes CAUTION
tasks that must be performed in conjunction
with other software. For example, instructions These indicate important information that, if
for the ChemDraw/Excel describes tasks that ignored, may lead to data loss or other serious
must be performed in conjunction with problems.
Microsoft Excel. For assistance, consult the
Excel online help or user’s guide. FEATURE
Conventions for this guide An asterisk (*) indicates that a feature is avail-
able in ChemBioDraw Ultra 12.0, ChemDraw
This guide uses several basic conventions to Ultra 12.0, and ChemDraw Pro 12.0 only.
help you quickly learn Chem & Bio Draw
A note indicates which features are available in
12.0.
ChemBioDraw Ultra 12.0, BioDraw Ultra
INSTRUCTIONS 12.0, and BioDraw Pro 12.0 only. Features not
Instructions are designed to help you navigate identified with a note or asterisk are available
through menus and screens. Items on screen in all versions.
appear in bold. For example, to open a new SHORTCUT KEYS
drawing template:
When a shortcut key sequence is given, the
1. Go to File>Open Templates>Amino Acids. Windows OS sequence is listed first, followed
This step asks you to select the File menu, by the Macintosh OS sequence (example: “Use
select Open Templates (in the File menu), and Shift+Ctrl+G or Shift+Command+G to ungroup
then select Amino Acids (in the Open Tem- objects”).
plates submenu).
Additional Information
These resources are available to help you get
started with Chem & Bio Draw 12.0:
4 Introduction
Chapter 1
QUICK REFERENCE CARD structures in Microsoft© Excel© for Windows.
The QRCs summarize commands and features. Chem & Bio Draw 12.0/Excel enables you to:
The cards are in the back of the Chem & Bio
• Add structures and data from Chem & Bio
Draw 12.0 printed manual.
Draw 12.0 or a ChemFinder database to an
ONLINE HELP Excel spreadsheet.
In Chem & Bio Draw 12.0, press F1 or go to • Search using the same features in Chem-
Help>Contents.
Finder.
TOOL TIPS
• Perform calculations on chemical struc-
This is the name or a short description of a tures.
tool. To see a tool tip, point to a tool.
STATUS BAR Converting Structures to Names
See the lower left corner of the Chem & Bio One of the most significant and useful features
Draw 12.0 window for useful information. in Chem & Bio Draw is Struct=Name. Draw or
open a chemically correct structure and Chem
Learning Chem & Bio Draw & Bio Draw displays the IUPAC name. See
Perhaps the best way to learn Chem & Bio Chapter 7: “Naming Structures” for more
Draw is to follow the tutorials found in this information.
guide. As you advance beyond the basics, you About ChemNMR
will find many powerful features to be quite
useful in drawing structures. Just a few of the Use this powerful feature to estimate proton
advanced features are described below: and carbon-13 chemical shifts in molecules
you draw. See “ChemNMR” on page 203.
Chemical structures in Excel
Chem & Bio Draw 12.0/Excel® provides a
unique plug-in to help you manage chemical

User Guide
6 Introduction
Chapter 1
2
Getting Started
This section will help you install Chem & Bio Requirements for install Chem & Bio Draw
Draw 12.0 and become familiar with the user 12.0 on a Macintosh® system:
interface. Operating System. Mac OS X 10.4 PowerPC,
Mac OS X 10.4 Intel, Mac OS X 10.5 Pow-
Installing Chem & Bio Draw erPC/Intel
Before installing Chem & Bio Draw, see the Browsers. Safari 1.4 and higher, Firefox 1.x,
ReadMe.html file and other ReadMe docu- Mozilla 1.7.5 and higher, Netscape 7.0.x
ments on the installation CD-ROM.
Screen Resolution. Chem & Bio 3D supports a
System Requirements screen resolution of 800 x 600 or higher.
Requirements for installing Chem & Bio Draw Site License Networks
12.0 on a Windows® system:
If you have a site license, see the network
Operating System. Windows 2000, XP Pro installation instructions at:
(32-bit only), Vista (32-bit only).
http://www.cambridgesoft.com/services/Desk-
Browsers. Microsoft Internet Explorer 7.x or topSupport/Documentation/NetworkInstalls/
6.x, Mozilla Firefox 1.5 and higher, Netscape
7.x, Mozilla 1.x The Work Area
Microsoft Office. Microsoft Office 2000, The work area appears whenever you launch
Office XP, Office 2003, Office 2007. Chem & Bio Draw 12.0. By default, the work
Screen Resolution. Chem & Bio 3D supports a area displays commonly used toolbars, the
PC screen resolution of 800 x 600 or higher.

User Guide
main menu, and document status bar. The
work area appears below:
a. title bar e. document window

b. Menu bar f. Main toolbar
c. BioDraw toolbar g. status bar
d. magnification controls
Figure 2.1 ChemBioDraw Ultra work area
Toolbars Tearing Off Toolbars

To display or hide a toolbar, select it in the The main toolbar has other toolbars extending
View menu. A check mark appears next to the from it. You can “tear off” these smaller tool-
toolbar name when it is visible. bars and place them anywhere on your screen.
To tear off a toolbar:
The Main Toolbar
1. Click the arrow on the lower right of a tool
Most common tools are on the main toolbar. in the main toolbar.
These include all tools necessary to draw and 2. While holding the mouse button down,
edit structures, reactions, and shapes. Go to point to the title bar, and release the button.
View>Show Main Toolbar.
8 Getting Started
Chapter 2
Docking and Floating Using Styles
You can dock or float any of the standard tool- To create a new document using a different
bars. When you dock a toolbar, it becomes style sheet or stationery pad:
attached to the drawing window. Whereas 1. Go to File>Open Style Sheets.
floating toolbars appear in front of the docu- 2. Choose a Style Sheet or Stationery Pad
ment window and you can move them where from the list.
you want.
Chem & Bio Draw 12.0 provides pre-defined
To dock a toolbar, do one of the following: style sheets or stationary pads in the
• Click and drag the toolbar to any edge out- ChemDraw Items folder. For example, the
side the drawing window. ACS Document 1996 is configured to create
• Right-click the toolbar and select Dock documents that are set with the bond lengths,
Toolbar. bond width, spacing, and fonts used in the 2-
column format of all ACS journals.
To float a toolbar, do one of the following:
For a list of the settings stored in these docu-
• Click and drag the docked toolbar into the ments, see Appendix A: “Preferences and Set-
drawing window. tings”.
• Right-click the toolbar and select Float Tool-
bar.
NOTE: Predefined style sheets or stationary
BioDraw Toolbar pads may restrict your options in unexpected
ways. For example, not all Save As... format
The BioDraw toolbar contains drawing tools
options are available. For general use, keep the
for adding biological and biochemical ele-
default settings.
ments to your drawings. BioDraw is available
in ChemDraw ActiveX Pro, ChemBioDraw
Ultra, and BioDraw (Pro and Ultra versions).
Opening Documents
See Chapter 4: “BioDraw” for more informa-
tion. To open a document, do one of the following:
• Go to File>Open. In the Open dialog box,
Documents select the name and location of the file and
A document is a workspace where you create click Open.
and edit structures. • In the File menu, choose the document
from the list at the bottom.
Creating Documents
Discarding Changes
You can create a new document using the
default settings, or use a Style Sheet or Statio- To retrieve the last saved version of a file, go
nery Pad with customized settings. To create a to File>Revert.
document, go to File>New Document.
Undo, Redo, and Repeat
Chem & Bio Draw 12.0 tracks your actions. To
undo, redo, or repeat your last action, select the

User Guide
appropriate option in the Edit menu. The num- below. Other windows are described through-
ber of actions that can be tracked is limited out this guide.
only by the amount of memory (RAM and vir-
tual memory) available. The Info Window
This window shows the size and position of the
NOTE: Chem & Bio Draw 12.0 tracks only pointer and anything you have selected. To
those actions you have performed since you last show or hide the window, go to View>Show
saved the document. Info Window.
Pointer. X and Y display the current mouse
coordinates. dX and dY indicate the change in
Saving Documents X and Y of a moved selection.
1. Go to File>Save. Selection. X and Y display the position of a
selection. W and H are the width and height.
2. Choose a folder in which to store the file.
3. Type a file name in the Save As text box. Other. Angle is the angle of a bond or rotation
4. Select a file format. of a selection. Dist is the bond length or the
distance a selection has moved. When resizing
5. Click Save.
an object, % indicates the current percentage of
the original size.
CAUTION
Chem & Bio Draw 12.0 uses the CDX file for- Periodic Table
mat by default. Other formats store a picture of Use the periodic table to insert atoms into
your drawing but may not retain relevant infor- structures. Go to View>Show Periodic Table
mation. For example, the EPS format does not Window.
store the chemical significance of the connec- Click a symbol to highlight the atom and acti-
tions between atoms and bonds. vate the Text tool. Drag across the table to
highlight each atom.
TO ADD AN ATOM
Selecting an open document
Select it in the periodic table and click an
The Window menu lists all open documents empty space in the document. The atom
and templates. The document you choose from appears in its chemically neutral form. For
the list becomes the active window. example, carbon appears as CH4 and hydrogen
appears as H2.
Windows TO LABEL AN ATOM
Windows are useful for viewing information Click an existing unlabeled atom.
about your drawing and even adding informa- TO CHANGE THE OXIDATION STATE
tion to it. To show or hide a window, select it
Using the symbol for the atom, click the atom
in the View menu. Windows cannot be docked.
in the document window.
Three commonly used windows are described
10 Getting Started
Chapter 2
TO CHANGE TO A DIFFERENT ATOM mouse over the character map to view a larger
Select the new atom in the periodic table and version of the characters in the top right corner
click the atom in the document you want to of the window. Click any character in the table
change. to enter it in the text box. The selected font
TO EDIT A LABEL (shown in the character map window) is
To modify the atom label, double-click the applied to that character only. It does not
atom in the document window. change the active font in the text box.
NOTE: Some element names conflict with NOTE: To cancel a selection, drag it to
Chem & Bio Draw 12.0 Hotkeys and may not be another character before releasing.
interpreted correctly.
The eight most recently used characters appear
at the top of the window. These characters
Character Map retain their font and are not affected by
Use the character map to add ASCII and other changes to the window. A character may
symbols to your document in various font appear more than once in this section if the
styles. To show or hide the map, go to versions use different fonts. Click the back but-
View>Show Character Map Window. ton to toggle among all the displayed charac-
The character map is active only when a text ters.
box is open for editing. With a text box open,

User Guide
12 Getting Started
Chapter 2
3
Basic Drawings
Chem & Bio Draw 12.0 provides a variety of bond is drawn in the direction you drag the
tools for drawing everything from simple cursor.
chemical structures to complex reactions. In
this section, we introduce basic drawing tech-
niques to help you create your first structures.
We also explain how to add features such as
arrows and shapes to enhance structures and Figure 3.2 Adding a bond by dragging
reactions. For more drawing features, see
“BioDraw” on page 35 and “Advanced Draw- Fixed Bonds
ing Techniques” on page 59. The Info window displays the bond length and
angle as you drag the bond. You can draw any
Bonds bond length or create any angle relative to the
The Main toolbar and Multiple Bonds toolbar X-axis. However, it is generally more useful to
offer numerous options for drawing bonds. draw bonds that are constrained to a fixed
Some of the tools are for drawing specific length and a fixed angle.
types of bonds while others represent nonspe- Drawing fixed length bond
cific bonds for drawing structures for database To draw bonds constrained to a fixed length:
queries.
1. Go to Object>Fixed Lengths and ensure that
Drawing bonds a check mark appears next to the Fixed
To draw the first bond of your structure, select Lengths command.
the solid bond tool in the Main toolbar and 2. Using the Solid Bond tool, begin drawing a
click in the document window. To draw structure.
another bond, click either end of the first bond.
The bonds in the new structure appear at
default lengths.
Drawing fixed angle bonds
Figure 3.1 Adding a bond to an atom When you fix bond angles, all bond that you
draw are constrained to angles that are multi-
You can draw a bond in any direction. Using a
ples of 15° relative to the X-axis.
bond tool, click and drag from an existing atom
or an empty area in the document window. The

User Guide
1. Go to Object>Fixed Angles and ensure that a Double Either Bonds
check mark appears next to the Fixed To draw a double either bond, use the double
Angles command. either bond tool from the Multiple Bonds tool-
2. Select a bond tool. bar or:
3. Begin drawing a structure. 1. Draw a bond using the Wavy Bond tool.
The bonds in the new structure appear at stan- 2. Click the center of the bond to create a dou-
dard 120° angles (relative to the X-axis). ble bond.
Changing fixed values 3. Click again to create a double either bond.
By default, bond lengths are drawn at .4167 in Triple Bonds
and bond angles in a chain are shown at 120° There are three ways to draw a triple bond:
by default.
To change the default fixed values: • Draw a bond using the Triple bond tool.
• Using the Solid, Dashed, or Bold bond tool,
1. Go to File>Document Settings and click the
drag from one end of an existing double
Drawing tab.
bond to the other end.
2. Enter a value in the Fixed Length text box.
• Using any bond or selection tool, point to
Use in, cm, pt, or iu for units (default is
an existing bond and type ‘3’.
.4167 in.).
3. Enter a value in the Chain Angle text box. Quadruple Bonds
4. Click OK. There are four ways to draw a quadruple bond:
• Draw a bond using the quadruple bond tool.
NOTE: To suppress fixed lengths and fixed • Using the Solid, Dashed, or Bold bond tool,
angles, press the ALT (Windows) or Option drag from one end of an existing triple bond
(Macintosh) key as you drag the bond. to the other end.
an existing bond and type ‘4’.
Bond Types
To change a quadruple bond into a single
Double Bonds bond:
There are four ways to draw a double bond: 1. Select any bond tool.
• Draw a bond using the Double bond tool. 2. Drag from one end of an existing quadruple
bond to the other. The quadruple bond
• Draw a single bond over an existing single
changes into a single bond corresponding to
bond.
the tool used to draw over the bond.
an existing bond and type ‘2’. You can also draw multiple bonds by
right-clicking a bond and selecting the bond
• Right-click any bond and select Dou- type from the shortcut menu, using the bond
ble>Plain in the context menu.
14 Basic Drawings
Chapter 3
properties dialog box, or using Hotkeys. See Editing Bonds
“Bond Properties” on page 127.
You can modify the appearance of chemical
bonds by:
NOTE: To reduce the bond order, select the
• Changing bond types
Eraser tool and click the bond.
• Changing bond alignment and orientation
• Moving Atoms
Dative and Wedged Bonds
• Layering bonds
Dative bonds and wedged bonds are drawn
with a fixed orientation in a document window. Changing Bond Types
To draw a dative bond: Change a single bond from one type to another
by doing either of the following:
1. Select the Dative Bond tool. • Select a bond tool and click the center of an
2. Drag from the positive to the negative end existing bond.
(arrow head) of the dative bond. • Right-click and select the new type from
the context menu.
To draw a wedged bond:
• Ctrl+click the bond.
1. Click one of the wedged bond tools.
Changing Double Bonds
2. Drag from the narrow end of the wedged
bond to the wide end of the wedged bond. To change one type of double bond to another:
3. 1. Select the Bold, Dashed, or Solid Bond

tool.
BOND ORIENTATION 2. Click a double bond.
• To change the orientation of the wedged The double bond changes to the new bond
bond, click the center of the bond using the type. One of the bonds in the double bond is
wedged bond tool. always a solid or dashed bond.
• To change the orientation of a dative bond,
click the center using the dative bond tool.
NOTE: If you click a tautomeric bond (solid/
COOH COOH dashed) a second time with the dashed bond
H tool, you create an aromatic double bond
H
(dashed/dashed).
HO CH 3 HO CH 3
NOTE: Chem & Bio Draw 12.0 treats hashed

wedged bonds with the narrow end in the plane
of the screen and the wide end behind the plane.

User Guide
Aligning Double Bonds 2. Release when one atom is on top of the
Double bonds can have one of three align- other. The bond between the atoms disap-
ments relative to other bonds— above, below, pears.
and centered.
NOTE: You can also move atoms using a selec-
Above tion tool. See “Moving Objects” on page 107.
Below
Bond Crossing
Centered When one bond crosses another, you can indi-
cate which bond is in front.
1. Click the bond tool used to create the exist- 1. Select the object to move to the front.
ing double bond. 2. Go to Object>Bring to Front.
2. To change the alignment, do one of the fol- The selected object now appears in front of all
lowing: other objects. Similarly, go to Object>Send to
• Click the center of the double bond. Back to position the bond behind other objects.
• Right-click, point to Bond Position on the
context menu, and choose the alignment.
Moving Atoms
1. Click a selection tool.
2. Point to the atom to move. A highlight box NOTE: For bonds with 3D coordinates, those
appears over the atom. coordinates determine the visible bond cross-
ings. Bring To Front and Send To Back have no
3. Shift+drag the atom.
effect.
Reducing Ring Size
To reduce the number of atoms in a ring, shift-
drag one atom on top of another atom. For Captions and Atom labels
example, you can convert cyclohexane to
cyclopentane. You can annotate simple hydrocarbon struc-
tures using captions and atom labels using the
1. Using a bond tool, point to an atom and text tool. For example, you can add the atom
Shift+drag.
16 Basic Drawings
Chapter 3
label “OH” and the caption “Phenol” to a Formatting captions and labels
drawing of toluene to create:
.
You can change a variety of text properties
OH such as color, font, size, and style.
1. Select the text object with a selection tool.
2. Go to Object>Object Settings. The object
dialog box opens.
3. Click the Captions or Atom Labels tab.
4. Select or modify the settings and click OK.
5. The change affects only the selected cap-
tion or atom label.
Phenol
Coloring text
1. Using the Benzene tool, click in the docu-
You can color some or all captions and atom
ment window. A benzene ring appears.
labels before or after you type them.
2. Using the Solid Bond tool, click one of the
benzene carbons to create toluene. 1. Select the Text tool.
3. Using the Text tool, click the end carbon on 2. Click where to place the text.
the methyl group of toluene. A text box 3. Choose a color from the Color menu.
appears. 4. Type the caption or atom label.
4. In the text box, type OH.
You can also color one or more captions or
5. Click outside the text box. labels or selected parts of them.
6. Using the Text tool, click below the draw-
ing and type “Phenol” in the text box. 1. Select the text to color.
2. Choose a color from the Color menu.
7. Click outside the text box.
Caption width
To edit the caption or atom label, click in the
To edit the width of a caption:
text box with the text tool and begin typing.
1. Set a caption using the Text tool. A resize
Repeating atom labels
handle appears on the right side of the cap-
You can repeat an atom label using the text,
tion.
bond, or ring tools.
2. Drag the resize handle to change the width
1. Click the Text tool. of the caption.
2. Label a single atom. Deleting Labels
3. Do one of the following: To delete an atom label, leaving the underlying
• Using the Text tool, double-click another bonds unchanged, do one of the following:
atom. • Select the Eraser tool and click the atom
• Using a bond, ring, or acyclic chain tool, label.
triple-click another atom.

User Guide
• With a selection, bond, or ring tool selected, You can also label several atoms at a time. For
point to the atom label and press the space- example, you can change neopentane (figure A
bar, Backspace, or Delete key. below) into methanetetraamine (figure B):
About Fonts
Chem & Bio Draw 12.0 uses the fonts installed
on your computer. If you open a document that
uses fonts that are not installed, the missing
fonts are replaced with the installed fonts.
Hotkeys and Nicknames
For simple structures, typing the atomic sym- To change neopentane into methanetetraamine:
bol in a text box is easy. However, for compli-
cated structures using Hotkeys and Nicknames 1. Create the neopentane structure.
2. Use Shift-click to select all the terminal car-
is easier.
bon atoms and press n on the keyboard.
Using Hotkeys
For a complete list of Hotkeys, see Shortcuts
Using Hotkeys, you can add functional groups
and Hotkeys in the online Help.
to your structures with one keystroke. For
example, to add tert-butyl to the end of a
hydrocarbon chain: NOTE: The Automatically Rectify Hydrogens in
Atom Labels feature (see “Setting Preferences”
1. Draw the chain. on page 20) does not affect Hotkeys. To add a
2. Hover the cursor where you want the func- substructure, press a hotkey. To change how
tional group. many hydrogens are added to the substructure,
3. Press ‘3’ (the hotkey for tert-butyl) on the select the hotkey again.
keyboard. ‘t-Bu’ is added to the structure.
4. Select ‘t-Bu’ in the structure and go to
Structure>Expand Label. Using Nicknames
Using Nicknames, you can add short names for
Using the Hotkeys n (nitrogen), O (oxygen), functional groups to use as an atom label or
and I (iodine), you can turn ethylbenzene into part of a label. When you label an atom with a
pyridin-2-yl hypoiodite. nickname, the expanded structure retains its
chemical significance.
Commonly used nicknames, such as Me, Et,
and Ph are stored in your ChemDraw Items
folder. You can edit this list within the GUI
18 Basic Drawings
Chapter 3
(however, you should not attempt to edit this However, since the Nickname “THP” is
file directly). defined, the label appears as “THPO”. See
“Aligning Text” on page 164.
NOTE: Nicknames may be edited in
ChemDraw Pro, ChemDraw Ultra, or Chem-
BioDraw Ultra 12.0 only. See “Generic Nick- Expanding Nicknames
names” on page 119. A nickname is a type of label. Therefore, you
expand and contract nicknames the same way.
When you expand a nickname into its struc-
You can assign Hotkeys to Nicknames. For
ture, the nickname itself disappears (unless the
example, in the Nicknames and Hotkeys pro-
nickname represents an amino acid or nucleic
vided, the Hotkey “4” labels an atom with
acid). Trifluoroacetone is shown here:
“Ph”, which represents a phenyl group.
Applying Nicknames
You may select a nickname from the Nick-
names list or type it in manually.
To select from the list:
1. Point to an atom.
2. Press the Hotkey “=” (equal sign). The
Nickname list appears.
You can use nicknames to select and help you
3. Select a nickname from the list. modify the functional groups they represent.
For example, assume you have a chain of three
TIP: You can jump to the approximately cor- amino acids– glycine, isoleucine, and leucine:
rect place in the Nickname list by typing the
first letter of the Nickname.
4. Click OK. After you expand the nicknames, you can

To type the nickname: select any of the amino acids by double-click-
ing its nickname, as shown:
1. Double click an atom with a bond tool or
click an atom with the Text tool.
2. Type the nickname in the text box.
NOTE: Nicknames are tokens and do not flip

orientation when applied to the left side of a
structure when using Automatic Justification.
For example, in the absence of a defined Nick-
name, the label “OTHP” appears as “PHTO”.

User Guide
To contract nickname, go to Structure>Con- 2. Click Delete Keyword.
tract Label. 3. Click OK.
Annotations Setting Preferences
Annotations are useful for adding text informa- You can specify how the captions and labels
tion that helps to identify your drawing in a look each time you use Chem & Bio Draw
database search. Annotations are categorized 12.0. Go to File>Preferences and click the
using keywords. There are several default key- Building/Display tab. Then, choose from these
words- Name, Description, Type, and Other options:
Info. You can also add your own keywords.
Automatic Atom Label Alignment. when this
feature is selected, the alignment of atom
NOTE: Annotations are available in ChemBio- labels will adjust according to the positions of
Draw Ultra 12.0, ChemDraw Ultra 12.0, and any bonds attached to the atom labels. For
ChemDraw Pro 12.0 only. example, ‘CH3’at the left end of a horizontal
bond changes to ‘H3C’.
To annotate an object: Automatically Rectify Hydrogens in Atom
Labels. When this feature is selected, hydro-
1. Select the object.
gens are added or removed from atom labels to
2. Go to Object>Annotate. The Annotate dia- preserve standard valences when you change
log box opens. your drawing. For example, if you increase the
3. In the Keyword list, do one of the follow- bond order in ethane to make ethylene, the
ing: ‘CH3’ changes to ‘CH2’.
• Select a keyword.
• Select Add New Keyword. NOTE: The Automatically Rectify Hydrogens in
Atom Labels feature does not affect Hotkeys. To
4. In the Content text box, enter the notes to
add a substructure, press a hotkey. To change
apply to the object or drawing.
how many hydrogens are added to the substruc-
5. Click OK. ture, select the hotkey again.
Deleting a keyword
When you delete a keyword, all the notes for
Formatting Atom Labels
that keyword are also deleted.
To set the default character style for atom
1. In the Annotate dialog box, select from the labels, go to File>Document Settings and click
Keyword list the keyword. the Atom Labels tab. You can modify the font
20 Basic Drawings
Chapter 3
style, baseline style, and whether terminal car- To activate chemical significance, right-click
bons and implied hydrogens appear. the label and select Interpret Chemically.
Analysis Data
You can add properties from the Analysis
Window to a caption and, if Auto-update is on
(Go to File>Document Setting>Auto-update
tab), the values will update as you modify the
structure.
To add analysis data to a caption:
Figure 3.3 Isobutane with a) terminal carbon labels
and implicit hydrogens shown, b) implicit hydrogens 1. Right-click the caption and select Analysis
hidden, and c) terminal carbons and implicit hydro- on the context menu.
gens hidden 2. Choose the properties to add.
To set the default for a document:
Rings
1. Go to File>Documents and Settings.
You can draw aliphatic and aromatic rings of
2. On the Atoms Labels tab, check the Show
different sizes and types.
Labels on Terminal Carbons checkbox.
3. Click OK. 1. In the Main toolbar, select a ring tool.
2. Click and drag in the document window to
To set the default for one or more structures: orient the ring.
1. Select and right-click the structure(s). If you click an atom or bond with a ring tool in
2. Click Object Settings in the context menu. an existing structure, the ring is fused to it.
The Object Settings dialog box appears.
3. On the atom Labels tab, check the box next Spiro and sprout rings
to Show Labels on Terminal Carbons. By default, clicking an atom in a ring using a
To add or remove a terminal carbon label, ring tool forms a spiro link.
right-click the atom and select or deselect
Show Terminal Carbon Labels.
Chemical Significance
Whenever possible, labels are recognized as
chemically significant by default. For example,
if you add a label, such as CH3OH to your
structure, you can attach bonds to it and the
label appears in the properties of the molecule.

User Guide
You can change this behavior so that a sprout To draw, click in the document window with
bond appears instead: either the cyclopentadiene or benzene drawing
tool. To draw a different orientation, Shift-
click in the drawing window.
Acyclic Chains
To draw long hydrocarbon chains:
1. Select the Acyclic Chain tool.
2. Click and drag in the document window in
the direction you want the chain to grow.
The number at the end of the chain indi-
1. Go to File>Preferences. cates how many atoms you have drawn.
2. On the Building/Display tab, check the box
next to Sprout Rings Instead of Spiro When Changing Chain Direction
Clicking. To change the direction as you draw, press the
Ctrl or Command key while drawing in the
Aromatic Structures direction you want.
Delocalized rings
You can draw a resonance delocalized ring NOTE: Release the mouse button before you
using any ring tool except for the cyclohexane release the Ctrl or Command key.
chairs.
1. Click a ring tool.
2. Press the Ctrl (Windows) or Command
(Macintosh) key and drag or click in the
document window.
Resonance structures
You can draw cyclopentadiene or benzene in
either of their two orientations:
Figure 3.4 Reversing chain direction
NOTE: If Fixed Lengths is off, use Ctrl+Alt or

Command+Option to reverse chain direction.
Fixed Angles must be on to reverse direction.
22 Basic Drawings
Chapter 3
FIXED LENGTH Objects, except for daggers and some symbols,
When Fixed Lengths is on, you can drag the can be rotated and scaled.
pointer on the acyclic chain tool to make any
angle relative to the X-axis. At a constant chain Arrows
length, the positions of the first bond and all You can customize arrows not only for length
subsequent odd-numbered atoms depend on and angle, but for arrowhead width and shape.
the direction you drag. Before releasing the You can also drag an arrow from its middle to
mouse button, you can change this position by create an arc of any length.
dragging in the opposite direction. When you mouse-over an arrow with the
FIXED ANGLE Lasso, Marquee, or an Arrow tool selected, the
When Fixed Angles is on, the angle the acyclic application switches to edit mode and adjust-
chain makes relative to the X-axis is con- ment handles appear on the arrow.
strained to 15-degree increments.
Adding chains to structures
To add an acyclic chain to an existing struc-
ture, click an atom in the structure. Click and
drag in the direction you want to draw the
chain.
Specifying chain length
To specify the exact length of a chain before
you draw it:
1. Select the Acyclic Chain tool.
2. Click an existing atom or an empty area in a
document window. The Add Chain dialog
box appears. Figure 3.5 Arrow adjustment handles
3. Type the number of atoms in the chain. Drag the adjustment handles to change the
4. Click Add. arrow length, angle, or shape. When changing
the angle of an arrow, you are restricted to
To add another chain of the same length any- multiples of 15° if the Fixed Angles is selected.
where in a document window, Alt-click (Win- Hold down the Alt or Option key to drag to any
dows) or Option-click (Macintosh) where you angle.
want the chain to begin.
Arrow Types
Arrows and Shapes There are many arrows types available, letting
you add a wide variety of reactions and annota-
Use the tools and tool palettes on the main
tions to your drawings.
toolbar to add shapes to your documents (A
tool palette is indicated on the main toolbar by Chem & Bio Draw 12.0 offers a variety of arc
an arrow). You can tear off the palettes and types and arrow types, such as crossed (no-go)
place them where you want.

User Guide
arrows, equilibrium arrows of unequal lengths, HOLLOW ARROWS
and elliptical arcs. You can rotate hollow arrows as well as
ARROW HEADS change their length and width. Changing the
There are three arrow head shapes available, arrowhead width also changes the width of the
solid, hollow, and angled. To change the line segment.
shape, right-click an existing arrow and choose You can modify arrows with a context menu.
the new shape from the context menu. Some of the context menu commands are also
ARC ARROWS
available on the Curves menu. Use the Context
menu to create arrows for which there are no
You can create an arc arrow one of two ways:
tools, such as bold-dashed or dipole.
• Click and drag the arc adjustment handle of CONNECTING ARROWS
a straight arrow. You can connect a new arrow to an existing
• Select an arc arrow from the Arrows pal- arrow at either end or at the midpoint.
ette.
You can customize arc arrows as easily as NOTE: The terms “left” and “right” in the
straight arrows. Here are a few examples: context menu are relative, and refer to the
direction the arrowhead is pointing.
For example, to draw a new arrow starting at

the midpoint of an existing arrow:
1. Select from the Arrows palette an arrow
type for the new arrow.
2. Place your cursor over the midpoint of the
existing arrow and hold down the Shift key.
3. With the shift key held down, draw the new
arrow starting from the existing arrow’s
midpoint.
Click a modified arrow (with the same arrow

tool) to undo all changes to the shape, but not
length, of the arrow.
NOTE: Click an unmodified arrow, or one that

has had only its length changed, to reverse its
direction.
24 Basic Drawings
Chapter 3
You can also drag existing arrows and connect Drawing Elements
them. Here are a few examples:
Drawing elements are simple shapes such as
circles and rectangles that you can add to your
drawing. Drawing elements cannot belong to a
structure. Therefore, if you double-click on a
bond, atom, or atom label with a drawing tool,
they are not selected. To group drawing ele-
ments with a structure, go to Object>Group.
See “Grouping Objects” on page 31.
The Info window indicates the length and
angle relative to the X-axis while you use any
of the drawing element types.
1. Select a rectangle tool from the Drawing
Finally, arrows can be rotated with the Struc- Elements toolbar.
ture Perspective tool as well as the Lasso or 2. Click and drag the box to the size you want.
Marquee. Combining these methods lets you Circles and Ovals
draw an unlimited number of arrows that are To draw a circle or oval:
otherwise difficult to create.
EQUILIBRIUM ARROWS
1. Select one of the circle or oval tools.
For equilibrium arrows, changing the length 2. Point to where you want the center of the
changes both arrows proportionately; changing circle.
the shape of the arrowhead changes both 3. Drag outward from the center.
arrowheads identically. To change the length RESIZING AND ROTATING
of only one arrow, hold down the Alt or Option You can modify rectangles, circles, and ovals
key. Two new adjustment handles appear. the way you modify arrows.
When you have created a unbalanced equilib-
rium arrow, only the shorter side can be 1. Point to a shape with its drawing tool or a
adjusted further.. selection tool to display adjustment han-
dles.
2. Click and drag to modify the shape.
Circles have only a radius adjustment, but you
can resize and reshape ovals and rectangles for
both length and width. Rectangles also have
corner handles that adjust length and width
proportionately.
Lines
Lines drawn with the line tool differ in two sig-
nificant ways from bonds drawn with the bond
tools:

User Guide
• Lines are not included in chemical interpre- When you drag the resize handle, the Info win-
tation of the drawing dow indicates the percentage enlarged or
• Lines that cross appear solid, bonds do not. reduced. When you drag the Rotation handle,
the Info window indicates the degree rotated.
To draw a line:
The Bracket Tools palette
1. In the Drawing Elements toolbar, select a
line tool. Brackets includes braces { }, brackets [ ], and
2. Click and drag in the drawing window parentheses ( ).
where you want the line. Single Brackets
Arcs You can draw a single bracket in any orienta-
Use the Arc tools to draw solid or dashed arcs tion. Select a single bracket tool from the
of different angles: 90°, 120°, 180°, and 270°. Drawing Elements palette.
To draw an arc: 1. Point where you want the bracket to start.
1. Do one of the following: 2. Drag from one end of the bracket to the
other end.
• In ChemDraw Standard, point to an Arc
tool and drag in the palette to select the Paired Brackets
angle. Paired brackets can only be placed in a vertical
• In other Chem & Bio Draw 12.0 applica- orientation. A rectangle or box defines their
tions, point to the Drawing Elements tool position.
and drag in the tool palette to select the To draw a paired brackets:
angle.
1. Select a paired bracket tool from the Draw-
2. Drag from left to right (for a convex arc) or ing Elements palette.
from right to left (for a concave arc). 2. Point where you want a corner of the
EDITING ARCS bracket.
To resize or rotate an arc. 3. Drag from one corner of the box diagonally
to the opposite corner.
1. Position the Arc tool over the arc. Drag
points appear on the ends and in the middle. Daggers
2. Drag either end of the arc to change its To draw a dagger:
length. 1. Select a dagger tool from the Brackets pal-
3. Drag the center point to change the curva- ette.
ture. 2. Click in the drawing window.
4. Use a selection tool to change its size or ori-
entation.
NOTE: To change the size of the dagger size
The Info window indicates the distance edit the Atom Label font size in the Text Settings
between the ends of the arc and the angle the dialog box.
clockwise end makes with the X-axis.
26 Basic Drawings
Chapter 3
Framing Objects properties, select Filled, Faded, or Shaded
under the Curve menu. To add color, select a
You can enclose your drawings or group struc-
color in the Color menu.
tures with a rectangle, brackets, parentheses, or
braces.
To enclose your object:
1. Select the drawing to enclose.
2. Go to Object>Add Frame
Pen Tools
The pen tools are useful for drawing freehand
curves and shapes. To draw a curve, select the
Draw curve tool on the Main toolbar (or go to
View>Other Toolbars>Pen Tools). Then, click
and drag your cursor across the drawing win-
dow.
NOTE: The pen tools are available in Figure 3.6 A freehand curve with different proper-
ChemBioDraw Ultra 12.0, ChemDraw Ultra ties applied; A) A simple curve; B) enclosed; C)
12.0, and ChemDraw Pro 12.0 only. filled; D) faded; E) shaded.
Selecting Objects
Editing curves Use the Lasso or the Marquee tool to select any
To edit a curve, click it using the Edit Curve object. You use the Lasso for freehand selec-
tool. To change the shape, click and drag a tion and the Marquee to select rectangular
handle. You can also change its size and color. regions.
To set one selection tool to behave like the
other, click the Lasso or Marquee tool while
holding the Alt or Option key down.
To toggle a selection tool and the last drawing
tool used, press Ctrl+Alt+Tab or Com-
mand+Option+tab.
If you haven’t used either selection tool, it
defaults to the Lasso tool.
When you select a structure or object, the
selection is displayed with a light blue frame
Freehand Shapes
To create a closed freehand shape, draw a
curve and go to Curves>Closed. To add curve

User Guide
around it with three types of selection handles. selected only if they are entirely within the
with a resize handle on each side and corner. rectangle.
Selecting entire structures
To select an entire chemical structure, dou-
ble-click a bond or atom in the structure using
a selection tool.
If the chemical structure or other object is part
of a group, the group is selected.
Selecting objects by clicking
1. Select the Lasso or the Marquee tool.
Figure 3.7 A) Drag this handle to rotate the object;
B) Drag any corner to resize; C) Drag any side
2. Point to an object in a document window.
handle to distort. A highlight box appears over the selected
object. If you point at a bond, the highlight box
The Lasso Tool
appears over the length of the bond.
Use the Lasso tool to make freehand selection
3. Click the object.
of irregular areas.
To select objects using the Lasso tool: The selected objects appear within the Selec-
tion Rectangle and the cursor changes to a
1. Select the Lasso tool. hand.
2. Press the mouse button while the pointer is
not over any object.
NOTE: If the bond or other object is part of a
3. Drag around part of a structure or other group you can select it as an individual object.
object. See “Grouping Objects” on page 31.
As you drag, a line appears that defines the
selection area. Bonds, structures, or other
objects are selected only if they are entirely Selecting multiple objects
within this area. The end points of the Lasso When you select multiple objects, each object
are connected when you release the mouse but- displays a selection box, so that you can see
ton. exactly what is chosen.
To add more objects to the selection, press
The Marquee Tool
Shift and select the other objects.
Use the Marquee tool to select objects and
To select all objects, go to Edit>Select All.
structures within a rectangular area.
Deselecting all objects
1. Select the Marquee tool.
2. Click and drag diagonally over the struc- To deselect all objects, do one of the follow-
tures or other object. ing:
As you drag, a rectangle appears that defines • Click an empty area outside the selection
the selection area. Bonds and other objects are rectangle.
• Press Esc.
28 Basic Drawings
Chapter 3
• Select a different tool. • resize freely (X and Y axis distortion) by
• Select another object without holding down holding the Shift key down while dragging.
Shift.
Rotating Objects
Deselecting one object
To deselect only one of several selected 1. Select an object to rotate. The Rotation han-
objects, hold down the Shift key and click the dle is at the top of the selection rectangle.
object with a selection tool. 2. Drag the Rotation handle clockwise or
counterclockwise.
NOTE: As shown in the figure below, objects To rotate an atom label with a structure, press
may appear within the borders of the selection the Ctrl or Command key while dragging the
rectangle but not be selected. structure.
NOTE: If an atom is unselected when a struc-

ture is rotated, the structure rotates around the
unselected atom.
To rotate a selected object by a specified angle:

1. Do one of the following:
Figure 3.8 Removing selected objects. Blue dots on
the surrounding rings indicate these rings have been • Go to Object>Rotate.
selected. The center ring has not been selected. • Double-click the rotation handle. The
Rotate Objects dialog box appears.
Resizing Objects
2. Enter a number and click either degrees CW
To resize a selected object, click and drag a for a clockwise rotation or degrees CCW for
handle.
counterclockwise rotation.
• resize proportionately by dragging any cor- 3. (Optional) To rotate the atom label text,
ner. select Rotate Atom Labels.
• resize with either X-axis or Y-axis distor- 4. Click Rotate. Objects are rotated around the
tion by dragging any side. center of the selection rectangle.

User Guide
To repeat the same rotation on any object in 2. Press an arrow key. The selected object
the document window: moves 1 point in the direction of the arrow.
1. Immediately after rotating an object, select
the other objects to rotate. NOTE: To move in a larger increment, hold
2. Go to Edit>Repeat Rotate. down the Alt or Option key while dragging the
Moving the center of rotation object. The selected objects move 10 points in
By default, an object turns around its center the direction of the arrow.
when you rotate it. However, you can move the
center of rotation so that the object rotates Moving Atoms
around an atom or some other location on the
You can move an atom in a chemical structure,
page.
click and drag it using a selection tool. The
To move the center of rotation: bonds connected to the atom stretch.
1. Select the object. A center of rotation indi- To move multiple atoms, select only the bonds
cator (‘+’) appears in the center of the that have atoms on both ends that you want to
object. move. The unselected bonds attached to the
2. While pressing the ALT key, click and drag selected atoms are stretched.
the indicator to another location.
3. To rotate the object, click and drag the rota- NOTE: You can also move atoms using the
tion handle. bond tool used to draw the atom. See “Moving
To reset the center of rotation to its default Atoms” on page 16.
position, deselect the object.
Moving Objects Copying Objects
1. Select an object to move using a selection 1. Select one or more objects.
tool. 2. Ctrl+drag or Option+drag the object(s) to
2. Click and drag the object to a new location. create a copy and position it.
To constrain the movement to the horizontal or
To constrain the copy to move only vertically
vertical direction, Shift+drag the selected
or horizontally while positioning it, hold down
objects.
the Shift+Ctrl or Shift+Option keys.
Small incremental movements are often useful
for aligning objects.To move an object a incre- Deleting Objects
mentally: To delete selected objects, do one of the fol-
1. Select the object. lowing:
• Press the Delete key.
• Go to Edit>Clear.
30 Basic Drawings
Chapter 3
Joining Objects To group objects so that the individual objects
in the group cannot be selected, you create an
To join two structures so that they share a
integral group. When you select any object in
bond:
an integral group, the entire group is selected.
1. Select a bond in the first structure. Grouping does not lock the position or orienta-
2. Shift+click to select the bond in the second tion of objects. Grouped objects maintain their
structure. relative positions when they are centered on
3. Go to Object>Join. the page, aligned or distributed.
To join two structures so that they share an Atoms and bonds making up a single chemical
atom: structure are always grouped. If you group part
of a structure with other objects, the resulting
1. Position the two chemical structures so that group contains the entire structure. If you add
the atoms you wish to fuse are oriented near atoms or bonds to a grouped structure, the new
each other. atoms and bonds are part of the group.
2. Select the two atoms to be joined. To group several objects:
3. Go to Object>Join.
1. Select the objects to group using a selection
tool.
NOTE: Attempts to fuse atoms that are not 2. Go to Object>Group.
approximately lined up will lead to incorrect To select an individual object within a group,
results. move the selection tool over an object until it is
highlighted and click once.
The object is selected, not the group.
NOTE: When you join two differently colored To select grouped objects, move the selection
bonds or atom labels, the color of the front tool over an object until it is highlighted and
object becomes the color of the resulting joined double click it.
object. When you join two atoms that are Ungrouping Objects
labeled, the front atom label becomes the atom To ungroup objects:
label of the resulting atom. For more informa-
tion about front to back ordering of objects, see 1. Select a group.
Chapter : “Page Layout”. 2. Go to Object>Ungroup or right-click the
group and select Group>Ungroup.
Integral Groups
Grouping Objects To create a group so that individual objects
A group is a collection of objects that act as a cannot be accessed:
single object. You can select all grouped 1. Select the objects.
objects by double-clicking with a selection
2. Go to Object>Group.
tool. Objects within a group can be selected
individually and manipulated while still 3. Right-click the group and select
remaining part of the group. Group>Integral.

User Guide
To restore an integral group to a regular group: Aligning Objects
1. Select the integral group. You can align objects vertically and horizon-
2. Right-click the group and deselect tally along their centers or edges.
Group>Integral.
Scaling Objects NOTE: Objects are aligned with the selected

object that appears highest on the page.
To resize objects:
1. Select the object(s). To align two or more objects:
1. Select the objects.
• Go to Object>Scale. 2. Go to Object>Align.
• Double-click a resize handle. The Scale
Objects dialog box appears.
NOTE: If you select only part of a structure or
3. Do one of the following
group with a selection tool, only that part is
• Select the first option to resize the object so used for the alignment operation, but the entire
that the bonds are the default length. structure or group is moved.
• Select the second option to resize the object
so that the bonds are the length specified in
the text box (you must enter a value.) Distributing Objects
• Select the third option to resize the object to Use the distribute commands to position three
a percentage of the current size. A value or more objects an equal distance apart.
greater than 100% enlarges it; a value less To distribute objects:
than 100% reduces it.
1. Select the objects. For reactants and prod-
4. Click Scale. ucts with different shapes, select the parts
of the objects to distribute.
Centering Objects 2. Go to Object>Distribute, and choose Verti-
To center an object (or group of objects) on the cally or Horizontally.
page:
Check Structure
2. Go to Object>Center on Page. You can check structures for errors in
valences, atom labels and defined nicknames.
The selected objects move so that the center of
the Selection rectangle is positioned at the cen- 1. Select a structure, part of a structure, or
ter of the page. caption.
2. Go to Structure>Check Structure.
32 Basic Drawings
Chapter 3
If a structure is incorrect, a message win- Disabling chemical warnings
dow appears.
Warnings are displayed by default; however,
you can turn them off. To disable the automatic
display of chemical warnings, go to
View>Show Chemical Warnings.
To disable the automatic error checking on a
specific object, right-click the object and dese-
lect Display Warnings on the context menu.
When Display Warnings is deselected for an
object:
• Red boxes are not displayed for question-
able objects.
• Problems are reported by the Check Struc-
3. To continue checking the structure, click ture command (Go to Structure>Check
Ignore. To ignore all subsequent errors, Structure).
click Ignore All. To stop checking for errors, To view a description of the problem, do one
click Stop. of the following:
Checking copied structures • Point at the warning with the mouse to dis-
play a tool tip that describes the error.
To analyze a structure on the Clipboard:
• Right-click the warning and choose Explain
1. Go to File>Preferences. This Warning.
2. On the General tab, click the Check Struc-
• Select the structure and go to
ture When Copying to Clipboard or Exporting
Structure>Check Structure.
check box.
This change affects all documents. Warning Preferences
To select which types of chemical warnings to
Chemical Warnings display:
Chem & Bio Draw 12.0 checks for correct 1. Go to File>Preferences.
chemical syntax as you draw. If it finds an 2. Click the Warnings tab.
error in your structure such as improper
3. Select the types of warnings and click OK.
valences, a wavy red box appears around the
questionable object. The box is displayed on-
screen only and does not print.

User Guide
34 Basic Drawings
Chapter 3
4
BioDraw
Chem & Bio Draw provides a variety of tools add more subunits as they are dragged and dis-
for you to create biology related drawings. play the subunit count.
Before reading this section, you should famil-
iarize yourself with the general behavior of NOTE: BioDraw tools are available in Chem-
Chem & Bio Draw 12.0 drawing tools. See BioDraw Ultra 12.0, BioDraw Ultra 12.0, and
“Basic Drawings” on page 13. BioDraw Pro 12.0 only.
BioDraw Tools
The BioDraw toolbar contains tools to draw BioDraw Templates
metabolic pathways, such as enzymes and BioDraw and ChemBioDraw Ultra include a
receptors. To display the BioDraw toolbars, go variety of templates that are useful for illustrat-
to View>Show BioDraw Toolbar. ing biological systems in full color for publica-
Standard shapes, such as circles, ellipses, and tion. To view the templates, go to File>Open
arrows, can be added from the Drawing Ele- Templates and select the template toolbar you
ments tool palette or the Arrows tool palette. want. A few of the available templates are
You can also use the Curve tool to create cus- shown below.
tom shapes.
Anatomy templates
As with Chem & Bio Draw 12.0 Drawing Ele-
ments, you can change the color of an object
with the Color menu, and the line and fill prop-
erties with the Curves menu. You can also
rotate, or change the size.
You create a BioDraw object by either clicking
or dragging on the page where you want it to
appear. Clicking gives you the default size and
shape, dragging allows you to not only to
enlarge the object, but also to distort it by drag-
ging on the x and y axes. Linear objects elon-
gate in the direction they are dragged. The
membrane and protein tools (DNA and helix)

User Guide
Animals a BioDraw object, you must use a selection
tool or the same tool used to create it.
Tool Customization Options
Bio Instruments 1-Substrate Enzyme size of the enzyme

“mouth”
Receptor width
G-protein, gamma shape

subunit
Helix Protein height, width of the

strands, width of the cylin-
ders, spacing
DNA height, width of the

strands, offset of the
second strand, spacing
Organelles
Membrane (line) size of subunit
(The overall length
remains constant, and the
number of subunits
changes in inverse propor-
tion to the size.)
Microorganisms Membrane (arc) length, arc, size of subunit
Membrane size of subunit

(ellipse)
Micelle size of subunit

For more information on using templates, see
“Templates” on page 73. Plasmid map Add/adjust markers and
Customizable Objects regions
The table below describes which BioDraw Ribosomes resize, color

objects you can customize.When customizing
tRNA resize, color
36 BioDraw
Chapter 4
These tools cannot be customized: The membrane line has one adjustment handle,
at its center, that you can drag to change the
2-Substrate Enzyme G-protein, alpha size of the membrane subunits.
subunit
Ion channel G-protein, beta

subunit
Immunoglobulin Golgi body
Endoplasmic Mitochondrion
reticulum
Figure 4.1 Drag the cursor to change the size of the
Cloud resize, color membrane subunits.
Membrane Line TIP: To change the length of the membrane,

1. Select the membrane line tool. select it and drag the left or right handle of the
2. Click and drag to draw a membrane line of selection box. You may then deselect it and
the size you want or just click for the readjust the subunit size.
default size.
When orienting the membrane, note that if Membrane Arc
Fixed Angles is selected, you are constrained to To create a membrane arc, click and drag in a
15 degree increments. To override the con- curve using the Membrane Arc tool.
straint, hold down the Alt or Option key as you
The membrane arc tool has three adjustment
drag.
handles:
• the handle at the starting point controls the
length
• the center handle controls the subunit size
• the handle at the leading edge controls the
arc
Helix Proteins
To create a helix protein:
1. Select the Helix Protein tool.
2. Drag in the document window or click to
draw the default size.
When orienting the protein, note that if the
Fixed Angles option on the Object menu is
selected, you are constrained to 15 degree

User Guide
increments. To override the constraint, hold DNA has four adjustment handles: height,
down the Alt or Option key as you drag. width of the strands, offset of the second
The helix protein has four adjustment handles: strand, and spacing
height, width of the strands, width of the cylin-
ders, and spacing.
Figure 4.3 DNA adjustment handles. A) height

adjustment; B) spacing; C) width; D) offset.
Coloring Residues
After you draw a protein or DNA strand, you
can color each residue using any of the color-
ing options-Shading, Fading, or Filled.
Figure 4.2 Adjustment handles on a helix protein. A)
1. Using the Marquee or Lasso tool, select a
height adjustment; B) width of strands; C) width of
cylinder; D) spacing between cylinders. residue to color.
2. Select the desired color from the Color
DNA Molecules
menu.
To create a DNA molecule:
3. On the Curves menu, select either Filled,
1. Select the DNA tool. Shaded, or Faded.
2. Drag in the work space or click to draw the tRNA
default size.
To create a tRNA molecule:
When orienting the DNA, note that if the Fixed
1. Select the tRNA tool.
Angles option on the Object menu is selected,
2. Click and drag in the workspace until the
you are constrained to 15 degree increments.
tRNA object is the desired size.
You can override the default by holding down
the Alt or Option key as you drag. Having drawn the tRNA molecule, you can
modify it as desired
Ribosomes A and B
These are two separate tools, available on the
BioDraw toolbar.
To draw either Ribosome A or Ribosome B:
38 BioDraw
Chapter 4
1. On the BioDraw toolbar, select a Ribosome ADDING REGIONS
tool. Regions represent the fragments in the plas-
2. Click and drag in the workspace until the mid. You can add as many regions to you map
Ribosome object is the desired size. as you want or have none at all.
Having drawn the object, you can modify its To add regions:
appearance. 1. Right-click the plasmid map and select
Plasmid Maps Regions in the context menu.
To draw a plasmid map, you first enter the 2. In the Regions dialog box, enter in the Start
number of base pairs you want your map to and End text boxes the base pair numbers
represent and then add markers.A simple plas- for a fragment. For example, if a fragment
mid map of an infectious R factor is shown includes all base pairs from 1 to 1000, type
below. 1 and 1000 in the text boxes.
3. If you want the Start and End base pair
numbers for the fragment to appear in the
drawing, select Add Markers At Region
Ends.
4. Click Add.
5. To add more regions, repeat steps 2-4.
6. Click OK.
ADDING MARKERS
Markers let you annotate base pairs in the plas-
mid map. For example, to label a specific base
NOTE: The tRNA and Plasmid Map tools pair or fragment, you add a marker to it.
require ChemBioDraw Ultra or BioDraw To add a marker:
Ultra.
1. Right-click the plasmid map and select
Markers in the context menu.
CREATING A PLASMID MAP 2. In the Markers dialog box, enter in the Posi-
1. On the BioDraw Toolbar, select the Plasmid tion text box the number for the base pair to
Map tool. which you want to add a marker.
2. Click in the drawing window where you 3. In the Label text box, enter the text to iden-
want to draw the plasmid map. The Insert tify the marker.
Plasmid Map dialog box opens. 4. click Add.
3. In the dialog box, enter the number of base 5. Click OK.
pairs you want in the map and click OK. MOVING MARKERS
The plasmid map is drawn. To move a marker label, click and drag the
label.

User Guide
RESIZING REGIONS acids. Then, you can expand, contract, or
you can resize region arrows to indicate differ- remove labels to complete the drawing.
ent base pairs or extend them outward to To draw a sequence:
emphasize them.
1. On the Main Toolbar, click the Sequence
1. Hover over the end of the region’s arrow icon and choose one of the following
using a selection tool. The arrow’s resize sequence tools:
handles appear and the cursor changes to a
Single-letter amino acid tool. Create a protein
double-arrow ( ). chain using a one-letter label to represent each
2. Click and drag a resize handle to adjust the amino acid.
size of the arrow. Three-letter amino acid tool. Create a protein
You can extend a region’s arrow outward as chain using three-letter amino acid labels.
shown below:
DNA tool. Create a DNA chain using labels
that represent each of the nucleic acids.
RNA tool. Create an RNA chain using nucleic
acid labels.
2. Click in the drawing window where you
want to start the sequence. A text box
appears.
3. In the text box, enter the single- or three-
letter label for the residue.
NOTE: For a list of all residue labels, see

“IUPAC codes” on page 42.
4. Repeat step 3 for each residue.

To extend an arrow, click and drag its center
5. When your chain is complete, click any-
handle as indicated by the cursor ( ) in the
where in the drawing window or choose a
figure above.
different tool.
ENHANCING THE DRAWING
EXPANDING SEQUENCES
A plasmid map is like any other drawing. You
After creating a sequence, you can expand the
can add color and shading to it, changing line
whole sequence or just specific labels.
widths, or modifying its text. You can modify
all or part of it. 1. Select one or more labels in the sequence.
(Hold down the Shift key to select more
Drawing sequences than one.)
You can draw protein and RNA sequences 2. Go to Structure>Expand Label.
using labels assigned to nucleic and amino When you expand a label into its structure, the
label appears below the structure.
40 BioDraw
Chapter 4
COLLAPSING LABELS To change the termini:
To collapse the structure back to its label (in
1. Using a selection tool, select the whole
the sequence):
sequence.
1. Double-click the label to select the struc- 2. Go to Object>Object Settings.
ture. 3. In the Object Settings dialog box, select the
2. Go to Structure>Contract Label. Atom Labels tab.
REMOVING RESIDUES 4. Under Amino-acid Termini, select either
When you remove a residue, the adjacent NH2/COOH or H/OH.
labels close, keeping the sequence intact. 5. Click OK.
1. If the label is expanded, collapse the struc- To hide or display the termini:
ture back to its label. 1. Using a selection tool, select the whole
2. Using a sequence tool, double-click the sequence.
label. 2. Go to Object>Object Settings.
3. Press DELETE on your keyboard. 3. In the Object Settings dialog box, select the
REPLACING RESIDUES Atom Labels tab.
To replace a residue, select the Marquee tool 4. Under Amino-acid Termini, select or dese-
and hover your mouse over it. Then, type the lect Show Sequence Termini.
new hotkey. 5. Click OK.
ADDING RESIDUES
Nonlinear sequences
You can add one or more residues to an exist-
ing sequence. By default, Chem & Bio Draw builds a
To add a residue: sequence from left to right across the page as
you continue to enter residue codes. However,
1. Choose the appropriate sequencing tool. you can add a carriage return to a sequence so
2. Select an existing label you want the new that it continues on the next line, such as:
label to be adjacent to.
3. Type the new label. The new label is added
to the right of the existing label.
NOTE: To add a label so that it is the farthest To create a nonlinear sequence:

left in the sequence, select the amino group
(protein sequence) or 3’ group (DNA/RNA 1. Draw the sequence.
sequence) 2. Use the sequencing tool to select the resi-
due you want at the end of the first line
(such as ‘His’ in the example above).
CHANGING AMINO ACID TERMINI
3. Press ENTER on your keyboard.
You can change the termini in the sequence or
even hide them altogether.

User Guide
Bonding from sequences 1. Draw a bond starting at the sequence label
from which you want to create a branch.
Sequence labels typically have two attachment
The Modify Nickname dialog box appears,
points. However, you can add attachment
displaying the sequence structure you
points so that the sequence branches.For exam-
selected.
ple:
2. In the Modify Nickname dialog box, dou-
ble-click the atom in the structure on which
you want to add the attachment point. A
new attachment point appears.
3. Click OK.
Although you modify the sequence in the
Modify Nickname dialog box, the structure for
When you add an attachment point, you spec- the label in the nickname library does not
ify the atom in the expanded label to which the change.
bond will attach. IUPAC codes
To bond from a sequence:
Use these codes to enter nucleotides and amino
acids in your sequence:
IUPAC nucle- Base IUPAC amino Three Amino acid

otide code acid code letter code
A Adenine A Ala Alanine

C Cytosine C Cys Cysteine
G Guanine D Asp Aspartic Acid
T (or U) Thymine (or E Glu Glutamic Acid
Uracil)
R A or G F Phe Phenylalanine
Y C or T G Gly Glycine
S G or C H His Histidine
W A or T I Ile Isoleucine
K G or T K Lys Lysine
M A or C L Leu Leucine
B C or G or T M Met Methionine
D A or G or T N Asn Asparagine
H A or C or T P Pro Proline
42 BioDraw
Chapter 4
V A or C or G Q Gln Glutamine
N any base R Arg Arginine
. or - gap S Ser Serine
T Thr Threonine
V Val Valine
W Trp Tryptophan
Y Tyr Tyrosine
Peptides Disulfide Bridges

The definition in the figure below was used for Creating a disulfide bridge between cysteine
the amino acid alanine. The unselected bond at residues is as simple as drawing a bond.
each end of the structure indicates the connec- Bridges between chains
tion points—nitrogen on the left and carbon on
To draw a disulfide bridge between two
the right.
chains:
1. Draw two chains, each containing cysteine.
2. Draw the bond between the cysteine resi-
dues.
You can draw a peptide chain by either:

• Stringing nicknames together.
Figure 4.4 Before drawing the disulfide bridge
• Stringing nicknames together in an atom

label with a bond attached.
• Stringing nicknames together without

bonds.
Figure 4.5 After drawing the disulfide bridge
Bridges within a chain
To draw a disulfide bridge within a chain:

User Guide
1. Draw a chain that includes two cysteine res- The bonded residues appear below:
idues, such as the one below:
2. Using the single bond tool, draw a bond

from one cysteine residue to the other.
44 BioDraw
Chapter 4
5
Tutorials
Overview To create the bonds:
The tutorials illustrate fundamental drawing 1. Go to Object>Fixed Lengths and Fixed
techniques. Each tutorial introduces new tech- Angles.
niques, or variations of techniques learned in
previous tutorials. We therefore suggest that NOTE: Fixed lengths and fixed angles lets you
you follow the tutorials in order. create structures with consistent bond lengths
Before you begin, review “Conventions for and angles. The fixed length dimension is set in
this guide” on page 4 to familiarize yourself the Drawing tab of the Document Settings dia-
with the terminology. You may also want to log box. The fixed angle dimension increments
use your quick reference card while you follow angles by 15 degrees.
the tutorials.
Chem & Bio Draw 12.0 checks for correct
chemical syntax as you draw. If there is an 2. Go to View>Show Main Toolbar.
error, a red box is displayed around the errone- 3. On the main toolbar, select the Solid Bond
ous object. (the red box appears on screen only tool.
and does not print). To disable the automatic 4. Position the cursor (+) anywhere in the doc-
warning on a specific object, right-click the ument window and click. A bond appears.
object and deselect Display Warnings on the 5. To add a second bond, click the right-end of
context menu. the bond you just created.
Tutorial 1: Drawing a Structure
In this tutorial, we explain how to draw the
structure below:
Figure 5.1 Attaching a bond to an existing bond

The two bonds form a 120-degree angle.
NOTE: The angle used when clicking to add

bonds is controlled by the Chain Angle setting
in the Drawing tab of the Document Settings

User Guide
dialog box. If this bond angle cannot be estab- ADDING A CAPTION
lished, the next smaller and logical bond angle We also want to name the molecule.
is used.
1. Using the Text tool, click below and to the
left of the structure. A text box appears.
6. To create a tertiary carbon, click in the same 2. In the text box, type “2-propanone”.
place as you did in step 5. 3. Press Esc or choose another tool.
.
Tutorial 2: Using Rings

In this tutorial you use rings to create the struc-
ture below:
Figure 5.2 Adding a third bond

CHANGING BOND ORDER
To create the double bond, either click and
drag over the vertical bond you drew in step 6
or simply double-click it.
Create a new document:

1. Go to File>New Document.
2. Go to File>Save As.
Figure 5.3 Adding a double bond 3. Type tut2.cdx in the appropriate text box.
ADDING ATOM LABELS 4. Select a folder in which to save the file.
1. Using the Text tool, click the end of the 5. Click Save.
double-bond shown below. A text box Create the ring system:
appears at the end of the bond.
1. Click the Benzene tool.
2. Shift-click in an empty area of the docu-
ment.
NOTE: Hold down the shift key to change
resonance structures when using the
2. Type an uppercase O in the text box. cyclopentadiene or benzene tools.
3. Close the text box by either pressing the 3. Point to the center of the lower right bond
Esc key or choosing another tool. in the benzene ring.
46 Tutorials
Chapter 5
4. Click to fuse another ring. 6. The create the double bond in the second
ring, hover the mouse over the bond and
type ‘2’ or simply click it.
Figure 5.4 Fusing rings

5. In the final structure, there is supposed to
be only one double bond in the second ring.
To correct the current structure, hover the 7. Using the bond tool, click the carbon atoms
mouse over one of the double bonds in the circled in the figure below. Three new
second ring and type ‘1’. Do the same for bonds will appear.
the other double bond.
8. Hover your mouse over one of the bond

Figure 5.5 To change the bond order, type ‘1’. shown below and type ‘2’. Do the same for
the other bond.

User Guide
9. Hover the mouse over the right-most termi- Tutorial 3: Fischer Projections
nal carbon and type the letter ‘o’ to create
the ketone functional group. This tutorial demonstrates creating a Fischer
projection of glucose (shown below).
10.To connect the left terminal carbons, select

the solid bond tool and click-drag a bond
from one carbon to the other.
The structure is complete.
Figure 5.6 Fischer projections

1. Go to File>Open Style Sheets and choose
ACS Document 1996.
Special Documents are stylesheets or station-
ary pads. They allow you to have pre-config-
ured settings for different tasks.
NOTE: In this tutorial, the ACS template pro-

vides the required settings for structures to be
published in all ACS journals: One-column lay-
out (Page Setting), Bonds with a Fixed length of
0.2 inches (Drawing Setting), Atom Labels in
10 point Arial or Helvetica font (Text Setting).
3. Type tut3.cdx in the appropriate text box.
4. Select a folder in which to save the file.
48 Tutorials
Chapter 5
5. Click Save. 1. To add a perpendicular bond, point to the
uppermost Chemical Warning box and click
To draw the first bond:
it.
1. Click the Solid Bond tool. Note that the red wavy box disappears as soon
2. Point in the document window. Drag down- as you add a bond.
ward vertically to draw the first bond. 2. Click again to add a horizontal bond in the
3. Point to the lower atom, and drag down- opposite direction.
ward again to draw the second bond. 3. Repeat steps 1 and 2 with each successive
The red wavy box appears because Show Chemical Warning box until all horizontal
Chemical Warnings is selected. We will keep it bonds are added.
selected for now.
4. Repeat step 3 three more times to draw a
total of five bonds.
Figure 5.8 Adding horizontal bonds to the backbone

Add labels to the first and last carbon atoms:
1. Select the Text tool.
2. Click the uppermost carbon atom to create a
text box, and type CHO.
3. Click the lower-most carbon atom, and type
Figure 5.7 Drawing the backbone CH2OH.
NOTE: When you drag the pointer along the

length of the bonds, the pointer alternates
between an arrow and a cross. The arrow indi-
cates you are pointing over the center of a
bond, and the cross indicates you are pointing
to an atom.
Add horizontal bonds to the second atom in the

Figure 5.9 Adding atom labels
string of bonds you created:

User Guide
Add the repeating labels for the hydrogens and View the basic properties of the structure and
hydroxyls: paste the information into your document:
1. Click the atom shown in A below and type 1. Click a selection tool to select the last struc-
the letter H. ture drawn. If the structure is not selected,
2. Double-click each of the other atoms double-click the structure.
labeled as hydrogen in B. 2. Go to View>Show Analysis Window.
3. In the Analysis window, click Paste. The
analysis information appears as a caption
below the structure.
Figure 5.10 Adding repeating atom labels
TIP: Double clicking with the text tool repeats

the last label.
3. Click one of the remaining atoms and type Figure 5.12 Fischer projection with analysis
O.oooo Save and close the document:
4. Double-click the remaining atoms to repeat 1. Go to File>Save.
the label. 2. Go to File>Close.
Figure 5.11 Completing the drawing
50 Tutorials
Chapter 5
Tutorial 4: Perspective 2. Go to Object>Rotate (or type Ctrl-R)
Drawings 3. In the Rotate Objects dialog box, enter 30
degrees for an angle and click Rotate. The
In this tutorial, we explain how to create a per- cyclohexane ring is rotated.
spective drawing by creating a model of α–D–
glucose as a Haworth projection.
Change cyclohexane to tetrahydropyran:

1. Click outside the structure to deselect it.
2. Point to the atom indicated in the figure
Figure 5.13 Perspective drawings below, and type the letter o.
Create a new document using the default style:
1. Go to File>Open Style Sheets>New Docu-
ment.
NOTE: If you are following the tutorials in

order, Chem & Bio Draw 12.0 will remember
your last drawing used the ACS style sheet and
open it as the default. Step 1 resets the default Figure 5.14 Adding an atom label with a HotKey
to New Document. Resize horizontally:
1. Go to Edit>Select All (or type Ctrl-A).
2. Go to File>Save As. 2. Using a selection tool, click-drag the right
3. Type tut4.cdx in the appropriate text box. side handle to resize the ring horizontally.
4. Select a folder in which to save the file. Release the mouse button when the ring is
is stretched about 200%.
5. Click Save.
Draw a ring:
1. Click the Cyclohexane Ring tool.
2. Click in an empty area of a document win-
dow. A cyclohexane ring appears.
Rotate the ring:
1. Go to Edit>Select All (or type Ctrl-A).
Resize the ring:

User Guide
1. Go to Edit>Select All (or type Ctrl-A). method is repeated here, with a slight varia-
2. Click-Drag the ring a corner adjustment tion.
handle increase the size of the ring to 1. Select the Solid Bond tool, point to the
150%. A dialog box appears, asking you atom shown in the figure below and double-
whether you want to scale the drawing and click to open a text box.
text settings. 2. Type OH.
3. In the dialog box, click No.
Add vertical bonds:
1. Click the Solid Bond tool.
2. Point to the atom shown in the figure below
and drag upward to create a bond.
Figure 5.15 Adding the OH labels

3. Move the pointer to the other atoms as
3. Point to the same atom, and drag downward shown, and triple-click to repeat the atom
to create another bond. label.
4. Repeat this procedure four more times, add-
ing the pairs of vertical bonds shown
below:
TIP: If placing the labels is difficult because of

the drawing size, go to View> Magnify.
Create OH labels:
You can use the repeating bond label technique
in Tutorial 4, or use Hotkeys. For the HotKey Add the CH2OH label:
method, just point and type “o”. The Text tool 1. Triple-click the upper atom of C5.
52 Tutorials
Chapter 5
2. Press the Enter (Windows) or Return (Mac- 3. Click to change to the new bond type.
intosh) key to open the atom label text box. 4. The cursor changes to a bold arrow as you
Type CH2 before the OH. point at the bond.
5. Click the Bold Wedge bond tool.
6. Click each of the ring bonds adjacent to the
bold bond.
For each bond, point slightly off center in the
direction that you want the wide end of the
wedge to be oriented and click.
TIP: If you move the pointer too far, the high-

light box disappears. If you find placing the
Figure 5.16 Adding the CH2OH label pointer difficult, go to View>Magnify.
NOTE: When used with a bond tool active,

Enter (Windows) or Return (Macintosh) is a NOTE: If the wedge is pointed in the wrong
Hotkey that opens a text box for the last atom direction, click the bond again to flip its orien-
labeled. tation.
Change the type of the front bonds: The resulting structure is shown in below:
1. Click the Bold Bond tool.
2. Point to the center of the bond shown
below.
Save and close the document:

1. Go to File>Save.
2. Go to File>Close.

User Guide
Tutorial 5: Newman Projections 2. Create a duplicate by holding down the Ctrl
(Windows) or Option (Macintosh) key
This tutorial demonstrates how to draw a New- while dragging the selection rectangle
man projection of ethane. upward to the right of the original.
The selection box disappears while you are
dragging.

1. Go to File>New Document. Figure 5.18 Creating a duplicate structure
Add a bond between the duplicated structures:
4. Select a folder in which to save the file. 1. Click the Solid Bond tool.
2. Click and drag from the tertiary carbon
5. Click Save.
atom of the lower fragment to the tertiary
Draw ethane: carbon of the upper fragment
:
2. In the document window, click and drag

NOTE: When connecting existing atoms, the
downward to create the first bond.
Fixed Length and Fixed Angles commands are
3. Point at the lower atom and click to add a ignored.
second bond.
4. Continue pointing at the same atom and
click again to add a third bond. When you release the mouse button, the ethane
structure is complete. Now, create its Newman
projection.
Drawing the Newman Projection
In this step, you will use the Orbital tool to
draw the hollow circle that is particular to
Newman Projections.
Figure 5.17 Creating the initial structure 1. Click the Orbital tool, and select the s
(Open) orbital.
Duplicate the structure:
2. Point to the left center carbon and drag out-
1. Click a selection tool. The last structure you
ward.
drew is selected.
The size of the orbital is constrained just like
bonds are. The constraint is based on a percent-
54 Tutorials
Chapter 5
age of the Fixed Length setting in the Drawing 2. Type 180 in the Angle text box and click
tab of the Document settings dialog box. Rotate.
Figure 5.19 Adding an orbital

Figure 5.20 After rotation
NOTE: Orbitals are not automatically With the rotated bonds still selected, change
grouped with the closest structure. To group the the layering of the structure so that the selec-
orbital with the existing structure so you can tion is in front.
move them as a unit, go to Object>Group. 3. Go to Object>Bring to Front (there is no vis-
ible change when you do this).
Move part of the structure to the front to over- Move the front part of the structure to create a
lap the orbital: Newman projection:
1. Click the Marquee tool. 1. Point within the Selection Rectangle so the
The orbital is selected. Click in the worksheet pointer changes to a hand.
to deselect it. 2. Drag the selection until the tertiary carbon
2. Point above the structure and drag around is centered within the orbital, as shown
the upper fragment to select the three below.
bonds. Do not select the bond connecting
the two fragments. You can Shift+click on
each bond separately, if that is easier.
NOTE: If chemical warnings are turned on,

you will see a red warning box when you over-
lay the structure, because the center atoms are
Rotate the selection: “on top of” each other.
1. Double-click the rotation handle to open the

Rotate Objects dialog box.

User Guide
3. Release the mouse button and click outside Drawing the structure
the Selection Rectangle to deselect the To draw the structure:
structure.
2. In the document window, click and drag
downward to create the first bond.
3. Point at the lower atom and click to add a
second bond.
4. Continue pointing at the same atom and
click again to add a third bond.
Figure 5.21 Completed Newman projection

1. Go to File>Save.
Tutorial 6: Stereochemistry Figure 5.22 Creating the initial structure

This tutorial demonstrates using Stereochemis- 5. Point to the bond shown in the figure below
try markers and the flip command. As you and type 9 (the Hotkey to sprout two
draw the structure below, you may notice that bonds).
some of the steps are similar to those needed
earlier to draw isobutane.
Create a new document.
1. Go to File>New Document.
2. Go to File>Save as.
Figure 5.23 Repeating the bond sprouting
5. Click Save.
Now, turn the single bond at the upper right
First, we draw the following structure: into a double bond using any of the methods
described in the earlier tutorials.
56 Tutorials
Chapter 5
Adding Atom Labels 2. Go to Object>Show Stereochemistry. The S
1. Double-click the alpha carbon atom and marker appears.
type NH2 in the text box that appears. Press
the Esc key when finished.
2. Add the O and OH with the text box or the
HotKey o.
3. Select the structure and go to Object>Flip

Horizontal. The R marker appears.
Adding Stereochemical properties

We now add stereochemical properties to the
structure. First, we change the carbon-nitrogen
bond to a solid wedge bond (tutorial 5 intro- 4. With the structure selected, go to Object>
duced the wedge bond tool; however, you can Rotate 180° Vertical.
also use a HotKey). Afterward, we display the
stereochemical markers, (R) and (S) for the
two isomers.
To add the solid wedge, point to the carbon-
nitrogen bond and do one of the following:
• Select the Wedge Bond tool, and click the
bond. The Wedged bond becomes hashed and the (R)
• Point to the bond and type the letter w. stereochemistry is preserved.
1. Go to File>Save.
Tutorial 7: Templates
Chem & Bio Draw 12.0 comes with an exten-
To add the markers: sive template library of predrawn structures
and images to help you work more quickly.
1. Select the entire structure with the Lasso or You can use a template to either start a new
Marquee tool. drawing or to modify one that already exists.

User Guide
In this tutorial, we use the phenanthrene tem- 1. Go to File>Open Style Sheets>New Docu-
plate to create peroxydibenzene. The template ment.
and final drawing are shown below: 2. In the Main toolbar, select the template
tool. The list of template palettes appears.
3. In the Aromatics palette, select the phenan-
threne template (it is in the fourth row, third
column).
4. Click anywhere in the document window.
Phenanthrene appears.
Now that phenanthrene is in the document, you
will want to remove two bonds from the center
ring and add two oxygen atoms.
To modify phenanthrene:
1. In the Main toolbar, select the Eraser tool.
2. Click the bottom bond in the center ring.
3. Click the double bond at the top of the ring.
It is now a single bond.
4. In the Main toolbar, select the Text tool.
5. Select one of the carbon atoms in the hydro-
carbon chain (what was the middle ring).
There are two simple steps to follow when 6. Type O to change it to an oxygen atom.
using a template. First, add the template to 7. Select the other carbon atom and change it
your drawing; second, modify the template to to an oxygen.
look the way you want.
To add the template for phenanthrene: Peroxydibenzene is now shown.
58 Tutorials
Chapter 5
6
Advanced Drawing Techniques
The advanced features in Chem & Bio Draw Mirror Images
are designed to either help you save time or to
perform functions that simply can’t be accom- You can reflect structures through planes per-
plished using the basic tools. For example, you pendicular to the X-axis or Y-axis. By copying
can see your drawing as 3D models or create a structure, you can create its mirror image to
stereoisomers at the click of your mouse. With represent racemic mixtures and other stereoi-
the Chem & Bio Draw 12.0 advanced drawing somers. You can also create a mirror image of
features, you can: a structure that has defined stereochemistry by
duplicating and rotating it.
• Create mirror images
To create a mirror image:
• Clean up structures
1. Draw a structure with defined stereochem-
• Add bonds to characters in atom labels
istry, for example, wedged bonds.
• Create bonds whose attachment is not
2. Select the structure and make a copy using
explicitly defined
Ctrl+Drag or option+drag.
• Add atom numbers 3. With the copy still selected, go to
• Contract and expand sections of structures Object>Flip Horizontal or Flip Vertical.
• View structure perspective To preserve the absolute stereochemistry while
• Create mass fragmentation, retrosynthesis, flipping, go to Object>Rotate 180º.
and synthesis drawings
• Draw with templates Coloring objects
• Create and edit templates You can select and color objects—specific
• Label functional groups with nicknames. bonds, part or all of a chemical structure,
boxes, curves, arrows, orbitals and reaction
mechanism symbols.
NOTE: The Clean Up Structure and template The border of objects that are shaded or filled,
features are available in ChemBioDraw Ultra such as white filled s-orbitals in the Orbitals
12.0, ChemDraw Ultra 12.0, and ChemDraw palette, are the same color as the shading or
Pro 12.0 only fill. The border of objects that are hollow, such
as circles and hollow boxes in the Drawing
Elements palette can be colored, but the inside
of the object cannot.

User Guide
To color an object: tures. For example, you can use the label “Ph”
to represent a phenyl functional group rather
than having to draw it. Labels are useful for
2. Do one of the following: drawing structures quickly or emphasizing a
• Click the Color button on the Style tool- part of your structure.
bar, and select the color from the menu
that appears.
NOTE: You can define nicknames in ChemBio-
• Choose a color from the Color menu.
Draw Ultra, Chem & Bio Draw 12.0 Ultra, and
• Go to Object>Object Settings and select Chem & Bio Draw 12.0 Pro only.
the color in the Drawing tab. Click OK
when finished.
You first add a label to part of your structure.
Coloring groups You can then expand the label to show the part
Chem & Bio Draw colors groups differently of the structure the label represents or reduce it
from integral groups. When you color an inte- back to the label.
gral group, its objects acquire the new color
but retain the original shading. When you color
Expanding Labels
a normal group, the new color is applied and If your structures contain defined nicknames,
the original shading is ignored. long atom labels, or contracted labels, you can
restore your structures to the expanded form.
Contracted:
Expanded:
Figure 6.24 A) The mitochondrion structure in its

default color; B) The structure colored blue as a
group; C) The structure colored blue as an integral
group. When you expand a label that contains a diva-
lent nickname, for example H-Ala-OH, the first
The new color applies to all structures in the
attachment is to the character to the left of the
group, even if the original colors of the objects
nickname (H). The second attachment is to the
in the group are not the same.
character to the right of the nickname (OH).
Labels To expand atom labels:
You can use labels to represent atoms, and 1. Select a selection tool.
define nicknames that help you draw struc-
60 Advanced Drawing Techniques

Chapter 6
2. Select the label to expand or double-click The label replaces the selected portion of the
the structure to expand all possible labels. structure.
3. Go to Structure>Expand Label. Your struc-
ture is redrawn in its expanded form.
Contracting Labels
You can compress an area of a structure and
replace it with a text label. Contracted labels
Figure 6.2 Contracted label
are similar to nicknames, but they are for one-
time use only, in the current document.
To create a contracted label: NOTE: If the area of the structure you contract
contains errors, an error dialog box appears.
1. Select the area of the structure to contract. Click Ignore to view other errors. Click Ignore
All to ignore all errors or Stop to end the con-
tract process.
Multiple atoms
Labels can comprise a group of atoms. When
Figure 6.1 Selecting a structure to contract you expand the label, it expands to create the
2. Go to Structure>Contract Label. The Con- structure.
tract Label dialog box appears. Expanded:
3. Type a label for the contracted structure and
click OK.
Contracted:

User Guide
Adding a Label of multiple atoms Objects” on page 32 and “Page Setup” on page
1. Using the text tool, click an atom in the 184.
structure where to place the label.
2. Type the formula (such as “CH2NHC3”). NOTE: The Clean up Structure command is
available in ChemBioDraw Ultra 12.0,
3. Using a selection tool, select the formula.
ChemDraw Ultra 12.0, and ChemDraw Pro
4. Right-click the formula and select Expand 12.0 only.
Label or go to Structure>Expand Label.
The Clean Up Structure feature follows these

rules:
• The Fixed Length setting on the Drawing
tab of the Document Settings dialog box
determines optimum bond lengths.
• A ring is redrawn only if all of its bonds are
selected.
• Multi-attached atom labels, variable attach-
ment points, and multi-center bonds cannot
be cleaned.
Figure 6.3 Adding bonds to a label
• Structures are rotated so that as many bonds
After the label expands, it behaves the same as possible are directed at a multiple of 15
way as any other part of the structure. degrees.
Clean Up Structure • Clean Up Structure preserves stereochemi-
cal meaning rather than the precise identity
You may find it difficult to draw atoms in the of wedged or hashed bonds, as shown
sterically correct position. Use the Clean Up below.
Structure command to redraw the structure so
that bond lengths are fixed and atoms are in the
correct location. Clean Up Structure does not
position molecules relative to other objects.
So, some overlap may occur.
For some compounds, the Clean Up Structure
command produces a structure that extends
beyond the bounds of the page. To view the
entire structure, scale the structure or increase
the size of the printed page. See “Scaling
Figure 6.4 Preservation of stereochemical meaning

Chapter 6
Using Clean Up Structure: Isomers of dibromobenzene can be represented
as:
1. Select the structure or part of the structure
to clean up.
2. Go to Structure>Clean Up Structure or type
Shift+Ctrl+K.
NOTE: The Clean Up Structure command

redraws your structure in iterations. Therefore,
you may need to select the command more than
Abbreviated
once.
notation for:
Attachment Points
You can draw polyhapto structures such as fer-
rocene ((Cp)2Fe), or an abbreviated notation
for different positional isomers of a compound,
using attachment centers. The procedure is
similar, and in both cases, the structure retains
chemical significance.
Multi-Center Bonds
To create a multi-center attachment point:
1. Select the structure whose center you want
defined as a multi-center attachment point.
2. Go to Structure>Add Multi-Center Attach-
ment.
An asterisk indicates a multi-center node.

The asterisk is not visible once a bond is drawn
to it. However, you can view the attachment
point using a bond or selection tool. See
“Viewing Attachment Points” on page 64.
Figure 6.5 Drawing a polyhapto structure To draw a bond to a multi-center attachment
point:
1. Click the Bond tool.

User Guide
2. Point to the asterisk and either click or drag a bond tool or a selection tool. The attachment
to create a bond. point is highlighted.
Atom Numbering
TIP: Go to Object>Fixed Lengths to either dis-
able or toggle Fixed Lengths to draw the bond You can add sequential numbering indicators
so that it extends from the ring. to atoms. The types of indicators are:
• Numbers (1, 2, 3, and so on)
• Text ending with a number (atom1)
Variable Attachment Points
• Greek letters in the Symbol font
To create a variable attachment point:
• Letters (a, b, c, and so on)
1. Draw the structural fragment to which to
The default indicator is numbers.
assign a variable attachment node.
2. Select the fragment.
TIP: To use text instead of numbers, number an
3. Go to Structure>Add Variable Attachment.
atom then edit the number. See “Editing Atom
4. Point to the asterisk in the structure and Numbers” on page 65.
drag to draw a bond.
NOTE: Either disable or toggle Fixed Lengths Showing Atom Numbers

to draw the bond so that it extends from the
ring. 1. Select one or more atoms to number.
2. While pointing to the selected atoms or
structure, do one of the following:
• Right-click or Control+click, point to Atom
on the context menu, and click Show Atom
Number.
• Type the HotKey ‘ (single quote).
3. For a single atom, do one of the following:
• Right- click and click Show Atom Number
from the context menu.
Figure 6.6 Using a variable attachment point • Type the HotKey ‘ (single quote).
Viewing Attachment Points Hiding atom numbers
After you draw a bond from a variable or
1. Select the atoms or structure.
multi-center attachment point, the asterisk dis-
2. Right-click or Control+click, point to Atom,
appears. To view an attachment point, position
and deselect Show Atom Number.
the cursor over the attachment point with either

Chapter 6
To remove an atom number indicator, do one 2. Click the appropriate position option, and
of the following: enter a value.
• Click the indicator with the Eraser tool.
• Point to the indicator with the Marquee or To position … Type a value for
Lasso tool and type Backspace or Delete. Position …
Editing Atom Numbers from the atom or bond by angle or by

To edit the atom number text and style: center to the indicator clock
center
2. Select the atom number indicator and type from the atom or bond by offset—hori-
the changes. center to bottom left of zontal and vertical
indicator baseline
NOTE: When you type in a new indicator, you
reset the counter for that structure to a new at specified coordinates absolute—horizon-
style. You may then continue numbering in that tal and vertical
style with the standard means. For example, if
you type α in a text box, then point to another
atom and use the context menu or HotKey, the
atom will be labeled β. Switching to another Structure Perspective
structure resets the counter. You can tilt molecules or portions of mole-
cules through three dimensions with the Struc-
3. To edit the atom number style, select the ture Perspective tool.
atom number indicator with the Text tool
and use the Text menu or Text formatting
toolbar.
Positioning Atom Numbers
Atom number indicators are positioned auto-
matically and move appropriately when you
modify a structure. You can reposition them by
dragging them to the desired position or use
To tilt a structure:
the Position Indicators dialog box.
To reposition an indicator: 1. Select the structure by dragging over it with
the Structure Perspective tool.
1. Right-click the indicator to move and click
2. Place the cursor inside the marked rectangle
the Position command on the context menu.
and drag in any direction.
The Position Indicators dialog box appears.
3. Use Shift+drag to limit the rotation to the X
or Y axes only.

User Guide
You can also select part of a complex molecule more bonds. When you release the mouse but-
and rotate it around a particular bond. ton, bonds that you cross are broken.
NOTE: Structure Perspective cannot be

applied to orbitals.
Flatten Command
To remove the Structure Perspective Tool
effect:
1. Select the structure with the Marquee or
Lasso Tool.
Figure 6.7 Using the mass fragmentation tool
2. Go to Object>Flatten.
By default, the line you draw disappears when
All z-coordinate information is removed from you release the mouse button.
the structure.
Mass Fragmentation NOTE: To draw a curved line or to keep the

line visible, hold down the Alt (windows) or
The Mass Fragmentation mimics the molecular Option (Macintosh) key while drawing. To keep
fragmentation in a mass spectrometer (but does the line visible, release the mouse button first.
not have any predictive qualities, so you must To draw a curved line, release the Alt or Option
specify what bonds are to be broken). key first.
NOTE: The Mass Fragmentation command is

When the line crosses a bond, the formula and
exact mass for the fragments on either side of
the bond are displayed as if the bond were
12.0 only.
homolytically broken. That is, a single bond
turns into a monoradical on each fragment; a
To fragment a structure, use the Mass Frag- double bonds turns into a pair of diradicals. If
mentation Tool to drag the cursor across one or multiple bonds are crossed, all fragments on
each side of the line are considered together. If
the only bond crossed is a ring bond, a single
formula/mass pair is displayed.
You can reposition the formula and mass dis-
plays (they are text objects), or delete them
altogether.

Chapter 6
Synthesis and Retrosynthesis Drawing Reactions
Chem & Bio Draw 12.0 includes two tools to To demonstrate how to draw reactions, we will
help you draw synthesis reactions. The Synthe- use this example:
sis tool draws synthesis reaction based on a
product structure that you specify. Alterna-
tively, the Retrosynthesis tool draws the reac-
tion with the product on the left and a broad
arrow pointing to the reactants. These tools are
in the fragmentation tools palette of the main
tools palette. Drawing an arrow
To demonstrate these features, we use the Starting with 2-propanone, draw the reaction
Beyer Method for quinolines, starting with the arrow:
structure below. 1. On the Main Tool toolbar, click the Arrow
tool to display the Arrow toolbar.
2. While holding the mouse button down,
move the mouse to the palette title bar, then
release the button. The palette becomes a
floating toolbar.
3. Click the third arrow from the left in the top
You can create either type of reaction using the
row.
appropriate tool and dragging through bonds
indicated by the dotted line. For example, if 4. In the document window, click and drag the
you use the retrosynthesis tool, you will create mouse horizontally to the right of the 2-pro-
the reaction: panone structure. The arrow appears.
6. Click above the arrow. A text box appears.
7. Type OH and press Esc. Realign the text
box as necessary using a selection tool.
Figure 6.8 Reaction created with the Retrosynthesis
tool
NOTE: If Show Chemical Warnings is turned
on (the default), a red box will appear around
the OH label when change tools or open another
text box indicating an error. Ignore this for now.
Figure 6.9 Reaction created with the Synthesis tool Add a charge symbol using the specialized
By dragging through the bonds in the structure symbols available in the Chemical Symbols
below (as indicated by the dashed lines), we tool palette:
can create either of two reactions, depending
on the tool that is used.

User Guide
1. In the Main Tool toolbar, click the Chemi- ored effects using the filled, faded, and shaded
cal Symbol tool. options. To use these effects:
2. Holding the mouse button down, select the 1. Select a block arrow from the Arrows pal-
circled Circle Minus symbol. ette and right-click it.
3. Point to the center of the OH label. Move 2. Select a color from the Color menu.
the cursor slightly right or left to select the
3. On the context menu, choose either Filled,
O.
Faded, or Shaded.
4. With the oxygen atom selected, drag the
charge symbol around the atom to the Drawing the product
desired position. We now create 4-hydroxy-4-methyl-2-pen-
tanone using a copy of the 2-propanone struc-
ture. You can also create the product from
scratch but you may find copying another
structure more convenient.
Copy the structure:
Objects added from the Chemical Symbols
palette are associated chemically with the 1. Select the 2-propanone structure and its
structure they are near. Note that the red caption.
valence error warning disappears when you 2. Press and hold the Ctrl (windows) or Option
add the minus charge. (Macintosh) key.
CURVED ARROWS The hand pointer with a plus sign indicates that
For some reactions, you may not want to be you are in the duplication mode of a selection
limited to drawing simple, straight arrows. In tool.
fact, you may need a variety of curved or col- 3. Drag the selection rectangle to the right and
ored arrows to enhance your drawings. You release the mouse button.
can curve most arrows found on the Arrows
toolbar. After you paste an arrow in your draw-
ing, click and drag the selection point in the
middle of the arrow.
As you drag the selection point, the size of the
arc appears, measured in degrees.
COLORED ARROWS
To color an arrow:
Figure 6.10 Duplicating a structure
1. In the drawing window, select the arrow to
color.
NOTE: To keep the copy aligned with the orig-
2. Select a color from the Color menu.
inal, hold Shift while dragging.
COLORING BLOCK ARROWS
For block arrows (those that aren’t made of
just simple lines), you can create various col- Modify the duplicate structure:

Chapter 6
1. Select the Solid Bond tool. hydroxy-4-methyl-2-pentanone, press the
2. Click the far right bond of the copied struc- Enter or Return key, and type 1 mole.
ture (Figure A). 2. Using the Text tool, add 2 Mole to the cap-
3. Point to a terminal carbon, shown in A tion for the reactant.
below. If the captions are not aligned properly under
4. Click the carbon atom until three bonds their structures, move them using a selection
appear, allowing a pause between each tool.
click. Adding a frame
To complete the drawing, add a shadowed box
NOTE: If you click too fast, the click is inter- around it:
preted either as a double-click, which opens a 1. Click the Drawing Elements tool.
text box or a triple-click, which duplicates your
2. In the Drawing Elements toolbar, select the
last atom label.
Rectangle (shadowed) tool.
3. Point to the upper left corner of the reaction
scheme. Click and drag diagonally down-
ward to the right to draw the box.
Grouping Objects
Some objects, such as arrows, are not associ-
ated with each other automatically. You can
manually group the objects together using the
Group command. You can then manipulate or
Figure 6.11 Adding multiple bonds to an atom move them as a single object.
5. Point to a terminal carbon atom, shown in To group objects:
Figure A below. 1. Click the Marquee tool.
6. Type capital OH. 2. Do one of the following:
• Draw a box around the arrow, caption and
symbol to select them.
• Click the arrow, then hold the shift key
down while you click the OH caption and
the charge symbol.
The Shift key lets you add objects to a selec-
tion without deselecting other objects.
Figure 6.12 Adding an atom label
Replace the product caption:
NOTE: If you click a selected object while
1. To update the product’s caption, select the holding Shift, that object is deselected.
caption with the Text tool and type 4-

User Guide
3. Go to Object>Group. Guidelines
For a reaction to be interpreted:
NOTE: You can select individual objects • Each reactant and product must contain at
within a group by clicking them. least one atom.
• Each reactant and product must be
Aligning the structures
described using a single label.
To align the structures: • Multiple reactants and products must be
linked by a “+” sign.
1. Select both structures with the Lasso or
Marquee. • Reaction conditions must reside completely
2. Go to Object>Align>T/B centers. within the left and right boundaries of the
reaction arrow.
The Reaction Interpreter
• The reaction cannot include a curved arrow.
The reaction interpreter identifies the reactants,
products, catalysts, and annotations in a reac- Drawing an Intermediate
tion. The interpreter color-codes each part to
help you identify them. In this tutorial, you draw the intermediate
structure shown below starting from a ring and
add arrows with the arrow and Draw Curve
tools.
NOTE: The Reaction Interpreter is available

in ChemBioDraw Ultra 12.0, ChemDraw Ultra
12.0, and ChemDraw Pro 12.0 only.
To use the reaction interpreter:

1. Go to View>Show Reaction Interpretation.
2. Hover your cursor over the reaction arrow.
The various parts of a reaction are color-coded
as follows: 1. Go to the File>New Document.
• Red–reactants 2. Go to File>Save As command.
• Magenta–products
• Cyan–Anything above the reaction arrow 5. Click Save.
• Blue–Anything below the reaction arrow Draw a ring:
1. Select the Cyclohexane Ring tool.

Chapter 6
2. Click in the document window to add a 4. Point to the same atom as in Step 2, (shown
ring. in Figure 6.15), and click twice (slowly) to
add two more bonds.
Delete an atom and its bonds from the ring:
1. Click the Eraser tool.
2. Click any atom, as shown in Figure 6.13 A.
Figure 6.15 Adding two bonds to an atom

Create a double bond:
5. Point to a bond, as shown in Figure 6.16,
and click.
Figure 6.13 Erasing an atom The double bond will initially form to the
inside. Click twice more to move it to the out-
side, as shown in Figure 6.16 B.
NOTE: Click the center of a bond to delete it or .
drag the eraser across multiple bonds to make

multiple deletions.
Add a bond: Figure 6.16 Creating a double bond

1. Click the Solid Bond tool. Add an atom label using a hotkey:
2. Point to an atom, as shown in Figure 6.14. 6. Point to the atom to label shown in figure A
3. Click to add a bond. below and type the letter o.
Figure 6.14 Adding a bond 7. Without moving the cursor, type a “-”
Add second and third bonds: (minus). The OH label changes to O–.
Complete the intermediate structure by adding

another OH:

User Guide
1. Point to the atom shown in Figure A below. width adjustment handles to adjust the
arrow as necessary.

• Type the letter o.
• Double–click the atom to open a text box,
and type OH.
The next step is to add arrows to indicate elec- Figure 6.18 Adjusting an arrow
tron flow. You add the first arrow using the Create the remaining arrows:
adjustable Arrows tool and the others using the
1. Select the Draw Curve tool.
Draw Curve tool.
2. Click just to the right of the O– atom label
1. Choose an upward curved arrow from the and drag to draw the arrow. Release the
Arrows palette. mouse button.
2. Point near the double bond where to indi-
cate the start of electron flow.
3. Drag to the right.
Figure 6.19 Drawing custom arrows

Refine the shape of the arrow:
Figure 6.17 Dragging an arrow

1. If the arrow isn’t exactly how you want it,
select the Edit curve tool to change its
4. Point to the arrow. Adjustment handles shape and position.
appear at the ends and in the middle. When you use the Edit curve tool to select
5. Drag the center up to decrease the curve. a curve, control handles appear that let you
You may also drag the ends or the point- change the shape of the curve.
2. Click and drag a terminal control handle (at
the end of the dotted line) to change the
shape of the curve at a particular location.

Chapter 6
3. Click and drag a midpoint control handle Templates
(at the middle of the dotted line) to move a
particular point in the curve. Chem & Bio Draw 12.0 includes an extensive
library of templates to help you quickly create
your own structures and reactions. You can use
a template either as a starting point for a new
drawing or to fuse structural features to an
existing drawing.
NOTE: Templates are available in ChemBio-

Draw Ultra 12.0, ChemDraw Ultra 12.0, and
ChemDraw Pro 12.0 only.
The templates you define are not limited to

Figure 6.20 Adjusting a curve atoms and bonds. Templates can contain any
features such as captions, colors, boxes, arcs,
4. To add an arrow head, go to Curves>Full
orbitals, arrows, reaction mechanism symbols,
Arrow at End.
and curves. You can also paste pictures from
5. Press Esc when you are finished. other applications into a template pane.
Selecting a template
Chem & Bio Draw 12.0 provides several ways
for you to select a template.
1. Go to File>Open Templates.
2. Select a template toolbar from the Main
toolbar.
3. Go to View>Templates> and select a tem-
plate toolbar from the list.
6. Create the remaining arrow as described
above to complete the intermediate as New Drawings
shown below.
1. Select the template to use.
2. In the document window, click and drag the
mouse until the template is oriented the way
you want or simply click in the window.
TIP: To modify template size while drawing it,

hold down the ALT key.

User Guide
Fusing a Template 6. In any drawing, select the Template tool on
the Main toolbar to use you palette.
In addition to starting new drawings, you can
use templates to add structural features to Modifying templates and palettes
existing drawings. To fuse a template to a MODIFYING A TEMPLATE
drawing, first select the template you want
1. Go to File>Open Templates and choose the
using the template tool. Then, click a bond in
palette from the list.
the existing drawing to add the template struc-
ture. 2. To modify a template, click in its template
pane and modify it in the document window
Customizing Templates as desired.
You can modifying any of the template pal- ADDING AND DELETING ROWS AND COLUMNS
ettes and creating your own palette. 1. in the palette, click in a pane where to add
Creating templates and palettes the new column or row or select the one to
When you create a palette, a set of empty tem- delete.
plate panes appear above the document win- 2. Select the appropriate option in the Edit
dow. The templates you draw for your palette menu.
appear in these panes. After you save your pal- ADDING A TEMPLATE
ette, it will contain the templates you have To add a template, click in an empty template
drawn. You can then select your palette from pane and begin drawing the template in the
the palette list in the Templates tool. document window. Go to File>Save.
To create a template palette: DELETING A TEMPLATE
1. Go to File>Open Style Sheets>New Tem- 1. Select the template pane for the template to
plates. delete.
2. Click in a template pane.
2. In the document window, select the entire
3. In the document window, draw a new struc- drawing.
ture. This will become a template in the 3. Go to Edit>Clear.
new palette. 4. Go to File>Save.
4. Click another template pane and draw Orienting Templates
another structure as desired. To make templates that you create simple to
5. After you draw all the templates in your use, orient the template structure so that you
palette, go to File>Save. can modify the bonds you use most often.
Resizing Template Panes
NOTE: Save your palette in the Chem & Bio To resize the Template panes in the Template
Draw 12.0 Items folder to ensure that it appears panel, drag the lower right corner of the Tem-
in the Main toolbar. plate panel. If needed, first click and drag the
resize handle.

Chapter 6
Defining Nicknames nicknames with two or more attachment
points, the numbering sequence of the attach-
A nickname is an alphabetic abbreviation that ment points determines the order in which
represents part of a structure. Nicknames are other parts of the structure are attached. For
useful for drawing large structures or struc- example, if you expand the structure H-Leu-
tures that repeatedly use similar features. OH, the hydrogen is bonded to the first attach-
ment point in leucine and the hydroxyl group
NOTE: The Nicknames feature is available in to the second.
ChemBioDraw Ultra 12.0, ChemDraw Ultra
Defining attachment order
When you define your own nickname, you first
draw the functional group structure and then
Chem & Bio Draw 12.0 comes with a library indicate the attachment points. The numbering
of nicknames for various commonly used func- order of the attachment points (for structures
tional groups and monomers. For example, if that have two) is determined by which bond
you typically draw protein structures, you may you draw first. For example, when the leucine
consider using amino acid nicknames in your nickname was created, the bond for the amino
drawings rather than drawing each amino acid attachment point was drawn first. Therefore, it
structure yourself. is numbered first.
.
NOTE: If you don’t know which attachment

point was drawn first, select the attachment
point you want labeled ‘1’ and go to
Object>Bring to Front. Then define the nick-
name.
For more information, see “Using Nicknames”

on page 18.
To define a new nickname:
Figure 6.21 Leucine, as found in the Nicknames
1. Create a structure containing the functional
Library
group to define as a nickname.
Attachment points 2. Select the functional group.
A nickname can have one or more attachment You must indicate the connection point for the
points that connect it to the main structure. functional group by selecting the new fragment
Attachment points must be single bonds. For

User Guide
without the bond connected to the attachment Symbol Nickname Element
point.
Am Amyl Americium
Np para-Nitrophenyl Neptunium
Pr Propyl Praeseodymium
To remove the overriding Nicknames, go to

File>List Nicknames and delete the overriding
nickname definition.
Deleting Nicknames
Figure 6.22 Adding a nickname. The arrow indi- You can also delete nicknames from the Nick-
cates the bond connected to the attachment point of names dialog box.
the nicknamed functional group. To delete a nickname:
3. Go to Structure>Define Nickname. 1. Go to File>List Nicknames.
The number of connection points is shown by 2. Select the nickname and click Delete.
radicals in the formula.
4. Type a short name for the nickname.
Troubleshooting Nicknames
5. Click OK. If the Define Nicknames command is disabled,
check for the following:
If you use a nickname that is the same as an
element name, a message indicates that the ele- • A connection point that is not present.
ment is replaced with the nickname. For exam- • More than two connection points that are
ple, using Ac for an acetyl group replaces the defined.
element Actinium. The Check Structure com- • A connection point that is not a single bond.
mand recognizes the label as an acetyl group
rather than Actinium. In Figure a below, the entire functional group
was selected. Because there is no atom that
The Nicknames list provides the following
indicates a connection point, you cannot define
default Nickname/Element conflicts:
a nickname. When a sulfonamide group is
Symbol Nickname attached to an unselected bond, you can define
Element
a nickname.
Ac Acetyl Actinium

Chapter 6
In Figure b, there is more than one attachment 3D Model
point on a single atom in a nickname.
Use a 3D model to paste a 3D version of the
structure into your drawing.
Incorrect Correct
1. Select the structure.
a 2. Go to Edit>Get 3D Model. The 3D structure
appears in the document window.
To view the model in Chem 3D, double-click
it.
NOTE: 3D Objects inserted in this way cannot

be transferred between platforms. For more
information see “File Formats” on page 153.
b
Chem & Bio 3D Preview options

The preview window displays structures in 3D
that you have selected (all structures if none
are selected). Chem& Bio 3D Preview works
only for chemical structures (not biological
structures). To view, go to View>Show Chem3D
Preview Window.
NOTE: For molecules that cannot be viewed in

3D Viewing the Chem & Bio 3D Preview window, “No pre-
As you create your drawing, you may be curi- view available” appears.
ous to see it in three-dimensions. There are two
features in Chem & Bio Draw that let you do
With the preview window open, you can
just that.
change the structure’s appearance several
ways, in either the document window the pre-
NOTE: Chem & Bio 3D must be installed on view window.
your computer to preview structures in three
In the document window
dimensions. Chem& Bio 3D Preview is avail-
able only in ChemBioDraw Ultra and Chem & Even with the preview window open, you can
Bio Draw 12.0 Ultra. still change your drawing in the document win-
dow to look how you want. You can alter the
structure, rotate it, or add new structures. The
preview window updates to reflect the
changes.

User Guide
In Chem & Bio 3D Preview 2. Edit the structure and close Chem & Bio
The preview window offers several options to 3D.
view structures. The edited structure appears in the ChemDraw
Launch Chem 3D. The structure will appear in document window.
Chem & Bio 3D as a model that you can edit.
Display Mode. Choose display options for the
ChemScript
model: wire frame, stick, ball & stick, cylindri- ChemScript is the cheminformatics Software
cal bonds, and space filling. Development Kit (SDK), a library of the
Select. Select the structure or parts of it. “chemical intelligence” programming scripts
that are prevalent throughout CambridgeSoft
Translate. Move the structure. products. ChemBioDraw Ultra lets you run
Rotate. Rotate the structure in three dimen- these scripts on the drawing in the active win-
sions (the image rotates only in the dow. You can use the scripts that are provided
ChemBio3D Preview). with ChemBioDraw Ultra, customize them, or
Zoom. Enlarge or reduce the apparent size of create your own. For more information on
the structure. ChemScript, see the ChemScript section in the
ChemBioOffice Desktop documentation.
Spin. rotate the structure horizontally in one
To run a script on the current drawing:
direction.
1. Go to File>Run ChemScript.
Rock. rotate the structure horizontally back
and forth. 2. In the Open dialog box, select the script and
click Open.
Returning to the document window
3. (Optional) To run the script again, go to
To exit the Chem & Bio 3D Preview, close the File>Re-run Previously Selected Chem-
preview window. Script.
To edit the 3D structure: ChemBioDraw Ultra also includes a library of
1. Double-click the 3D structure. Chem & Bio sample scripts for you to use. Go to File>Chem-
3D opens. Scripts and select an option.

Chapter 6
7
Naming Structures
Chem & Bio Draw 12.0 incudes two features Struct=Name
to help you generate structures and chemical
names—Name>Struct and Struct>Name. Struct=Name is designed to interpret a wide
These two features provide unprecedented variety of chemical structures. This means that
ability and convenience to create and name you can draw a structure in the document win-
structures. Collectively, these features are dow and, using the Convert Structure to Name
called Struct=Name. command, Struct=Name will provide its name.
It also updates the name whenever you modify
Struct>Name generates systematic names for
the structure.
chemical structures. using the Cahn-Ingold-
Prelog rules for stereochemistry. Using this
option, you can generate the name of structures NOTE: Struct=Name is available only in
you have drawn. ChemBioDraw Ultra and ChemDraw Ultra.
Name>Struct is a comprehensive algorithm for
converting English chemical names into chem-
ical structure diagrams. It is designed to inter- Unsupported structures
pret chemical names as they are actually used Although quite useful, this feature has a few
by chemists. In other words, it recognizes the limitations for interpreting some structures
shorthand and slang of everyday usage, in such as:
addition to recognizing most of the official
• Sulfones and chalcogen analogs
IUPAC, IUBMB, and CAS rules and recom-
mendations. In addition, it has an extensive • Polymers
algorithm for identifying common typing
• Isotopically modified compounds
errors to help accurately generate structures.
• Radicals, ions, and radical ions
NOTE: Struct>Name and Name>Struct are Supported Structures
available only in ChemBioDraw Ultra and
ChemDraw Ultra. However, the nomenclature types
Struct=Name will interpret include:
• Stereochemistry
Principal group in rings and chains
• Carboxylic Acids

User Guide
• Peroxy acids • Identifying the base chain of the molecule
• Amide derivatives of acids • Identifying and building substituents
• Carbonic acids • Nomenclature of groups cited only by pre-
• Nitric acids fixes
• Acid Halides • Heteroacyclic compounds
• Carboxylic Esters • Naming of substituent groups
• Salts • Locants
• Anhydrides • Name generation (alphabetization, punctua-
tion, etc.)
• Hydrazides
• Imides Ringed structures
• Amides Struct>Name supports the these types of
ringed structures:
• Hydrazines
• Nitriles • Carbomonocyclic structures
• Amines and Imines • Heteromonocyclic structures
• S, Se, and Te Acids • Fused polycyclic structures
• S, Se, and Te Esters • Fused polycyclic trivially-named struc-
tures
• S, Se, and Te Acid Halides
• Ring fusions of multiple rings
• S, Se and Te Amides • Ring fusions of two multiple ring systems
• Sulfides and chalcogen analogs • Ring fusions of more than two ring sys-
• Sulfoxides and chalcogen analogs tems
• Heteroatomic acids (P, B, As) • Bridged monocyclic structures
• Heteroatomic esters • Spiro ring systems
• Heteroatomic acid halides Some of these ring structures are defined
• Aldehydes and chalcogen analogs below.
• Ketones and chalcogen analogs RING ASSEMBLIES
• Alcohols and chalcogen analogs A ring assembly consists of two or more cyclic
• Hydroperoxides systems that are directly joined to each other
by single or double bonds. All the cyclic sys-
• Peroxides
tems are the same and are either a single ring,
Non-ringed structures fused system, alicyclic von Baeyer system,
• Isolating and naming the functional groups spiro system, phane system, or fullerene. Also,
80 Naming Structures
Chapter 7
the number of ring junctions is the number of element) independent bridged fused ring sys-
cyclic systems minus 1. tems. An example appears below.
Figure 7.25 The bridged fused ring system 9,10-

epidioxyanthracene
Other compounds
• Phosphorous and Arsenic compounds
• Si, Ge, Sn, and Pb compounds
• Boron compounds
Figure 7.23 An example of a ring assembly struc-
ture: 1,1':2',1''-terphenyl • Organometallic compounds
FUSED RING SYSTEMS Stru1,1':2',1''-terphenylct=Name generates
Struct>Name supports fused ring systems of names with proper CIP stereochemistry
two or more rings such as the structure below. descriptors. It has no theoretical limits to the
size of the structures that can be named.
Using Struct=Name
To insert the name of a structure into your
drawing:
1. Select the drawing for which you want to
insert a name.
2. Go to Structure>Convert Structure to Name.
The name of the structure appears as a cap-
tion under your drawing.
Figure 7.24 cyclopenta[ij]pentaleno[2,1,6- Auto Update
cde]azulene is a fused ring system
Chemical properties, including the chemical
BRIDGED FUSED RING SYSTEMS
name and analysis, can be included in a cap-
Chem & Bio Draw 12.0 supports bipodal (both
tion, and will update when you modify the
bivalent and polyvalent) simple acyclic
structure. To toggle the auto-update feature,
(chained) homogeneous (atoms of only one
right-click the caption and select Auto-update.
A check mark appears next to the command
when it is selected. Successive clicks toggle
the command on and off.

User Guide
When auto-update is on (default) the label for obtaining structures for trade or common
updates each time you modify the structure. names.
NOTE: For large complex structures, it may NOTE: Because the syntax of German is simi-
take the new label a few seconds to appear on lar to that of English, Name=Struct can also
the screen, depending on the speed of your pro- interpret many German names.
cessor. You do not have to wait for the new label
to appear before continuing to modify your
structure. Converting Names to Structures
To place a structure into the document window
using the structure name, you can either type
Name=Struct the name or paste the name from the clipboard.
Name=Struct creates structures from chemical converting typed names
names you provide. To type the name and convert it to its structure:
1. Go to Structure>Convert Name to Structure.
NOTE: Name=Struct is available only in
The Insert Structure dialog box appears.
ChemBioDraw Ultra and ChemDraw Ultra.
2. Type the name (example: 2-bromobenzoic
acid).
Name=Struct recognizes most organic nomen-
clature. It also recognized inorganic chemistry,
NOTE: You can also copy a name to the clip-
especially when the rules closely match those
board and type Crtl+V or Command+V to
for organic chemistry. However, there area few
paste the name into the dialog box.
types that are not supported:
• Coordination complexes
3. To place the name below the structure,
• Polyboranes select Paste name below structure.
• Polymers 4. Click OK.
• Some highly-bridged ring systems, includ- Converting Clipboard names
ing fullerenes and porphyrins/porphines
To paste a name on the clipboard as a struc-
• Some stereochemistry designators: +, -, +/- ture:
, +-, D, L, DL, endo, exo, syn, anti, r, t, c
1. Click in the document window.
Although some trade names are supported, 2. Go to Edit>Paste Special>Name as Struc-
Name=Struct is not intended to interpret trade ture. The structure appears in your docu-
or common names. A chemical database, such ment.
as ChemBioFinder.com, is more appropriate
Converting captions
You can convert a caption in the drawing area
to a structure.
Chapter 7
1. Select the caption.
Hydrazines S, Se, and Te Acid
2. Go to Structure>Convert Name to Structure.
Halides
Supported Structures
Struct=Name can name compounds in the fol- Hydroperoxides S, Se, and Te
lowing classes of structures: Acids
Ketones and chalcogen S, Se, and Te

Principal groups in rings and chains analogs Esters
Acid Halides Amide derivatives Nitriles
of acids
Ringed structures
Alcohols and chalcogen Anhydrides
analogs Bridged monocyclic struc- Heteromonocy-
tures clic structures
Aldehydes and chalcogen Carbonic acids
analogs Carbomonocyclic structures Ring fusions of
only two rings
Amides Imides
Fused polycyclic trivially- Ring fusions of
Amines and Imines Nitric acids
named structures two multiple ring
systems
Carboxylic Acids Peroxy acids
Carboxylic Esters Salts Other compounds
Heteroatomic acid halides Sulfides and chal- Boron compounds Si, Ge, Sn, and Pb
cogen analogs compounds
Heteroatomic acids (P, B, Sulfoxides and Organometallic compounds Phosphorous and

As) chalcogen analogs Arsenic
compounds
Heteroatomic esters Peroxides
Hydrazides S, Se and Te
Amides

User Guide
Chapter 7
8
Chemistry Features
Chemical Analysis Molecular Weight. The average molecular
mass of the structure, where atomic masses are
The Analysis window displays the chemical based on the natural abundance of all isotopes
formula, exact mass, molecular weight, m/z, of the element.
and elemental analysis for the entire document,
a structure, part of a structure, or a caption in m/z. Mass/charge, where charge =1. The
Formula style. weights of the most common isotopes and a
To view analysis information, go to graphical representation of the isotopic abun-
View>Show Analysis Window.
dance is shown.
Values for selected objects in the document The molecular weight shown takes the isotopes
window are shown. If no structure is selected for each atom and their natural abundance into
in your document, values for the entire docu- account. Where there is more than one abun-
ment are shown. dant isotope, this feature computes multiple
molecular weights. Low abundance combina-
You can have this window open as you draw in
tions (whether because the isotope is in low
the document. It shows the current values as
abundance or because it includes many moder-
you draw.
ate-abundance contributions) are not taken into
The Decimals setting applies to Exact Mass, account.
Molecular Weight, and m/z only.
Elemental Analysis. The percent by weight of
Formula. The molecular formula showing the each element in the structure.
exact number of atoms of each element in the
To paste information about a structure as a
molecule and charges, radicals, and isotopes.
caption:
Exact Mass. The exact molecular mass of the
structure, where atomic masses of each atom 1. Click the check boxes for the information
are based on the most common isotope for the that you want.
element. 2. Click Paste.

User Guide
The information appears as a multiline caption The HotLink information and the data itself are
below the structure. You can edit this informa- continually updated.
tion with the text tool.
Using the ChemBioFinder HotLink
The HotLink displays information for any
structure that is shown in the document win-
dow. If you have more than one structure, the
HotLink displays information for the structure
you select. If none of the structures are
selected, no HotLink information appears.
To open the ChemBioFinder HotLink:
1. Select a structure of interest.
2. Go to View>Show ChemBioFinder HotLink
Window.
Figure 8.1 Structural analysis

Stereochemistry
The information updates as you edit the struc- Show Stereochemistry calculates the absolute
ture. You can show or hide the information: stereochemistry according to the Cahn-Ingold-
Prelog (CIP) priority rules. For more informa-
1. Using any tool, right-click the caption. tion about the CIP rules, see “Cahn-Ingold-
2. Point to Analysis, and select or deselect the Prelog” on page 194.
item to show/hide.
Only tetrahedral and double-bond stereochem-
istry are supported, and only non-racemic ste-
ChemBioFinder HotLink reochemistry is interpreted. Stereochemical
CambridgeSoft maintains a vast database of indicators for aromatic bonds are not dis-
compounds and their properties. ChemBio- played.
Draw 12.0 and ChemDraw Ultra 12.0 provide The stereochemistry feature calculates and dis-
a live Internet connection to the database, plays the following:
which includes a variety of valuable informa-
(R), (S). Standard tetrahedral stereochemistry
tion such as:
(r), (s). Tetrahedral stereochemistry deter-
• Links to available data resources such as
mined by other stereochemical centers. For
the CambridgeSoft ChemIndex.
example: cis-decalin and myo-inositol.
• Basic properties such as molecular weight
and formulae. (E), (Z). Standard double-bond stereochemis-
try
• Names and synonyms
• Chemical identifiers such as CAS Registry Displaying Stereochemistry Indicators
Numbers and ChemACX IDs.
1. Select the entire structure.
2. Right-click and click Object Settings.
86 Chemistry Features
Chapter 8
3. In the Drawing tab, under Atom Indicators Formatting Indicators
and Bond Indicators, select Show Stere- The atom label settings determine the font
ochemistry. style and size of the terms. A setting on the
The stereo-centers are marked as shown in the Building/Display tab of the Preferences dialog
following example. box determines whether or not the term will be
displayed in parentheses. (The default is to dis-
play parentheses.)
Removing Indicators
To remove an indicator, click it using the
Eraser tool.
Positioning Indicators
Stereochemistry indicators are positioned auto-
matically and move appropriately if a structure
is modified. However, you can move them
either by dragging them or by indicating an
exact location.
To indicate an exact location:
1. Select the indicator to move.
2. Right-click and choose Position. The Posi-
tion Indicator dialog box appears.
3. Click the appropriate option, and type a
value, described below:
To Position … Type a value for

the position by…
from the atom or bond angle, in degrees

Figure 8.2 Stereochemistry indicators
center to indicator or
If you make changes to the drawing that affect center clock, in clock time
the stereochemistry, the stereochemistry is
recalculated. from the atom or bond offset, horizontal
center to bottom left of and vertical
Hiding Indicators
indicator baseline
1. Select the indicator to hide.
2. Right-click and choose Hide Indicator. at specified coordinates absolute, horizontal
and vertical

User Guide
Relative Stereochemistry pairs. However, drawing this requires only one
structure:
You can specify relationships between groups
of stereocenters within a molecule.
NOTE: ChemBioDraw Ultra, Chem & Bio

Draw 12.0 Ultra, and Chem & Bio Draw 12.0
Pro support ISIS-compatible stereochemistry.
This notation enables you to describe stere-

ochemical properties and individual stereo-
centers rather than the entire molecule. As a
result, you can illustrate properties of several
enantiomers using only a few (or even just
one) structure. The notation is illustrated
below: Figure 8.3 beta-Cypermethrin
Two stereo-centers have the &1 designation
because of their fixed relative configuration:
when one is (R) the other must be (S). As a
result, they form a group. The third stereo-
center varies independently and is designated
&2. Group numbers are incremented automati-
cally. To see all the beta-cypermethrin stereoi-
somers, go to File>Open Samples>b-
Cypermethrin.
To indicate stereochemistry for a group:
1. Select all atoms in the group using
To add stereochemical notation to a structure, Shift+click.
go to Structure>Enhanced Stereochemistry. 2. Go to Structure>Enhanced Stereochemistry
The power of this notation becomes clear when and select a stereochemistry marker.
you draw complex enantiomers. For example,
See “Displaying Stereochemistry Indicators”
beta-cypermethrin is a mixture of four distinct
on page 86 for information on showing and
stereoisomers consisting of two enantiomeric
hiding indicators.
Chapter 8
You can save enhanced stereochemistry nota- or atom label with a selection tool. To group the
tion in any of these formats: CDX, CDXML, orbitals with the structure, go to Object>Group.
MOL V3000, RXN V3000, SKC, TGF. See “Grouping Objects” on page 31.
NOTE: Mol V3000, SKC, and TGF are avail- S-orbitals

able in ChemBioDraw Ultra, Chem & Bio
To draw an s orbital:
Draw 12.0 Ultra and Chem & Bio Draw 12.0
Pro only. 1. Hold down the mouse button over the
Orbital tool and drag to select the s-orbital
tool from the palette.
When saving to SKC or TGF format, the indi-
2. Click an atom in the drawing where the
cators are converted into corresponding Data
orbital will be centered.
SGroups. Whenever you open SKC or TGF
files containing such Data SGroups, they are Sigma Orbitals
converted into true Enhanced Stereochemistry To draw a σ-orbital:
values.
1. Hold down the mouse button over the
Chemical Annotations Orbital tool and drag to select the σ-orbital
tool from the palette.
Chem & Bio Draw 12.0 provides the following 2. Click an atom in the drawing where the
tools and tool palettes that enable you to add orbital will be centered.
chemical annotations to your documents:
Single Lobe Orbitals
Orbital tools palette. Draw orbitals. To draw a single lobe orbital:
Chemical Symbol Tools palette. Draw charges,
radicals, and other symbols.
Orbital tool and drag to select the single
Orbitals lobe orbital tool from the palette.
2. Click an atom where the narrow end of the
You draw orbitals so that the node appears
orbital is to be attached.
first. Then you can change the background
color, shading, and solid color using the Color p-orbitals
menu. To draw a p orbital:
Display the Info window to view the orbital’s 1. Hold down the mouse button over the
length and angle relative to the X-axis while Orbital tool and drag to select the p-orbital
you draw it. To constrain the length and angle tool from the palette.
of an orbital, go to Object>Fixed Lengths or
2. Click an atom where the node of the orbital
Fixed Angles.
is to be attached.
Hybrid Orbitals
NOTE: Orbitals are not normally part of the
structure they are drawn near and are not To draw a hybrid orbital(‘sp3’):
selected when you double-click a bond, atom,

User Guide
1. Hold down the mouse button over the Lone Pair
Orbital tool and drag to select the hybrid- Use the lone pair symbol to indicate a lone pair
orbital tool from the palette. of electrons common in Lewis structures.
2. click an atom where the node of the orbital
is to be attached.
Chemical Symbols tool and drag to select
d-orbitals the lone pair from the palette.
To draw a d orbital(‘dxy’): 2. Click and drag the atom to where you want
the lone pair. The lone pair is offset from
the atom at a fixed position.
Orbital tool and drag to select the d-orbital
tool from the palette. Radical
2. Click an atom where the node of the orbital Use the radical symbol to indicate a single
is to be attached. non-bonded electron.
dz2-orbitals 1. Hold down the mouse button over the
To draw a dz orbital:
2- Chemical Symbols tool and drag to select
1. Hold down the mouse button over the the radical from the palette.
2. Click and drag the atom to where you want
Orbital tool and drag to select the dz2-
the radical symbol.
orbital tool from the palette.
2. Click an atom where the node of the orbital Radical Cation and Radical Anion
will be attached. Use the charge radical symbols to represent
radicals that are charged.
Chemical Symbols
When you attach a symbol (other than H-dot or Chemical Symbols tool and drag to select
H-dash) to an atom, it remains at a fixed dis- the symbol from the palette.
tance from the central character of the atom 2. Click and drag the atom to where you want
label, even when you move the symbol. the symbol.
However, you can place unattached symbol
To add a radical cation or radical anion symbol
anywhere and resize them.
in a horizontal orientation, click an atom.
H–dot and H–dash
Charge Symbols
To represent a hydrogen atom that is coming
To draw a charge and associate it with a struc-
out of the plane toward you along the Z axis,
ture:
use the H–dot symbol.
To represent a hydrogen atom that is directed 1. Hold down the mouse button over the
backwards into the plane away from you along Chemical Symbols tool and drag to select
the Z axis, use the H–dot symbol. To insert H– the charge symbol from the palette.
dots and H–dashes, click an atom. 2. Click and drag the atom to which you want
the charge to correspond.
Chapter 8
The number of hydrogen atoms increases or 1. Select the chemical symbol.
decreases as appropriate for the addition of the 2. Drag the rotation handle on the chemical
charge. symbol.
Attachment Points See “Rotating Objects” on page 29.
The ability to indicate an attachment point is
useful in polymer-bound combinatorial synthe- Chemical Properties
sis, protein chemistry, and other situations. The You can enter predicted values for the physical
Chemical Symbols toolbar includes four stan- and thermodynamic properties of a chemical
dard attachment point drawing tools that allow structure of up to 100 atoms.
you to indicate a point of attachment while
maintaining chemical meaning.
NOTE: Chemical properties are available in
The properties are calculated using the most

reliable methods for the given structure. Log P
and CMR values based on literature values
rather than a calculation are included in the
report file.
The reported properties are:
Figure 8.4 Attachment point symbols
Boiling Point. Reported in Kelvin at 1 atm.
The bead tool are specifically intended to indi-
Melting Point. Reported in Kelvin at 1 atm.
cate attachment to a resin. Any of these tools
may be used for variable attachments in que- Critical Temperature. The temperature above
ries (see “Attachment Points” on page 63); but, which the gas form of the structure cannot be
only the diamond tool shows rank numbers. liquefied, no matter the applied pressure (Tc).
This means that, as you add diamond symbols Reported in Kelvin.
to a structure, the points will have sequential Critical Pressure. The minimum pressure that
numbers. must be applied to liquefy the structure at the
Rotating a Symbol critical temperature (Pc). Reported in bars.
You can rotate the radical anion, cation, and Critical Volume. The volume occupied at the
lone pair symbols around the same end from compound’s critical temperature and pressure
which they were originally drawn. For exam- (Vc). Reported in cm3/mol.
ple, the radical cation symbol is rotated and Gibbs Energy. The Gibbs free energy, ΔG, for
resized from the charge. The Info window the structure. Reported in kJ/mol at 1 atm and
shows the angle that one of the ends of a sym- 298.15K.
bol makes with the X–axis as you rotate.
Henry’s Law. The inverse of the logarithm of
To rotate a chemical symbol:
Henry’s law constant [-log (H)] (no units).

User Guide
Heat of Formation. ΔHf, for the structure. To create a stoichiometry grid:
Reported in kJ/mol at 1 atm and 298.15K.
1. Draw a reaction, or open a file containing a
tPSA. Calculation of polar surface area based reaction, and select the entire reaction.
on fragment contributions. 2. Go to Structure>Analyze Stoichiometry. The
CLogP. /CMR. Use CLogP to calculate grid appears under the reaction.
n-octanol/water partition coefficient (log Pow).
LogP values based on literature rather than cal-
NOTE: If a catalyst or condition label is dis-
culations are included in the report file.
played above the reaction arrow, right+click
Use CMR to calculated Molar Refractivity. the label and deselect Interpret Chemically in
MR values based on literature rather than cal- the context menu before creating the grid.
culations are included in the report file.
To enter data in the grid:

NOTE: CLogP and CMR values appear only
in ChemBioDraw Ultra and ChemDraw Ultra. 1. Select the Text tool, and click where to
enter the data.
Viewing Chemical Properties

1. Select the structure whose properties you
want to view.
2. Go to View>Show Chemical Properties Win-
dow. The Chemical Properties window
appears.
3. To paste the basic properties into your doc-
ument, click Paste.
4. To create a report and view results for other
fragmentation methods click Report. The Figure 8.5 Entering data in the Grid
report is produces as a text file.
2. Set the limiting compound. If the default
Stoichiometry Grid setting is incorrect, right-click or control-
click the word ‘No’ in the limiting row, and
Use the Stoichiometry Grid to calculate sto- select Set Limiting from the context menu.
ichiometric data for a reaction. The grid is 3. Enter values for all reactants, as applicable.
filled in as you modify a reaction drawing. If you are using units other than the
NOTE: The stoichiometry grid is available in

Chapter 8
defaults, type in the units along with the You can edit the grid for presentation with the
values (no space required). context menu, showing or hiding either rows or
columns. You can also change the color of the
text.
Value Comments
TLC
Limiting? Indicates the limiting reactant.
Only one reactant may be speci- The TLC Tool lets you depict thin layer chro-
fied as limiting. matography plates. The tool creates a rectangu-
lar plate with an origin line, solvent front, and
Sample Mass Mass of reactant. Default units: g. one or more lanes. The lanes can be populated
with spots of different Rf, size, shape, or color.
%Weight Reactant purity. Defaults to
100%.
NOTE: The TLC tool available in ChemBio-
Volume Default units: ml. Requires either Draw Ultra 12.0, ChemDraw Ultra 12.0, and
a molarity or a density to also be ChemDraw Pro 12.0 only.
entered.
To create a TLC plate:
Molarity Default units: M
1. Select the TLC tool from the Main toolbar.
Density Default units: g/ml 2. Drag in any direction from the point of ori-
gin. The number of lanes is a function of
After you enter the minimum amount of infor- the width of the plate you create.
mation required, the values are calculated. As
you continue entering information, or edit
inputs, the values are recalculated.
NOTE: Entered values are in bold-face; calcu-

lated values are in normal font.
Reactants Products
Formula C3H 6O2S C2H4O Formula C5H 10O3S
MW 106.14 44.05 MW 150.20
Limiting? Yes No Equivalents
Equivalents Expected Mass 114.26g
Sample Mass Entered values Expected Moles 760.76mmol
%Weight Measured Mass
Molarity Purity
Density 807.50g/l 788.00g/l Product Mass
Volume 100.00ml Product Moles
Reactant Moles 760.76mmol 760.76mmol %Yield
Reactant Mass 80.75g 33.51g
Figure 8.6 Calculated stoichiometric values

User Guide
You can modify the plate as follows:
If you want to... then...
If you want to... then... Delete a spot. Click the spot with the
Eraser tool.
Change the height Drag a border or corner.
or width of the If you erase all spots in a
plate. lane, the lane will be
deleted.
Move the origin or Click and drag the origin or
solvent front. solvent front line. Display or set the 1. Right-click or Control-
Rf for a spot; add click on a spot.
Show or hide the Right-click or Control-click a custom spot 2. Point to TLC Spots,
origin, solvent in the plate and select the and take the appropri-
front, borders, or appropriate action. ate action.
side ticks.
Use the Transparent option To display Rf for all spots,
right-click or Control-click
to overlay the TLC plate on
a scanned plate. in the plate and select
Show Rf from the TLC
Change the order Drag the origin tick to the Spots submenu.
of lanes. new location. Change the style 1. Right-click or Control-
or color of a spot. click in a spot.
Add, delete, or 1. Position the cursor on
2. Choose the style or
duplicate a lane. the lane you want to
color.
delete or duplicate (or
between lanes to add). To change the style for all
2. Right-click or Control- spots, Right-click or
Control-click in the plate
click in the plate.
and choose the style from
3. Select the appropriate the TLC Spots submenu.
action.
You can also delete lanes
with the Eraser tool.
Move a spot. Drag the spot. The Rf
displays as you drag.
Duplicate a spot. Ctrl+drag or Option-drag

the spot.
Chapter 8
Resizing Spots
If you want to... then...
You can resize spots by holding down the Shift
Enlarge or “smear” Shift+drag the spot. When key while pointing at an edge of the spot. Drag
a spot. you position the cursor on the left or right sides of the spot to adjust the
a spot and press “Shift”, width only. Drag from the top to adjust the
the cursor assumes one of height. Drag from the bottom to adjust the tail.
three shapes, depending Dragging from any of the other four corners
on how it is positioned: will scale all three values.
• Cross arrows, used to
Custom Spots
enlarge a spot.
• Horizontal arrow, The TLC tool can create the most common
used to widen a spot. spot shapes. Other types of spots, such as
smears, can be reproduced as custom spots.
• Vertical arrow, used to The Set Custom Spot command lets you insert
elongate a spot or cre- a graphic file for a spot. Typically, these files
ate a crescent. would be produced by scanning a TLC plate
Rf Display and saving the spots in a library of spot shapes.
Right-click a spot and select Show Rf to indi- ChemNMR

cate the spot’s retention value. By default, the
ChemBioDraw Ultra and ChemDraw Ultra
value is set to Rf to two decimal places.
include ChemNMR as an optional add-on fea-
To move the tag ture. Using ChemNMR, you can estimate and
Either click and drag the tag using a selection display proton and Carbon-13 chemical shifts
tool or Right-click or Control-click the tag and for a selected molecule.
choose Position. Then edit the values in the
Position Indicators box.
NMR Shifts
To view 1H or 13C NMR information:
Editing the Rf value
Select the tag with the Text tool and edit the 1. Select a structure.
value. 2. Go to Structure>Predict 1H-NMR Shifts or
Predict 13C-NMR Shifts.
If you change the Rf the spot will move to the
new position indicated. ChemNMR redraws the molecule with the esti-
If you edit the Rf to have different precision, mated shifts and displays the information and
that precision will be preserved.

User Guide
line spectrum in a new window as shown The selection rectangle surrounds the selected
below. objects.
10 8 6 4 2 0
PPM
5. Go to Structure>Make Spectrum-Structure
Assignment.
The selected atoms and bonds in the structure

are associated with the selected spectral peaks.
Viewing Spectral Assignments
Assigning Structures to Spectra
1. Click the Lasso or Marquee tool.
ChemBioDraw Ultra lets you assign structures 2. Place the pointer over a peak. The assigned
to spectra. You can then display the structure atoms or bonds are highlighted.
associated with a specific peak by placing the
pointer on that peak.
1. Open a spectral file.
2. Draw the structure or structures to assign to
the spectrum.
3. Select specific atoms and bonds in the
structure.
4. Shift-click the peak or peaks to which you
want the structure assigned.
Figure 8.7 Viewing spectrum-structure assignments
Chapter 8
Removing Spectral Assignments Updating the ChemNMR database
To remove spectrum to structure assignments: Once you have an SDF file that contains the
supplementary, follow these steps to update the
1. Click the Lasso or Marquee tool. ChemNMR database:
2. Select the objects from which to remove the
1. Exit Chem & Bio Draw.
assignment.
2. Locate the Chem & Bio Draw ChemNMR
3. Go to Structure>Clear Spectrum-Structure.
directory. By default, the directory is at:
Custom Shift Correction Data C:\Documents and Settings\All
Users\Application Data\
You can add your own shift correction data for
CambridgeSoft\ChemOffice2010\
proton prediction to supplement the existing
ChemDraw\ChemNMR
data that the ChemNMR algorithm uses. You
provide your data in an SDF file and then use 3. Open a DOS prompt:
the file to update the Chem & Bio Draw Chem- • In Windows XP, go to Start>Run and
NMR database. enter cmd in the Run window. Click OK.
Using a third-party tool, such as ACD Labs • In Windows Vista, go to Start and enter
software or MestreNova, you may be able to cmd in the search field. Press the Enter
create your SDF file with the supplementary key.
data already included (Consult your applica- 4. at the DOS prompt, navigate to the Chem-
tion’s user manual for instructions). Alterna- NMR directory in step 2.
tively, you can use ChemBioFinder to add your 5. Enter the command:
data to an SDF file. MakeChemNMRUserDB.exe <input file>
NMR DATA FORMAT <resource directory> <output directory>
The correction data that you add to your SDF where
file must be in this format:
• <input file> is the full path and filename
> <SHIFT> of the SDF file that contains the correction
<atom_id>,<shift_value>,<ignored> data.
• <resource directory> and <output direc-
For example: tory> are the full path to the ChemNMR
directory.
> <SHIFT1>
2,9.61,0.0 6. Restart Chem & Bio Draw.
Restoring Default NMR Data
> <SHIFT2> If you want to stop using your own data, you
3,8.92,0.0 can restore Chem & Bio Draw to its original
The correction data for each molecule must settings.
appear after the molecule’s structural data. For To restore the original settings:
example, if your SDF file includes benzene,
the NMR data must immediately follow the 1. Exit Chem & Bio Draw.
benzene structural data. 2. Locate the ChemNMR directory.

User Guide
3. Delete the files Ushiftdb5H1.txt and Example supplementary data
Usimilvecx.h1. The example below represents an SDF file that
4. Restart Chem & Bio Draw. includes supplementary NMR data for two
structures. The supplementary data follows the
structure data and is shaded gray for clarity.
ACD/Labs07190711112D
14 14 0 0 0 0 0 0 0 0 15 V2000
5.7578 -1.9992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7578 -3.3267 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6062 -1.3275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6062 -3.9825 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3.4547 -1.9992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4547 -3.3267 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9094 -1.3275 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
8.0609 -1.9992 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
6.9094 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.3031 -1.3275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3031 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1516 -1.9992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1516 -3.3267 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -1.3275 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 2 0 0 0 0
1 7 1 0 0 0 0
2 4 2 0 0 0 0
3 5 1 0 0 0 0
4 6 1 0 0 0 0
5 6 2 0 0 0 0
5 10 1 0 0 0 0
7 8 1 0 0 0 0
7 9 2 0 0 0 0
10 11 1 0 0 0 0
10 12 1 0 0 0 0
12 13 2 0 0 0 0
12 14 1 0 0 0 0
M ZZC 1 5
M ZZC 2 6
M ZZC 3 4
M ZZC 4 1
M ZZC 5 3
M ZZC 6 2
M CHG 2 7 1 8 -1
M ZZC 7 9
M ZZC 8 13
M ZZC 9 10
M ZZC 10 7
M ZZC 11 8
M ZZC 12 11
M ZZC 13 12
M END
> <ID>
1
Chapter 8
> <solvent>
d6-DMSO
> <SHIFT1>
2,9.61,0.0
> <SHIFT2>
3,8.92,0.0
> <SHIFT3>
6,9.01,0.0
> <SHIFT4>
10,3.11,0.0
> <SHIFT5>
11,1.16,0.0
> <SHIFTS>
5
$$$$ TH
> <solvent>
d6-DMSO
> <SHIFT1>
2,9.6,0.0
> <SHIFT2>
3,8.91,0.0
> <SHIFT3>
6,9.11,0.0
> <SHIFT4>
10,2.75,0.0
> <SHIFT5>
11,1.17,0.0
> <SHIFT6>
12,2.41,0.0
> <SHIFTS>
6
$$$$

User Guide
ACD/Labs07190711112D
15 15 0 0 0 0 0 0 0 0 16 V2000
7.1683 -1.9521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.1683 -3.2484 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.0438 -1.2962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.0438 -3.8887 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.9194 -1.9521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9194 -3.2484 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.2927 -1.2962 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
9.4171 -1.9521 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
8.2927 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
3.7950 -1.2962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7950 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2489 -2.1708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1401 -1.5149 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -2.1552 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.1401 -0.2186 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 2 0 0 0 0
1 7 1 0 0 0 0
2 4 2 0 0 0 0
3 5 1 0 0 0 0
4 6 1 0 0 0 0
5 6 2 0 0 0 0
5 10 1 0 0 0 0
7 8 1 0 0 0 0
7 9 2 0 0 0 0
10 11 1 0 0 0 0
10 12 1 0 0 0 0
12 13 1 0 0 0 0
13 14 2 0 0 0 0
13 15 1 0 0 0 0
M ZZC 1 5
M ZZC 2 6
M ZZC 3 4
M ZZC 4 1
M ZZC 5 3
M ZZC 6 2
M CHG 2 7 1 8 -1
M ZZC 7 9
M ZZC 8 14
M ZZC 9 10
M ZZC 10 7
M ZZC 11 8
M ZZC 12 11
M ZZC 13 12
M ZZC 14 13
M END
> <ID>
2

Chapter 8
> <solvent>
d6-DMSO
> <SHIFT1>
2,9.6,0.0
> <SHIFT2>
3,8.91,0.0
> <SHIFT3>
6,9.11,0.0
> <SHIFT4>
10,2.75,0.0
> <SHIFT5>
11,1.17,0.0
> <SHIFT6>
12,2.41,0.0
> <SHIFTS>
6
$$$$

User Guide
Chapter 8
9
ChemDraw/Excel
ChemDraw/Excel is an add-in for Microsoft© SD file. MDL SDFiles are supported only in
Excel© for Windows. ChemDraw/Excel ChemBioDraw Ultra 12.0, ChemDraw Ultra
enables you to: 12.0, and ChemDraw Pro 12.0 only
• Add chemical structures and other data Chem & Bio Draw 12.0 databases. Imports all
from Chem & Bio Draw 12.0 or a Chem- fields stored in the main form. Molecular
Finder database to an Excel spreadsheet. weight and formula fields are not imported
• Search using the same search features as because ChemDraw/Excel calculates them.
ChemFinder. Each structure is named Structure <n>, where
n is a unique number.
• Perform calculations on chemical struc-
tures.
NOTE: To import CFW files into Excel, save
When you install the add-in, a ChemOffice them with the “allow CAL/OLE Automation
menu is added to the Excel menu and a toolbar access” security setting checked. See “Setting
appears. Security Options” in Chapter 3 of the Chem-
Finder manual for details.
Setting Up ChemDraw/Excel
When you install ChemDraw or Chem & Bio
When you import a table, structure data are
Draw, ChemDraw/Excel is also installed. To
transformed into structure drawings in the first
open a ChemOffice worksheet, go to
column, and all other fields are imported in
ChemOffice12>New ChemOffice Worksheet.
separate columns.
When a worksheet is active, ChemDraw/Excel
appears in the title bar and the Chem & Bio To import a table:
Draw 12.0 toolbar is active. 1. In Excel, select the cell where you want the
import to start. The upper left corner of the
Importing Tables import is at this cell. Data is filled down
ChemDraw/Excel lets you import from: and to the right.
2. Go to ChemOffice12>Import/Export>Import
MDL SDFiles. Imports all records in the file.
Table. The Import Table dialog box appears.
Each structure is given the name stored in the

User Guide
3. Type or select the file name to import and Error. “ChemFinder is not running, would you
click Open. All records are added to your like to start it up?”
spreadsheet. Do the following:
1. Click Yes. The message “After loading your
NOTE: You can import a table only into a new desired database and performing your
ChemOffice worksheet. search, return to Excel and redo the opera-
tion.” appears.
2. Click OK. ChemFinder opens.
Converting Worksheets 3. Open a database and perform a search.
You can convert a normal Excel worksheet 4. Return to Excel and go to
into a ChemDraw/Excel worksheet. Go to ChemOffice12>Import/Export>Import Chem-
ChemOffice12 >Convert Worksheet. Finder List.
“ChemDraw for Excel” appears in the Excel Error. “No database loaded in ChemFinder.
title bar. Load a database and perform your search.
Then return to Excel and redo the operation.”
Upgrading Workbooks
ChemFinder is running, but no database is
Older ChemDraw/Excel workbooks may be loaded. Do the following:
incompatible with the latest add-in. Therefore,
you may need to upgrade them. To upgrade, go 1. Click OK. ChemFinder moves to the front.
to ChemOffice12>Upgrade Workbook. 2. Open a database and perform a search.
3. Return to Excel and go to
Importing Hit Lists ChemOffice12>Import/Export>Import Chem-
Finder List.
You can search records in ChemFinder and
import the hit list structures with data into Error. “Form has no database or hit list has no
Excel using the Import ChemFinder List com- records. Load a database and perform your
mand. ChemFinder must be open with a hit list search. Then return to Excel and redo the oper-
present. ation.”
To import a hit list: 1. Click OK. ChemFinder moves to the front.
1. Go to ChemOffice12>Import/Export>Import 2. Open a database and perform a search.
ChemFinder List. 3. Return to Excel and go to
2. In the message box, click Yes to import the ChemOffice12>Import/Export>Import Chem-
hit list. The records are imported into Excel. Finder List.
Error Messages Exporting Tables

If all conditions required to use the Import
ChemDraw/Excel lets you export tables to
ChemFinder List command are not met, one of
MDL SDFiles. The first column of the area to
the following error messages may appear.
export must have the word “Structure” in its
104 ChemDraw/Excel
Chapter 9
top cell. Structures outside the first column SMILES Strings
will be discarded.
You can insert SMILES strings into cells and
To export data: convert them to structures.
1. Select the cells to export, including the cell
that contains the word “Structure”. NOTE: This feature is available in ChemBio-
2. Go to ChemOffice12>Import/Export>Export Draw Ultra 12.0, ChemDraw Ultra 12.0, and
Table. ChemDraw Pro 12.0 only.
3. In the Save Table To dialog box, type the file
name and click Save.
1. Type or paste the SMILES strings into one
Adding Structures or more cells.
2. Select the cells to convert.
You can add chemical structures from any file
format supported by Chem & Bio Draw 12.0 to
a spreadsheet. The names of added structures NOTE: (Optional) To keep the original text,
are retained. If the structure does not have a copy and paste it elsewhere.
name, Chem & Bio Draw 12.0 assigns the
name: “Structure <n>”, where n is a number 3. Go to ChemOffice12>Convert>SMILES to
unique to the worksheet. Molecule. The cell will display a text string
The simplest way to insert a new structure in a starting with “Structure” followed by a
cell is by using Chem & Bio Draw 12.0. number.
1. Double-click in a cell. The ChemDraw for 4. To display the structure, click the Show
Excel dialog box appears. Pictures icon. If the cell did not contain a
2. Click Yes. Chem & Bio Draw 12.0 opens. valid SMILES string, the string remains.
3. Draw the structure.
Adding Structures by Name
4. In Chem & Bio Draw 12.0, go to File>Exit
and Return to New Molecule. The new struc- You can type or paste the names of chemicals
ture appears in the cell. into cells and convert them into structures.
Adding a Structure From a File 1. Enter the names into cells.

2. Select the cells to convert.
1. In Excel, select the cell into which you
want to add the structure.
NOTE: (Optional) To keep the original text,
2. Go to ChemOffice12>Molecule>Load. The copy and paste it elsewhere. This command can
Choose Molecule To Load dialog box also convert names generated from Excel for-
appears. mulas.
3. Type or select the file name of the structure
to add and click Open.
3. Select ChemOffice12>Convert>Name To
Molecule.

User Guide
If the cell contains a name supported by Normal Searches
Name=Struct, the structure appears with the
Use a normal search to find full structures and
given name as the name of the cell.
substructures that match the one you define in
4. To show the structure, select the cell and the search dialog box.
choose ChemOffice12>Picture>Show.
1. Select a cell containing the label Structure.
Saving Structures 2. Go to ChemOffice12>Search>Normal.
You can save a chemical structure to a separate 3. The ChemDraw for Excel dialog box
file. appears.
4. Select the Search Tab.
1. In the spreadsheet, select the cell containing
5. Click in the empty window and draw the
the structure.
structure for which you want to search.
2. Go to ChemOffice12>Molecule>Save. The
6. Select the Normal tab at the bottom of the
Save to File dialog box appears.
dialog box.
3. Select an existing file or enter a new file
7. For Search Type, select either Full Structure
name and click Save.
or Sub Structure.
Searching 8. For Filter Type, select to either include or
exclude hits.
You can search for structures based on the cri-
9. Enter a formula query.
teria and search function you use. ChemDraw/
Excel offers three basic search functions: 10.Click Search. The hit list is displayed in a
column named Match. Items matching the
• Normal search search criteria are labeled as TRUE.
• Similarity search
Similarity Searches
• R-Group Analysis
Perform a similarity search to find structures
Opening a database with features corresponding to a structure of
Before searching, you must open the structure your choosing. For more information about
database. similarity searching, see the ChemFinder
User’s Guide.
1. In Excel, go to ChemOffice12>New To search for similarity:
ChemOffice Worksheet.
2. Go to ChemOffice12>Import/Export>Import 1. Select a cell containing the label Structure.
Table or Import ChemFinder list and select 2. Go to ChemOffice12>Search>Similarity. The
the file to import. ChemDraw for Excel dialog box appears.
After you open a database, you can search for 3. Select the Search Tab.
structures. 4. Click in the empty window and draw the
structure for which you want to search.
5. Select the Similarity tab.
6. Select the Search Type.
106 ChemDraw/Excel
Chapter 9
7. Select the Sort Results order. the analysis results; the hydroxyl groups for
8. Select the Similarity Percent value. o-, m-, and p-cresol.
9. Click Search. The hit list is displayed in a
column named Similarity. Items matching
the search criteria are labeled as TRUE.
R-Group Analysis
An R-group analysis returns all molecules in
the query database that include a template
structure that you provide. For example,
assume you want to find all molecules in the
database that include toluene in its structure,
such as p-cresol or o-xylene (assuming your • The functional group found at each Rn posi-
database includes these molecules). Simply tion for each search result. For a given
draw toluene as your template and the analysis returned molecule, view across its row to
will return all molecules that contain at least view the functional group at each R-group
one toluene structure. position. In this example, the search results
Interpreting Analysis Results consist of a hydrogen and hydroxyl group
for R1, R2, and R3.
To illustrate, we will assume that you have a
small database that consists of four molecules: Working with Structures
o-, m-, and p-cresol, and bromobenzene. Fur-
ther assume you want to run an R-group analy- ChemDraw/Excel lets you rename structures
sis on this database to find all the molecules and use the clipboard to cut, copy, and paste
that contain toluene in its structure. You will structures.
find that the results include three main parts:
Naming Structures
• The list of molecules that contain the tolu-
Excel recognizes certain characters as formu-
ene template. In this example, the results
las. To prevent the system from interpreting a
include o-, m-, and p-cresol. Bromobenzene
chemical structure name as an Excel formula,
is not included because it does not contain
you can rename a structure.
the template.
To name a structure:
• The toluene template with all variations of
R-group attachments that were found in the 1. Select the structure.
database. In this example, the attachments 2. Go to ChemOffice12>Molecule>Name All
are represented by functional groups. These Selected. The Name Molecule dialog box
are the locations of the R-groups found in appears.
3. Type the name and click OK.

User Guide
Using the Clipboard Resizing Structures
You can cut, copy, and paste structures using 1. Select the cells whose pictures you want to
the clipboard. resize.
To cut a structure from a cell: 2. Select Resize Picture on the ChemOffice
1. Select the structure. menu. Resize handles appear on the
selected structures.
2. Go to ChemOffice12>Molecule>Cut. The
structure is removed from the cell and is 3. Click-drag the resize handles to resize a
placed on the clipboard. picture. Any changes you make to a picture
is proportionately reflected in the other pic-
To copy a structure from a cell:
tures.
1. Select the structure. 4. To end resizing, click a cell and the pictures
2. Go to ChemOffice12>Molecule>Copy. are deselected.
The structure remains in the cell and a copy is
placed on the clipboard.
NOTE: When pictures are resized larger than
To paste a structure: their cells, use Align Pictures to enlarge the
1. Select the area where you want to paste the cells. Align Pictures does not make cells
structure. smaller.
2. Go to ChemOffice12>Molecule>Paste. The
structure is pasted from the clipboard.
Displaying Structures
ChemDraw/Excel Functions
ChemDraw/Excel supplies a variety of func-
ChemDraw/Excel lets you select whether to
tions that return information about chemistry
display structures. You can also adjust the size
objects in a specified cell.
of cells to display their entire contents.
To show structures:
NOTE: Functions that report chemical proper-
1. Select the cells in which you want to dis- ties are available in ChemBioDraw Ultra 12.0,
play or hide structures. ChemDraw Ultra 12.0, and ChemDraw Pro
2. Select ChemOffice12>Picture>Show or 12.0 only.
Hide.
Aligning Structures
A structure may be too big for its cell or be NOTE: The surface area and volume calcula-
improperly positioned. To correct the problem, tions are performed with Michael Connolly's
select the Align All Pictures command. program for computing molecular surface
To align structures, go to ChemOffice12>Pic- areas and volume (M.L. Connolly. The Molecu-
ture>Align Pictures. The cells adjust to display lar Surface Package. J. Mol. Graphics 1993,
their entire contents. 11).
108 ChemDraw/Excel
Chapter 9
To insert a ChemDraw/Excel function into Result: 1-(2,3-dihydro-1H-inden-2-yl)propan-
your worksheet: 2-one
1. Select an empty cell.
2. Go to Insert>Function. The Insert Functions NOTE: Some CambridgeSoft product pack-
dialog box appears. ages and levels allow unlimited structure-to-
3. In the Category dropdown list, select name conversions, while others impose a daily
ChemDraw Functions.
limit on conversions.
4. Select the function to insert from the list
and click OK. A dialog box appears.
Chemical composition
5. Enter the structure cell reference for which
you want to calculate properties in the When this function is called with just a cell ref-
Structure box. erence, it displays the elemental percent by
weight for all elements in the structure. When
6. If the function takes a second argument,
this function is called with a cell reference and
enter it in the Element type box. Element
an atomic symbol, it displays the fraction by
type arguments are optional.
weight of the given element in the structure.
7. Click OK.
Functions
Each property is calculated using the “best
available” method. If the cell reference argu- CHEM_COMPOSITION(cell ref)
ment does not point to a valid structure cell, CHEM_COMPOSITION(cell ref, atomic sym-
#N/A appears in the cell. bol)
All ChemDraw/Excel functions are described Examples
below.
In cell: =CHEM_COMPOSITION(A2)
Chemical name Result: C,82.72;H,8.10;O,9.18
Displays systematic names for chemical struc- In cell: =CHEM_COMPOSITION(A2, "C")
tures with support for the Cahn-Ingold-Prelog Result: 0.827188133
rules for stereochemistry.
Chemical formula
Function
Displays the chemical formula for the struc-
CFW_CHEMICAL_NAME(cell ref) ture(s) in the cell.
Example Functions
In cell: =CFW_CHEMICAL_NAME(A2) CHEM_FORMULA(cell ref)
CHEMPROPSTD_MOL_FORMULA(cell ref)
Examples
In cell: =CHEM_FORMULA(A2)
Result: C12H14O
In cell: =CHEMPROPSTD_MOL_FORMULA(A2)

User Guide
Result: C12H14O Number of atoms
Molecular weight When this function is called with just a cell ref-
erence, it displays the total number of atoms in
Displays the average molecular mass of the the structure. When this function is called with
structure, where atomic masses are based on a cell reference and an atomic symbol, it dis-
the weighted average of all isotope masses for plays the number of atoms of the given ele-
the element. ment in the structure.
Units Functions
atomic mass units CHEM_NUM_ATOMS(cell ref)
Functions CHEM_NUM_ATOMS(cell ref, atomic symbol)
CHEM_MOLWEIGHT(cell ref) Examples
CHEMPROPSTD_MOL_WEIGHT(cell ref)
In cell: =CHEM_NUM_ATOMS(A2)
CHEMPROPSTD_MASS(cell ref)
Result: 27
Examples In cell: =CHEM_NUM_ATOMS(A2, "C")
In cell: =CHEM_MOLWEIGHT(A2) Result: 12
Result: 174.23896 Number of hydrogen-bond
In cell: =CHEMPROPSTD_MOL_WEIGHT(A2)
acceptors
Result: 174.238960
In cell: =CHEMPROPSTD_MASS(A2) Displays the number of hydrogen-bond accep-
tors based on topology.
Result: 174.238960
Function
Exact mass
CHEM_NUM_HBACCEPTORS(cell ref)
Displays the exact molecular mass of the mole-
cule, where atomic masses of each atom are Example
based on the most common isotope for the ele- In cell: =CHEM_NUM_HBACCEPTORS(A2)
ment. Result: 1
Units Number of hydrogen-bond donors
g/mole
Displays the number of hydrogen-bond donors
Function based on topology.
CHEMPROPSTD_EXACT_MASS(cell ref) Function
Example CHEM_NUM_HBDONORS(cell ref)
In cell: =CHEMPROPSTD_EXACT_MASS(A2) Example
Result: 174.104465 In cell: =CHEM_NUM_HBDONORS(A2)
Result: 0
110 ChemDraw/Excel
Chapter 9
SMILES string Example
Displays the SMILES string for the structure. In cell: =ISREACTION(A2
Result: True
Function
CHEM_SMILES(cell ref) Boiling point
Example The boiling point for the molecule at one atm.
In cell: =CHEM_SMILES(A2) Units
Result: O=C(C)CC(C1)Cc2c1cccc2 Kelvin
Formal charge Functions
Displays the net charge on the molecule. CHEMPROP_BOILING(cell ref)
CHEMPROPPRO_BOILING_POINT(cell ref)
Function
CHEMPROPSTD_FORMAL_CHARGE(cell ref) Examples
In cell: =CHEMPROP_BOILING(A2)
Example
Result: 540.059
In cell: =CHEMPROPSTD_FORMAL_CHARGE(A2
In cell:
Result: -1 =CHEMPROPPRO_BOILING_POINT(A2)
Does cell have a structure drawing? Result: 540.059
Returns TRUE if the cell has a ChemOffice/ Melting/freezing point
Excel structure drawing (including reaction
The melting/freezing point for the structure at
drawings), returns FALSE otherwise.
1 atm.
Function
Units
ISSTRUCTURE(cell ref)
Kelvin
Example
Functions
In cell: =ISSTRUCTURE(A2)
CHEMPROP_FREEZING(cell ref)
Result: False
CHEMPROPPRO_MELTING_POINT(cell ref)
Does cell have reaction drawing? Examples
Returns TRUE if the cell has a ChemOffice/ In cell: =CHEMPROP_FREEZING(A2)
Excel structure drawing of a reaction drawings, Result: 331.31
returns FALSE otherwise.
In cell:
Function =CHEMPROPPRO_MELTING_POINT(A2)
ISREACTION(cell ref) Result: 331.31

User Guide
Vapor pressure Functions
The vapor pressure for the structure at 25° C. CHEMPROP_CRITICAL_TEMP(cell ref)
CHEMPROPPRO_CRITICAL_TEMPERATURE(c
Units
ell ref)
Pa
Examples
Function
In cell: =CHEMPROP_CRITICAL_TEMP(A2)
CHEMPROPPRO_VAPOR_PRESSURE(cell ref) Result: 615.351
Example In cell:
=CHEMPROPPRO_CRITICAL_TEMPERATURE(
In cell:
A2)
=CHEMPROPPRO_VAPOR_PRESSURE(A2)
Result: 0 Result: 615.351
Critical pressure Critical volume

The minimum pressure that must be applied to The volume occupied at the compound's criti-
liquefy the structure at the critical temperature. cal temperature and pressure.
Units Units
bar cm3/mole
Functions Functions
CHEMPROP_CRITICAL_VOLUME(cell ref)
CHEMPROP_CRITICAL_PRESSURE(cell ref)
CHEMPROPPRO_CRITICAL_VOLUME(cell ref)
CHEMPROPPRO_CRITICAL_PRESSURE(cell
ref) Examples
Examples In cell: =CHEMPROP_CRITICAL_VOLUME(A2)
In cell: Result: 562.5
=CHEMPROP_CRITICAL_PRESSURE(A2) In cell:
Result: 49.8035 =CHEMPROPPRO_CRITICAL_VOLUME(A2)
=CHEMPROPPRO_CRITICAL_PRESSURE(A2)
Gibbs Free Energy
Result: 49.804
The Gibbs free energy for the structure at
Critical temperature 298.15 K and 1 atm.
The temperature above which the gas form of Units
the structure cannot be liquefied, no matter the
kJ/mole
applied pressure.
Functions
Units
CHEMPROP_GIBBS(cell ref)
Kelvin
112 ChemDraw/Excel
Chapter 9
CHEMPROPPRO_GIBBS_FREE_ENERGY(cell Ideal Gas Thermal Capacity
ref)
The constant pressure (1 atm) molar heat
Examples capacity at 298.15 K for an ideal gas com-
In cell: =CHEMPROP_GIBBS(A2) pound.
Result: 84.77 Units
In cell: J/[mole K]
=CHEMPROPPRO_GIBBS_FREE_ENERGY(A2)
Functions
Result: 84.77
CHEMPROP_IDEAL_GAS(cell ref)
Henry's Law Constant CHEMPROPPRO_IDEAL_GAS_THERMAL_CAPA
The inverse of the logarithm of Henry's Law CITY(cell ref)
constant.
Examples
Functions In cell: =CHEMPROP_IDEAL_GAS(A2)
CHEMPROP_HENRY_LAW_CONSTANT(cell ref) Result: 201.036
Example In cell:
=CHEMPROPPRO_IDEAL_GAS_THERMAL_CAP
In cell: ACITY(A2)
=CHEMPROP_HENRY_LAW_CONSTANT(A2)
Result: 201.036
Result: 4.78182
LogP
Heat of Formation
The logarithm of the partition coefficient for n-
The heat of formation for the structure at octanol/water.
298.15 K and 1 atm.
Functions
Units
CHEMPROPPRO_LOGP(cell ref)
kcals/mole
CLOGP_DRIVER_PARTITION_COEFFICIENT
Functions (cell ref)
CHEMPROP_HOF(cell ref) Examples
CHEMPROPPRO_HEAT_OF_FORMATION(cell
In cell: =CHEMPROPPRO_LOGP(A2)
ref)
Result: 2.233
Examples In cell:
In cell: =CHEMPROP_HOF(A2) =CLOGP_DRIVER_PARTITION_COEFFICIEN
Result: ^-105.73 T(A2)
=CHEMPROPPRO_HEAT_OF_FORMATION(A2) Molar refractivity
Result: -105.73
The molar refraction index.

User Guide
Units Function
cm3/mole CHEMPROPSTD_CONNOLLY_ACCESSIBLE_AR
EA(cell ref)
Functions
CHEMPROPPRO_MOL_REFRACTIVITY(cell Example
ref) In cell:
CLOGP_DRIVER_MOL_REFRACTIVITY(cell =CHEMPROPSTD_CONNOLLY_ACCESSIBLE_A
ref) REA(A2)
Result: 428.557
Examples
In cell:
NOTE: The default probe radius used in the
=CHEMPROPPRO_MOL_REFRACTIVITY(A2)
calculations is 1.4 angstroms.
Result: 53.305
In cell:
=CLOGP_DRIVER_MOL_REFRACTIVITY(A2) Connolly Molecular Surface Area
Result: 5.3297
The contact surface created when a spherical
Water solubility probe (representing the solvent) is rolled over
the molecular model.
Prediction of the water solubility of the struc-
ture at 25° C. Units
Units Angstroms2
mg/L Function
Function CHEMPROPSTD_CONNOLLY_MOLECULAR_ARE
A(cell ref)
CHEMPROPPRO_WATER_SOLUBILITY(cell
ref) Example
Example In cell:
=CHEMPROPSTD_CONNOLLY_MOLECULAR_AR
In cell: EA(A2)
=CHEMPROPPRO_WATER_SOLUBILITY(A2)
Result: 212.294
Result: 0
Connolly Solvent Accessible NOTE: The default probe radius used in the
Surface Area calculations is 1.4 angstroms.
The locus of the center of a spherical probe
(representing the solvent) as it is rolled over Connolly Solvent-Excluded Volume
the molecular model.
The volume contained within the contact
Units molecular surface.
Angstroms2
114 ChemDraw/Excel
Chapter 9
Units Example
Angstroms3 In cell:
=CHEMPROPSTD_PRINCIPAL_MOMENT(A2)
Function
Result: 249.546 1409.279 1658.824
CHEMPROPSTD_CONNOLLY_SOLVENT_EXCLU
DED_VOLUME(cell ref) Balaban index
Example Function
In cell: MOLECULAR_TOPOLOGY_BALABAN_INDEX(c
=CHEMPROPSTD_CONNOLLY_SOLVENT_EXCL ell ref)
UDED_VOLUME(A2)
Result: 170.277 Example
In cell:
Ovality =MOLECULAR_TOPOLOGY_BALABAN_INDEX(
The ratio of the molecular surface area to the A2)
minimum surface area. The minimum surface Result: 29909
area is the surface area of a sphere having a
value equal to the solvent-excluded volume of Cluster count
the molecule. Computed from the Connolly
Function
Molecular Surface Area and Solvent-Excluded
Volume properties. MOLECULAR_TOPOLOGY_CLUSTER_COUNT(c
ell ref)
Function
Example
CHEMPROPSTD_OVALITY(cell ref)
In cell:
Example =MOLECULAR_TOPOLOGY_CLUSTER_COUNT(
In cell: =CHEMPROPSTD_OVALITY(A2) A2)
Result: 1.428947 Result: 13
Principal Moments of Inertia (X, Y, Z) Topological index

The moments of inertia when the Cartesian Function
coordinate axes are the principal axes of the
molecule. MOLECULAR_TOPOLOGY_MOLECULAR_TOPOL
OGICAL_INDEX(cell ref)
Units
Example
grams/mole Angstroms2
In cell:
Function =MOLECULAR_TOPOLOGY_MOLECULAR_TOPO
CHEMPROPSTD_PRINCIPAL_MOMENT(cell LOGICAL_INDEX(A2)
ref) Result: 1998

User Guide
Number of rotatable bonds Example
In cell:
Function
=MOLECULAR_TOPOLOGY_SHAPE_ATTRIBUT
MOLECULAR_TOPOLOGY_NUM_ROTATABLE_B E(A2)
ONDS(cell ref) Result: 11.076923
Example
Shape coefficient
In cell:
=MOLECULAR_TOPOLOGY_NUM_ROTATABLE_ Function
BONDS(A2) MOLECULAR_TOPOLOGY_SHAPE_COEFFICIE
Result: 2 NT(cell ref)
Polar surface area Example

In cell:
Function
=MOLECULAR_TOPOLOGY_SHAPE_COEFFICI
MOLECULAR_TOPOLOGY_POLAR_SURFACE_A ENT(A2)
REA(cell ref) Result: 0
Example
Sum of degrees
In cell:
=MOLECULAR_TOPOLOGY_POLAR_SURFACE_ Function
AREA(A2) MOLECULAR_TOPOLOGY_SUM_OF_DEGREES(
Result: 17.07 cell ref)
Radius Example
In cell:
Function
=MOLECULAR_TOPOLOGY_SUM_OF_DEGREES
MOLECULAR_TOPOLOGY_RADIUS(cell ref) (A2)
Example Result: 28
In cell: Sum of valence degrees
=MOLECULAR_TOPOLOGY_RADIUS(A2)
Result: 4 Function
MOLECULAR_TOPOLOGY_SUM_OF_VALENCE_
Shape attribute DEGREES(cell ref)
Function Example
MOLECULAR_TOPOLOGY_SHAPE_ATTRIBUTE In cell:
(cell ref) =MOLECULAR_TOPOLOGY_SUM_OF_VALENCE
_DEGREES(A2)
Result: 40
116 ChemDraw/Excel
Chapter 9
Topological diameter Total valence connectivity
Function Function
MOLECULAR_TOPOLOGY_TOPOLOGICAL_DIA MOLECULAR_TOPOLOGY_TOTAL_VALENCE_C
METER(cell ref) ONNECTIVITY(cell ref)
Example Example
In cell: In cell:
=MOLECULAR_TOPOLOGY_TOPOLOGICAL_DI =MOLECULAR_TOPOLOGY_TOTAL_VALENCE_
AMETER(A2) CONNECTIVITY(A2)
Result: 7 Result: 0.001157
Total connectivity Wiener index
Function Function
MOLECULAR_TOPOLOGY_TOTAL_CONNECTIV MOLECULAR_TOPOLOGY_WIENER_INDEX(cel
ITY(cell ref) l ref)
Example Example
In cell: In cell:
=MOLECULAR_TOPOLOGY_TOTAL_CONNECTI =MOLECULAR_TOPOLOGY_WIENER_INDEX(A
VITY(A2) 2)
Result: 0.009821 Result: 249

User Guide
118 ChemDraw/Excel
Chapter 9
10
Query Structures
A query is simply a search for information that To perform a query, you first draw the query
is stored in a database. If you have ever structure in Chem & Bio Draw. You then enter
searched the Internet using a Web browser, the structure in a database application such as
then you have performed a simple query. The ChemBioFinder 12.0. The application then
query parameter is the alphanumeric text you searches one or more databases that you spec-
enter in the search engine text field and the list ify and returns the query results.
of Web sites that are returned is the query
result. Search limitations
A query structure is a parameter you use to Several factors determine the search results
search chemical databases (the database must that are returned. To get the results you expect,
include structures for the query to be useful). you must first ensure that the structure you
The query structure can include bond and atom draw accurately represents the query you want
properties that you specify to narrow or to perform. For example, if your query struc-
broaden the list of search results. Here are two ture requires that no carbon atoms in an aro-
query structure examples: matic structure can be part of any ring, you are
likely to return no results or an error, depend-
ing on the query system used.
Your search application you use can also affect
your query. If the application does not accu-
rately interpret your query structure or the
structures in the database, you may receive
inaccurate results.
Generic Nicknames
Figure 10.1 Two example structure queries. A) The
results will include any connected atom at the loca-
A generic nickname represents a nonspecific
tion specified by ‘R’; B) The results will include attachment. It can be either an unspecified
either a single or double bond at the location speci- atom, functional group, or structural feature.
fied by ‘S’D’. When you perform a query, the query will look
for structures based on the type of generic
nickname you use and where it is located in the

User Guide
query structure. Records that match the query • Right-click the atom, point to Insert Generic
structure are returned in the search results. Label on the context menu, and click the
label you wish to insert on the sub-menu.
NOTE: The nicknames feature is available in Generic Nickname Hotkeys
12.0, and ChemDraw Pro 12.0 only. You can assign hotKeys to generic nicknames
just like other nicknames. For information on
assigning a Hotkey to a nickname, see “Cus-
For example, the query structure below uses tomizing Hotkeys” on page 167.
the letter ‘Q’ to indicate that a nonhydrogen,
noncarbon atom must appear at the specified Defining Generic Nicknames
location. You cannot define the meaning of a generic
nickname because generic nicknames can rep-
resent multiple (and perhaps an infinite num-
ber of) substituents. Generic nicknames have
meaning only in the context of the search sys-
tem you are using.
The generic nicknames recognized as chemi-
cally meaningful are listed in the Generic
Nicknames file in the ChemDraw Items folder.
To edit the generic nickname files, open the
Other generic nicknames may be used to indi- Generic Nicknames file in a text editor and
cate other types of query criteria. The generic make your changes. Follow examples in the
nicknames that Chem & Bio Office 12.0 sup- file for the correct format.
ports is listed below (all are recognized as
chemically significant).
NOTE: If you check a structure that has a
• A: represents one atom only. generic nickname, a message is displayed
• M: represents metal. because the structure contains variable substit-
uents. If you ignore this message, the generic
• Q: represents an atom that is neither hydro-
nicknames are ignored and the chemical for-
gen nor carbon.
mula, mass, etc. are reported as if the atom
• X: represents any halide. label containing the generic nickname were not
• R: unrestricted; represents zero or more selected.
connected atoms of any kind.
To label an atomic position with a generic
nickname, do one of the following: Atom Properties
• Double-click the atom to open a text box, Atom properties determine what structural fea-
and type in the nickname. tures are allowed at the site of an atom. For
example, you can specify that a carbon atom
must be part of a ring, have at least two attach-
120 Query Structures

Chapter 10
ments, have no attachments, or perhaps be a assigned, a character for each property appears
specific isotope. You can specify a wide vari- adjacent to the atom.
ety of properties for any atoms in your query
structure.
NOTE: The atom properties feature is avail-

Ultra 12.0, and ChemDraw Pro 12.0 only.
Figure 10.1 This structure illustrates a variety of

Assigning atom properties possible atom properties that can be assigned. The
icons in the structure are described throughout this
To assign properties to selected atoms in a
guide.
structure:
The list below describes the query property for
1. Select one or more atoms. each indicator. For more information, see
2. To open the Atom Properties dialog box, do “Query Indicators” on page 121.
one of the following: *—Substituents: Free Sites (followed by the
• Right-click, select Atom Properties. number of free sites)
• Go to Structure>Atom Properties. U—Substituents: Up to (followed by the maxi-
• Press the Hotkey “/ ”. mum number of substituents)
X—Substituents: Exactly (followed by the
3. In the Atom Properties dialog box, select number of substituents)
the properties to associate with the selected
H—Implicit Hydrogens
atom(s).
R—Ring Bond Count
4. Click OK.
S—Unsaturation
Query Indicators C—Reaction Change
Query indicators display the atom properties T—Reaction Stereo
that you assign to a structure, as the figure L—Translation
below illustrates. If more than one property is (none)—Abnormal Valence
Viewing indicators for an atom or bond

Except for the substituents query properties,
the characters indicate that a given property is
applied, but not the value of that property.
To find the value of a query property setting:
1. Select the atom.
• Right-click, point to an atom, and point to
the appropriate property.

User Guide
• Go to Structure>Properties and view the Hiding a query indicators
settings on the Atom Properties tab. To hide an indicator:
Showing indicators for a structure 1. Right-click the indicator.
To display query indicators for a structure: 2. Choose Hide Indicator on the context menu.
1. Select the structure. Removing Atom Properties
2. Right-click and go to Atom> or Bond>Show
Query Indicator on the context menu.
To remove all properties from an atom:
To display query indicators for an atom or 1. Select the atom.

bond: 2. Go to Structure>Atom Properties.
3. Click Use Defaults.
1. Right-click the atom or bond.
2. Choose Show Query Indicator on the context To remove specific properties from an atom,
menu. do one of the following:
Positioning Query Indicators • Right-click the atom. In the context menu,
Query indicators are positioned automatically select Atom Properties and choose the prop-
and move appropriately if a structure is modi- erties to remove.
fied. You can reposition them by dragging • Go to Structure>Atom Properties and click
them to the desired position or with the Indica- the atom properties to remove.
tor Position dialog box. • With query indicators shown, click the
To reposition an indicator numerically: appropriate query indicator with the eraser
1. With a selection tool, click the indicator to tool.
move. Atom Property Options
2. Right-click and choose Position. The Posi-
tion Indicator dialog box appears. The properties you can assign to atoms are
described below.
3. Click the appropriate Position option, and
type a value:
NOTE: These features are available in Chem-
BioDraw Ultra 12.0, ChemDraw Ultra 12.0,
To Position … Type a value for… and ChemDraw Pro 12.0 only.
from the atom or bond angle, degrees or
center to indicator cen- clock, o’clock Substituents
ter
A substituent is defined as a non-hydrogen
from the atom or bond offset, horizontal and atom connected by a bond of any order. The
center to bottom left of vertical substituents properties specify the number of
indicator baseline substituents that may be bonded to the selected
at specified coordi- absolute, horizontal atoms.
nates and vertical For example, in the figure below, the carbonyl
carbon (B) has a substituents count of two, the

Chapter 10
alpha carbon (A) and the aldehyde oxygen. ble. An explicit hydrogen and its bond are visi-
(hydrogen atoms are not counted). The alde- ble.
hyde oxygen has only one substituent.
Figure 10.2 Substituent count. Figure 10.3 A) examples of implicit hydrogens; B)

The substituent count atom property lets you an explicit hydrogen.
specify the number of bonds to an atom in the The Implicit Hydrogens property specifies
target structure. This includes bonds already whether additional, implicit hydrogen atoms
drawn in the query structure. may be attached to the selected atoms. If
The various substituent options are described implicit hydrogen atoms are not allowed, all
below. valences to that atom must be filled by bonds
to non-hydrogen atoms.
Unspecified. This is the default. The target
base determines the search. Some databases
find compounds with any substitution at this NOTE: The implicit hydrogens property is
atom; other databases (including DARC) find available in ChemBioDraw Ultra 12.0,
only compounds with substitution exactly as ChemDraw Ultra 12.0, and ChemDraw Pro
drawn. 12.0 only.
Free Sites. Finds compounds in which the
selected atoms may contain a range of substitu-
ents up to the number specified plus the num- Option Search Result
ber of bonds as drawn. A value of zero finds a
substituent count as drawn. You can also use Allowed Default. Finds compounds
the Free Sites symbol in the Query toolbar to regardless of whether
apply free sites. hydrogen atoms are attached
to the selected atoms.
Up to. Finds compounds in which the selected
atoms may contain a range of substituents up Not Finds compounds with no
to the number specified. allowed additional hydrogen atoms
Exactly. Finds compounds in which the attached to the selected atoms.
selected atoms contain the exact number of
substituents as specified, up to 15 substituents. Ring Bond Count
The Ring Bond Count specifies the number of
Implicit Hydrogens
bonds attached to an atom that are part of rings
An implicit hydrogen is a hydrogen atom in of any size. For simple cases, this also speci-
which it or its bond is implied but is not visi-

User Guide
fies the maximum number of rings in which an Unsaturation
atom can reside. The Unsaturation property specifies whether a
multiple bond is attached to the selected atoms.
Option Search Result
Any Default. Finds compounds in
which the selected atoms can be a Unspecified Default. Finds compounds
member of any type of ring, or a regardless of whether a multiple
member of no ring at all. bond is attached to the selected
atoms.
No ring Finds compounds in which the
bonds selected atoms are acyclic. Must be Finds compounds that do not
absent have a multiple bond attached
As drawn Finds compounds in which the to the selected atoms.
selected atoms reside in the same
type and number of rings as Must be Finds compounds that have at
drawn. present least one multiple bond (double,
triple or aromatic) attached to
Simple ring Finds compounds in which the the selected atoms.
selected atoms is a member of
only one ring (the atom has two Reaction Change
ring bonds). The Reaction Change property specifies
whether a change occurs at selected atoms
Fusion Finds compounds in which the after a reaction. This property is meaningful
selected atoms lies at ring fusions only when searching a database that contains
(the atom has three ring bonds). chemical reactions. In ChemFinder, only the
Spiro or Finds compounds in which the
higher selected atoms is a member of a
spiro or higher linkage (the atom
has four or more ring bonds).

Chapter 10
product atom is checked. The stereo designa- 1. To display the Query tools, go to
tion is ignored on reactants. View>Other Toolbars>Query Tools or click
the Query Tools icon on the Main Tool pal-
NOTE: The reaction change property is avail- ette.
able in ChemBioDraw Ultra 12.0, ChemDraw 2. Click the Free Site tool on the Query tools
Ultra 12.0, and ChemDraw Pro 12.0 only palette.
3. Click the atom to which you want to apply
free sites.
4. Continue to click the atom to increase the
Option Search Result free site number.
May be Default. Finds all reactions To reduce the number of free sites, hold the Alt
anything regardless of any change to or Option key while clicking the atom.
selected atoms after a reaction. You can also change the free sites using the
Atom Properties dialog box or the shortcut
Must be as Finds all reactions that are menu. See “Atom Properties” on page 120.
specified changed at the selected atoms
exactly as specified by the reac- Reaction Stereo
tion center property in the Atom The Reaction Stereo property specifies that the
Properties dialog box. selected atoms are stereocenters in a reaction.
This property is only meaningful when search-
ing a database containing chemical reactions.
Figure 10.4 The reaction change indicator is circled

Figure 10.5 The reaction stereo indicator is circled
in the figure above.
in this example.
Free Sites
A free site query lets you specify the maximum Option Search Result
number of substituents a result can have. How-
ever, it also requires that the bonds in the Any Default. Finds all compounds
results appear exactly as they appear in the regardless of the stereochemistry
query structure. at the selected atoms.
NOTE: The Free Sites feature is available in Inversion Finds compounds in which the
ChemBioDraw Ultra 12.0, ChemDraw Ultra selected atoms have an inverted
12.0, and ChemDraw Pro 12.0 only. stereo configuration after a reac-
tion.
To increase the number of free sites:

User Guide
hexa-deuterobenzene—by specifying a nuclide
Option Search Result at any location.
Retention Finds compounds whose
selected atoms have an NOTE: The isotopic abundance property is
unchanged stereo configuration available in ChemBioDraw Ultra 12.0,
after a reaction. ChemDraw Ultra 12.0, and ChemDraw Pro
12.0 only.
Translation
The Translation property specifies what is
required to match in the structure query and
possible database hits in a Markush DARC Option Search results
query.
Unspeci- Default
fied
Option Definition
Any For ChemFinder, the same as
Equal Default. Matches specific to default. Included for compati-
specific or generic to generic bility with other systems
terms. where the default may be
different.
Broad Translates specific query atoms to
corresponding superatoms in the Natural Indicates an isotopically
database. unmodified nuclide.
Narrow Translates query superatoms to Enriched Indicates a mixture of isotopi-
corresponding specific atoms or cally substituted and isotopi-
groups in the database. cally unmodified nuclides.
Any Translates generic or specific Deficient Indicates a depleted label, that
terms to any term. is, the nuclide is present in less
than the natural ratio.
For more information, see the Markush DARC
User Manual. Nonnatural Indicates an isotopically
Isotopic Abundance substituted nuclide, that is,
The Isotopic Abundance property lets you dis- essentially all the molecules
tinguish between different isotopic com- of the compound have only
pounds—for example between mono- and the indicated nuclide.
Abnormal Valence
The Abnormal Valence property specifies
whether selected atoms can have a valence
other than normal. “Normal” valences for each

Chapter 10
element are defined in the Isotopes Table file show the properties that have been assigned to
in the Chem & Bio Draw 12.0 Items folder. it.
NOTE: The Abnormal Valence atom property NOTE: The bond property feature is available
does not provide a visual indicator. in ChemBioDraw Ultra 12.0, ChemDraw Ultra
.
Option Search Result Assigning Bond Properties

Not allowed Default. Finds compounds where To define bond properties:
the selected atoms only have 1. Select one or more bonds in a structure.
valences that are normal for that 2. Do one of the following:
element. If necessary, hydrogen
atoms are added to or removed • Right-click, point to Bond on the context
from the atom before transferring menu, point to the property you want, and
it to the chemical database. If the choose the desired options.
Check Structure When Copying to • Go to Structure>Properties. On the Bond
Clipboard or Exporting preference Properties tab, select the desired properties
is turned on, an error message from the drop-down lists and click OK.
warns of abnormal valences.
• Point to bond and press the Hotkey “/ ”.
Allowed Finds compounds with the The Bond Properties dialog box appears.
specific valence drawn. In the Bond Properties dialog box, select
the properties to associate with the selected
atoms. Click OK.
NOTE: If Abnormal Valence is Allowed, any
The character that appears depends on which
Invalid Valence messages for those atoms are
query properties have been assigned. If more
ignored by the Check Structure command.
than one property is assigned, more than one
indicator appears adjacent to the atoms. See
“Query Indicators” on page 121.
Bond Properties The indicators are:
Assigning query properties to bonds is similar
.
to assigning query properties to atoms. Bond Indicator Bond Query Property

query indicators that appear next to a bond
Any Bond Types: Any
S/D Bond Types: Single/Double
D/A Bond Types: Double/Aromatic

User Guide
Removing Bond Properties
Indicator Bond Query Property
To remove all query properties from one or
S/A Bond Types: Single/Aromatic more bonds:
1. Select the bonds.
Rng Topology: Ring
2. Go to Structure>Bond Properties.
Chn Topology: Chain 3. Click Use Defaults.
The bond properties are removed and the indi-
R/C Topology: Ring or Chain
cators do not appear.
Rxn Reaction Center To remove specific bond properties:
1. Select the bond.
Viewing Bond Properties 2. Do one of the following:
The descriptor for the Reaction Center query • Right-click, point to the appropriate prop-
property indicates that the property is applied, erty, and click the property to remove.
but not the value of the property. • Go to Structure>Bond Properties and click
To find the value of a query bond property set- the bond property to remove.
ting:
Bond Property Options
1. Select the bond.
2. Do one of the following: The properties you can assign to bonds are
described below.
• Right-click, point to Bond Properties, and
select to a property. Bond Types
• Go to Structure>Bond Properties. This property specifies the bond type of the
selected bonds. The default bond type corre-

Chapter 10
sponds to the current type of the bond (single, saved to a given file format, it is converted to
double, etc.) as drawn. the closest equivalent that is supported.

Topology
Single (all) Finds compounds with the The Topology property specifies the ring envi-
and Dative bond type you select for the ronment of the selected bonds.
selected bonds.
Double or Finds compounds whose Option Search Result
Double Bold selected bonds are double.
Unspecified Default. Finds compounds
Double Finds compounds whose regardless of environment.
Either selected bonds are double
Ring Finds compounds where the
bonds and have either cis/
selected bonds are part of a
trans stereochemical configu-
ring.
ration.
Chain Finds compounds where the
Aromatic Finds compounds whose
selected bonds are part of a
selected bonds are aromatic.
chain (and are specifically
Tautomeric Finds compounds whose not part of a ring).
selected bonds are tautomeric.
Ring or Chain Finds compounds where the
Triple Finds compounds whose selected bonds are part of
selected bonds are triple. either a ring or a chain.
Quadruple Finds compounds whose
Reaction Center
selected bonds are quadruple.
The Reaction Center property specifies how
Any Finds compounds regardless the selected bonds are affected in a reaction.
of the bond type of the This property is only meaningful when search-
selected bonds. ing a database containing chemical reactions.
S/D Finds compounds whose
selected bonds are single or Option Search Result
double.
Unspecified Default. Finds compounds
D/A Finds compounds whose
regardless of whether the
selected bonds are double or
selected bonds are affected by
aromatic.
the reaction.
S/A Finds compounds whose
Center Finds compounds where the
selected bonds are single or
selected bonds are affected by
aromatic.
a reaction, but the type of
change is unspecified.
NOTE: Not all bond types are supported in all
file formats. When an unsupported bond type is

User Guide
1. Open an atom label text box.
2. Type an open bracket (“[“) followed by a
Make/Break Finds compounds where the list of elements separated by commas (“Cl,
selected bonds are either bro- Br, I”), followed by a close bracket (“]”).
ken or created in a reaction. 3. Close the text box.
Change Finds compounds where the
bond order of the selected
bonds changes in a reaction.
Make& Finds compounds where the
Change selected bonds are formed, bro-
ken, or undergo a change in
bond order.
Not Center Finds compounds where the
selected bonds are not part of
Figure 10.6 An element list as an atom label
the reaction center.
The figure below shows a query structure cre-
Not Modi- Finds compounds where the
ated to find compounds matching the follow-
fied selected bond’s orders do not
ing criteria:
change, but which may or may
not be part of the reaction cen-
ter.
Unmapped Finds all compounds.
Element Lists
By labeling an atom position with a list of ele-
ments, you specify that one of these elements
must match in the structure for which you are (A) indicates that the atom must match any
searching. An example of an element list is: atom except hydrogen. The indicator (B) near
the bond indicates that the bond must be single
or double, S/D. The element list (C) specifies
that one of these elements must match in the
The elements in the list must be separated by
target structures.
commas. A space after each comma and brack-
ets are optional. Element Not-Lists
The element not-list specifies that the elements
NOTE: An element list may contain only in the list match must not match in the struc-
atomic symbols, plus D (deuterium) and T (tri- ture for which you are searching. Commas
tium). must separate the elements in the element not-
list. A space after each comma and brackets are
To create an element list: optional.

Chapter 10
The word NOT must be in all-caps and must be To enclose structures with brackets:
followed by a space. Alternatively, the word
1. To display to Bracket toolbar, go to
NOT may be replaced with a minus sign.
View>Other Toolbars>Bracket.
For example:
2. On the Bracket toolbar, select one of the
double bracket tools.
3. To draw the brackets, click and drag across
Figure 10.7 Element NOT lists the structure you want to enclose.
This method will give a default value for com-
NOTE: An element not-list may contain only ponent order, multiple group repeat count, or
atomic elements, plus D (deuterium) and T (tri- SRU label.
tium).
Setting Bracket Properties
To create an element not-list: You can change the properties of brackets by
the context menus or Bracket Properties dialog
1. Open an atom label text box. box.
2. Type an open bracket, the word NOT, and a To use the Bracket Properties dialog box:
space (“[NOT”) followed by a list of ele-
ments separated by commas (“Cl, Br, I”), 1. Select a bracket using a selection tool.
followed by a close bracket (“]”). 2. Go to Structure>Bracket Properties. The
Bracket Properties dialog box appears.
Polymers The Flip Type option appears only for ladder
Polymers are indicated by brackets, parenthe- polymers. See “Flip Type” on page 134.
ses, and braces that enclose repeating struc- You can customize the text that appears to the
tures or structural fragments. The bracket bottom right of the bracket for the following
properties lets you specify the context and ori- bracket types.
entation of the repeating units. • Component (c#)—the component order
must be a non-negative integer, and is dis-
NOTE: The polymer feature is available in played as the letter “c” followed by an inte-
ChemBioDraw Ultra 12.0, ChemDraw Ultra ger (or “c” alone if an order of zero is
12.0, and ChemDraw Pro 12.0 only. specified).
• Multiple Group (#)—the repeat count must
For example: be a positive integer.
• SRU (n)—the SRU label can be any text.
You can also edit the text for these bracket
usage types directly in the document using the
Text tool. You cannot edit the text displayed
for other bracket usage types.

User Guide
Bracket Usage als are known, but the exact structure of the
reaction product is not.
Representations of polymers are either struc-
ture-based or source-based. The type of You can create a source-based representation
bracket you use depends on which type of rep- by enclosing a structure in “Monomer (mon)”
resentation you need. brackets.
A source-based representation of poly(vinyl
Structure-based Polymers
chloride) is shown in below:
Structure-based representations enclose only
part of a structure within brackets. One or more
bonds cross each of the enclosing brackets.
The crossing bonds “match up”, making the
polymer structure more explicit.
You create a structure-based polymer represen-
tation by enclosing a portion of a structure in
brackets with a bracket type of SRU (n). The You can use “Mer (mer)” brackets for compo-
subscript “n” is recommended by IUPAC to nents of a copolymer where those individual
denote structure-based representations of components are known not to repeat them-
unknown size, but you can edit the text using selves or they alternate with the other compo-
the text tool. nents. For example:
A structure-based representation of
poly(vinyl chloride) is shown in below:
You can also use the bracket usage types Copolymers represent substances with more
“Crosslink (xl)”, “Graft (grf)”, and “Modifica- than one repeating unit. In general, you can use
tion (mod)” to represent specific types of bracket type “Component (co)”. You can also
repeating units in a structure-based representa- use “Copolymer, alternating (alt)”, “Copoly-
tion. mer, random (ran)”, and “Copolymer, block
Source-based Polymers (blk)” to represent different specific types of
Source-based polymer representations enclose copolymers in a source-based representation.
an entire discrete chemical substance in brack- The bracket type, “Mixture, unordered (mix)”
ets. The mode of polymerization may be obvi- may be used to represent a collection of sub-
ous from context, or it might be unknown. stances that may all be present, but not neces-
Source-based representations are useful when sarily in known amounts. Bracket type
describing processes where the starting materi-

Chapter 10
“Component (c)” indicates individual mixture You can edit the numeric repeat count with the
elements, as shown below. text tool. Examples are shown in below.
Figure 10.8 Brackets used to indicate mixtures

Bracket type “Mixture, ordered (f)” is prima-
rily used to describe manufacturing processes,
where the ordering of components is a critical
part of the process (and where a different
ordering might produce a different final prod-
uct. As with unordered mixtures, individual Figure 10.9 Brackets to indicate multiple groups
elements of an ordered mixture should be sur-
ANALYSIS
rounded by brackets with a bracket usage of
“Component (c)”. Unlike with unordered mix- Because multiple group brackets represent a
tures, however, components of ordered mix- specific repeat count (unlike the unknown
tures must represent their ordering. You can do repeat count of the other bracket types), it is
this by editing the “c” label with the text tool to possible to calculate accurate molecular
include a number (“c1”, “c2”, and so on.) weights (and related data) for such structures.
That data is displayed in the Analysis window
You use the bracket type, “Multiple Group (#)”
as with any other structure.
to indicate that the enclosed items are repeated
a specific known number of times. Multiple Repeat Pattern
group brackets may enclose entire structures,
For simple linear polymers, the repeating units
or may enclose a portion of the structures only.
may connect head-to-tail or head-to-head (or
their repeat pattern might be a mixture or
unknown). You can also assign this property to
brackets.
Because of its prevalence, the head-to-tail type
is assumed to be the default Repeat Pattern,

User Guide
and does not receive any special annotation on • Parentheses or braces may be used instead
the brackets, as shown below. of brackets
• Brackets can be omitted if not needed for
clarity, for example with O1-3
To create a link node:
2. Type in the following format:
[CH2]3-7
Flip Type
For ladder polymers (those polymers with two
connecting bonds on each side), the connection
order may be undefined. You can assign the
Flip Type property to define it. This property is
appropriate only for brackets with exactly two
Figure 10.10 Head-to-tail repeat pattern. A and B crossing bonds.
represent the polymers shown. C represents a
Because of its prevalence, the No Flip type
mixture of A and B.
does not receive special annotation. The figure
Link Nodes below illustrates a flip type in ladder polymers.
You can specify a variable-length chain or ring

by indicating that one of the atoms can be
repeated some number of times using link
nodes.
NOTE: The link nodes feature is available in

Link nodes must have exactly two connecting Alternative Groups

bonds. The atom label must conform to the fol- You can create a search query that contains
lowing conditions: variable functional groups or substructures.
• It must consist of a generic name or no Instead of submitting multiple queries on
more than a single element symbol. structures that share a common substructure,
• The last part of the label in the form: num- you can submit a single query with the parent
ber hyphen number, with the number and structure. The parent structure can have attach-
hyphen subscripted

Chapter 10
ment points to a list of alternative groups that To define an alternative group:
you can define.
1. Go to View>Other Toolbars>Query Tools to
open the Query toolbar.
NOTE: The alternative groups feature is avail- 2. Click the Alternative Group query tool and
able in ChemBioDraw Ultra 12.0, ChemDraw drag with the tool to create an area large
Ultra 12.0, and ChemDraw Pro 12.0 only. enough to draw the alternative groups.
3. Type a title, such as R1, in the Alternative
Alternative groups, sometimes called R- Group Title box, then draw the substructure
Groups or G-Groups (Generic Groups), are fragments in the Alternative Group box.
shown below.
Figure 10.11 Defining an alternative group

Specify where the fragments should bond to
the parent structure on the alternative group
label by defining Attachment Points.
• Select the diamond shaped Attachment
Point tool on the Chemical Symbols palette
(View>Other Toolbars>Chemical Symbols),
and click a substructure fragment where
you want to place the attachment point.
• Point to a substructure fragment where you
Defining Alternative Groups want to place the attachment point and
You can create alternative group definitions press the Hotkey “.” (period).
(R, G, etc.) that represent a set of substituents, An attachment point symbol appears.
each of which is used in the query.

User Guide
2. Repeat for all fragments. Multiple Attachment Points
You can also use R-groups that contain more
than one attachment point, such as the one
below:
For this type of R-group, you will need to indi-

Figure 10.12 Adding attachment points. An attach-
cate in your table the attachment point order. If
ment point symbol has been applied to the nitrogen
atom.
you have well-defined multiple attachment
points on your structure fragments, you can
When you create a parent compound that con- search for specific materials. This type of
tains an alternative group you defined, an search is especially useful for searching for
attachment point symbol appears next to the conformationally similar structures.
label. The attachment point number matches
For example, assume you want to find the two
that found in the definition.
compounds in figure A below but not the two
compounds in figure B.
Figure 10.13 Structure with R-group table

The number displayed in the attachment point
symbol is the attachment rank order. See the
example in Multiple Attachment Points.
Figure 10.14 Multiple attachment points

By specifying the attachment point order, you
can exclude the unwanted compounds.
To specify the attachment points order:

Chapter 10
1. Draw the parent structure shown below drawings the numbering of attachment points
is implicit and the numbered attachment rank
indicators are superfluous.
NOTE: Attachment rank indicators are avail-

2. Create an alternative group box labeled
“R1”.
To hide the attachment rank indicators and
3. Draw the structure fragments and label
remove the numbers from the attachment
them with attachment points.
points:
When the alternative group definition is com-
1. Go to File>Preferences.
plete, the attachment point symbols appear in
the parent compound. 2. In the Preferences dialog box, click Build-
ing/Display.
3. Deselect Show Attachment Rank Indicators.
This change affects all documents.
The figure below shows an alternative group
definition and a parent structure with the
attachment rank indicators hidden.
t
Figure 10.15 R-groups with multi-attachment points

By numbering your attachment points, you
have unambiguously specified that the methyl
group must be adjacent to the amine group.
The conformations that are not of interest are Figure 10.16 Hidden attachment indicators
excluded.
Attachment Point Numbering
Attachment Rank Indicators Numbered attachment points let you specify
You can hide the attachment rank indicators if precisely how the structure fragments are con-
required. For example, in publication-quality nected to your parent structure.

User Guide
The numbering of the attachment points is You can define your search query more con-
related to the front to back order of the attach- cisely with the anonymous alternative group.
ment points. By labeling an atom position as a list of sub-
To set the order of the attachment points, click structures you specify that one of these sub-
the ends of the bonds in the order you want to structures must match in the structure for
number them using the Attachment Point tool. which you are searching. Commas must sepa-
The last point clicked has the highest number. rate the items in the anonymous alternative
To change the ordering of the attachment group. A space after each comma and the
points do one of the following: brackets are optional. Examples of anonymous
alternative groups are shown below.
• Click the attachment points with the
Attachment Point tool.
• With a selection tool, select the bond to
which the attachment point is connected
and go to Object>Bring to Front or Send To
Back.
Figure 10.17 Anonymous alternative groups
The attachment point numbers are highest in To create anonymous alternative groups:
the front.
Anonymous Alternative 2. Type an open bracket “[”followed by a list
of elements, fragments, nicknames, or
Groups generic nicknames separated by commas,
followed by a close bracket “]”.
NOTE: Anonymous alternative groups are
available in ChemBioDraw Ultra 12.0, Expand Generic Structures
ChemDraw Ultra 12.0, and ChemDraw Pro You can generate multiple structures from an
12.0 only. abbreviated combinatorial structure with the
Expand Labels tool. The tool is designed for
Anonymous alternative group are a cross “small” expansions, and is limited to a maxi-
between an element list and an alternative mum of 500 generated structures. For large
group. Element lists are restricted to single ele- combinatorial expansions, use
ments, but anonymous alternative groups can CambridgeSoft’s CombiChem for Excel.
contain any structure that can be represented
by text. Nicknames and generic nicknames are NOTE: This feature is available in ChemBio-
allowed in anonymous alternative groups. Draw Ultra 12.0, ChemDraw Ultra 12.0, and
Anonymous alternative groups are shortcut ChemDraw Pro 12.0 only.
notation for regular alternative groups, elimi-
nating the need to specify a name such as
“R1”.

Chapter 10
Four kinds of abbreviated combinatorial defi- Definitions are expanded into multiple com-
nitions may be used: plete molecules. If more than one site is
present in the selection, the expansion will
definition example include all permutations of substitutions.
Expansions are generated in a new document.
Alternative To expand a generic structure:
Groups and
R-tables 1. Select one or more generic structures to
expand.
NOTE: For alternative group/R-tables, both

the alternative group label and the table must
be selected. If the label is selected but not the
table, the label will not be modified by the
expansion, and will appear as a label in all gen-
Anonymous erated structures.
Alternative
Groups
2. Go to Structure>Expand Generic Structure.
The structures are generated in a new docu-
ment.
R-Logic Queries
After you have your generic structure and a set
Element
of R-groups, you can use them to run queries
Lists
against a structure database. This is called an
R-Logic query.
When you run an R-Logic query, you search
for structures that all have the generic structure
and a combination of your R-groups. The com-
binations are based on a Boolean expression
that you define. To prepare an R-Logic search,
go to Structure>R-Logic Query to open the R-
Variable Logic Query dialog box.
Attachment
To define a query, select one or more R-groups
in your structure and how many times it must
occur. You can also indicate that, if the first R-
group condition is met, another R-group must
also be found before the structure is returned as

User Guide
a result. For example, consider the following other must be a hydrogen to return a positive
structure: result.
Atom-to-Atom Mapping
You can create correspondences between
atoms in different structures for use in creating
queries for searching a reaction database. The
reactions mapped can be single or multi-step.
You can assign atom-to-atom mapping for cre-
ating records for a reaction database and for
creating queries for searching a reaction data-
base.
NOTE: Atom-to-atom mapping is available in

This structure indicates that both R1 sites must
consist of either a fluorine or chlorine atom
and that the R2 site must be either a bromine or You can assign atom mapping in two ways:
iodine atom. • Automatic mapping (go to Structure>Map
Assume you want to find all structures in your Reaction Atoms).
database that have either a F or Cl atom at both • Manual mapping, using the Reaction
R1 locations and either Br or I at R2: Atom-Atom Map tool on the main tools
palette.
1. Go to Structure>R-Logic Query.
2. In the R-Group dropdown list, select R1. During either type of mapping process, the
mapping algorithm perceives and assigns a
3. For Occurrence range, select 2. This indi-
reaction center for the reactants and products.
cates that two instances of an R1 group must
occur in a structure for it to be returned as a When a reaction map is established, you can
result. point to an atom in one structure with the
Reaction Atom-Atom Map tool selected to
4. For If R(i), select R2. This indicates that the
highlight the mapped atom in the other struc-
R2 location must consist of either Br or I. ture.
5. Click Add.
Displaying and Printing
6. Click OK.
To make the symbols always appear and print
Rest H on the atoms when mapping reactions:
Select Rest H in the R-Logic Query dialog box 1. Go to File>Preferences.
to indicate that, if you have two possible R-
2. In the Preferences dialog box, click the
group locations, and only one is filled, the
Building/Display tab.

Chapter 10
3. Select Always Display and Print Reaction Manual Mapping
Mapping. In situations that require manual mapping of
4. Click OK. atoms, you can use the Reaction Atom-Atom
Map tool. This might be necessary when the
Deselect Always Display and Print Atom Map-
automatic mapping is applied to complicated
ping to show the symbols only when you select
reactions, and gives incorrect results. In these
the Reaction Atom-Atom Map tool. When this
cases you can manually readjust the reaction
option is deselected, atom mapping symbols do
mapping.
not print, even though a reaction map has been
created. The figure below shows the initial mapping
being amended by using the Reaction Atom-
Automatic Mapping Atom Map tool.
To create a reaction map:
1. Draw the reaction you want to map and
select the reaction.
TIP: Double-click the arrow with a selection

tool to select the entire reaction.
2. Go to Structure>Map Reaction Atoms.

Figure 10.19 Automatic mapping to be amended
The symbol Rxn appears next to the bonds in When you manual map reactions with the
the reactant and product that are perceived by Reaction Atom-Atom Map tool, you can sup-
the algorithm as being modified by the reac- press automatic re-mapping of atoms other
tion. These symbols are bond properties that than your target atom.
are applied. For more information about the
To suppress automatic re-mapping:
Reaction Center bond property, see “Bond
Properties” on page 127. 1. Go to File>Preferences.
2. On the General tab, select Automatic Reac-
tion Mapping.
3. Click OK.
To use the Reaction Atom-Atom Map tool to
supplement the automatic mapping:
1. Click the Reaction Atom-Atom Map tool
on the Query toolbar.
2. Point to the atom in the reactant whose
mapping you want to establish. For exam-
ple, in the following drawing you would
point to the acyclic carbon adjacent to the
Figure 10.18 Automatic reaction mapping ether oxygen.

User Guide
3. Drag from the reactant atom to the corre- Stereochemical Symbols
sponding product atom.
There are three types of flags that indicate ste-
The remaining atoms are mapped based on the reochemistry:
manual mapping.
Racemic. A racemic mixture.
Absolute. A pure enantiomer of known config-
uration.
Relative. A pure enantiomer of unknown con-
figuration.
See “Relative Stereochemistry” on page 88 for
changes in Chem & Bio Draw 12.0.
The default atom label size for the document
determines font and size for stereochemical
flags.
NOTE: The stereochemical symbols feature is

12.0 only.
To draw a stereochemical flag:

Figure 10.20 Finalized mapping
You can continue to set or change the mapping 1. To display the Query tools, go to
for other atoms in the reaction if necessary View>Other Toolbars>Query Tools or click
until you get exactly the mapping you want. the Query Tools icon on the Main Tool pal-
ette.
Clearing Reaction Mapping
2. On the Query tools palette, click the tool for
To clear all reaction mapping: the flag you want to use.
1. Select the structures whose mapping you 3. Click next to the structure to which you
want to remove. want to assign the flag.
2. Go to Structure>Clear Reaction Map.
Exporting Reaction Mapping
3D Properties
Reaction mapping and reaction center percep- 3D queries are particularly useful in pharma-
tion information are stored in the native file cophore searching where the user is looking
format (*.cdx.) You can open the file in Chem for a 3D relationship among atoms and bonds,
& Bio Draw 12.0 for transfer to other applica- for example in a series of potential receptor
tions that read atom mapping such as Chem- ligands. To create a 3D query, you add geome-
Finder. You can also copy mapped reactions to tries (lines, planes, etc.) and constraints (speci-
these same applications using the Clipboard. fied as ranges) to a query structure. For

Chapter 10
example, you might specify that two atoms
must be between 4 and 5 Å apart, or that two Option Search Result
planes must be separated by 80-100 degrees. Plane Defines the best-fit plane for
the selected points, or for a
NOTE: The 3D Properties feature is available point and a line.
in ChemBioDraw Ultra 12.0, ChemDraw Ultra Exclusion Defines an exclusion sphere
12.0, and ChemDraw Pro 12.0 only. Sphere around a point. If more than
one point is selected, the exclu-
To assign 3D properties to a structure: sion sphere is around the first
selected point, and the subse-
1. Select the structure or substructure. quent points are allowed within
NOTE: Because some 3D properties specify an the exclusion sphere when the
order, use Shift+Click to select them in the query is evaluated. Indicated as
order you want. a range, in Å, beginning at 0.
2. Go to Structure>Add 3D Property and select Normal Defines the normal from a

an option from the table below. defined plane in the direction
of a point.
NOTE: In the table, points may be atoms, Point Defines a point positioned at a
centroids or points. Lines may be lines or specified distance from a first
normals. point in the direction of a sec-
ond point (in order), or in the
direction of the normal.
Centroid Defines a point positioned at
Angle Defines an angle constraint the average position of all other
between three points (in order). points selected.
Indicated as a range.
All constraint values can be edited with the
Dihedral Defines a dihedral (torsional) text tool. Only exclusion spheres show the
angle constraint among four change visually.
points (in order), between two When you create a point, a dialog box is dis-
lines, or two planes. Indicated played. Specify the distance from the first
as a range. selected point to the calculated point. The dis-
Distance Defines a distance constraint tance may be specified as an absolute value in
between two points, a point and Å or as a percentage of the distance between
a line, or a point and a plane. the selected points. Negative values indicate
Indicated as a range, in Ang- that the calculated point is further from the sec-
stroms. ond point than the first point is, rather than
Line Defines the best-fit line for the being between them.
selected points. Geometry and constraint objects update
dynamically when you change the structure;

User Guide
they cannot be moved independently. They
may be used with CDX, MOL, SKC, and TGF Exported Query ISIS™ Mol Rxn
Properties
files (full read-write compatibility); they are
not compatible with other formats. They can, • Allowed X X X
however, be saved in print-only formats such
as TIFF. Ring Bond Count
Export Compatibility • Any X X X
Because query properties are useful only in a • No ring bonds
chemical database, you must transfer your X X X
structures from Chem & Bio Draw 12.0 into • As drawn X X X
your search system. Not all file formats sup-
port the same query properties and not all • Simple ring X X X
chemical databases support the same file for-
mats. Consult the documentation for your data- • Fusion X X X
base to see which file formats are supported.
The following table lists the query properties • Spiro or higher X X X
that Chem & Bio Draw 12.0 writes to SKC,
TGF, and Clipboard file formats. The CDX is Unsaturation
the preferred format to use to retain all query
properties in a drawing. • Unspecified X X X
.
• Must be absent
Exported Query ISIS™ Mol Rxn
Properties • Must be present X X X
Atom Properties Reaction Change
Substituents • May be any- X X
thing
Unspecified X X X
• Must be as X X
• Free Sites b b b specified
• Up to Reaction Stereo
a a a
• Any X X
• Exactly Xc Xc Xc
• Inversion X X
Implicit Hydrogens
• Retention X X
• Not allowed X X X
Translation

Chapter 10
Exported Query ISIS™ Mol Rxn Exported Query ISIS™ Mol Rxn
Properties Properties
• Equal • Double Bold h h h

• Broad • Aromatic X X X
• Any • Tautomeric i i i
• Narrow • Triple X X X
Abnormal Valence • Quadruple l l l

• Not Allowed X X X • Any X X X
• Allowed X X X • S/D X X X
Bond Properties • D/A X X X
Bond Type • S/A X X X

• Single X X X Topology
• Dashed X d X • Unspecified X X X
• Hashed d d d • Ring X X X
• Wedged Hashed X X X • Chain X X X
• Bold X e e Reaction Center
• Wedged X X X • Unspecified X X
• Wavy X X X • Center X X
• Hollow Wedged e e e • Make/Break X X
• Dative f f f • Change X X
• Double Xg X X • Make&Change X X
• Double Either X X X • Not Center X X

User Guide
b—Free Sites counts of zero translated to
Exported Query ISIS™ Mol Rxn “Substitution as drawn”; all other Free Sites
Properties
values written as substitution counts equal to
the total current valence plus the free sites
Other Query Attributes
value.
• Generic Nick- Xj Xj Xj c—Substituent counts of greater than 5 are
names translated to “6 or more”
• Element Lists Xko Xko Xko d—Converted to Wedged Hashed
e—Converted to Wedged
• Element Not Xk Xk Xk f—Converted to a Single, with a positive
Lists charge applied to that atom at the base of the
• Alternative X Xm dative bond and a negative charge applied to
Groups the atom at the point of the dative bond
• Anonymous n n g—Interpreted by ISIS™ as unspecified cis/
Alternative trans stereochemistry
Groups h—Converted to Double
• Link Nodes p p p i—Converted to S/D
j—Only M, X, Q, A; others written as aliases
• Bracket proper- X X X k—Truncated to the first 5 elements
ties
l—Converted to single.
• Atom-Atom X X m—An RG file will be created automatically.
mapping
n—Converted to non-anonymous alternative
• Variable groups.
Attachment o—Lists of greater than 5 elements converted
Positions to alternative groups.
3D query properties p—The low end of the repeat range is always
treated as 1.
a—Converted to the appropriate number of
exact substituents

Chapter 10
11
Sharing Information
Chem & Bio Draw 12.0 includes many of the For more information, see “Autoscaling” on
standard system commands for transferring page 149.
information within and between documents, If you are pasting the Chem & Bio Draw 12.0
and between Chem & Bio Draw 12.0 and doc- drawing into a document from which you are
uments created using other applications. planning to print to a PostScript printer, see
You can transfer information using: “Transferring PostScript (Macintosh)” on page
151.
• the Clipboard
• drag and drop Text Line Notation
• file formats Use text line notation to expand a line of text
When you drag-and-drop Chem & Bio Draw into the structure that it represents. A SMILES
12.0 information, or use the clipboard, the string is a line of text that represents the struc-
object you are copying can be edited. ture of a molecule. Several software packages
use SMILES strings to enter and store chemi-
The Clipboard cal structure information.
You can use the clipboard to transfer part or all

information within an active document win- NOTE: Text line notation is available in Chem-
dow between applications on the same com- BioDraw Ultra 12.0, ChemDraw Ultra 12.0,
puter or on a network. Use the standard copy- and ChemDraw Pro 12.0 only.
and-paste or cut-and-paste tools to transfer
information to any application that supports A SMIRKS string describes chemical reactions
these tools. The information is transferred as a in text. If you select a reaction and use the
drawing object. Double-click the object to edit Copy As SMILES command, a SMIRKS string
it in Chem & Bio Draw 12.0 is copied to the clipboard. If you use the Paste
You may also use the Copy As tool to translate Special SMILES command when a SMIRKS
a selected structure to a SMILES, SLN, or string is on the clipboard, a reaction is pasted
InChI™ string. into your document.
If the Clipboard contains structures and you Creating SMILES Strings
are pasting into another Chem & Bio Draw
To create the SMILES string for a structure:
12.0 document, the pasted information is
scaled to the settings in the current document. 1. Select the structure.

User Guide
2. Go to Edit>Copy As>SMILES. Pasting SMILES
The SMILES string is transferred to the Clip- You can convert that text string into a struc-
board. ture.
To paste a SMILES string as a structure:
1. In the source file where the SMILES string
is located, select the SMILES string and
press Ctrl+C.
2. In Chem & Bio Draw 12.0, go to
Edit>Paste Special> SMILES.
Creating SLN Strings

You can copy a structure to the Clipboard as an
SLN string for export to a Tripos application.
Figure 11.1 Using SMILES strings
To copy a structure as an SLN string:
To display the SMILES string, paste the string
in a document window. 1. Select a structure.
2. Go to Edit>Copy As>SLN.
When the SMILES string is on the Clipboard,
you can transfer it to another application that The Structure is copied to the clipboard as an
can interpret SMILES strings. SLN String.
If you copy more than one structure from
Chem & Bio Draw 12.0 to the Clipboard, the
SMILES string are separated by a period.
SMILES supports an alternate notation for aro-
matic structures using lowercase letters. Chem
& Bio Draw 12.0 generates this type of
SMILES string for any structure drawn with
explicit aromatic bonds, either by using the
Aromatic bond type in the Atom Properties
dialog box, or by placing a circle within any Figure 11.3 SLN strings
ring structure.
Creating InChI™ Strings
Chem & Bio Draw 12.0 supports* the IUPAC
International Chemical Identifier (InChI™)
protocol.
*. InChI™ is a trademark of the International

Union of Pure and Applied Chemistry.
Figure 11.2 Aromatic SMILES notation InChI™ Material in Chem & Bio Draw 12.0
is © IUPAC 2005.
148 Sharing Information

Chapter 11
To copy structures as InChI™ strings to other 2. Drag the selection out of the document win-
documents. dow onto the desktop. The file appears on
the desktop.
1. Select the structure.
2. Go to Edit>Copy As>InChI. To view the file contents, double-click its icon.
To use contents in a document, drag the file
You may copy only legitimate InChI™ struc-
into an open window of an application that
tures. If you attempt to copy a structure not
supports drag-and-drop.
supported by the InChI™ protocol, a warning
informs you that the structure is not supported.
Transferring Objects
Creating InChIKey strings
In this section, we explain how some features
Chem & Bio Draw 12.0 supports Standard in Chem & Bio Draw 12.0 behave when you
InchIKey, available in InChI 1.02. An transfer objects using the Clipboard or drag
InChIKey string is a condensed digital repre- and drop from one document to another.
sentation of an InChI string. All InChiKey
AUTOSCALING
strings are the same length whereas InChI
strings are not. This standard makes InChIKey When you transfer objects, the objects are
strings useful for Web searching and database scaled to match the document settings of the
indexing. destination document.
To copy a structure as an InChIKey string to BONDS
other documents: When a structure is copied (or moved) to
another document, the structure adopts the new
1. Select the structure. document’s fixed length value. However, it
2. Go to Edit>Copy As>InChIKey. retains its scaling factor.
For more information on InChI™ and For example, assume the Fixed Length is set to
InChIKey, see www.iupac.org/inchi/. 1.0 cm in a source document. A benzene ring is
resized to 200%. The bond length is then 2.0
Drag-and-Drop cm. In the destination document, the Fixed
You can use drag-and-drop to copy objects to Length set to 1.7 cm. When the benzene ring is
other documents. To use this feature in other pasted into the destination document, the
applications, they must support drag-and-drop. bonds are scaled by a factor of 2 to a final bond
The object is transferred as a Chem & Bio length of 3.4 cm.
Draw 12.0 object and can be edited. ATOM LABELS
Scrap and clipping Files Atom labels are scaled the same way as bonds.
You can use clipping files (Macintosh) and For example, in the source document, the atom
scrap files (Windows) to copying parts of a label font size is set to 16 points. One or two
drawing to other applications without having atom labels in the source document are resized
to save the file in Chem & Bio Draw 12.0. to 8 points, a ratio of 8:16 or a scale factor of
0.5. The destination document has an atom
To create a scrap or clipping file:
label font size is set to 14 points. When the
1. Select an object in a document. atom label is pasted into the destination docu-

User Guide
ment, the font size is scaled by a factor of 0.5 To change the settings in the destination docu-
to give a final atom label font size of 7 points. ment to match the settings in the source docu-
CAPTIONS ment, click Change Settings.
Chem & Bio Draw 12.0 autoscales captions All of the settings in the destination document
using the ratio of the fixed length in the desti- are changed to match those of the source docu-
nation document to the fixed length in the ment. All of the colors in the Color palette of
source document times the caption font size. the destination document are changed to those
The font size of the caption can be any size and specified in the source document.
is not related to the setting in the Settings dia- To scale the objects from the source document
log box. This assures that captions are always to the settings in the destination document,
in proportion to the bonds with which they are click Don’t Change Settings.
pasted. The settings from the source document are
For example, if the source document has a scaled to those in the destination document
fixed length of 1.0 cm and the destination doc- using the ratios given above.
ument has a fixed length of 2.0 cm, and the
caption you are pasting is 12 points, then the NOTE: If the source document was created in
resulting caption size after autoscaling is (2.0 a ChemDraw version earlier than 3.0, the name
cm /1.0 cm) x 12 points = 24 points. of the document appears as “Unknown” in the
NON-BOND OBJECTS AND COLOR dialog box.
All objects that are not affected by settings in
the Document Settings dialog boxes, such as
arrows and boxes, are scaled to maintain the Embedding Objects (Windows)
same proportions to bonds that were present in
the source document. Chem & Bio Draw 12.0 supports the Object
With the exception of the foreground and Linking and Embedding (OLE) protocol on
background color, the colors present in the Windows. This lets you edit structures that are
selection to be pasted are added to the destina- pasted in other types of documents. Chem &
tion document’s Color palette if they are not Bio Draw 12.0 is an OLE server, which means
already present (up to a maximum of 20 total it can create OLE objects that can you can
colors). The background color in the destina- copy and paste into other OLE client applica-
tion document is unchanged, and all objects tions.
colored using the foreground color are changed When you transfer drawing from Chem & Bio
to match the foreground color in the destina- Draw 12.0 into another document type that
tion document. supports OLE, you can open the drawing and
edit it from within the client application.
PASTING TO AN EMPTY DOCUMENT
If you paste a Chem & Bio Draw 12.0 drawing For example, to edit a drawing inserted into
into an empty document and the settings Microsoft Word for Windows version 6.0 or
between the documents are different, the later, do one of the following:
Change Settings dialog box appears. • In Word, select the drawing and go to
Edit>CS ChemDraw Drawing Object.

Chapter 11
• Double-click the drawing. one who uses a PostScript printer, you can turn
the preferences off.
The Chem & Bio Draw 12.0 tools and menus
replace those of Word. Use the tools to edit the To deselect the PostScript preferences:
drawing. 1. Go to File>Preferences.
When you have finished making changes, click 2. Deselect Include PostScript and Include
in another area of the Word document. The ChemDraw LaserPrep.
Word tools and menus are restored.
To transfer only a few drawings to another
Edit Graphic Object (Macintosh) document, select Include PostScript and Include
ChemDraw Laser Prep in the Preferences dialog
Chem & Bio Draw 12.0 supports the Edit box.
Graphic Object (EGO) protocol for editing
The PostScript commands and the ChemDraw
structures pasted into other types of docu-
Laser Prep are transferred with each drawing.
ments. When you drag an object from Chem &
The transferred drawings can be printed inde-
Bio Draw 12.0 into another type of document
pendently of Chem & Bio Draw 12.0.
that supports the EGO protocol, or copy it with
the clipboard, you can double-click the object If you do not check the Include PostScript
and it appears in a Chem & Bio Draw 12.0 check box when printing to a PostScript printer
document window. When you close the docu- Chem & Bio Draw 12.0 sends QuickDraw
ment window, any changes you made are commands to the printer. For more informa-
reflected in the other document. tion, see “Printing Background Color” on page
171.
NOTE: As of this writing, versions of Microsoft
Word after 5.0 do not support EGO. NOTE: You can also transfer drawings to a
document in a remote location whose printer
cannot be initialized.
Transferring PostScript
To print to a non-PostScript printer, deselect
(Macintosh)
Include PostScript and Include ChemDraw Laser
To obtain the highest quality drawings possible Prep on the General tab of the Preferences dia-
on a PostScript printer, Chem & Bio Draw log box.
12.0 creates a screen representation and a Post-
Script representation of your drawing. Exporting
For best print quality under all circumstances, You can export Chem & Bio Draw 12.0 draw-
you will want to leave the Include PostScript ings in various file formats and open them in
and Include ChemDraw Laser Prep preferences other applications. Conversely, Chem & Bio
selected (default) when you copy and paste to Draw 12.0 recognizes a variety of file formats
other applications. and can open documents created in other appli-
If you never plan to print to a PostScript printer cations.
or never plan to give your document to some- To export a file:

User Guide
1. Go to File>Save As. Other format options are noted in format
2. In the Save As dialog box, do the follow- descriptions.
ing:
Importing
a. Type a name for the file and choose a
location in which to save it. Use “Go To You can import graphics or documents from
ChemDraw Items” to quickly locate the other applications into Chem & Bio Draw
ChemDraw Items folder. 12.0.
b. Select a file format. Objects
c. Click OK or Save. Inserted objects are OLE files and can be
Some file formats do not support atom labels resized and rotated but cannot be flipped. Since
that contain nicknames or structural fragments. an object is embedded, you can edit it in its
When you save in these formats, Chem & Bio native application from within the drawing
Draw 12.0 expands all atom labels and saves window.
the file using the expanded form. Files
The following formats do not support nick- When you insert a file, the file becomes part of
names or structural fragments: the drawing. You can edit it only if it is in a
• Connection Table Chem & Bio Draw 12.0 format.
• MSI MolFile To insert a file:
• SMD 1. Go to Edit>Insert File.
2. In the Open dialog box, select the file type
from the drop down menu.
NOTE: Some versions of Chem & Bio Draw
3. Select the file and click Open. The file is
12.0 do not support all the formats listed.
embedded in the drawing.
To insert an object:
Some formats can be saved with different
options. If a format has no save options, 1. Go to Edit>Insert Object.
Options is grayed out. The following text- 2. In the Insert Object dialog box, click Create
based formats can use the Text Options: from File.
• ChemDraw XML 3. Browse to the file you want to insert and
click OK.
• CML
• Connection Table
• ISIS/TGF NOTE: If you select file type “All files” and
choose a file type that Chem & Bio Draw 12.0
• ISIS/Reactions
does not support (such as TXT) you will get an
• MDL MolFile error message, and the file will not be embed-
• Accelrys MolFile ded.
• SMD

Chapter 11
To create a new object: allow data to be attached to any object. When
saving to MDL formats, this data will be lost
1. Go to Edit>Insert Object.
unless the object meets the rules noted above.
1. Click Create New.
2. Select the Object Type.
4. Enter the data in the text box under the
3. Click OK. object.
ISIS™ compatibility Modifying Attached Data
ChemBioDraw Ultra 12.0, ChemDraw Ultra Chem & Bio Draw 12.0 treats attached data as
12.0, and ChemDraw Pro 12.0 support ISIS/ normal text for most purposes. However, two
Sketch including R-Logic and leaving groups. additional commands appear on the context
menu when attached data is selected.
Attached Data
Chem & Bio Draw 12.0 supports associating • Select Linked Objects changes the selection
text fields with objects such as atoms and to include all of the objects associated with
bonds by defining a “field name”. The feature the data.
is compatible with the “Data SGroup” in MDL • Position opens up the same dialog that is
formats, and will be converted to Data used to position ObjectTags, allowing you
SGroups when saved in MDL formats if a field to position the data relative to the associ-
name is specified and it is attached to: ated structure.
• a collection of atoms and bonds, or

• a single set of brackets NOTE: Positioning information is lost when
saving to MDL formats.
If it is attached to a collection of atoms and
bonds and a set of brackets, it will be converted
to two different Data SGroups.
Graphics export border preference
To attach data to objects:
You can specify the size of the border when
1. Select an object. exporting pictures. This preference affects the
2. Go to Object>Attach Data. output of all graphical formats, including but
The Attach Data dialog box appears. not necessarily limited to: WMF, PICT, EPS,
3. Enter the field name and click OK. TIFF, GIF, BMP, and PNG. It applies to the
clipboard and saved files. The default value is
2 points (0.278 in; 0.071 cm).
NOTE: Field names cannot be edited in Chem
& Bio Draw 12.0 after they are created. While File Formats
Chem & Bio Draw 12.0 will allow any field
Chem & Bio Draw 12.0 supports importing
name length, MDL formats have restrictions
and exporting the file formats listed below. To
that users should be aware of before creating
export in one of these formats, use the Save
names. Likewise, Chem & Bio Draw 12.0 will
As... option. Not all formats are supported in all

User Guide
Chem & Bio Draw 12.0 products. Also see
“Importing” on page 152. Format Import Export
MDL MolFile (MOL)a YES YES

Format Import Export
MDL RGFile (RGF)a YES YES
ChemDraw (CDX) YES YES
(Macintosh)Accelrys YES YES
ChemDraw XML (CDXML) YES YES MolFile (MSM)
ChemDraw 3.5 (CHM) YES YES PICT (Macintosh) YES YES
ChemDraw 2.0 and YES NO Portable Network Graphics YES YES

ChemDraw 2.1 (CHM) (PNG)
ChemDraw Template (CTP)a YES YES Standard Molecular Data YES YES
(SMD)a
ChemDraw Template Style YES YES
Sheet (CTS)a Structure-Data file (SD)a YES YES
ChemDraw Stationary Pads/ YES YES Galactic Industries (SPC)a YES NO

Style Sheets (CDS)
Windows Metafile YES YES
Connection Table (CT)a YES YES (EMF, WMF)
Chemical Markup Language YES YES TIFF file (TIF) YES YES
(CML)a
a available in ChemBioDraw Ultra 12.0,
Bitmap (BMP) YES YES ChemDraw Ultra 12.0, and ChemDraw
Pro 12.0 only
Encapsulated PostScript NO YES
(Macintosh) Transferring Across Platforms
PostScript (EPS) (Windows) Use the following procedures to transfer
between Macintosh and Windows. From the
Graphic Image Format (GIF) YES YES following table, determine the versions of the
Chem & Bio Draw 12.0 software between
ISIS (SKC, TGF, RXN)a YES YES which you want to transfer documents and fol-
low the appropriate instructions.
JCAMP (JDX, DX)a YES NO When you transfer files across platforms, fonts
are not transferred. If a font in the transferred
JPEG (JPG, JPEG) YES NO document is not available, Chem & Bio Draw
MDL V3000 MolFile (MOL) 12.0 substitutes fonts for those that are avail-
YES YES
able on the new platform.

Chapter 11
Macintosh to Windows Windows to Macintosh
To open a Chem & Bio Draw 12.0 file in Win- To open a Chem & Bio Draw 12.0 file on a
dows that was created on a Macintosh, follow Macintosh that was created in Windows, fol-
the instructions for the appropriate versions low the instructions for the appropriate ver-
shown in the table below. sions shown in the table below.
From Macintosh To Windows Instructions From Windows To Instructions

Version Version Version Macintosh
Version
≥ 4.0 ≥ 4.0 Save as
ChemDraw ≥ 4.0 ≥ 4.0 Save as the
and add .cdx default
to the file ChemDraw
name. (.cdx).
≥ 4.0 3.x Save as ≤ 3.5.x ≥ 4.0 Save as
ChemDraw ChemDraw
3.x and add 3.x (.chm).
.chm to the
file name.
≤ 3.5.x = 3.x Save as
ChemDraw
and add .chm
to the file
name.

User Guide
Chapter 11
A
Preferences and Settings
You can customize Chem & Bio Draw 12.0 by • Sprout rings (as opposed to spiro rings).
configuring Preferences and Document Set-
• The default style sheet is changed to I/Draw
tings for the way you work.
Styles.cds.
Preferences allow you to change the default
behavior of certain options that apply to every To activate the I/Draw mode, go to File>Prefer-
open document. Document Settings allow you ences and click I/Draw.
to change the default behavior of options that
will affect only the active document. Setting Preferences
Preferences affect how Chem & Bio Draw 12.0
Theme Options works, regardless of the document with which
The theme defines the appearance of the Chem you are working.
& Bio Draw GUI but does not affect any of the 1. To open the Preferences dialog box, go to
functions. By default, Chem & Bio Draw 12.0 File>Preferences.
is installed with the version 12.0 theme. How- 2. To restore the default settings, click Use
ever, other themes such as Classic and I/Draw Defaults.
are also available.
Default Document Location
To change themes:
You can set the default file directory shown in
1. Go to File>Preferences and select the Gen- the Open dialog box each time you want to
eral tab. open a file.
2. Select a theme in the Theme dropdown list.
1. Go to File>Preferences. The Preferences
3. Click OK. dialog box appears.
4. (Macintosh only) Exit and relaunch Chem 2. Click the Directories tab.
& Bio Draw 12.0.
3. Click the Use Documents Location check-
box and type in or browse to the location to
I/Draw
use.
The I/Draw theme changes the look of the
Default Open File Format
Main and Ring toolbars. However, in addition
to changing these toolbars, you can select the I/ To set the default file format in the Open dia-
Draw mode to activate two other helpful fea- log box:
tures:

User Guide
1. Go to File>Preferences. The Preferences label is with Alt+Enter or Option+Return. To
dialog box appears. close the text box, click outside the text box or
2. Click the Open/Save tab. select another tool.
3. Click Use Default File Format in the Opening To change the default:
Files section, and choose the desired file 1. Go to File>Preferences.
format.
Setting the Default Tool TIP: In Macintosh OS X, the Preferences dia-
log box is on the ChemDraw menu.
You can choose which tool is selected when
you open documents.
1. Go to File>Preferences. The Preferences 2. Choose the appropriate option on the Build-
ing/Display tab:
dialog box appears.
2. Click the Open/Save tab.
3. Under Opening Files, select a tool. To change the Select …
default for …
Autosave
Atom Label text Require Alt+Enter or
You can configure Chem & Bio Draw 12.0 to Option+Return to Cre-
periodically save an open documents at a spec- ate New Line in Atom
ified time interval you set. Labels
1. Go to File>Preferences. The Preferences Caption text Require Alt+Enter or
dialog box appears. Option+Return to Cre-
2. Click the Open/Save tab. ate New Line in Cap-
3. Click the Autosave Every checkbox and tions
enter the minutes to use. 3. Click OK.
The time starts counting down after the first Bitmap Fonts (Macintosh)
change is made.
When text appears in a document on the
Default File Format screen, it can appear using either a bitmap or a
1. Go to File>Preferences. The Preferences TrueType font.
dialog box appears. To use bitmap fonts, if they are available:
2. Click the Open/Save tab. 1. Go to File>Preferences.
3. Click the checkbox next to Use Default File 2. Select Use Bitmap Fonts When Available.
Format in the Saving Files section and
choose a format from the list. Text drawn using Bitmap fonts looks better
and appears more quickly than text drawn
New Lines and Closing Text Boxes using TrueType fonts. However, the size and
position of text drawn using Bitmap fonts
The default way to create a new line in a cap-
change somewhat when printed.
tion text box is with the Enter or Return key.
The default way to create a new line in an atom
158 Preferences and Settings

Appendix A
For accurate correspondence between what To add a path to a ChemDraw Items folder:
you see on the screen and what is printed, dese-
1. Go to File>Preferences. The Preferences
lect Use Bitmap Fonts When Available.
dialog box appears.
This change affects all documents.
2. Click the Directories tab.
Highlight Box Tolerance 3. Click Add New, browse to a location, and
click OK. A new path is added to the list.
You determine the size of the highlight box
and how close you must get to activate an 4. To rearrange the search order, click Move
object by setting the Tolerance. The default Up and Move Down.
setting for the Tolerance is 5 pixels. At this set- 5. To delete a path, click Remove. To delete all
ting, the highlight box appears on bonds if the added paths, click Default Paths.
pointer is located 5 pixels or less from any
Accessing Documents Quickly
point on the bond.
To set the Tolerance: If have a file that you always want readily
available to you whenever you launch Chem &
1. Go to File>Preferences. Bio Draw 12.0, save the file in the ChemDraw
2. On the General tab, select or type the toler- Items directory. Files in this directory appear
ance. This change affects all documents. in the Templates list. By default, the directory
The ChemDraw Items Folder is at:
C:\Documents and Settings\All
The location of the ChemDraw Items folder is Users\Application Data\
based on your operating system. If you are CambridgeSoft\ ChemOffice2010\
using ChemOffice 2009, the folder is at: ChemDraw\ChemDraw Items.
Windows XP. C:\Documents and Settings\All Whenever you need to open the file, go to
Users\ApplicationData\CambridgeSoft\ File>Open Templates and select the file name
ChemOffice2009\ChemDraw\ from the list.
Windows Vista. C:\Program
Data\CambridgeSoft\ChemOffice2009\Chem Customizing Toolbars
Draw The look and arrangement of toolbars are
Macintosh. By default, the ChemDraw Items defined by a set of XML files. If you are famil-
Folder is in the same folder as your Chem & iar with editing XML files, your can modify
Bio Draw 12.0 application. the toolbar for the way you work. You can
The folder contains the preferences, Hotkeys, remove, rename, and resize buttons; change
nicknames, and isotopes files; scripts, and the button icons, or move them from one toolbar to
generic nicknames file. It also contains tem- another. You can also create or delete toolbars.
plate documents and template Stationery Pads. The toolbar schema
You can have multiple ChemDraw Items fold-
ers. This is useful in corporate installations for The Toolbars.xsd file, located in the Toolbars
maintaining personal files such as nicknames directory, contains the schema definitions for
and standard templates. all the toolbars. These include definitions (but

User Guide
not the content) for the toolbars, the pop-up Caption and label text settings. set text
text, and the status bar text. options such as the font used for atom labels
and captions
The toolbar XML files
Color settings. set available colors for objects
The Toolbars directory contains the subdirec- and the document background
tory where the toolbars xml files are stored.
The files are stored according to the skins in Print/Page Setup. set options such as the page
which they are used. These are the files you size used and text displayed in footers
will most commonly edit to customize the tool- You can apply document settings in the fol-
bars. lowing ways:
• Customize settings for the entire document
Editing the XML files
using the Document Settings dialog box
Since the files are xml-based, you can edit • Apply settings to the entire current docu-
them using any xml or text editor. After you ment from an existing document.re
save them, exit and restart Chem & BioDraw.
Your changes will take effect. • Apply settings to selected objects in the
current document from an existing docu-
CAUTION ment
Create a backup of all XML files that you Default Styles
intend to edit.
Chem & Bio Draw 12.0 saves default styles as
either a style sheet (Windows) or stationary
Editing toolbar icons pad (Macintosh). When you launch Chem &
Bio Draw 12.0, the last style sheet or stationery
In addition to customizing the toolbars, you pad used opens as the default. If you choose
can also replace the icons themselves. For different one, that file becomes the default.
example, you can replace the eraser icon with You can set a default that is not changed:
the word “Erase”.
1. Go to File>Preferences(Macintosh:
ChemDraw).
NOTE: All images files you use as icons must
be in .png format. 2. On the Open/Save tab, browse to the
default style sheet (stationery pad).
3. Deselect Opening Any Style Sheet(Statio-
nery Pad) Changes Default.
Document and Object Settings
4. Click OK.
Document and object settings are user-defin-
able settings that are applied to the current doc- To view the default style, click the File menu.
ument. Settings include: The New menu item displays the name of the
Style Sheet or Stationery Pad.
Drawing settings. set drawing options such as
the fixed length used to draw bonds

Appendix A
Saving Customized Styles The settings in the active document window
change to those found in the style sheet or sta-
Every new document created with Chem &
tionery pad that you choose.
Bio Draw 12.0 uses a style sheet or stationary
pad file to obtain its document settings. These
files can also contain predefined objects. When NOTE: Applied settings are for the current
you create a new document, you actually create document only. To make them the default set-
an untitled copy of the style sheet or stationary tings for all documents you open, go to
pad. Any changes you make to the copy do not File>Open Style Sheets.
affect the file itself.
You can create a style sheet or stationary pad To apply the document settings from a docu-
with your own customized setting by saving it ment or style sheet not listed in the menu:
as a CDS file. If you store the CDS file in the
ChemDraw Items folder, it appears in the Open 1. Go to File>Apply Document Settings
Templates menu (under the File menu). from>Other. The select document dialog
To save a document’s setting as a Style Sheet box appears.
or Stationery Pad: 2. Open the appropriate folder and select a
document or Style Sheet/Stationery Pad.
1. Go to File>Save As. The Save As dialog
3. Click Open.
box appears.
2. Name the file and change the type (in OS Applying Object Settings
X: format) to CD Style Sheet (cds) or You can apply settings from another document
ChemDraw Stationery pad. to selected objects in the current document.
3. To save the file in the ChemDraw items You can apply the chosen settings to the
folder, click Go To ChemDraw Items. selected objects only, or to all new objects
drawn in the current document.
4. Click Save.
To apply object settings:
Settings From Other Documents
To apply document settings to the active win- 2. Go to Object>Apply Object Settings from
dow that are contained in a different document, and choose the document from which to
go to File>Apply Document Settings from and apply the settings. A dialog box appears:
choose the document from which to apply the 3. Do one of the following:
settings.
• To selected object only, click No.
• To selected an object and any new objects
you draw, click Yes.
Drawing Settings
Drawing settings affect how bonds and other
objects are drawn. You can configure the
drawing settings for an entire document or for
a particular object as follows:

User Guide
• For the entire document, go to File>Docu- Bold Width setting must be greater than the
ment Settings and select the Drawing tab. Line Width setting. The end of a wedge is 1.5
• For an object, use the Object Settings dialog times the bold width
box. Line Width. Set the width of all bonds, lines,
Changes made to the drawing settings affect and arrowheads in the drawing.
the active document window only. Drawing Margin Width. Change the amount of space
settings can be saved in style sheets or station- surrounding all atom labels that will erase por-
ary pads. tions of the bonds to which they are attached.
To apply settings from other documents to The margin width also determines the amount
your document, go to File>Apply Document of white space surrounding the front bonds in a
Settings. bond crossing. See “Bond Crossing” on page
Chain Angle. Set the angle (from 1 to 179 16.
degrees) between bonds created by the Acyclic Hash Spacing. Set the spacing between the
chain tool or modified by the Clean Up Struc- hashed lines used when wedged hashed bonds,
ture command. hashed bonds, dashed bonds, dashed arrows, or
See, “Acyclic Chains” on page 22 and “Clean dashed curves are drawn.
Up Structure” on page 62.
Bond Spacing. Set the distance between the
lines in double or triple bonds. The distance is
set either as:
• The percent of the length of the bond Units. Set the units used in the Object Settings
(between 1 and 100). This allows for pro- dialog box to centimeters, inches, points, or
portional spacing if different bond lengths picas.
are used.
Atom and Bond Indicators. Set which indica-
tors to display. See “Atom Numbering” on
page 64 and “Stereochemistry” on page 86.
Configuring Documents
• An absolute value you choose in the units 1. Go to File>Document Settings.
specified for your document. 2. Click the Drawing tab and configure the set-
Fixed Length. Constrain the bonds drawn to tings.
the length you specify. This also adjusts the 3. Click OK.
preferred bond length when you use the Clean TERMINAL CARBON LABELS
Up Structure command. By default, Chem & Bio Draw 12.0 does not
See “Drawing fixed length bond” on page 13 display terminal carbons. To display them:
and “Clean Up Structure” on page 62.
1. Go to File>Document Settings.
Bold Width. Set the width of the line used 2. Select the Atom Labels tab.
when bold and wedge bonds are drawn. The

Appendix A
3. Check the box next to Show Labels On Ter- Formatting Captions
minal Carbons.
Text settings affect how captions and atom
Configuring Objects labels for the current document are drawn and
To configure the drawing settings for a formatted.
selected object: Formatting options include:
1. Select the object. • font (font type)
2. Go to Object>Object Settings. • size (font size)
3. Configure the settings and click OK. The • style (font and baseline style)
settings you chose are applied only to the
selected object. • line spacing
• alignment
Analysis and Properties
Setting Font parameters
You can paste fundamental structure properties
Changing text formats in the Document Set-
directly into your drawing.
tings dialog box affects the current document
There may be a time where you may decide to only. You can also change settings for individ-
change the names of these properties. For ual objects by using the Object Settings dialog
instance, you may consider using “MW” rather box, the Text menu, or the Style toolbar.
than “Molecular Weight” to save room on the
To edit the document text settings for captions
page. How these properties are named and
and atom labels:
updated is controlled by the document settings.
The changes you make apply only to the prop- 1. Click File>Document Settings.
erties you paste in your drawing. The names in 2. In the Document Settings dialog box, click
the Analysis and Chemical Properties dialog Captions or Atom Labels.
boxes remain unaffected. 3. Change the settings as desired. The options
To change the names of the properties: are described in the following sections.
1. Go to File>Document Settings. 4. Click OK.
2. Select the Auto-update tab. 5. The formatting is applied to the current
3. In the Analysis window, select the property document.
whose name you want to change. Setting the Baseline Style
4. In the Label text box, type the new name.
You can specify the following baseline styles:
5. Repeat steps 3-4 as desired for the Chemi-
cal Properties window. Normal. Use this for standard text.
6. Select Automatically update upon chemistry Superscript. Reduces the text size by about
changes if you want the property values to 25 percent and raises its baseline.
be updated when you modify your drawing. Subscript. Reduces the text by about
7. Click OK. 25 percent and lowers the baseline.

User Guide
Formula. Formats in a way that is appropriate To open the object settings dialog box, do the
for most chemical formulas, that is, numbers following:
are subscripted. You must, however, capitalize
1. Select a caption or atom label.
manually.
2. Go to Object>Object Settings. The Object
You can apply several styles to the same Settings dialog box appears.
selected caption. You can also apply multiple
styles to different portions of a single caption. Captions
You specify the caption justification and line
Style Indicators spacing on the Captions tab of the Object Set-
Select any text in the document window and go tings dialog box. All text in a single caption
to Text>Style to view the styles that have been must have the same justification and line Spac-
applied to it. A check indicates the style ing.
applies to all the selected text. A hyphen indi- There are four available justifications:
cates the style applies to only some of the Flush Left. creates left-justified caption text.
selected text.
Centered. creates centered caption text.
Specifying Line Spacing Flush Right. creates right-justified caption
You can specify the three types of line spacing: text.
Automatic. Consistently spaced lines of text Justified. creates right-left justified caption
based on the height of the tallest character in text.
the entire caption. This is the default line spac- Atom Labels
ing.
Use the Centered, Flush Left, Flush Right,
Variable. Lines of text with different spacing Stacked Above, or Automatic justifications to
based on the tallest character and the lowest create labels that identify atoms and functional
descender in each line. groups in your chemical structure without
Fixed. Consistently spaced lines using a spac- obscuring bonds or other atom labels.
ing that you specify.
NOTE: When using Stacked Above justifica-
Aligning Text
tion, enter the tokens from top to bottom using
You can set the alignment of captions and Alt+Enteror Option+Return to go to a new line.
atom labels to justify text to suit your needs. If you change the justification after the label is
The options available depend on whether you entered, it will in most cases generate a warn-
are aligning captions or atom labels. Apply set- ing.
tings in the Object Settings dialog box.

Appendix A
Examples of the atom label justifications are If you label C5, the tokens are placed from
shown below. right to left because there are bonds to the right
of the atom:
You can force an entire multi-atom label to be

a token by defining it as a nickname. This pre-
vents the label from flipping when applied to
the left side of a structure.
For example, if you define the Nickname CH3,
and label C5 with the combined label and nick-
name NCH3, the final orientation is CH3N
instead of H3CN. In this case, the Nickname,
Figure A.1 Atom label justification. A) stacked CH3, is a token.
above; B) centered; C) flush left; D) flush right.
If you label C1, the second and third tokens are
Automatic Alignment placed above the first token since there are
When you justify atom labels automatically, bonds below the atom.
Chem & Bio Draw 12.0 breaks the label into If you label C4, the second and third tokens are
tokens. A token consists of an uppercase letter placed below the first token.
followed by any numbers or lowercase letters.
The first token is attached to the atom and the
rest of the label appears without obscuring
other parts of the chemical structure.
For example, to create N-methylpiperidine,
label an atom in cyclohexane with the atom
label NCH3, which contains the three tokens, N,
C and H3. If you label C3, the tokens are placed
from left to right because there are bonds to the
Changing the Default Format
left of the atom.
Each new caption or atom label uses default
document settings for the font, size, and style
of captions and atom labels.
You can change the format by:
• Changing the document settings for subse-
quent drawings in the current document.

User Guide
• Choosing a new format for an individual Changing Text Spacing
caption or label from the Text menu or tool- You can change the text settings for a specific
bar before you type. caption or atom label. The setting change is
• Selecting text and applying a new format to applied to the selected object only. You can
an individual label after you type. also choose whether to have the settings
applied to the selected text and to all subse-
Settings for New Text
quent text you type.
To specify the text settings for new captions
To change the text settings for a specific cap-
and atom labels in the current document:
tion or atom label:
1. Select the text to change with a selection
2. Click Captions or Atom Labels in the Docu- tool.
ment Settings dialog box. 2. Set the appropriate options on the Text
3. Select the appropriate options. menu.
4. Click OK.
To change only part of a single caption, select
These settings affect all new captions or atom the part you want to change with the Text tool.
labels in the current document. To use these To specify a font and size for selected text, do
settings in new documents save them in a style one of the following:
sheet (Windows) or stationery pad (Macin-
tosh). For more information, see “Saving Cus- • Choose the font and size from the Text
tomized Styles” on page 161. menu.
• Right-click and choose the font and size
Formatting a Caption or Label
from the right-click menu.
You can set the text format for an individual
• Select the font and size from the drop-down
caption or atom label before you type. The for-
menus on the Style Toolbar.
mat change is applied to the current text only.
To set the text format before you type: Fractional Character Widths
On the Macintosh, you can choose to have the
1. Select the Text tool and click in the docu-
spacing between characters as close to propor-
ment window. A text box appears.
tional as possible. If you are printing to a Post-
2. To set the text format do one of the follow- Script printer, this option improves the font
ing: appearance.
• Go to Text> Font, Style or Size. To set fractional widths:
• Set the format options on the Style toolbar.
3. Type the text in the text box.
2. Click the Hdr/Ftr tab in the Document Set-
The format is applied to the typed text. Any tings dialog box.
subsequent text you type is formatted accord- 3. Click Fractional Widths.
ing to the default document settings for the
current document.

Appendix A
Specifying the Margin Width • “Bond”: Hotkeys used to modify bonds
You can adjust the white space surrounding the • “Generic”: Hotkeys used to select tools and
atom label so that some of the attached bond is open dialog boxes
hidden.
Each Hotkey is encoded in this format:
<Hotkey key="{key}"
command="{command}" value="{value}"
description="{description}”/>
key
Key is the keyboard key that invokes the com-
mand. You can assign a particular key to dif-
To adjust the white space: ferent functions as long as the functions are
defined in different object types. For example,
1. Go to File>Document Settings. The Docu- ‘b’ changes an atom to Boron in the Atom
ment Settings dialog box appears. object type, a bond to bold in the Bond object
2. Click the Drawing tab. type, and could be assigned to the Benzene tool
3. Type a new Margin Width value. in the Generic object type. You can use any
4. Click OK. key except the hard-coded keys: function keys,
Enter, Space, Backspace, and arrow keys.
The margin width is applied to all subsequent When you edit the xml file, remember that, if
drawings in the current document. you create capital and lowercase Hotkeys for
the same object type, the Hotkey will be case-
Customizing Hotkeys sensitive. If a key appears more than once in
If you are familiar with XML, you can custom- the file for the same object type, the one closest
ize the set of Chem & Bio Draw Hotkeys. You to the end of the file takes precedence.
can modify the existing Hotkeys and even cre- command
ate your own.
Command is any one of the predefined com-
To customize Hotkeys, you must open the mand names. All available commands are
Chem & Bio Draw Hotkeys text file hot- described in the hotkeys.xml file.
keys.xml in a text editor. By default, this file
is in the folder:
NOTE: You cannot add to the command list.
C:\Documents and Settings\ All
Users\Application Data\
CambridgeSoft\ChemOffice2010\ value
ChemDraw\ChemDraw Items
This is the parameter value associated with the
The Hotkeys in the file are organized by command. For example, if the command is
object type: LABELTEXT, the value is the label that
• “Atom”: Hotkeys used to modify atoms appears. If the command is BONDDISPLAY,
the value corresponds to the bond display type.

User Guide
To create a hotkey that switches to a particular • CYCLOHEXANE
tool, choose TOOLMODE for a command and • CYCLOHEPTANE
use any of these command names for a value:
• CYCLOOCTANE
• LASSO • CYCLOHEXANECHAIR1
• MARQUEE • CYCLOHEXANECHAIR2
• 3DTRACKBALL • CYCLOPENTADIENE
• MASSFRAG • BENZENE
• ERASER • TLCPLATE
• TEXT
• SOLIDBOND
NOTE: The features that are available
• MULTIBOND depends on the level of Chem & Bio Draw 12.0
• DASHEDBOND you are using.
• PEN
• HASHEDBOND description
• ARROW This text is useful for whenever you edit the
• HASHEDWEDGEDBOND hotkey.xml file. The tool description explains
• ORBITAL what each Hotkey does.
• BOLDBOND Editing the hotkeys.xml file
• DRAWINGELEMENTS To customize Chem & Bio Draw Hotkeys:
• WEDGEDBOND 1. Determine whether you want to create or
• BRACKET edit an Atom, Bond, or Generic Hotkey
type.
• HOLLOWWEDGEDBOND
2. Open the hotkeys.xml file in a text editor.
• CHEMICALSYMBOLS
3. Navigate to the appropriate Hotkey list in
• WAVYBOND the hotkeys.xml file.
• ARC 4. Either add or a new Hotkey entry using the
• TABLE appropriate format and values or edit an
• QUERY existing hotkey in the list.
• ACYCLICCHAIN 5. Save the hotkeys.xml file.
• SNAKINGCHAIN 6. Close and reopen Chem & Bio Draw 12.0.
• TEMPLATE Working with Color
• CYCLOPROPANE
You can create full color presentations of your
• CYCLOBUTANE chemical drawings to appear on your monitor,
• CYCLOPENTANE print on a color printer, or create 35mm slides
using a film printer.

Appendix A
Most computers can display any of 16 million The Color palette
colors, but the number of colors that can
Use the color palette to specify the color of
appear at any one time may be limited by your
objects and text in the document in the active
monitor and display card.
window. A palette is stored in every document
What you can color and style sheet (called a “stationery pad” for
Macintosh users). You can use style sheets or
In Chem & Bio Draw 12.0, you can change the stationary pads to create a series of documents
color of the background, foreground, or indi- with the same color scheme.
vidual objects:
Customizing Colors
Background Color. The color of the document
Changes you make to the color palette affect
window. By default, the background color is
the current document only. You can save up to
white.
20 colors. For more information, see “Saving
Foreground Color. The color of object you Customized Styles” on page 161.
draw. By default, the foreground color is black.
Individual objects. You can assign colors to NOTE: If you select an object or group that
objects to help then stand out against other contains multiple colors, a check mark appears
parts of your drawing. next to each of the colors in the Color menu.
The check mark alerts you that a change would
Changing colors
affect more than one color.
You can change the color of the background,
foreground, groups, or objects to emphasize
parts of your drawing. To change the color palette in the current docu-
ment:
Background and foreground
The background and foreground define the col- 1. Go to File>Document Settings. The Docu-
ors used in your drawing. To change the col- ment Settings dialog box appears.
ors: 2. Click the Colors tab.
3. Click the color to change (either Back-
1. Go to File>Document Settings and select the
ground or Foreground) and select Other.
Colors tab.
The Color dialog box opens.
2. Select the Background and Foreground col-
4. Click the new color in the Basic Colors or
ors.
the Custom Colors section.
3. Click OK.
5. Click OK. The color is changed to the new
color and added to the Color menu.
NOTE: Changing the foreground color does
To add a customized color:
not affect objects you have colored.

User Guide
1. In the Color dialog box, click Define Cus- 3. Click New Color.
tom Colors.
Figure A.3 The Macintosh Color Picker dialog box

4. Use one of the icons on the left to select a
method of defining your color, then select a
color.
Figure A.2 Setting custom colors. A) Color refiner For more information about the Macintosh
box; B) Luminosity box. color options, see your System documentation.
2. Click a color in the Color Refiner box to set 5. Click OK. The new color appears in the
the hue and saturation. Colors tab in place of the original color and
The pointer turns into a cross hair when you is added to the color menu.
click. You can drag to a different region to To add a new color to the Color menu:
change the hue and saturation.
1. Click New Color or Set Other Color on the
3. Click in the Luminosity box to set the
Color tab. The Color Picker dialog box
brightness of the color.
appears.
4. If necessary, change the hue, saturation,
2. Click a color in the Color Wheel.
luminosity, and RGB components by typing
the values in the text boxes. 3. If necessary, adjust the hue, saturation,
brightness, and RGB components by typing
5. Click Add to Custom Colors.
in the values.
6. Click OK.
4. Click OK. The new color is added to the list
Macintosh Color Settings of Other Colors.
To change the palette of colors used in the cur- Removing Colors
rent document:
To remove a color from the Color menu:
1. Go to File>Document Settings. The Docu-
1. Click the color. A highlight box appears
ment Settings dialog box appears.
around the color.
2. Click the Colors tab. 2. Click Remove Color.

Appendix A
Objects that were drawn in the removed color commands and the ChemDraw LaserPrep File
are changed to the foreground color. with the pictures.
The Macintosh High Resolution Clipboard
Templates and Color
supports high-resolution printers. Most appli-
The background and foreground colors used in cations support the High Resolution Clipboard.
a template from the template pop-up palette are Because this was not always the case in the
not used when the template is drawn in a docu- past, this preference continues to be available
ment window. However, any other colors used for users to turn off if an application being
in the template are added to the color palette of used does not support the High Resolution
the current document if they are not already Clipboard.
present. This is part of the autoscale feature. If you are unsure if the application uses a High
For more information, see “Autoscaling” on Resolution Clipboard, try transferring pictures
page 149. with this check box selected and deselected,
and see which picture prints with higher qual-
Saving Color palette Settings
ity.
You can save the Color palette in a style sheet If you are printing to a non-PostScript printer,
or stationery pad. The Color palette is saved in deselect Include ChemDraw LaserPrep and
addition to other document settings such as Include PostScript to reduce the size of each
page setup settings, text settings, and drawing picture. Do not deselect this option if the docu-
settings. ment will ever be printed to a PostScript
Printing Background Color printer.
Printers that use the PostScript page definition
Print Background Color controls whether the language use the PostScript representation.
background color contained in your document The PostScript representation describes objects
is printed. by using mathematical shapes that can be pre-
To change whether the background color is cisely imaged at whatever resolution is used by
printed: your printer. The PostScript representation cre-
1. Go to File>Preferences. ated by Chem & Bio Draw 12.0 is composed of
2. Click Print Background Color. two parts, the PostScript commands and the
ChemDraw Laser Prep. The ChemDraw Laser
3. Click OK.
Prep contains specific instructions that enable
Macintosh Print Preferences the printer to interpret the PostScript com-
mands contained in a Chem & Bio Draw 12.0
When you print a document, Chem & Bio document.
Draw 12.0 creates a QuickDraw representation
INCLUDE POSTSCRIPT
and a PostScript representation of the docu-
ment contents. To transfer Chem & Bio Draw 12.0 pictures to
another document that will be printed on a
If you are transferring information to another
PostScript printer:
application from which you print Chem & Bio
Draw 12.0 pictures, you include PostScript 1. Go to File>Preferences.
2. Click Include PostScript.

User Guide
3. Click OK. Document Settings
When Include PostScript is deselected, no Chem & Bio Draw 12.0 includes a library of
PostScript commands are generated. This usu- document settings based on those found in
ally results in lower quality printing, particu- many well-known scientific publications. For
larly of drawings cut and pasted into other example, some journals may require submitted
applications. However, because the representa- articles be formatted with specific margins,
tion used for printing when Include PostScript fonts, page size, etc. If you plan to submit your
is not selected is the same as that used for document to a specific journal, open in Chem
drawing to the screen, better correspondence & Bio Draw 12.0 the style sheet for that jour-
between the screen and printed output may be nal. If you want, you can also create style
observed. sheets of your own.
INCLUDE CHEMDRAW LASER PREP
Selecting the include ChemDraw Laser Prep NOTE: “Style sheets” are called “stationary
lets you print to a printer that cannot be initial- pads” in the Macintosh operating system.
ized using Chem & Bio Draw 12.0. If you cre-
ate drawings with this option off, they will not
print on PostScript printers without the use of To create your own style sheet:
Chem & Bio Draw 12.0. 1. Create a new document.
To include ChemDraw Laser Prep: 2. Enter the settings in the Page Setup, Draw-
1. Go to File>Preferences. ing, Text Settings, and Color palette dialog
2. Click Include ChemDraw Laser Prep. boxes.
3. Click OK. 3. Go to File>Save As.
4. In the Save As dialog box:
When you select Include ChemDraw Laser
a. Select the Chem & Bio Draw 12.0 style
Prep, you should also select Include Post-
sheets or stationary pads file format.
Script.
b. Type a name for the document.
c. Select the ChemDraw Items folder as
the location for saving the template.
5. Click OK or Save.

Appendix A
Publishing Documents
This following table contains a sample struc-
ture for each of the style sheets used in many
popular publications.
ACS Document 1996
• Fixed Length: 14.4 pt

• Bold Width: 2 pt
• Line Width: 0.6 pt
• Margin Width: 1.6 pt
• Hash Spacing: 2.5 pt
• Chain Angle (degrees): 120
• Bond Spacing (% of length): 18
• Atom Label Font (Win/Mac): /
• Atom Label Size: 10 pt
• Caption Font (Win/Mac): /
• Caption Size: 10 pt
• Drawing Area (Width x Height): 540 pt x 720 pt
• Page Size: US Letter
• Reduction (%): 100

User Guide
Adv. Synth Catal.
• Fixed Length: 17 pt
• Line Width: 1 pt
J.Chin. Chem. Soc.
HO
• Bold Width: 2.5 pt
• Margin Width: 2 pt
O H • Hash Spacing: 2.5 pt
N • Atom Label Font (Win/Mac): /
HO • Atom Label Size: 12 pt

Appendix A
J. Mol. Mod. (1 column)
• Fixed Length: 14.4 pt

HO • Bold Width: 2 pt
N • Atom Label Font (Win/Mac): Times New Roman/
HO Times
• Caption Font (Win/Mac): Times New Roman/
Times
• Drawing Area (Width x Height): 8.5 cm x 25.4 cm
(1 column); 17 cm x 25.4 cm (2 column)

User Guide
New Document
HO • Fixed Length: 30 pt
O H • Chain Angle (degrees): 120
N • Atom Label Size: 10 pt
HO
• Drawing Area (Width x Height): 7.5 in x 10 in
• Page Size: US Letter or A4 (as selected)
New Slide
• Drawing Area (Width x Height): 7.5 in x 10 in

Appendix A
Phytomedicine
HO • Fixed Length: 20 pt
• Line Width: 1pt
O H • Hash Spacing: 3 pt

User Guide
RSC
• Fixed Length: 0.43 cm

HO • Bold Width: 0.056 cm
• Line Width: 0.016 cm
• Margin Width: 0.044 cm
• Hash Spacing: 0.062 cm
O H
• Drawing Area (Width x Height): 8.9 cm x 25.4 cm
(1 column); 19 cm x 27.7 cm

Appendix A
Science of Synthesis
;
HO
O H
HO
• Drawing Area (Width x Height): 19.79 cm x 27.15
cm
• Page Size: A4

User Guide
Synthesis, Synlett
HO
• Drawing Area (Width x Height): 12 cm x 26.7 cm
• Page Size: A4
Verlag Helvetica Chimica Acta
HO
O H • Hash Spacing: 2 pt
• Bond Spacing (% of length):14
• Drawing Area (Width x Height): 368 x 720 pts

Appendix A
Wiley Document
; • Fixed Length: 17 pt
HO • Bold Width:2.6 pt
• Line Width:0.75 pt
O H • Chain Angle (degrees): 120
• Bond Spacing (% of length):18
N • Atom Label Size: 12 pt
HO • Caption Size: 12 pt
• Drawing Area (Width x Height): 19.79 x 27.15 cm
• Page Size: A4

User Guide
Appendix A
B
Page Layout
The presentation quality of your document is The size of drawing area displayed depends on
affected by how chemical structures and other the size and resolution of your monitor. In
objects are placed on the page. Effective layout some cases you can see the entire document.
of a drawing includes proper alignment of If you magnify a document, the drawing area
chemical structures and other objects, appro- size and drawing objects become bigger. If you
priate page size, and page orientation. The increase the magnification so that the page size
page layout tools include setup of the page and becomes bigger than the screen, scroll bars
the use of the ruler, tables, layering, aligning, become available.
and distributing commands.
Setting up Pages
The Drawing Area
You can create two types of documents:
The document window is not necessarily the
Pages. A single document containing one or
same size as the drawing area of the page. A
more sheets, each of which is printed on a sin-
document window, in most cases, actually cov-
gle piece of paper.
ers only a portion of the drawing area.
The following options allow you to set the Posters. A single large document, composed of
drawing area displayed on your screen. as many pieces of paper as necessary.
• Document Settings and Page Setup let you Paged Document Setup
modify the page, margins, headers, footers, To create a document with one or more pages:
document type, and size.
1. Go to File>Document Settings. The Docu-
• View menu options: Actual Size, Show
ment Settings dialog box appears.
Document, Magnify, and Reduce.
2. On the Layout tab, check that Pages is
• Magnification Controls: enlarge and reduce
selected.
• Dragging to enlarge the drawing area. 3. Specify the number of pages in the Docu-
• Windows: Point to a border or corner of a ment Size section. The size of the pages is
document window and drag to resize. determined by the Page Setup settings. For
• Macintosh: Drag the Size box in the lower more information, see “Page Setup” on
right corner of the document window. page 184.
4. Type the Margin settings. The units of the
margins are set in the Preferences dialog

User Guide
box. The paper size minus the margins 5. Type additional information in the Text box
determines the drawing area. from the following:
5. Create Headers and Footers as described in file name. &f
Headers and Footers.
page number. &p
6. Click OK. A new document opens, using
your settings. date printed. &d
time printed. &t
Poster Documents Setup
6. Position the text horizontally by typing the
You can create a poster by creating a single appropriate characters listed below. Any
large drawing area, which will be printed on as text following these characters is appropri-
many separate pages as necessary. When you ately aligned.
set the document size and how much each page
overlaps, Chem & Bio Draw 12.0 calculates centered. &c
the number of pages needed and the margin right. &r
sizes. You can set registration marks, which left (default). &l
mark the overlap setting on each page, to use
as a guide when assembling the poster from the Page Setup
separate pages.
You can customize the size, orientation and
To create a poster document: margins for the document page. To setup the
1. Go to File>Document Settings. page, go to File>Page Setup. Options for cus-
2. On the Layout tab, click Poster. tomizing the page appear below:
3. Type the Height, Width, and Page Overlap. Paper. Choose the size of the paper on which
The number of pages and the margin you want to print the document and the printer
dimensions are calculated. tray where the paper is located.
4. Select whether to Print Registration Marks. Orientation. Select either Portrait or Land-
5. Create Headers and Footers. scape.
6. Click OK. Margins. By default, all margins are set to 0.5
inches.
Headers and Footers
Printer. Click to select a printer and set prefer-
In poster documents, only one header and ences. You can also choose the printer in the
footer appear for the entire document. Print Options dialog box, as described below.
To create headers and footers:
1. Go to File>Document Settings. Printing
2. Click the Hdr/Ftr tab. Chem & Bio Draw 12.0 uses the standard sys-
3. Enter the position from the edge of the page tem commands to print documents. The
that you want the header or footer to appear. options that you have available to you depend
4. Type the text to appear in the header or on the printer that you are using. See your
footer. printer’s documentation for more information.
184 Page Layout

Appendix B
In general, to print a document: Scaling
1. Go to File>Page Setup. Some printers include an option to reduce or
2. Make all appropriate selections for the enlarge your drawings by a variable percentage
printer you are using and click OK. (25-400%). This option scales all objects and
3. Go to File>Print. text in the document window by the percentage
specified. This is not a change in magnifica-
4. Make your selections in the Print dialog
tion. The size of objects is changed relative to
box and click OK.
the paper size, margins, and orientation you
To print a document from Windows Explorer have specified.
or from the Finder: The enlarge or reduce option is useful for
1. Select the document you want to print. changing the size of the available drawing
2. Go to File>Print. The Chem & Bio Draw area, while keeping the images on the screen at
12.0 application is opened and the Print dia- the normal size when you are drawing. If your
log box appears. document is set so that the drawing fills the
page on one printer and you use another printer
3. Make your selections in the Print dialog
that requires larger margins, the drawing my
box and click OK.
disappear off the edge of the document win-
Print Options dow. You can reduce the size of the drawing
with the reduce option so that it fits in the doc-
Select Printer. This window lists all printers ument window.
connected to your computer. You can either
use the default printer or select another printer. Saving Page Setup Settings
Print to File. The document is saved as a .prn You can save page setup settings in a style
file that also includes your printer preferences. sheet or stationary pad. Whenever you open a
The document can then be sent later to a style sheet or stationery pad, these settings are
printer. used. The settings are saved in addition to the
Find Printer. Click to map to a printer that is text settings, drawing settings, and the color
not currently listed in the Select Printer win- palette.
dow.
35mm Slide Boundary Guides
Page Range. Select the pages you want to
print. If you wan to print only specific parts of If you make 35mm slides from a hard copy of a
your document, select the parts using the selec- document or from a screen shot, you can dis-
tion tool and then choose Selection in the Print play boundary lines that appear on your screen
Options dialog box to print. positioned at 7 inches and 10.5 inches to match
the 2:3 ratio for the 35 mm slide format. These
Number of copies. By default, only one copy is
guides help you keep your drawing within this
printed.
region to maintain the proper ratio, but are not
printed. The drawing area of the page must be
at least 7 x 10.5 inches for these boundary lines
to be visible.

User Guide
To display the 35mm slide boundary lines: 2. Go to View>Magnify or press F7.
1. Go to File>Preferences. The magnification occurs around the center of
2. Select the Building/Display tab. the selected object. The magnification percent-
3. Select the Show 35mm Slide Boundary age appears in the Magnification control on the
Guides check box. General toolbar.
4. Click OK. Actual Size
Two 35mm Slide Boundary Guides appear in To return to the actual size from any other
the same orientation you have chosen in the magnification, go to View>Actual Size.
Page Setup dialog box. These guides appear in Reduce
every document. To reduce the magnification:
Viewing Drawings 1. Select an object around which you want to

reduce the magnification.
You can use a close-up view of objects in your
reaction scheme to make sure they are properly
NOTE: If you do not select an object, the last
positioned. At times, you may want to reduce
object drawn is the center point of the magnifi-
your view so that you can move groups of
cation.
objects around the page. You can change the
magnification to perform these functions using
the Magnify and Reduce commands in the 2. Go to View>Reduce.
View menu, the Zoom tool, or the magnifica-
The reduction in magnification appears in the
tion controls.
Magnification drop-down list.
Magnification You can reduce the magnification until the
entire page fits on the screen. In the reduced
Magnifying your drawings changes how large
view, you can continue to use all of the draw-
or small it appears without changing its actual
ing tools. In particular, you can use a selection
dimensions. You can either select a value in
tool to rearrange the drawing to take better
the magnification dropdown list or enter your
advantage of the space available.
own value between 1% and 999%.
Show Document
Magnify
Show Document reduces the magnification
1. Select an object you want to keep in view as until the entire page is visible in the document
you magnify the drawing. window.
To view the entire drawing area in a document
NOTE: If you do not select an object, the last window at once, go to View>Show Document.
object drawn is the center point of the magnifi- The Magnification control shows the reduction
cation. in magnification that was required to have the
entire page appear on the screen.
186 Page Layout

Appendix B
The Magnification Control As you move the pointer, ruler guides appear
on each ruler, indicating the position of the
Where the magnify and reduce commands let
pointer.
you quickly increase or decrease the magnifi-
cation, the magnification control lets you be
more precise using a numeric value.
To use the magnification controls in Windows,
select a value from the dropdown list or type a
value.
To use the Magnification controls in the Mac-
intosh, do one of the following:
• Select a value from the drop-down list.
• Select Other from the drop-down list. In the
dialog box that appears, type a value and
click OK.
Rulers
Use the rulers to position objects a measured Figure B.4 How rulers indicate position. A) The
distance away from a reference point or create cursor; B) Ruler guides indicating vertical and hori-
objects of an approximate size. To set the ruler zontal location of the cursor.
units, go to File>Preferences and select the
When you select an object, two guides appear
General tab.
in each ruler. The four guides together show
Displaying Rulers the height and width of the selected object.
To toggle rulers on and off, go to View>Show
Rulers. The rulers appear along the top and left
The Crosshair
edges of the document window. Use the crosshair to align objects relative to
each other and to space objects an equidistant
apart. The axes of the crosshair can be moved
within a document window.
Displaying the Crosshair
To toggle the Crosshair on and off, go to
View>Show Crosshair.
To assist you in aligning objects, the Crosshair
includes grid lines that extend from the major
division marks on each axis.
You can also show the rulers while the
crosshairs are displayed so that you can see the
unit measurement associated with each divi-
sion on the crosshair axes.

User Guide
Moving the Crosshair In either case, if a bond or side of the object is
1. Position the pointer where the Crosshair parallel to one of the axis, it disappears when it
axes intersect. is exactly positioned over a Crosshair axis.
The pointer changes to an arrow when it is near 3. Select a second object.
the center of the crosshair. 4. Drag the second object to the crosshair axis
2. Click and drag the crosshair. or grid line and align it to the first.
To constrain crosshair to move in the X- or Y- You can also move selected objects in small
direction, shift+drag the crosshair. increments to align them with the Crosshair
using the arrow keys available on some key-
Positioning Objects boards:
To align two or more objects do anyone of the To move 1 point, select the objects and press
following: an arrow key. To move in 10pt increments,
• Move the Crosshair axes and align it with hold down the Alt key (Windows) or the
the object. Option key (Macintosh) while you press the
• Select an object and drag it until it is arrow key.
aligned with either axis of the Crosshair, or
a grid line.
188 Page Layout

Appendix B
C
Chemical Interpretation
Chem & Bio Draw 12.0 converts lines, charac- compounds. For example, if you’re investigat-
ters, and other symbols into chemically meaning organic acids, a compound with the struc-
ingful figures as you work. This occurs in the tural formula CH3COO would probably
background, but you can also choose to view represent acetic acid. Present the same formula
this chemical data. Chem & Bio Draw 12.0 in a paper on transition metal chemistry, and
uses the data when exporting to file formats you might be describing a novel methylated
that support only a subset of the notations that cobalt oxide. If you had asked Chem & Bio
Chem & Bio Draw 12.0 does. Draw 12.0 to interpret it beforehand, you
This section describes how Chem & Bio Draw would have received a message reporting a
12.0 interprets what you draw. valence error, and you might have been
prompted either to add a negative charge or to
Chemical Intelligence change the capitalization.
Chem & Bio Draw 12.0 was designed as a tool Chem & Bio Draw 12.0 can offer only sugges-
to aid in chemical communication. Most chem- tions. If you and your audience understand
ists would understand AcOo-C6H4COOH what you are trying to depict, then you can
immediately, whether or not they recognized it ignore these suggestions. In many cases, you
as aspirin. Most computer programs, however, can teach Chem & Bio Draw 12.0 to under-
require what is known as a “complete connec- stand the notation you’re using. For more
tion table,” in this case, a collection of 21 information, see “Applying Nicknames” on
atoms connected by 5 double bonds and 16 sin- page 19.
gle bonds in a specific pattern. Chem & Bio
Draw 12.0 takes what makes sense to a chemist
Database Conventions
and converts it into what makes sense to Most databases require not only that you draw
another application. a structure in a way that makes sense, but that
This chemical intelligence can be used as a you draw it in the way that the database
sophisticated “spelling” checker for chemical expects it. Consider ferrocene, which is repre-

User Guide
sented in at least four different ways in major Bond Conventions
databases:
The following table describes the chemical
conventions Chem & Bio Draw 12.0 recog-
nizes.
Bond Description
Single bond, unspecified stereo-

chemistry.
Single bond, “down” stereochem-

istry (into the plane of the paper,
away from the viewer), from the
first drawn atom to the second
drawn atom.
Single bond, “up” stereochemistry

(out of the plane of the paper,
toward the viewer), from the first
drawn atom to the second drawn
atom.
Single bond, mixture of “up” and

“down” stereochemistries in some
unspecified proportion.
Dative bond. Often used to indicate

polar bonds, such as the N-O bond
in pyridine N-oxide.
Figure C.5 Representations of ferrocene Double bond, with cis/trans stere-

A successful search in one database might not ochemistry as drawn.
produce any results in another. When in doubt,
consult the documentation for the conventions Double bond, with cis/trans stere-
your database uses. ochemistry unknown.
Tautomeric bond, either single or

double according to rules of
tautomerism.
190 Chemical Interpretation

Appendix C
+*/
Aromatic bond, part of a delocal- A series of any combi-

ized resonance system. nation of the above.
Triple bond. Chem & Bio Draw 12.0 analyzes atom labels
from left to right, applying standard valence
Quadruple Bond. rules to determine which atoms are bonded
together. The exception is with an atom label
A single bond near a closed circle is recog- in Automatic alignment on the left side of a
nized as aromatic: compound. This type of atom label is displayed
in reverse (H3CO instead OCH3) and is parsed
from right to left. Standard valences for each
atom are defined in the Isotopes Table.
By definition, a “simple” atom label has all
bonds attached to the first (or last) character. A
multi-attached atom label has bonds connected
Atom Labels
to more than one character, or has all of its
A simple atom label may contain any of the bonds attached to a character in the middle of
following: the atom label. Multi-attached atom labels are
always parsed from beginning to end, but the
A single element. beginning might be on the right if the atom
label was in Automatic style and on the left
side of the original structure:
A multi-attached label
that is parsed from left
An element and some to right.
number of hydrogen
atoms.
A multi-attached label
that is parsed from
right to left.
A nickname.
A bond attached to the

open parenthesis of a
repeating group is
treated as if bonded to
Repeating units within the first of those
parentheses. groups.

User Guide
Draw 12.0, and generates an error message if
A bond attached to the
you try to analyze it. Generally, empirical for-
close parenthesis or
mulas (C2H6 and H2SO4) are not recognized,
repeat count of a
repeating group is but structural formulas (CH3CH3 and
treated as if bonded to HOSO2OH) are.
the last of those Molecular weight and elemental analyses of
groups. empirical structures is possible, but the Expand
Label command does not work with them.
Multiple fragments within a single label can be Empirical structures are discarded when they
specified in the following ways: are transferred to other applications that
require unambiguous structures.
Implicitly, using standard Chemically-significant text must be entirely in
valence rules. formula or, for isotopes and charges, super-
script style. Chem & Bio Draw 12.0 does not
Explicitly, using a space, recognize a chemical formula embedded
period (unsuperscripted or within a larger block of text.
unsubscripted), bullet, or
combination.
If you draw a bond, add an
atom label, and then delete the
An unsuperscripted, unsub- bond, you have a chemically
scripted integer at the start of meaningful text block whose
a fragment is recognized as a font, size, and style match other
stoichiometric multiplier and atom labels.
is treated as if the appropriate
number of fragments were
drawn explicitly. If you create a caption with the
text tool and set it to Formula
style, you have a chemically
Chemically Significant Text
meaningful text block whose
Often, it is simpler to write a chemical formula font, size, and style match other
like MeOH or H2O than it is to draw out an captions.
entire atoms-and-bonds structure. Chem & Bio
Draw 12.0 correctly interprets any unambigu-
Charges
ous structural formula. For example,
CH3COCH2CH3 is recognized as methyl ethyl Charges may be created as part of a textual
ketone and MeOH is recognized as methanol. atom label or with the appropriate symbol from
On the other hand, C6H6 might mean benzene, the Chemical Symbols palette. Charges are
or it might mean one of over 200 other iso- always assigned to a specific element in the
mers. C6H6 is not recognized by Chem & Bio atom label, whose acceptable valences become

Appendix C
those of the similar isoelectronic neutral ele-
A “floating” charge placed
ment
.
within a delocalized system is
recognized by the Analyze
A charge following an element Structure function, but is
is assigned to that element. discarded when saved to
formats that require all charges
A charge that does not follow to be associated with specific
an element is assigned to the atoms.
next element.
Isotopes and Elements
By default, all isotopes are recognized in the
Charges that follow a monova- full Table of the Elements. This data is pro-
lent element with a repeat vided by CRC Press, Inc. Isotopes are defined
count are assigned to the in the Isotopes Table file. You can edit this file
element before that element.
in any text editor to add new isotopes.
Charges that follow other

repeating units are distributed A superscripted
among those units. number before the
element symbol indi-
cates isotope numbers.
Charges may be superscripted.
Isotopes can be
Multiple charges are recog- included anywhere that
nized appropriately. regular elements can.
Charges may have repeat

Deuterium and Tritium
counts as long as both the
can be indicated by
charge and the repeat count are
their one-letter
superscripted.
symbols.
A “floating” charge placed
with the Chemical Symbols Radicals
Tool is assigned to the nearest
Radicals are indicated with the appropriate
atom. If no atom is within the
distance set as the Fixed
symbol from the Chemical Symbols palette. As
Length, the charge is ignored with charges, they are assigned to the nearest
and not assigned to any atom. atom. Radicals always occupy one free

User Guide
valence, in addition to any charge effects. Two atom that is disregarded during chemical cal-
examples are: culations but still lets you create diagrams that
look meaningful to an experienced chemist. A
Ph few examples are shown below:
Ph C C O
η3 or π-Allyl complex:
Ph
H-Dot/H-Dash
M
H-Dot and H-Dash symbols from the Chemical
Ferrocene, a π-Aryl complex:
Symbols palette indicate the stereochemistry
of a single hydrogen atom. These symbols are
most commonly used in fused systems, such as
below:
Complexes Cp2TiCl2, another π-Aryl complex:

Compounds with electron pairs can act as
Lewis bases, bonding with Lewis acids that are Cl Cl
electron-deficient. Similar behavior can be Ti
seen between lone pairs and metals.
The best representation of these types of inter-
action is with a dative bond from the electron-
pair donor to the acceptor. With a plain bond η-C5H5Mn(CO):
instead of the dative bond, a valence error
would be reported. The dative bond more accu- CO
rately represents the electron donation. OC CO
Complexes may also be represented with
explicit lone pairs and without any bonds. Mn
If you use a simple bond to indicate a complex,
you may want to set Abnormal Valence to
Allowed in the Atom Properties dialog.
Cahn-Ingold-Prelog
Multi-center Attachments
Absolute stereochemistry is calculated for tet-
Multi-center attachments are meaningful only rahedral atoms and double bonds according to
when created using Structure>Add Multi-Center the Cahn-Ingold-Prelog (CIP) priority rules.*
Attachment. This command creates a pseudo-

Appendix C
The CIP rules are designed to order ligands by Rule 5. R precedes S
their priority and determine a descriptor based Chem & Bio Draw 12.0 checks differences up
on the orientation of the ordered ligands in to 15 atoms distant from the stereocenter.
space.
Stereochemical Indicators
A ligand is an entity attached to a stereocenter.
After the ligands are ranked, an indicator is
For example, a tetrahedral carbon has four
assigned as shown in the following table.
ligands corresponding to its four substituents.
When a tetrahedral carbon is in a ring, it still
has four ligands: the two ligands outside the Stereo- Indicator
ring, a third consisting of the ring “unpeeled” center
clockwise, and a fourth consisting of the ring
“unpeeled” counterclockwise. Double bond Z if the highest ranking ligand
of each pair are on the same
Five rules used to determine the priority of side of the bond; otherwise E.
ligands are summarized below in simplified
Tetrahedral When the lowest-ranking
form. For more detailed information, see the
atom ligand is located behind the
references. They are checked sequentially as
central atom:
follows:
Rule 1. Higher atomic number precedes lower • R when remaining 3 ligands
are arranged clockwise in
Rule 2. Higher atomic mass precedes lower descending order
Rule 3. cis precedes trans • S when remaining 3 ligands
Rule 4. Like pairs of descriptors precede unlike are arranged counterclock-
pairs wise in descending order
• r or s is used for pseudo
asymmetric atoms
*. R.S. Cahn, C.K. Ingold, and V. Prelog,
“Specification of Molecular Chirality”,
Angew. Chem., Int. Ed. Engl. 1966, 5, 385-
Stereochemical Flags
414 (errata: 1966, 5, 511); Angew. Chem. While the chirality of a specific stereocenter
1966, 78, 413-447. can be indicated with the appropriate wedged,
V. Prelog and G. Helmchen, “Basic Principals
of the CIP-System and Proposals for a Revi-
hashed, or plain bond, sometimes it is useful to
sion”, Angew. Chem. 1982, 94, 614-631; indicate the relative stereochemistry of a mole-
Angew. Chem. Int. Ed. Engl. 1982, 21, 567- cule as a whole, considering the relationship
583. between all stereo-centers. Stereochemical
P. Mata, A.M. Lobo, C. Marshall, and A.P. flags apply to the nearest structure; if no struc-
Johnson, “The CIP Sequence Rules: Analy-
ture is within the distance specified by the
sis and Proposal for a Revision.” Tetrahe-
dron:Asymmetry. 1993, 4, 657-668.

User Guide
Fixed Length value, the stereochemical flag is
not assigned to any structure.
Figure C.8 The Racemic flag indicates a mixture of

the exact stereoisomer as drawn and its enantiomer.
Polymer Representations
Figure C.6 The Absolute flag indicates the exact Polymers are represented by brackets used to
stereoisomer as drawn. enclose repeated structures or structural frag-
ments. Bracket properties specify the orienta-
tion and context of the repeating units. An
explanation of the bracket properties is given
in “Setting Bracket Properties” on page 131.
NOTE: The polymer drawing feature is avail-

References
“Graphic Representations (Chemical Formu-
lae) of Macromolecules (Recommendations
Figure C.7 The Relative flag indicates the exact
1994)” Pure Appl. Chem., 66, 2469-2482
stereoisomer as drawn, or its enantiomer. (1994).
“Source-Based Nomenclature for Copolymers
(Recommendations 1985)” Pure Appl. Chem.,
57, 1427-1440 (1985). Also available at: http://
www.iupac.org/publications/books/pbook/Pur-
pleBook-C7.pdf.

Appendix C
“Basic Definitions of Terms Relating to Poly-
mers (1974)” Pure Appl. Chem., 40, 479-491 Message Description
(1974) Also available at: http://www.iupac.org/
An atom in this Displayed in cases where a
reports/1996/6812jenkins/index.html.
label has an place cannot be found to place
Also see the Guide for the authors of papers invalid valence. a bond or a bond cannot be
and reports in polymer science and technology found to place an atom. Valid
from IUPAC. valences for each element are
listed in the Isotopes Table
Analysis Messages
file.
When a structure cannot be analyzed fully, two
general types of messages are displayed: ChemDraw can’t Displayed when text is found
interpret this that cannot be identified as an
• Status messages that report a problem that label. element, nickname, generic
may not affect the final analysis nickname, or alternative
• Critical messages that may affect the final group name.
analysis
Parentheses Displayed when parentheses
don’t match. cannot be matched into nested
Message Description
open-close pairs.
There are too Displayed for every unlabeled
This label has Displayed when a plus and
many bonds to atom with more than four
conflicting or minus charge have been
this unlabeled filled valences. Filled
unassignable assigned to the same element,
Carbon. valences include sum of bond
charges. charges have been assigned in
orders, charge, radicals, and
more than one way, or a
free sites. Aromatic bonds
charge has been assigned to a
count 1.5 each, rounded down
nickname, generic nickname,
unless it is the only bond to
or Alternative Group name.
the atom. Charge is signed
and includes charge implied
Formula cannot Displayed for every label that
by dative bonds. The Substit-
be computed for contains a generic nickname,
uents query property treats
queries. an element list or an alterna-
free sites, up to and exactly
tive group. This is a status
the same way: an atom with
message only; analysis
two explicit bonds and
continues as if the problem-
“Substituents: Up To 3” or
atic label were not selected.
“Substituents: Exactly 3” or
“Substituents: Free Sites 1”
has three filled valences.

User Guide
Message Description Message Description
Text not in Displayed for the first caption This isolated Displayed for unlabeled
Formula style that is not an atom label or bond is probably single bonds unattached to
won’t be inter- Alternative Group name, and not intended to other bonds. All bonds are
preted. which contains any text not in have chemical interpreted chemically,
Formula, Subscript, or Super- significance. usually as C2H6, and may
script style. This is a status cause unexpected results if
message only, and appears intended as a graphical line
only once regardless of how only. This is a status message
many captions are in the only.
selection.
The atom is very Displayed for any atom that is
This named Displayed for any structure close to another nearly touching another atom
alternative within an Alternative Group atom or bond. or bond but not bound to it. If
group contains Box where the structure lacks a bond really was intended,
no attachment an attachment point. This is a the analysis of the structure
point. status message only. produces incorrect results.
This is s status message only.
This named Displayed for any Alternative
alternative Group Box whose contained The stereocenter Displayed for any asymmetric
group contains structures have varying has no stereocenter without attached
fragments with numbers of attachment bonds specified. wedged, hashed, dashed, or
inconsistent points. Since all structures bold bonds. This is a status
valences. within an Alternative Group message only, and appears
Box are to be used inter- only when Show Stereochem-
changeably, they must have istry is tuned on and there is at
the same number of attach- least one other wedged,
ments. This is a status hashed, dashed, or bold bond
message only. in the structure.
This named Displayed for any Alternative There is a Displayed for any
alternative Group Box that is empty. This valence and odd-membered ring drawn as
group contains is a status message only. charge error a delocalized system (with a
no fragment. somewhere in circle in the middle), where
this aromatic there is no corresponding
Part of a mole- Displayed for any Alternative system. associated charge. For
cule is outside of Group Box whose border example, a delocalized repre-
the alternative crosses part of a structure. sentation of cyclopentadiene
group definition. This is a status message only. must include either a negative
charge or a multicenter
attachment.

Appendix C
Message Description
The stereocenter Displayed for any stereo-

has conflicting center (tetrahedral atom,
or ambiguous asymmetric double bond,
stereobonds etc.) where the absolute stere-
specified. ochemistry cannot be deter-
mined from the structure as
drawn. For example, this
message would be shown for
a carbon atom attached by
bold bonds to four different
ligands. This message is
displayed only when Show
Stereochemistry is also turned
on.
This label has an Displayed for every label that

unrecognized has a numeric superscript
isotopic mass. immediately preceding an
atomic symbol, where the
superscripted number does
not correspond to a recog-
nized isotope. For example,
24CH .
3

User Guide
Appendix C
D
Property Calculations
You can calculate predicted values of selected least squares analysis. This method allows a
physical and thermodynamic properties for calculation of logP with a standard devia-
structures of up to 100 atoms. The following tion of 0.43 logP units and can handle mol-
topics describe how the values are determined. ecules containing hydrogen, oxygen,
nitrogen, sulfur, halogens and phosphorus
NOTE: The property calculations plug-in is atoms. If this method is applied to mole-
available for ChemBioDraw Ultra, ChemDraw cules with internal hydrogen bonds, the
Ultra, and ChemDraw Pro only. standard deviation is 0.83 LogP units.
Henry’s Law
LogP Two methods are used to predict Henry’s Law
constant.
Three fragmentation methods are used to pre-
dict the logP values. • The first is an approach based on the bond
contribution method. This method uses 59
• Method one is based on 94 atomic contribu- bond contribution values and 15 correction
tions evaluated from 830 molecules by least factors. The contributions were calculated
squares analysis. This method works with a by least squares analysis using a data set of
standard deviation of 0.47 logP units and 345 chemicals. This method estimates with
can handle molecules containing hydrogen, a mean error of 0.30 units and a standard
oxygen, nitrogen, sulfur and halogens. deviation of 0.45 units and can handle mol-
• Method two is an extension of method one ecules containing carbon, hydrogen, oxy-
but is based on 120 atomic contributions gen, nitrogen, sulfur, phosphorus and
evaluated from 893 molecules by least halogens.
squares analysis. In addition to the atoms • In the second method, Henry’s Law con-
introduced for method one, it can handle stant is estimated from an equation found
molecules that contain phosphorus and using linear regression. Multifunctional
selenium atoms. This method works with a compounds were omitted from this study.
standard deviation of 0.50 logP units. This method should not be used for com-
• Method three is based on 222 atomic contri- pounds where distant polar interaction is
butions calculated from 1868 molecules by present.

User Guide
Molar Refractivity Topological Polar Surface Area
Molar refractivity—Two fragmentation The polar surface area of a molecule (mea-
methods are used to estimate the molar refrac- sured in square angstroms) can be used to pre-
tivity value. dict of pharmaceutical transport properties in
the body. Historically, this property has been
• Method one includes 93 atomic contribu-
calculated using time-consuming 3D tech-
tions evaluated from 504 molecules by
niques. However, but a recent paper has pro-
using a constrained least squares technique.
vided a remarkably accurate way of predicting
This method works with a standard devia-
it very rapidly. Chem & Bio Draw 12.0 imple-
tion 1.27 cm3/mol and can handle mole-
ments a more innovative algorithm*.
cules containing hydrogen, oxygen,
nitrogen, sulfur and halogens. Other Properties
• The second method is an extension of
Normal Boiling Point and Melting Point. Esti-
method one that includes 120 atomic contri-
butions evaluated from 538 molecules by mated in K using two methods.
using a constrained least squares analysis • Joback's fragmentation method.
technique. In addition to the atoms intro- • The Joback method as modified by Stein.
duced for method one, this method can han- All boiling points are estimated for a pres-
dle molecules with phosphorus and sure of 1 atm.
selenium atoms. This method works with a
Miscellaneous properties. Heat of Formation,
standard deviation of 0.77 cm3/mol. Gibbs Free Energy, Ideal Gas Thermal Capac-
CLogP and CMR ity, Freezing Point, Critical Temperature, Criti-
cal Pressure, and Critical Volume are
Specific algorithms for calculating LogP and estimated using Joback’s fragmentation
molar refractivity from fragment-based meth- method.
ods developed by the Medicinal Chemistry
Project and BioByte.
*. The algorithm is based on:
Ertl, P., Rohde, B., and Selzer, P., 2000. Fast
NOTE: CLog P and CMR are available in Calculation of Molecular Polar Surface
ChemBioDraw Ultra and ChemDraw Ultra Area as a Sum of Fragment Based Contribu-
only. tions and Its Application to the Prediction of
Drug Transport Properties. J.Med.
Chem.43: 3714-3717.
202 Property Calculations

Appendix D
E
ChemNMR
ChemNMR provides a detailed protocol of the
NOTE: The ChemNMR Feature is available in estimation process applied. It gives substruc-
ChemBioDraw Ultra and ChemDraw Ultra tures as names, compound classes in most
only. cases, substituents in form of a linear code,
respectively.
The data set for the 1H NMR Shift tool cur-
ChemNMR estimates chemical shifts for all rently contains 700 base values and about 2000
hydrogen or carbon atoms for which additivity increments. The 13C NMR Shift tool is based
rules are available. Following a hierarchical on 4000 parameters. It also implements models
list, it first identifies key substructures of a for ethylenes (cis/trans) and cyclohexanes
molecule. A substructure provides the base (equatorial/axial).
value for the estimated shift. For example, ben-
zene would be identified as the key substruc- ChemNMR Limitations
ture of trinitrotoluene.
The program handles the following elements:
When a substructure is a ring system not avail-
H, D, He, Li, Be, B, C, N, O, F, Ne, Na, Mg,
able in the data, ChemNMR approximates its
Al, Si, P, S, Cl, Ar, K, Ca, Sc, Ti, V, Cr, Mn,
base shift using embedded rings and, if neces-
Fe, Co, Ni, Cu, Zn, Ga, Ge, As, Se, Br, Kr, Rb,
sary, it will disassemble the ring into acyclic
Sr, Y, Zr, Nb, Mo, Tc, Ru, Rh, Pd, Ag, Cd, In,
substructures.
Sn, Sb, Te, I, Xe, Cs, Ba, La, Ce, Pr, Nd, Pm,
ChemNMR views remaining parts of the mole- Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, Hf,
cule as substituents of a substructure. Each Ta, W, Re, Os, Ir, Pt, Au, Hg, Tl, Pb, Bi, Po,
substituent adds to or subtracts from the base At, Rn, Fr, Ra, Ac, Th, Pa, U, Nep, Pu, Am,
shift of the substructure to which it is attached. Cm, Bk, Cf, Es, Fm, Md, No, Lr. Functional
Additivity rules determine the increment of groups are expanded automatically.
each contribution. If an increment for a substit-
In the case of 1H NMR, it estimates shifts of
uent cannot be determined, ChemNMR uses
about 90% of all CHx-groups with a standard
embedded substituents—smaller structural
deviation of 0.2.-0.3 ppm. The use of polar sol-
units with the same neighboring atoms. Or, it
vents may strongly increase these deviations. It
will use increments of identical or embedded
does not estimate shifts of hydrogen atoms
substituents of a corresponding substructure by
bonded to heteroatoms because they are signif-
assuming that the effects of the substituents are
icantly affected by solvents, concentration,
of the same magnitude.
impurities, and steric effects.

User Guide
In case of 13C NMR, it estimates over 95% of Pretsch, E.; Fürst, A.; Badertscher M.; Bürgin,
the shifts with a mean deviation of -0.29 ppm R.; Munk, M. E. J. Chem. Inf. Comp. Sci.
and standard deviation of 2.8 ppm. 1992, 32, 291-295.
Bürgin Schaller, R.; Pretsch, E. Anal. Chim.
NMR References
Acta 1994, 290, 295.
Sources for Chem & Bio Draw 12.0 NMR data Bürgin Schaller, R.; Arnold, C.; Pretsch, E.
include the following publications: Anal. Chim. Acta 1995, 312, 95-105.
Fürst, A.; Pretsch, E. Anal. Chim. Acta 1990, Bürgin Schaller, R.; Munk, M. E.; Pretsch, E.
229, 17. J. Chem. Inf. Comput. Sci.1996, 36, 239-243.
204 ChemNMR
Appendix E
F
Technical Support
Telephone and Internet technical support is You can deliver your form to Technical Sup-
available to registered users. Be sure to provide port using either of:
your serial number. Online: www.cambridgesoft.com/services/mail
Technical Support on the internet includes E-mail: support@cambridgesoft.com
answers to frequently asked questions (FAQs)
and general information. You can find it at: Locating your serial number
http://www.CambridgeSoft.com/services/ For Windows users, the serial number is on the
Other resources are also available: outside of the Chem & Bio Draw 12.0 box. For
Macintosh users, the serial number is on a card
1. Chem & Bio Draw 12.0 Readme file. This
inside the box. You can also find the serial
file includes known limitations or conflicts.
number online or in the Chem & Bio Draw
2. Review System requirements. See the menu:
beginning of this manual for minimum
ONLINE
requirements for installing and running
Chem & Bio Draw 12.0. If you have downloaded Chem & Bio Draw
12.0, you can find your serial number at the
3. If you still need assistance, fill out a copy of
CambridgeSoft Web site.
the CS Software Problem Report Form at:
1. Go to www.cambridgesoft.com.
http://www.cambridgesoft.com/services/mail.
2. Log into your CambridgeSoft account.
When you fill out the form:
3. Click My Downloads in the list of Services.
• Try to reproduce the problem before con-
WINDOWS
tacting us. If you can reproduce the prob-
lem, please record the exact steps that you In Chem & Bio Draw for Windows, go to
took to do so. Help>About. The serial number is under the
license name.
• Record the exact wording of error mes-
sages. MACINTOSH
In Chem & Bio Draw 12.0 for Macintosh,
• Record what you have tried to correct the choose About CS ChemDraw in the Apple
problem. menu. The serial number appears at the bottom
left.

User Guide
206 Technical Support
Appendix F
G
Shortcuts and Hotkeys
Hotkeys are organized into atom labels, bond
Atom Label Key
types, and functions such as adding a charge or
displaying a bond. Shortcuts are organized by H h
the menu on which the command is found.
Nicknames are listed alphabetically by abbre- Q* q
viation in two tables. Each listing is a link to a
Br b
page that displays the structure and full name.
A navigation bar at the bottom of the page lets I i
you step through the section or return to the
listings. R r
n-Bu 1
NOTE: You can modify Hotkeys and Nick-
names. The tables in this section refer to the K k
default values.
S s
s-Bu 2
Atom Keys
Use atom keys to insert atoms in a drawing Me m
using your keyboard. For example, place your Si S
mouse over an atom and press ‘3’ to add a tert-
butyl group. t-Bu 3
N n
Atom Label Key
TMS t
A a
C c
F f
Na N
Ph P or 4
X x
Ac A or 5

User Guide
Atom Label Key Function Key
Cl C or l Position a double bond to the r

right
O o
Change to wedged bond w
COOCH3 E
Bring bond to front f
D d
Change to hashed bond H
OTs T
Open a bond properties text box / (slash) or ?
CH2OH 6
Change to hashed-wedged bond h
Et e
P p Function Hotkeys
B B Function Key
Bond Hotkeys Add an attachment . (period)

point
To modify a bond, place your mouse over the
bond and select a key listed below. Add an atom number ‘ (single quote)
Function Key
Add a negative -
charge
Change to single bond 1
Add a positive +
Change to dashed bond d charge
Change to double bond 2 Sprout one bond 0
Change to wavy bond y Sprout two bonds 9
Change to triple bond 3 Sprout three bonds 8
Position a double bond to the l Display the Atom / (slash) or ?

left Properties dialog
box
Change to quadruple bond 4
Display the Choose = (equals)
Center a double bond c Nickname dialog
box
Change to bold bond b
208 Shortcuts and Hotkeys

Appendix G
Function Key Command Key Combination
Open an atom label <Enter> Undo Ctrl+z

text box.
Redo Shift+Ctrl+z
Remove an atom <Backspace>,
label. <Delete> or <space> Repeat last Ctrl+y
command
Shortcuts Clear Delete
Below is a list of key combinations for a vari-
ety of common tasks. View
File
Command Key Combination
Command Key Combination Actual size F5
Create a new document Ctrl+n Magnify F7
Open a document Ctrl+o Reduce F8
Save a document Ctrl+s Fit to window F6
Save a document as... Shift+Ctrl+s Toggle ruler F11
Print a document Ctrl+p Toggle crosshair Ctrl+h
Page setup Shift+Ctrl+p Object

Close a document Ctrl+w
Command Key Combination
Exit Chem & Bio Draw Alt+F4
Toggle fixed length Ctrl+L
Edit Toggle fixed angles Ctrl+E
Command Key Combination Select multiple objects Shift+Click (with

Lasso, Marquee, or
Cut Ctrl+x Structure Perspec-
tive tools
Copy Ctrl+c
Group selected objects Ctrl+g
Paste Ctrl+v
Ungroup objects Shift+Ctrl+g
Select all Ctrl+a

User Guide
Command Key Combination Command Key Combination
Join selected objects Ctrl+J Automatic justifica- Shift+Ctrl+M

tion
Bring to front F2
Plain Ctrl+
Send to back F3
Bold Ctrl+B
Flip horizontal Shift+Ctrl+H
Italic Ctrl+I
Flip vertical Shift+Ctrl+V
Underline Ctrl+U
Rotate 180° horizontal Alt+Shift+Ctrl+H
Formula Ctrl+F
Rotate 180° vertical Alt+Shift+Ctrl+V
Subscript selected F9 (in a label)
Rotate... (opens Rotate Ctrl+R character, or next
Objects dialog box) character typed
Scale...(opens Scale Ctrl+K Superscript selected F10 (in a label)
Objects dialog box) character, or next
character typed
Structure
Adds a degree sign Alt+248 (in a label)
(°)
Command Key Combi-
nation
Drawing
Clean up structure Shift+Ctrl+K
Command Key Combina-
Convert name to structure Shift+Ctrl+N tion
Convert structure to name Alt+Ctrl+N Copy a selected object Ctrl+drag
Text Copy a selected object Shift+Ctrl+drag
(constrained to X and Y
Command Key Combination axes)
Flush left Shift+Ctrl+L Distort (limit resize to X or Shift+drag (with

Y axis) resize handle)
Center Shift+Ctrl+C
Toggle the Lasso and the Ctrl+Alt+Tab
Flush right Shift+Ctrl+R previous drawing tool
Justified Shift+Ctrl+J

Appendix G
Command Key Combina-
tion
Change direction of a chain Ctrl+Drag (with

alkane chain
tool)
Change orientation of Shift+Click

double bonds (with saturated
double-bond ring
tools)
Create resonance delocal- Ctrl+Click (with

ized ring ring tools except
chairs)
Remove a curve segment Alt+Shift+Click

(with the pen
tool)

User Guide
Nicknames
Ac-Me
Ac Bz c-C7H13 cyclopropyl DPIPS i-C4H9
Ad BOM c-C8H15 Cys DPTBS i-C5H11
Ala Bs c-Hx Dan DTBMS i-Pr
Alloc Bt C10H20 DEAE DTBS Ile
Allyl Btm C10H21 DEIPS Et Im
Am Bu Cbz DMIPS Fmoc Leu
Arg Bzh cHx DMPM Gln Lys
Asn Bzl CoA DMPS Glu m-C6H4
Asp BzOM Cy DMTr Gly m-Phenylene
Benzoyl c-C3H5 cyclobutyl DNP His m-Tolyl
Benzyl c-C4H7 cycloheptyl Dnp i-Am MDIPS
Bn c-C5H9 cyclooctyl Dns i-Bu MDPS
Boc c-C6H11 cyclopentyl DNS i-C3H7 Me
MEM-Xyl
MEM n-Pr Phenyl s-Butyl TBDMS Thr
Mes N3 Pht s-C4H9 TBDPS TIPDS
Met neo-Am Piv s-C5H11 TBMPS TIPS
MMTr neo-C5H11 PMB SEM TBS TMS
MOM Np PMBM Ser TDS Tos
MPM o-C6H4 PNB SES Tf trans-

Cinnamyl

Appendix G
MEM-Xyl
Ms o-Phenylene Poc t-Am Tfa Troc
MTM o-Tolyl PPi t-BOC TFA Trp
n-Am p-C6H4 Pr t-Boc Thexyl Trt
n-Bu p-Phenylene Pro t-Bu THF Ts
n-C3H7 p-Tolyl Pv t-Butyl Thf Tyr
n-C4H9 Ph s-Am t-C4H9 THP Val
n-C5H11 Phe s-Bu t-C5H11 Thp Xyl

User Guide
Appendix G
H
The CambridgeSoft Web Site
The CambridgeSoft Web site is a valuable free access to ChemBioFinder.com, Che-
source of helpful information. There you can: mACX.com, ChemClub.com, and the e-mail
edition of ChemNews. To register online, go to
• Register your software.
Online>Register Online. The CambridgeSoft
• Search for chemical information by name Professional Services page opens in your
or ACX number; or, insert a structure into a browser.
worksheet.
• Get technical support, documentation, soft- User’s Guide
ware downloads, and more. The Online menu also provides a way for you
You can navigate to the site directly from to easily find current and previous versions of
Chem & Bio Draw by selecting the appropriate all CambridgeSoft documentation. To access
option in the Online menu. the CambridgeSoft Manuals page, go to
Online> Browse CambridgeSoft Documentation.
Registering Online The Desktop Manuals Web page appears. You
To activate any Chem & Bio Office 2009 can select PDF versions of the CambridgeSoft
application, register with the CambridgeSoft manuals from the dropdown list.
Web site to receive a registration code. Upon
filling out a registration form, you will receive NOTE: If you do not have a CambridgeSoft
the registration code by e-mail (this registra- User account, you will be directed to a sign-up
tion scheme does not apply to site licenses). page first.
If your serial number is invalid or you do not
have an internet connection, contact
CambridgeSoft Support to receive a registra- Technical Support
tion code. The online menu link Browse CambridgeSoft
You may use your Chem & Bio Office 12.0 Technical Support also opens the
application a limited number of times while CambridgeSoft Professional Services page.
waiting for the registration process to finish. Here you can find a variety of Desktop Support
After you reach the limit, you must register the resources including the CambridgeSoft
software. Knowledge Base, product Downloads, Q&A,
In addition to registering your software, you FAQ, Documentation, and so on.
can request literature, or register for limited

User Guide
1. Go to Online>Browse CambridgeSoft Tech- The Find Structure from ACX number dialog
nical Support. The Professional Services box appears.
Web page opens. 2. Type the ACX registry number.
2. Click Desktop Support. 3. Click OK. The structure appears in your
Suppliers on ACX.com document.
ChemACX (Available Chemicals Exchange) is To find a structure by name:

a Webserver application that accesses a data- 1. Go to Online>Find Structure from Name at
base of commercially available chemicals. The ChemACX.com.
database contains catalogs from research and 2. In the dialog box, type either a chemical
industrial chemical vendors. name or trade name.
You can use Chem & Bio Draw 12.0 to link to 3. Click OK. The structure appears in your
the chemacx.com database record of suppliers document.
for compounds that you draw.
ACX Numbers
1. In Chem & Bio Draw 12.0, select a struc-
ture you have drawn that you want to look 1. To Find an ACX number for a structure:
up. 1. Select the structure.
2. Go to Online>Find Suppliers on Che- 2. Go to Online>Find ACX Numbers from
mACX.com. Structure.
The ChemACX.Com page opens in your The ACX number appears in the Find ACX
browser with information on the selected struc- Numbers from Structure dialog box.
ture.
For more information on using the ChemACX Chem & Bio 3D ActiveX Control
Web site, see the ChemOffice Enterprise http://www.cambridgesoft.com/services/Desk-
Workgroup & Databases Manual. topSupport/Documentation/Chem3DControl/
ACX Structures and Numbers SciStore.com
Chem & Bio Draw 12.0 searches ACX and SciStore offers life science desktop software,
returns information about related structures enterprise solutions, chemical databases, and
and numbers. You can place the returned infor- consulting services to biotechnology, pharma-
mation in your document. ceutical, and chemical industries. Visit SciS-
ACX Structures tore at www.scistore.com.
There are two ways to find ACX structures, by CambridgeSoft.com
ACX number or by name.
To open the CambridgeSoft Home Page, go to
To find a structure by ACX number:
Online>Browse CambridgeSoft.com. Check the
1. Go to Online>Find Structure from ACX Num- CambridgeSoft Web site for new product
ber. information. You can also get to Chem-
News.Com, and other pages through
CambridgeSoft.Com.
216 The CambridgeSoft Web Site

Appendix H
Using the ChemOffice SDK The ChemOffice SDK page contains docu-
mentation, sample code, and other resources
The ChemOffice Software Developer’s Kit
for the Application Programming Interfaces
(SDK) lets to customize your applications.
(APIs).
To browse the ChemOffice SDK, go to
Online> Browse ChemOffice SDK.

User Guide
218 The CambridgeSoft Web Site
Appendix H
Index
Numerics alternative groups 134
attachment point numbering 137
13
C, 1H shifts, estimating 95 attachment point symbol 136
35 mm slide boundary lines 185 attachment rank indicators 136
3D model 77 defining 135
3D query properties 142 description 134
3D viewing 77 multiple attachment points 136
analysis 133
A information 85
abnormal valence 126 messages 197
absolute flag, drawing 142 analysis and properties 163
accessing documents 159 analysis messages 197
ACS Document 1996 173 analysis results, interpreting 107
ACX information, finding 216 analysis window 85
acyclic chains anion, drawing 90
changing direction 22 anonymous alternative groups 138
drawing 23 apply settings command 161
adding applying object settings 161
3D query property 142 arcs 26
a template 74 drawing 26
chemical names 79 resizing 26
frames 69 arrows
rows and columns 74 adjustment handles 23
structures 105 autoscaling 150
structures by name 105 changing direction 24
structures in ChemDraw/Excel 105 cursor types 23
adjustment handles 23 hollow arrows 24
Adv. Synth.Catal. 174 rotating 25
advanced drawing techniques 59 undo 24
aligning objects assigning
align submenu 32 atom mapping 140
overview 32 asymmetry, see stereochemistry indicators
rulers 187 195
with crosshair 188 atom
aligning structures 70 , 108 ,
numbers 64 65
aligning text 164 query properties 120
alignment, automatic 165 atom label text boxes, closing 158

User Guide
,
atom labels 164 191 attachment points, viewing 64
automatic justification 165 attachment rank indicators, showing 137
justification 164 auto update 81
layering 167 automatic
margin width 167 alignment 165
multi-attached 61 drawing of structure 82
specification 191 justification, atom labels 165
text boxes, creating new line 158
autosave 158
white space 167
autoscale
atom labels, adding 10
template color 171
atom numbers when transferring 149
editing 65
showing and hiding 64 B
atom properties background and foreground 169
abnormal valence 126 background color, printing 171
,
description 120 122 128 , Balaban index 115
implicit hydrogens 123
in query structures 120 baseline style, captions 163
options 122 benzene ring
reaction changes 124 changing orientation 22
reaction stereo 125 drawing 22
resetting defaults 122 BioDraw 9
ring bond count 123 drawing a helix protein 37
substituents 122 drawing a membrane arc 37
unsaturation 124 drawing a membrane line 37
viewing 121 drawing DNA 38
atom, changing to a different 11 templates 73
atom, to add an 10 BioDraw objects
atoms color 35
moving 30 customizing 36
line and fill properties 35
atom-to-atom mapping 140
attached data 153 BioDraw templates 1 35 ,
bitmap fonts (Macintosh) 158
attachment point
defining 135 bitmap fonts, using when available 158
numbering 137 bitmapped
symbol 136 printing quality 161
,
tool 91 135 boiling point 111
attachment points 63 75 , calculation 202
definition 91
attachment order 75
numbering 137 bold width 162
attachment points, multiple 136 bond crossings
changing 16
220 Index
white space 162 exact mass 85
bond properties formula 85
defining 127 molecular weight 85
query indicators 127 CambridgeSoft Web site, accessing 216
reaction center 129 CambridgeSoft.com 216
removing 128 caption text boxes
topology 129 closing 158
types 128 creating new line 158
viewing 128 captions 164
bond spacing, description 162 analysis information 85
bond types autoscaling 150
in queries 128 ,
formatting 163 166
bonding from sequences 42 formula 163
bonds inserting from structure 79
adding to an atom label 62 justification 164
autoscaling 149 setting font, size and styles 166
changing type 15 subscript 163
double either 129 superscript 163
drawing 13 carbon-13 shifts, see 13C, 1H shifts, esti-
editing 15 mating 95
fixed angle 13 cation, drawing 90
layering 16 CDX see file formats 10
margin width 162
chain angle, description 162
multi center attachment 63
orientation for dative or wedged bonds 15
chain length 23
quadruple 14 specifying 23
selecting 28 changing
types 190 default settings 161
border of page 183 changing bond type 15
braces 26 character map 11
brackets charges
drawing 26 specifications 192
paired 26 symbols, drawing 90 , 192
single 26 check structure
tool 26 overview 32
usage 132 checking chemistry 32
C Chem & Bio 3D 77 78 ,
Chem & Bio 3D preview 78
Cahn-Ingold-Prelog 194 Chem & Bio 3D preview options 77
calculating Chem & Bio 3D, launching 78
chemical properties 91 Chem & Bio Draw
elemental analysis 85

User Guide
SDK 78 critical temperature 202
Chem 3D 78 critical volume 202
ChemBioFinder hotlink 86 freezing point 202
ChemBioFinder.com 216 Gibbs free energy 202
heat of formation 202
ChemClub.com 215
Henry’s Law 201
ChemDraw ideal gas thermal capacity 202
customizing 157 LogP 201
Hotkeys file 167 molar refractivity 202
ChemDraw Items folder thermal capacity 202
location 159 TPSA 202
ChemDraw items folder using 91
description 159 chemical symbols
isotope table 126 rotating 91
scripts 161 chemical syntax checking 33
templates 73
chemical warnings 33
ChemDraw laser prep 171 disabling 45
ChemDraw/Excel 103 suppressing 33
adding structure files 105 chemically significant text 192
adding structures 105
chemicals, purchasing online 216
adding structures as SMILES 105
adding structures by name 105 chemistry
aligning structures 108 of ChemDraw 189
converting old worksheets 104 chemistry checking 32
exporting to SDFiles 104 ChemNews.Com 216
functions 108 ChemNMR
get ChemDraw list command 104 example supplementary data 95 98 ,
import hit list error messages 104 NMR shifts 95
importing tables 103 using 95
naming structures 107 ChemNMR database 97
searching 106 ChemNMR directory 97
starting 103 ChemNMR, about 5
chemical composition 109 ChemOffice SDK, accessing 217
chemical formula 109 ChemProp
chemical intelligence 189 critical pressure 202
chemical interpretation 189 ChemScript 78
chemical name, structure from 82 chirality, see stereochemistry, flags 195
chemical properties 92 clean up structure 62
boiling point 202 clearing
chemical properties 91 mapping 142
CLogP 202 spectrum-structure assignments 97
CMR 202 stereochemical markers 86
222 Index
clearing reaction mapping 142 name to structure 82
, , , ,
Clipboard 33 82 108 127 142 147 , , converting names to structures 82
148, 149 converting worksheets 104
clipboard 82, 107, 147 copy
clipping files 149 as SLN command 148
CLogP 92, 202 with clipboard 147
closing text boxes 158 copying objects 30
cluster count 115 creating
Hotkeys 167
CMR 92
SLN strings 148
color
critical pressure, calculation 202
autoscaling 150
changing 169 critical pressure, definition 91
menu 169 critical pressure 112
overview 168 critical temperature, calculation 202
saving settings 171 critical temperature, definition 91
color palette 169 critical temperature 112
colored arrows 68 critical volume, calculation 202
coloring critical volume, definition 91
block arrows 68 critical volume 112
colors, customizing 169 crosshair
,
colors, maximum number of 150 168 169 , displaying 187
commands moving 188
new 9 using to align objects 188
open 9 curved arrows 68
save 10 curves 27
complexes 194 autoscaling 150
configuring documents 162 custom shift correction data 97
configuring objects 163 customized settings, saving 161
Connolly molecular surface area 114 customizing
Connolly solvent accessible surface area ChemDraw 157
114 saving document settings 161
Connolly solvent-excluded volume 114 customizing colors 169
contracting labels 61 customizing toolbars 159
conventions cycloalkane rings, converting to delocal-
text 4 ized rings 22
convert name to structure, limitations 82 cyclohexane chair ring tool 21
convert structure to name, automatic cap- , ,
cyclohexane ring tool 46 51 70
tions 79 cyclopentadiene ring tool 21
converting cyclopentadiene ring, changing orientation

User Guide
22 cross hairs 187
cyclopentadiene rings, drawing 22 rulers 187
cyclopropane ring tool 21 displaying and printing 140
displaying structures 108
D dissociation tool 67
daggers 26 distributing objects 32
data Sgroup, support for 153 disulfide bridges 43
database conventions 189 document
database conventions, in structure drawings location, default 157
189 posters 184
dative bonds, drawing 15 setting up multi-paged 183
default document and object settings 160
atom properties, resetting 122 document settings 172
bond properties, resetting 128 Adv. Synth.Catal. 174
changing 161 J. Mol. Mod. 175
document location 157 new document 176
file format 157 new slide 176
stationery pad 170 overview 160
default document location 157 phytomedicine 177
default file format 158 RSC document 178
Science of Synthesis 179
default format
Synthesis/Synlett document 180
changing 165
Verlag Helvetica Chimica Acta 180
default open file format 157 Wiley document 181
default save file format 158 document setup
default styles 160 multiple-paged documents 183
defining alternative groups 135 posters 184
defining nicknames 75 document window
deleting drawing area 183
delete key 30 enlarging 183
nicknames 76 reducing 183
objects 30 documentation web page 215
rows and columns 74 documents
delocalized rings, drawing 22 creating 9
,
deselecting objects 28 29 saving 10
deselecting one object 29 Does cell have a reaction drawing? 111
detecting errors Does cell have a structure drawing? 111
check structure command 32 d-orbitals, drawing 90
error checking 33 DOS prompt 97
disable chemical warnings 33 , 45 double bond
displaying changing type 15
224 Index
drawing 14 drawing settings
orientation 16 changing defaults 161
double either bonds, drawing 14 margin width, effect on atom labels 167
drawing margin width, effect on bond crossing 162
acyclic chains 22 duplicating objects 30
arcs 26 Dz2- orbitals, drawing 90
arrows 67
benzene and cyclopentadiene rings 22 E
,
charge symbols 90 192 edit 11
curves 27 editing
daggers 26 atom numbers 65
database conventions 189 bond type 15
d-orbitals 90 bonds 15
double bonds 14 embedded objects 150
double either bonds 14 generic nickname file 120
dz2-orbitals 90 query indicators 122
fixed angle bonds 13 element
free sites 125 recognized 193
hybrid orbitals 89
element lists 130
mirror images 59
nonlinear sequences 41 element Not-lists 130
p-orbitals 89 elemental analysis
quadruple bonds 14 caption 85
radicals 90 description 85
reaction intermediates 70 embedding objects 150
reactions 67 empirical formulas 192
resonance delocalized rings 22 enantiomers, describing 88
rings with fixed length 21 enlarge
sequences 40 document window 183
sigma orbitals 89 page size 185
single bonds 13 error checking 33
single lobe orbitals 89
s-orbitals 89
error messages 104 197 ,
stereochemical symbols 142
exact mass
structure automatically from name 82 caption 85
triple bonds 14 definition 85
drawing a structure tutorial 45 Excel tables, exporting 104
drawing area 183 expanding labels 60
expanding 60
drawing elements
autoscaling 150
export compatibility 142
color 25 exporting
fill patterns 25 compatibility 144
mapping 142

User Guide
query properties 144 in queries 123
query structures 144 freezing point, calculation 202
using file formats 151 fusing a template 74
exporting reaction mapping 142
G
F G groups 134
FAQs generic groups 134
online, accessing 215 generic nicknames 119 120 ,
technical support 205
,
generic structures, expanding 138 165 ,
file formats
CDX 10
201 , 202
MDL MolFile V3000 153
get ChemDraw/Excel list 104
native 10 getting started tutorial 45
file formats, table 153 Gibbs free energy, definition 91
Fischer projections tutorial 48 Gibbs free energy 112
fixed angle bonds 13 grouping objects 31 69 ,
fixed lengths groups
description 162 integral 31
scaling 32 guidelines 70
flatten command 66 H
flip type 134
hash spacing, description 162
flush left justification 164
H-Dot and H-Dash 194
flush right justification 164
specification 194
font
headers, creating 184
imaging speed 158
new captions 166 heat of formation, definition 92
footers, creating 184 Henry's Law constant 113
formal charge 111 Henry’s Law 201
format Henry’s law, definition 91
atom labels 164 hiding atom numbers 64
text 163 hiding palettes 8
formula command hiding query indicators 122
description 85 high resolution
using 163 non-PostScript printing 161
fractional character widths 166 high resolution printing 171
framing objects 27 highlight box
free energy selecting 28
calculation 202 highlight box tolerance 159
definition 91 home page, CambridgeSoft 216
free sites Hotkeys 159
drawing 125
226 Index
creating 167 isotopes and elements 193
hotkeys.xml file 167 isotopes table file 126
hotkeys .xml file 168 isotopes text file 126
hot-linked properties 81 isotopic abundance 126
how to use this guide 4
hybrid orbitals, drawing 89 J
hydrogens, implicit 123 J. Mol. Mod. 175
hyphens, font submenu 163 J. Mol. Mod. (1 column) 175
I J.Chin. Chem. Soc. 174
Joback’s Fragmentation method 202
I/Draw 157 joining objects 31
implicit hydrogens 123 joining structures 31
imported objects, selecting 28 justification
importing atom labels 164
using file formats 151 captions 164
importing hit lists 104
importing tables 103
K
importing tables to ChemDraw/Excel 103 Kekule structures 22
in Chem & Bio 3D preview 78 L
InChI strings, copy as 147
lab supplies, purchasing online 216
InChIKey strings, copy as 149
label, to edit a 11
include ChemDraw LaserPrep 151
indicators
,
labels 10 60
automatic terminal carbons 162
atom numbering 64
auto-update 81
query, editing 122
contracting 61
query, positioning 122
,
stereochemistry 86 195
expanding 60
Lasso tool
stereochemistry, positioning 87
selecting objects 28
Info window 10
displaying fixed angles 13
launch Chem & Bio 3D 78
insert name as structure 82 layering
atom labels 167
inserting
name as structure 82
Lewis dot symbol, see lone pair symbol 90
integral groups, creating 31 ligand, defined 195
intermediates 70 limitations, name-to-structure 82
internet, CambridgeSoft web site 216 line width 162
ISIS lines, drawing 25
V3000 support 153 link nodes 134
isotopes LogP 201
specifications 193 lone pair symbol 90

User Guide
M molecular weight
caption 85
m/z, displaying 85 definition 85
,
magnification control 183 186 187 , moving
magnifying ,
atoms 16 30
with magnification control 187 crosshair 188
with View menu 186 objects 30
, ,
Main toolbar 8 13 21 multi-attached atom labels command 61
MakeChemNMRUserDB.exe 97 multi-center attachments 63 194 ,
manual mapping 141 multi-center attachments, see also variable
clearing 142 attachments 63
overview 141 multi-center bonds 63
mapping multiple atoms 61
atom 140 multiple atoms, adding a label of 62
automatic 141 multiple attachment points 136
clearing 142
multiple-paged documents, setup 183
exporting 142
manual 141 N
reaction 140
name
margin width
inserting as structure 82
adjusting 162
of structure, inserting 79
description 162
effect on bond crossings 162
name to structure see Name=Struct 82
setting 167 name, automatic structure from 82
specifying 167 Name=Struct 82
margin width, specifying 167 converting 82
Marquee tool 27 28 , limitations 82
mass fragmentation tool 66 67 , naming structures 107
native file format 10
mass/charge, displaying 85
maximize objects 186 new document 176
melting point, definition 91 new drawings 73
messages new lines in captions 158
analysis 197 new slide 176
status 197 Newman projections tutorial 54
mirror images, creating 59 nicknames 18 207 ,
modifying a template 74 defining 75
modifying templates and palettes 74 defining peptides 43
deleting 76
molar refractivity 202
troubleshooting 76
molar refractivity 113 NMR data
molecular mass, definition 85 restoring default 97
228 Index
NMR, see ChemNMR, spectra 95 or labels
nonlinear sequences 41 formatting 166
non-PostScript printing orientation
high resolution 161 benzene ring tool 22
Macintosh 151 cyclopentadiene ring tool 22
non-ringed structures 80 double bonds 16
normal searches 106 orienting templates 74
number of hydrogen-bond acceptors 110 ovality 115
number of hydrogen-bond donors 110 overlap, multipaged documents 184
number of rotatable bonds 116 oxidation state, changing 10
numbering atoms 64 P
O page
objects border 183
3D rotation 25 overlap 184
aligning 188 page definition language
copying 30 quickdraw 161
deleting 30 page setup
distributing 32 saving settings 185
framing 27 paged documents 183
grouping 31 paired brackets 26
joining 31 palette
moving 30 arcs 26
selecting 27 brackets 26
ungrouping 31 color 169
using crosshair with 187 showing 8
using rulers with 187 single bonds 13
objects ungrouping 31 tearing off 8
OLE 150 palettes, creating 74
Online menu parentheses 26
browse SciStore.com 216 pen tools 27
CambridgeSoft home page 216 peptides, defining with nicknames 43
ChemBioOffice SDK 217
periodic table 10
CS Chem3D technical support 215
lookup suppliers on SciStore.com 216
perspective drawings tutorial 51
,
register online 215 217 phytomedicine 177
picture layers
open documents 10
open templates 10 atom labels 167
opening plasmid map 39
ChemDraw/Excel 103 adding markers to 39
resizing regions 40
opening a database 106

User Guide
polar surface area 116 preferences 171
polymer representations 196 printing background color 171
polymers 131 properties
flip type 134 atom in searching 120
repeat pattern 133 atom, abnormal valence 126
source-based 132 , ,
atom, description 120 122 128
structure-based 132 atom, implicit hydrogens 123
p-orbitals, drawing 89 atom, query 120
positioning atom, reaction changes 124
crosshair 187 atom, reaction stereo 125
objects 30 atom, resetting defaults 122
query indicators 122 atom, ring bond count 123
rulers 187 atom, substituents 122
stereochemistry indicators 87 atom, unsaturation 124
bond 127
positioning atom numbers 65
bond query indicators 127
positioning query indicators 122 bond types 128
posters, setup 184 bond, reaction center 129
PostScript bond, removing 128
commands 151 bond, topology 129
printing 161 proton shifts, see 13C, 1H shifts, estimating
preferences 95
drawing, see Drawing settings 161 publishing documents 173
include ChemDraw LaserPrep 151
include PostScript 151 Q
initialize PostScript printer 151 quadruple bonds 14
overview 157
queries
print 171
multiple rings 134
require CTRL+ENTER 158
require Option+Return 158 query indicators
text, see text settings 161 editing 122
use bitmap fonts when available 158 query properties
preferences and settings 157 3D 142
principal moments of inertia (X, Y, Z) 115 exported 144
printing query structures 119
exporting 144
background color 171
ChemDraw laser prep 171 quick reference card, description 5
drawing elements fill 25 QuickDraw
effect of PostScript commands 151 print quality 160
high-resolution non-PostScript 161 quickdraw
overview 184 bitmapped image 161
PostScript atom labels 171
230 Index
R replacing residues 41
repositioning
R groups 134 stereochemistry indicators 87
racemic flag, drawing 142 reset defaults
radicals 193 atom properties 122
drawing 90 bond properties 128
specification 193 residues
radius 116 replacing 41
reaction atom-to-atom mapping 140 resizing
reaction center 129 arcs 26
reaction changes 124 template panes 74
reaction intermediates 70 resizing and rotating 25
reaction interpreter 70 resizing objects 29
reaction mapping resizing structures 108
automatic 141 resizing template panes 74
clearing 142 resonance delocalized rings, drawing 22
exporting 142 resonance structures 22 46,
manual 141 Rest H 140
overview 140 retrosynthesis tool 67
reaction stereo 125 returning to the document window 78
reactions 67 reversing actions 9
red boxes on objects 33
reduce
,
Rf display 94 95
R-group analysis 107
document window 183
object 186
,
ribosome 38 39
page size 185 ribosomes A and B 38
references 196 ring assemblies 80
registration marks 184 ring bond count 123
registration, online 215 ,
ringed structures 80 83
relative flag, drawing 142 rings
relative stereochemistry 88 drawing with fixed length 21
remove rings tutorial 46
colors 170 R-logic queries 139
removing atom properties 121 rotate
removing bond properties 128 chemical symbols 91
command 29
removing colors 170
dialog box 29
repeat command, rotations 29 objects 29
repeat pattern 133 rotating objects 29
repeating actions 9 RS, see stereochemistry indicators 195
repeating atom labels 17

User Guide
RSC 178 selecting multiple objects 28
RSC document 178 selecting objects 27
ruler guides 187 by clicking 28
rulers selection tool
showing 187 deleting 30
running scripts 78 deselecting objects 28 , 29
highlight box 28
S joining 31
sample code, SDK web site 217 sequences
save command drawing 40
default file format 158 nonlinear 41
saving setting
defaults 161 preferences 157
structures in ChemDraw/Excel 106 setting bracket properties 131
saving changes automatically 158 setting font parameters 163
saving color palette settings 171 setting preferences 20 157 ,
saving customized settings 161 setting the baseline style 163
saving customized styles 161 setting up ChemDraw/Excel 103
saving documents 10 settings
saving page setup settings 185 document 160
saving structures 106 settings for new text 166
scaling settings from other documents 161
fixed length 32 shape attribute 116
objects 32 shape coefficient 116
when transferring information 149 sharing information 147
scaling objects 32 shortcut keys 4
Science of Synthesis 179 structure 210
SciStore.com 216 text 210
scrap files 149 shortcuts 207 209,
scripts 78 show
SDK Online, accessing 217 atom numbering 64
searching 106 show crosshair 187
ChemDraw/Excel 106 show document 183 186 ,
export compatibility 144 show rulers command 187
selecting show stereochemistry 86
bonds 28 showing atom numbers 64
entire structure 28 showing palettes 8
with lasso 28 Sigma orbitals, drawing 89
with marquee 28 similarity searches in ChemDraw/Excel
selecting an open document 10 106
232 Index
single bonds, drawing 13 relative 88
single brackets 26 removing markers 87
single lobe orbitals, drawing 89 see also indicators 195
showing 86
site license 7
terms supported 86
SLN strings 148
stereochemistry tutorial 56
copy as 147
stoichiometry grid 92
SMILES strings 105
editing with the context menu 93
copy as 147
setting the limiting compound 92
creating 147
viewing clipboard 148 , ,
Struct=Name 5 79 82
SMILES string 111 Struct=Name, structure types supported 83
SMIRKS, overview 147 structure
checking 32
S-orbitals, drawing 89
chemical warning 33
source-based polymers 132 clean up structure command 62
specifying line spacing 164 converting to name 79
specifying the margin width 167 selecting 28
spectra shortcut keys 210
removing assignments 97 show stereochemistry 86
spectrum-structure assignments structure perspective 65
removing 97 structure perspective tool, using with ob-
viewing 96 jects 25
spiro and sprout rings 21 structure-based polymers 132
squiggly bond tool see tools, wavy bond 13 structures
starting ChemDraw/Excel 103 adding by name 105
stationery pad displaying 108
default 170 style indicators 164
document settings 170 style sheet
page setup settings 185 document settings 160
saving document settings 158 page setup settings 185
Status 5 saving document settings 161
, ,
status bar 5 8 160 style sheets
status messages 197 color palette 171
stereochemical flags 195 style, caption 163
stereochemical indicators 195 styles, default 160
stereochemical symbols, drawing 142 subscript command 163
stereochemistry substituents 122
drawing mirror images 59 sum of valence degrees 116
flags 195 superscript command 163
,
indicators 86 195 supplier, finding online 216
indicators, repositioning 87

User Guide
supported structures 79 83 , TLC spots
suppress chemical warnings 33 45 , crescent 95
SVG 1 custom, about 95
syntax checking 32 custom, adding 94
display or set Rf 94
Synthesis and retrosynthesis 67
enlarged 95
Synthesis, Synlett 180 resizing 95
Synthesis/Synlett document 180 Rf, about 95
system requirements 7 tails 95
T wide 95
tolerance
technical support 205 effect on highlight box 159
templates 73 tool tips 5
BioDraw 1 35, toolbar schema 159
coloring 171
toolbar XML files 160
creating 74
customizing 74
toolbars
deleting 74 customizing 159
new drawings 73 icons, editing 160
orientating 74 tearing off 8
overview 73 tools
resizing panes 74 acyclic chain 22
tutorial 57 alternative group 135
templates and color 171 arc 26
attachment point 135
terminal carbon labels 162
BioDraw 9
text bold bond 13
atom label format 164 bold wedge bond 13
atom labels, automatic justification 165 bond 13
formatting 163 bracket 26
shortcut keys 210 cyclohexane chair 21
text box
closing 158
cyclohexane ring 46 51 , , 70
cyclooctane ring 21
creating new line 158 cyclopentadiene ring 21
text conventions 4 cyclopropane ring 21
text line notation 147 dashed bond 13
text settings dative bond 13
captions, font, size, and style 166 dissociation 67
changing defaults 161 hashed bond 13
text spacing, changing 166 hashed wedge bond 13
theme options 157 hollow wedge bond 13
lasso 28
TLC 93
Marquee 28
234 Index
,
mass fragmentation 66 67 unsaturation 124
reaction atom-to-atom mapping 140 unspecified atom properties, in queries 123
retrosynthesis 67 unsupported structures 79
setting the default tool 158
up to, in queries 123
structure perspective 65
wavy bond 13
upgrading workbooks 104
topological index 115 use defaults
atom properties 122
topological polar surface area 202
bond properties 128
topology 129 bracket properties 131
total connectivity 117 user guide, online 215
total valence connectivity 117 using nicknames 18
trackball tool 65
transferring across platforms 154 V
transferring information V3000, support for 153
across platforms 154 vapor pressure 112
keeping in scale 149 variable attachment points 64
transferring objects 149 Verlag Helvetica Chimica Acta 180
transferring PostScript (Macintosh) 151 view
translation 126 shortcut keys 209
translation (query property) 126 viewing 92
triple bonds, drawing 14 analysis information 85
,
tRNA 3 38 spectrum-structure assignments 96
troubleshooting viewing drawings 186
online 215
troubleshooting nicknames 76
W
Tutorial 1 (Drawing a Structure) 45 warning preferences 33
Tutorial 2 (Using Rings) 46 warnings, chemical 33
Tutorial 3 (Fischer projections) 48 water solubility 114
Tutorial 4 (Perspective Drawings) 51 Web site, CambridgeSoft, accessing 216
Tutorial 5 (Newman Projections) 54 wedged bonds, drawing 15
Tutorial 6 (Stereochemistry) 56 what you can color 169
Tutorial 7 (Templates) 57 What’s New 1
tutorials 45 white space, adjusting in atom labels 167
types of bonds 190 Wiener index 117
Wiley document 181
U Window menu 10
undo, redo, and repeat 9 Windows to Macintosh 155
ungroup command 31 work area 7
ungrouping objects 31 working with color 168

User Guide
working with structures 107 ideal gas thermal capacity 113
X LogP 113
melting/freezing point 111
xml files, editing 160 molecular weight 110
Z number of atoms 110
sum of degrees 116
zooming, see changing perspectives 186
topological diameter 117
exact mass 110
heat of formation 113
236 Index
CambridgeSoft
Solutions
featuring
E-Notebook
D ESKTOP S OFTWARE
E NTERPRISE S OLUTIONS
C HEMICAL & B IOLOGICAL

R ESEARCH I NFORMATICS
L ABORATORY, D EVELOPMENT &

M ANUFACTURING I NFORMATICS
K NOWLEDGE M ANAGEMENT
S CIENTIFIC D ATABASES
CAMBRIDGESOFT
Vision, Passion
Research, Discovery, Development,
CambridgeSoft Software, Solutions and Databases

SOLUTIONS
& Innovation
Trials and Manufacturing
Motivated by Vision
Innovation is an organizational must in pharmaceutical, biotechnology, and chemical industries.
Effective new ideas, developed through collaboration and communication, free from organizational
boundaries, will determine your long-term success. In today’s connected world, information flow
within organization can be overwhelming. Large amounts of data—some structured and some
unstructured—can cloud an R&D organization’s ability to focus on what is important. Since 1986,
CambridgeSoft has been solving the problem of electronic storage and communication of chemical structures, models, and informa-
tion. Starting with ChemDraw, then broadening to ChemOffice in 1992 and BioOffice in 2004, CambridgeSoft extended its software to
include enterprise wide solutions with ChemOffice Enterprise in 1998, E-Notebook in 2000 and biology with BioAssay in 2001. Today,
CambridgeSoft products are used by hundreds of thousands of chemists, biologists, scientists, and engineers who work in pharmaceutical,
biotechnology, and chemical industries, including government and academic research. These systems work within your research, discov-
ery, development, trials and manufacturing, and information technology to help you capitalize on your organization’s intellectual assets. By
turning information into explicit knowledge, you accelerate innovation and drive organizations forward.
Created with Passion

Chemists, biologists, scientists, and engineers need timely, convenient access to critical information,
whether structured or unrefined. CambridgeSoft, which began by helping scientists manage desktop
chemical and biological information with Chem & Bio Draw, now addresses enterprise-wide scientific
information problems with Chem & Bio Office Enterprise and Workgroup. These solutions are flexible
and powerful to deal with today’s complex projects which span functional organizations and geographi-
cal boundaries. Eliminating data barriers and bringing information to all—in the form they need to interpret it—aligns all of the mem-
bers of your teams, focusing their collective knowledge and diverse skills toward the common goals of problem solving and innovation.
The results can be dramatic:
· Information transparency and group collaboration improve productivity and reduce costs.
· Faster and smarter research decisions cut time to market and increase productive efforts.
· Empowered employees contribute increased value to the research, discovery, development, trials and manufacturing organization.
Advanced through Innovation

When your research, discovery, development, trials and manufacturing organization is
able to respond swiftly and effectively to opportunities and market changes, promote innovation and
accelerate product delivery, you are working smarter to outpace your competitors. As the speed of busi-
ness continues to accelerate, leading organizations constantly seek faster and better informed decision
making as well as new business efficiencies. For the individual chemist, biologist, scientist, and engi-
neer who needs to capture, organize, and communicate chemical and biological data, through the complex and widespread workgroup
and enterprise scientific information systems needs, CambridgeSoft Solutions can help.
CAMBRIDGESOFT
Chem & Bio Office Desktop

KNOWLEDGE CHEMICAL,
MANAGEMENT BIOLOGICAL
Desktop
Chemistry Biology BioAssay &

E-Notebook E-Notebook ChemBioViz
Process Workflow BioSAR

E-Notebook LIMS Enterprise
Enterprise
Compliance DocManager
E-Notebook Enterprise
Chem & Bio Office KNOWLEDGE MANAGEMENT

Enterprise
Research organizations thrive when information is easily captured, well organized and readily avail-
E-Notebook Enterprise able. E-Notebook Enterprise streamlines record keeping with rigorous security and efficient archiv-
Chemistry & Biology ing, and facilitates text and structure searching. E-Notebook provides organizations with a powerful
mechanism to transfer mission criticalwork product from shared drives to a well-organized, compli-
Analytical Services ant and searchable Oracle application. MS Office, chemical structures and workflow support
modules are provided for the full range of research and development activities.
Sample Management
Workflow LIMS LABORATORY INFORMATICS

Compliant DB Laboratory Informatics includes Workflow LIMS for instrumentation automation, Compliant DB for stor-
age of your data and the Oracle Cartridge which is the industry’s only enterprise content manage-
Oracle Cartridge ment system developed by a large pharmaceutical company.
BioAssay Enterprise BIOLOGICAL INFORMATICS

BioDraw Finding structural determinants of biological activity requires processing masses of biological
assay data. Scientists use BioAssay Enterprise and BioSAR Enterprise to set up biological models
BioSAR & BioViz and visualize information. The BioViz application allows you to create graphical representations
of data.
Registration Enterprise CHEMICAL INFORMATICS

ChemBioFinder Managing huge data streams is a key challenge. Registration Enterprise organizes information
Enterprise about new compounds according to an organization's business rules.
SOLUTIONS
to Enterprise Solutions
LABORATORY & SCIENTIFIC
MANUFACTURING DATABASES
Inventory ChemACX The Merck

Enterprise Database Index
Registration GxP Sigma-Aldrich

Enterprise Validation MSDS
Compliant ChemBioFinder
Oracle Cartridge
or SQL DB SDMS Gateway
MANUFACTURING INFORMATICS
Inventory Enterprise CambridgeSoft’s Inventory Enterprise application is designed to manage the
chemical, reagent, sample and compound tracking needs of large multi-site
Materials Management
chemical and pharmaceutical laboratories. Inventory Enterprise is an Oracle-based,
Compliance Management ChemOffice Enterprise product that is designed for multiple users with diverse
container types, racks, and multi-well plate formats.
ChemDraw & Chem3D DESKTOP SOFTWARE

ChemFinder & ChemInfo Success begins at the desktop, where scientists use ChemOffice, ChemDraw, BioOffice and
BioDraw to pursue ideas and communicate with the natural language of chemical structures,
BioDraw, BioAssay & biological pathways, and models. Scientists organize information and manage data with E-
BioViz Notebook and Inventory. ChemBio3D provides modeling, ChemBioFinder aids searching, while
BioOffice adds BioDraw, BioAssay and BioViz. All are integrated with Microsoft Office to speed
Inventory & E-Notebook research tasks.
ChemBioFinder Gateway SCIENTIFIC DATABASES

Good research depends on reference information, starting with the structure-searchable
The Merck Index
ChemACX Database of commercially available chemicals and Sigma-Aldrich MSDS. The Merck
ChemACX Database Index and other scientific databases provide necessary background about chemicals, their prop-
erties, and reactions.
Development PROFESSIONAL SERVICES

Training & Support CambridgeSoft's scientific staff has the industry experience and the chemical and biological
knowledge to maximize the effectiveness of your information systems.
ENTERPRISE &
Chem & Bio Office Enterprise

Integrated Research, Discovery, Development,
Desktop to Enterprise Development and Testing
Since the company's founding, CambridgeSoft's desktop soft- Building on productivity software, CambridgeSoft created enter-
ware, starting with its industry-leading Chem & Bio Draw, has prise applications to meet the needs of an everexpanding research
been the cornerstone application for scientists who draw and and development community that relies on data sharing across sci-
annotate molecules, reactions, and pathways. This suite of enter- entific disciplines, research campuses, and even oceans as global-
prise applications has developed and now provides solutions in all ization has increased demands. Since the software takes advantage
areas of discovery. of the latest web based technologies, it is deployed readily
throughout a research and development organization. Using the
Research and Discovery integrated suite, scientific teams are well armed to solve the daily
challenges of development. These teams include scientists who
Researchers can record and share their experimental
scale up and design manufacturing procedures,toxicologists who
information using E-Notebook, while protecting intellectual prop-
determine the metabolic fate of drugcandidates, formulation sci-
erty with digital signatures and 21 CFR Part 11 compliance. They
entists who determine drugdosing and delivery systems, as well as
can design both single experiments or design combinatorial
many others.
libraries of compounds. They can find and purchase reagents in
ChemACX database, store and use them from Inventory, record
Trials
newly made compounds within a proprietary Registration system,
record the results in BioAssay, analyze the results with BioViz, and A suitable drug candidate is one that has the desired activity to
generate reports linking activity and structure with BioSAR. provide disease therapy while meeting drug safety requirements,
can be manufactured in a cost effective and reproducible fashion
Virtually every aspect of discovery, from synthesis planning, under 21 CFR Part 11 and Good Manufacturing Processes
library enumeration, reagent selection, primary and secondary (GMP) guidelines, and is stable under normal formulation and
screening, in vivo testing, through to analysis of results and report- storage conditions. With a drug candidate in hand, the final chal-
ing is covered by this integrated application suite. lenge is to determine safety and efficacy in a patient population.
All specifications subject to change without notice.
US 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390 EMAIL info@cambridgesoft.com
EU 00 800 875 20000 UK +44 1223 464900 JP 0120 146 700 WWW www.cambridgesoft.com
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, BioOffice, BioDraw & ChemBioFinder are trademarks of CambridgeSoft Corporation ©2009
WORKGROUP
and Workgroup Solutions

Trials and Manufacturing Workflow
Manufacturing management and informatics solution, covering electronic note-
books, biological screening and chemical registration over your
Manufacturing requires the transfer of data and batch process
intranet. ChemBioOffice Enterprise Ultra includes E-Notebook for
records from the pilot plant studies using Inventory, E-Notebook,
record keeping, BioAssay for low and high throughput screening
and Registration systems under Good Laboratory and
with integrated plate inventory, BioSAR for SAR reports,
Manufacturing Processes (GxP).
Registration System, Inventory for reagents and biologicals, and
ChemACX database of available chemicals. Technologies include
The handling of materials, including chain of custody require-
ChemDraw ActiveX and Oracle Cartridge.
ments, material documentation, material workflow, such as avail-
ability states and recertification dates, are tracked and handled by
the system.
Chem & Bio Office Workgroup
Chem & Bio Office Workgroup Ultra is a comprehensive knowl-
These systems meet the requirements and provide the basis to edge management and informatics solution, covering electronic
manage materials and records during clinical trials. Clinicians can notebooks, biological screening and more over your intranet.
design and record results from protocols, and all of these web
based software systems provide the access required by clinicians Chem & Bio Office Workgroup Ultra includes E-Notebook
who are removed from the sponsoring company. for record keeping, BioAssay for low and high-throughput screen-
ing, BioViz for visualization, Inventory for reagents and ChemACX
Chem & Bio Office Enterprise database of available chemicals. Technologies also include SQL
Chem & Bio Office Enterprise is a comprehensive knowledge- Server for affordability and ease of administration.
KNOWLEDGE
Overview &
E-Notebook’s Flexible Architecture
E-Notebook E-Notebook Architecture

Used for collaboration and knowledge sharing, regulatory compli- E-Notebook Enterprise edition is a globally-deployable, Oracle-
ance, intellectual property protection, LIMS,document manage- based application designed for everyone from small research
ment, project management, and workflow support, E-Notebook is groups to global organizations. Oracle Cartridge manages chemical
the leader in a new class ofapplications. Configurable, multi-pur- structures and reactions in a common data repository, layered with
detailed security and is 21CFR Part 11 Compliant (audit trails,
pose, and enterprise-scalable, it provides a solution to a large set of
digital signatures). The enterprise edition works with procurement
requirements across R&D and manufacturing. E-Notebook's foun- databases and services including ChemACX database and Inventory
dation layer of features includes support for 21 CFR Part 11, 37 management systems to save time locating chemicals and entering
CFR and GxP compliance, on top of which a widely configurable structures.
design interface provides support for specific scientific and regula-
tory workflows. Because this diverse portfolio of requirements is Flexible and Configurable Architecture
met in a single applicationplatform, E-Notebook both lowers the The E-Notebook architecture is designed to provide organizations
total investment required to meet these needs, and provides a sub- with an unparalleled level of flexibility. A powerful configuration
stantial increase in productivity due to a far more integratedenvi- layer is provided to make it possible to modify substantially the
ronment for scientists and technical staff. look and feel of the application in order to meet very diverse work-
flows. Detailed workflow support in the same application is pro-
E-Notebook Architecture vided for researchers in early stage discovery through early clinical
development even though the requirements for these groups are
CambridgeSoft’s E-Notebook provides a comprehensive, easy-to- totallydifferent. Beyond configuration, a rich API is provided for
use interface designed to replace paper laboratorynotebooks in a custom development and system integration.
variety of settings. Underneath is a fullyconfigurable, secure sys-
tem for organizing the flow ofinformation generated by your E-Notebook is also in production with integrated inventory sys-
organization. Scientists can enter chemical reactions, Microsoft tems including CambridgeSoft’s Inventory manager, as well as
documents (Word, Excel, PowerPoint), spectra, biological data in-house systems, analytical data capturing systems, and com-
and images, and other types of information and documents. It also pound registration systems. E-Notebook supports limiting access to
allows you to search by text, chemical substructure, metadata tags, certain information at the project or group level if desired, as secu-
organizational hierarchy, or other keys. rity is granular. Information can be shared or secured as desired
throughout the framework.
MANAGEMENT
General R&D
IP Protection and Regulatory Compliance
General R&D
• Replace Shared Drives with Oracle
CambridgeSoft’s E-Notebook is a solution that enables
pharmaceutical and biotechnology companies to improve the
efficiency of the process from diseased target identification to prod- • DMPK, Screening Biology, Genetics, and Microscopy
uct launch. Its core Oracle database manages the workflow to be
compliant with Good Laboratory Practices (GLP), Good
• LIMS, Method Execution, 21 CFR Part 11, GxP
Manufacturing Processes (GMP), and the FDA’s 21 CFR Part
11; while the client interface is highly configurable and flexible.
Anywhere a shared drive is used, E-Notebook can offer a better
Development and Testing
solution.
CambridgeSoft’s Enterprise E-Notebook meets the needs of ever
Through the R&D process, using CambridgeSoft’s E-Notebook in expanding research and development communities that rely on
each subsequent stage adds increasing scientific and economic data sharing across scientific disciplines and campuses as globaliza-
value by providing workflow automation and knowledge sharing. tion has increased demands.
Research and Discovery E-Notebook allows custom integration of a large array of modules,
in-house applications, lab instruments, and back-end data storage
E-Notebook Enterprise is capable of providing knowledge manage-
to provide a true end-to-end solution for development and testing.
ment, chemical- and biological-focused solutions in virtually all
Designing workflows and calculations is much faster and requires
areas of discovery. Researchers can record and share their experi-
far less programming using the E-Notebook than existing lab infor-
mental information, while protecting intellectual property with
mation systems. End users include scientists and process chemists
digital signatures and 21CFR Part 11 and 37 CFR compliance.
who scale up and design manufacturing procedures, toxicologists
who determine the metabolic fate of drug candidates,
• Chem & Bio Draw—draw and annotate molecules,
formulation scientists who determine drug dosing and
reactions, and biological pathways
delivery systems, as well as many others.
• ChemACX—find and purchase reagents
• Inventory—store and track reagents and samples
• Registration—record newly made compounds
• BioAssay—model complex protocols and record results A suitable drug candidate has the desired activity to provide dis-
from biological testing ease therapy while still meeting safety requirements, can be man-
• BioSAR—generate reports linking activity with structure ufactured in a cost effective fashion under 21 CFR Part 11 and
• BioViz—analyze biological results GMP guidelines, and is stable under normal
formulation and storage conditions. The handling of
Virtually every aspect of discovery process—from synthesis materials, including chain of custody requirements, material
planning, library enumeration, reagent selection, primary and documentation, material workflow, such as availability states and
secondary screening, in vivo testing, through to analysis of results recertification dates, are tracked and handled by the
and the reporting of data—is covered by the integrated E-Notebook application. CambrideSoft’s E-Notebook meets these
E-Notebook solution. requirements under Good Laboratory and Manufacturing
Processes (GxP) and provides the basis to manage materials and
records during clinical trials.
KNOWLEDGE
Chemistry &
Electronic Journal and Record Keeping,
Chemistry
• Chemical Synthesis, Scale-up and Analytical
Under the R&D value chain, chemistry can be further
divided into three separate stages: synthetic chemistry
(research/discovery), analytical chemistry (pre-clinical) and • 37 CFR Electronic Signatures
process chemistry (development). The flexibility and configura-
bility of E-Notebook enables a successful data repository, analysis, • Service Requests and Discovery Workflow
sharing, reporting, and searching efficiently and paper-free.
Process Chemistry
Synthetic Chemistry
The objective of process research is to identify efficient processes
Synthetic Chemists take advantage of many features tied into a
for the synthesis of active pharmaceutical agents at the scale
smooth interface within CambridgeSoft’s Enterprise E-Notebook. required for clinical trials and commercial use. It is necessary to
Reactions are drawn with in-place editing; a stoichiometry grid provide precise descriptions of these processes so that they can be
dynamically fills with the formulas, molecular weights, and chem- executed by different groups in different locations. It is also
ical names. Reagents can also be imported from other systems, required that such processes be compliant with Good Laboratory
such as available chemicals from the ChemACX database or Practices (GLP), Good Manufacturing Processes (GMP) and the
Registration system. FDA's 21 CFR Part 11 regulation. E-Notebook's process chemistry
modules are designed to support these dual workflow and
CombiChem is one important aspect of library generation for regulatory compliance needs of process chemists.
Synthetic Chemists. For some, E-Notebook serves as the complete Reaction Properties
CombiChem solution, taking advantage of features such as the
enumeration of products from a virtual library on a flexible plate
layout, a multiple reaction site checker, and multiple step parallel
synthesis. Others simply import a list of compounds from an
external source or SDFile so that they can record and calculate
data on a library-wide stoichiometric table.
Analytical Chemistry
E-Notebook serves as a repository for analytical data, and it also
acts as a communication portal with which scientists and analysts
communicate with each other. Scientists can create and send
service requests directly to an analyst with the click of a button.
Paper is eliminated: when results are obtained, the analyst can
send the images and chromatograms directly back to the scientist's
E-Notebook.
PowerPoint Integration
MANAGEMENT
Biology
DMPK, Screening Biology, Microscopy
Discovery Biology
These scientists are involved at the very start of the drug
discovery process, as genomics and genetics are essential
disciplines used when identifying a disease target. This work is • DMPK, Screening Biology, Genetics, and Microscopy
methodical but unscripted, and so requires an electronic note-
book pallet that is as free form as its paper predecessor. This is
• LIMS, Method Execution, 21 CFR Part 11, and GxP
where the benefit of E-Notebook's flexibility is unmistakable.
While the system can be set up with rigid form based data entry
appropriate for later stage research and development, discovery Assay & Screening Biology
biology configurations are typically open and boundless. Genomic One of E-Notebook's strengths is its ability to integrate with exist-
map and DNA, RNA and protein sequence files can be dragged- ing electronic methods of data capture, including using it with
and-dropped into E-Notebook, sequencing results can be sent CambridgeSoft’s BioAssay module to provide full screening exper-
directly from instruments to electronic experiments, and protocols imental support. In addition to this, Microsoft Word and Excel
and data can be managed with familiar tools such as Microsoft are also embedded directly in E-Notebook, as is image and movie
Word and Excel. capture. Scientists benefit from the functionality of these tools
implanted in a rich, searchable environment. Biological experi-
The beauty of capturing data in E-Notebook is that ments can be managed and organized in a way that is not possi-
information can be compiled and viewed in a meaningful way. For ble with a traditional file system.
example, the creation of a new biological strain entails many steps,
potentially involving nonconsecutive workdays of various individ- In vivo Experiments/Animal Management
uals. E-Notebook can generate customized reports that meaning- In vivo experiments are important aspects of target discovery and
fully summarize the process in real time. These reports are validation, and are critical paths to determine the
navigable—clicking on each step will bring you to the efficacy of selective therapeutic candidates. CambridgeSoft’s E-
corresponding experiment. Notebook becomes the centralized location to collect, store and
Database Structure interpret in vivo experiment results. Again, when used with
BioAssay, the full end-to-end experimental workflow is supported,
from creation, to data analysis and quality control, to summary
and reporting. In conjunction with in vivo experiments, animal
housing and breeding can also be tracked. Traditionally, the work-
flow consists of paper-based record keeping across the animal
facility, lab bench, and researchers desktop. With E-Notebook,
paper tracking and recording is eliminated. Instead, form tools can
be designed to:
• Track animal status

• Track animal pedigree
• Record Genotype
• Create mating records
• Create litter records
KNOWLEDGE
Analytical Services &

Electronic Journal and Record Keeping
Formulation and Validation

• Service Request Workflow
E-Notebook's formulation module is designed to support the dual
workflows and regulatory compliance needs of formulation engi-
neers. The flexibility allows any number of formulations to be • Sample Management
created, and security allows only designated administrators to
create a new formulation.
• Method Execution Framework
Analytical & Quality Control
Analytical and Quality Control Laboratories must execute defined
procedures to test material that may be administered during pre- Pharmacokinetics (DMPK)
clinical and clinical trials. This work must also be compliant with
There is a holistic approach to Drug Metabolism and
both GxP and 21 CFR Part 11. Templates for standard analytical
Pharmacokinetics. No single study describes the behavior of a
tests are provided and analytical procedures are implemented as
compound; it is the combination of data from disparate experi-
E-Notebook forms, which are easily designed and controlled.
ments that represents the pharmacological profile for a com-
Equally important, E-Notebook provides workflow enforcement
pound. It is here where E-Notebook reveals one of its most signifi-
that monitors data entry and ensures that the forms are complet-
cant capabilities: the reporting feature. E-Notebook reports are
ed in sequence for proper method execution.
flexible: any field (e.g. compound ID, study type, etc.) can be used
to query the system and any field (e.g. conclusion, dose, etc.) or
For example, rules can be configured such that the 'Day 3' form
field aggregate (e.g. average radioactivity) can be displayed in the
of a multi-day process will not accept any entries unless all
report. Reports are dynamic and navigable: results are displayed
required fields on the 'Day 2' form are first completed. The forms
with links that provide quick access to experiments.
can contain automatic calculations to compute totals, averages,
differences, and much more. E-Notebook can further streamline
Reports are viewed directly in the E-Notebook interface, but they
the procedure by allowing for electronic management of solutions,
can also be exported to Microsoft Word or PDF to share with
equipment, and other resources that are needed for experiments.
those who do not have E-Notebook access.
Drug Metabolism Inventory Enterprise
E-Notebook supports the DMPK laboratories in testing the metab-

olism and longevity of compounds in various in vitro and in vivo
models. DMPK data capture needs can vary significantly, and the
flexibility of the E-Notebook solution addresses this. For example,
an in vivo enzyme induction test may create relatively small
amounts of data for which scientists utilize E-Notebook integra-
tion with Microsoft Excel. Conversely, large quantities of data,
such as those generated by in vitro enzyme inhibition studies, are
often collected and analyzed by applications such as BioAssay.
Therefore, integration with BioAssay and Excel are fundamental to
DMPK E-Notebook usage.
MANAGEMENT
Sample Management
Compliance Execution and Sample Tracking
Drug Safety / Toxicology

• Track & Barcode Samples
Paper notebooks have traditionally been considered to be the
record source for the entirety of an experiment, but they often
miss non-experimental information generated shortly after con- • Create Any Report from Database
ception. For example, toxicology studies are often initiated not
by the scientist who ultimately runs the experiment, but instead • Full Audit Trail
by a manager or coordinator who assigns the study to the scien-
tist. Important material related to this first step in the process,
such as ideas, emails, and other communications are often left out Sample Login
of traditional paper notebooks. The E-Notebook toxicology work-
E-Notebook is able to easily configure sample logins (registration of
flow addresses this concern: studies are first created by a manager,
sample, assignment of barcode label, and initiation of sample
and subsequently assigned to the scientist for execution.
tracking) by incorporating CambridgeSoft’s Inventory application.
Through E-Notebook, forms can be created to keep track of newly
Compliance Execution
synthesized or acquired compounds, tracking their physical prop-
E-Notebook is also useful for capturing the Standard Operating erties and tests, and assigning unique identifiers. New compounds
Procedure (SOP) corresponding to the experiment. These docu- are entered directly via the E-Notebook form, and chemical, along
ments are often stored separately from the actual data, leading to with non-chemical, data is kept alongside the sample. When a
error and confusion, thus causing risk to the validity of the data. proprietary compound is registered, if desired, it is compared for
Storing and displaying procedures and other related documents in uniqueness via a configurable, stereoselective duplicate check and
concert with the data eliminates this risk and helps build perspec- assigned a registry number.
tive on the study.
Sample Tracking
Sample Lifecycle Management
Tracking samples, requesting analysis and establishing chain of
E-Notebook can manage the entire sample lifecycle through tight custody can all be simply managed within the E-Notebook inter-
integration with Inventory. Sample lifecycle management is essen- face. E-Notebook serves as a repository for analytical data and
tial for the registration, testing, evaluation, and reporting in vari- experiments, linking such data directly to the sample ID, and it
ous analytical and manufacturing stages. Manual tracking of sam- acts as a communication portal with which scientists and analysts
ples and test results is labor-intensive and time-consuming; and communicate with each other during the service request lifecycle.
compliance with GxP guidelines requires expensive manual Scientists create and send service requests directly to an analyst
audits. with the click of a button. Paper is eliminated: when results are
obtained, the analyst can send the images and chromatograms
The controlled flexibility of CambridgeSoft’s E-Notebook is well directly back to the scientist's E-Notebook (which appear in the
suited for these detail and compliance-oriented environments. person's E-Notebook inbox, and are then accepted into the experi-
E-Notebook’s Sample Lifecycle Management module is compliant ment if desired). To establish chain of custody, each step of sam-
with Good Laboratory Practices (GLP), Good Manufacturing ple ownership is tracked, recorded and made compliant with
Processes (GMP) and 21 CFR Part 11. FDA's 21 CFR Part 11.
L A B O R AT O RY
Workflow LIMS,
Visual LIMS, Lab Automation,
Workflow LIMS Automation • Service Request Workflow allows scientists to

CambridgeSoft’s Workflow LIMS is a scientific data and communicate as they work
workflow management tool for lab automation and in silico
experimentation. Workflow LIMS eliminates the need for custom • Direct Communication from E-Notebook to create
programming by providing a visual experiment design and work-
tasks and send results
flow layout with built-in laboratory automation and analytics.
By using Workflow LIMS, researchers can connect their • Method Execution Framework to enable standard
laboratory processes, instruments, and decision points in a operation procedures and compliance
conceptual manner that directly couples to instrumentation— for
both automation and data gathering—and provide
Applied Technologies and Benefits
real-time results. The Workflow LIMS solution enables a
scientific team to design procedures, execute those procedures, Workflow management enables discovery teams to rapidly trial
capture the results and integrate lab equipment to automate part new procedures, capture best practices and scale successful designs
or all of the process. Procedures typically revolve around lab activ- from a manual prototype right up to a fully automated high-
ities, but may also draw in decision support tools on a scientist's throughput lab. But discovery and research, by its very nature,
desktop, and queries/updates to databases. demands that processes be flexible and that workflow execution
rapidly adapt to new techniques and equipment.
Interactivity and Integrity
1. The modeling environment, Workshop Configuration Editor, Conventional laboratory information workflow applications can-
in which the scientific team models the capabilities of the lab - for not meet this requirement because of their heavyweight configu-
example, the kind of basic processes which are available in the lab, ration needs, their lack of adaptability and the cost and complex-
and their inputs and outputs. ity of integrating them with rapidly changing lab technology.
2. The design environment, Workbench, in which researchers Workflow LIMS addresses these problems by providing a visual,
create workflows from these basic processes. easy-to-use environment for describing processes and building
3. The runtime Operations Manager, which manages the assign- workflows out of those processes, enabling scientists to rapidly
ment of tasks to agents, tracks the progress of tasks and workflows, trial new procedures, and by offering a rapid development tool kit
and manages the storage of captured data. for equipment integration which supports gradual automation to
4. The agent tier, made up of a number of applications that han- minimize up-front costs and ongoing risk.
dle specific types of task, either manually (through a user inter-
face), or automatically (by driving equipment through a control CambridgeSoft’s Workflow LIMS simplifies even manual lab pro-
interface or performing automated data processing). cedures by managing the breakdown of a procedure into tasks, and
5. The monitoring tier consists of a reporting tool that by automating the majority of data capture and transfer tasks; but
provides historical utilization information, and a live activity by capturing process as well as data, Pathways reduces the costs
viewer that allows scientists to drill into individual workflows and risks of implementing discovery techniques, and enables
and samples. companies to accelerate the entire discovery process.
I N F O R M AT I C S
Compliant DB & Oracle Cartridge

Compliant Storage and Chemical Data Management
Compliant DB
• Develop Centralized Validated Storage and
CambridgeSoft’s Compliant DB is the industry's enterprise GxP Compliant Storage
content management system developed by a large pharmaceutical
company. It serves as an electronic library that collects, organizes,
• Store Documents, Machine Files & Chemical Objects
warehouses, indexes and safely archives all your structured and
unstructured electronic records. From raw data and laboratory
reports to compliance records, Compliant DB also will support any • Oracle Cartridge is compatible with Linux, Solaris,
of CambridgeSoft’s workflow solutions, including E-Notebook, AIX and Windows and includes structure searching,
BioAssay, and Inventory. As its name implies, Compliant DB is fully property predictions and nomenclature
compliant with the requirements of 21 CFR Part 11 for
electronic records and electronic signatures.
Oracle Cartridge
Compliant DB can be used directly over your company's intranet, The CambridgeSoft Oracle Cartridge is used by all ChemOffice
extranet, or over the Internet with a simple web browser. Enterprise applications for storing, searching, and analyzing chem-
Complaint DB gives your organization a secure, 21 CFR Part 11 ical data. It can also be used in the development of your custom
compliant centralized electronic library for all electronic data files. Oracle applications. Chemical structure and reaction data is diffi-
Not only can machine-readable instrument data files be stored,
cult to manipulate without utilizing special software, and Oracle
but also images, multimedia files, presentations, human-readable
data cartridges define new, recognized data types. CambridgeSoft’s
word processing and Adobe PDF documents, spreadsheets and
hundreds of other formats. This data can serve as source data Oracle Cartridge utilizes this technology, making it possible to
(instrument data to BioAssay), and also repository. Although manipulate chemical structure and reaction data from within
Compliant DB can operate as a stand-alone application, only Oracle, improving portability and consistency in applications.
CambridgeSoft provides fully-integrated Knowledge Management Since the Oracle Cartridge is accessed through native Oracle SQL,
and Enterprise Informatics applications integrated with compliant programmers can interact with chemical structure data directly in
storage. Compliant DB makes this possible. the database.
Workbench Sample
The CambridgeSoft Oracle Cartridge supports CDX, CDXML,
MolFile, MolFile v.3000, RXN and SMILES formats, making it
flexible enough to be included with both new and legacy data
applications, without the need for file conversion. Chemical infor-
mation can originate from either ChemDraw or ISIS Draw, E-
Notebook, Inventory, or Registration. Oracle Cartridge has extensive
support for stereochemistry, relative stereochemistry, tautomers
and structure normalization. There is also a built-in structure enu-
merator (for nonspecific structures), basic property predictors,
nomenclature algorithms (name=struct), and dynamic utilities for
molecular file format conversions.
BIOLOGICAL
BioAssay, BioViz,
Assay Screening and Visualization
BioAssay
• Effectively manage data from complex biological
For modeling complicated in vivo experiments, or
assays involved with lead optimization
supporting an ultra-HTS platform, BioAssay has become the lead-
ing choice for managing biological experimental data. It is the
• Scalable HTS & HTTS
only application of its kind to provide a best-of-breed solution for
both ultra-high volume laboratories and lower-throughput set-
tings. BioAssay includes support for laboratory automation, calcu- • Use BioDraw to document cellular pathways
lation, and statistics, and also complicated low and medium
throughput assays such as animal models and in vivo experiments.
BioDraw
BioAssay is designed to tackle the needs of high and low through-
Diagramming and presenting cellular pathways is made easier and
put screening biologists alike by providing an application flexible
more effective with BioDraw. Formerly called Pathworks,
enough to model any assay, regardless of complexity, through an
BioDraw does for biologists what ChemDraw has done for
easy-to-use interface for importing, storing and analyzing the data.
chemists—saving time and producing a more professional
The software supports the quick set-up of biological models, auto-
representation of the science.
mated calculations and curve fitting, data validation, and the cre-
ation of customized structure activity reports.
BioDraw makes drawing and annotating biological pathways
quick and easy, adding a level of uniformity and detail which is
BioAssay Extends E-Notebook
unmatched. Common pathway elements such as membranes,
BioAssay Enterprise is a scalable, flexible biological screening solu- enzymes, receptors, DNA and reaction arrows are built into the
tion utilizing Oracle’s role based security and the Oracle Cartridge. BioDraw toolbar. BioDraw also allows the import of images in
When used as part of ChemOffice Enterprise, BioAssay is integrat- GIF, PNG or JPEG formats. BioDraw offers many ways to share
ed with E-Notebook for experimental data, Inventory Enterprise for your drawings and accompanying data. Users can export data to
plate tracking and management, Registration Enterprise for the reg- Microsoft Office applications for inclusion in presentations and
istration of new compounds and BioSAR Enterprise for customized grant proposals or save data as an image file for use in journal
reporting. article submission.
BioAssay Ultra is designed to deliver much of the functionality of our

enterprise level applications, without a widespread roll-out.
BioAssay Ultra, coupled with BioViz, offers a user friendly inter- Draw Biological
Pathways
face for importing, viewing, validating, and plotting your biolog-
ical assay data from your desktop.
• BioAssay effectively manages data from complex biological assays

involved with lead optimization.
• BioViz integrates with BioSAR for one step in-depth data Plot Assay Data
analysis from a BioSAR report.
BioSAR & BioDraw

Data Mining and Pathway Drawing
BioSAR
• BioSAR is a catalog driven mining and structure-
BioSAR Enterprise, a strategic must for any discovery
activity analysis program
organization interested in serious data mining, is a data dictionary
driven structure-activity analysis program. Users may choose
among assays registered in the dictionary or search for assays • BioSAR provides both form and table views within
of interest. a simple and powerful web interface
The power of BioSAR lies in the researcher’s freedom from • BioViz provides one-step in-depth analysis of
dependence on IT support for dynamically working with all avail- several variables
able scientific data. For example, once an assay is registered into
the data-dictionary, it is automatically included in the powerful
analysis framework. By reducing the time between question and
answer, BioSAR gives researchers the ability to explore new ideas
• BioSAR is a catalog driven data-mining and structure
and avoids this issue by placing SAR report creation in the
activity analysis program.
researcher’s control.
• BioSAR provides both form and table views within a
simple and powerful web interface.
BioSAR Enterprise allows the researcher to create custom reports
• BioDraw makes it easy to draw and annotate
and views of their data. You decide what is displayed, and BioSAR
biological pathways including common elements such as mem-
takes care of the rest.
branes, enzymes, receptors and DNA.
While most SAR tools provide only a table-based interface,
BioViz
BioSAR provides both a form view and table view, and connects to
BioViz for high-dimensional analysis. BioSAR merges the sophisti- BioViz with ChemFinder transforms the numbers in your database
cation of a powerful data catalog technique with knowledge into graphics on your screen. Retrieve or search for a set of com-
gained through years of working closely with scientist users. The pounds, choose the data you want to see, whether it is biological
result is a SAR application that is as intuitive as it is powerful. test results in Oracle tables, physical property values calculated
Security within BioSAR Enterprise is highly granular; different automatically or prices in a catalog, and BioViz will generate an
roles exist for administrators, publishers, and browsers. interactive window showing a scatterplot, histogram, or other
useful data graphic.
Administrators may add assays to the data catalog engine, publish-
ers may create reports and publish them, and browsers may use The Plot Window, the key to data visualization in BioViz, is able
data query and analysis. Most data mining tools provide a mech- to show two variables plotted against each other in a scatterplot
anism to store queries, but the interface for creating queries is too with each point representing a structure from the current hit list.
complex. With BioSAR, each set of assays is a complete report If you, for example, modify the list by performing a search, the
with a query form, a view form, and a table view, combining the plot updates to show the new set of points. You can drag a rectan-
convenience of a ChemFinder or ISIS application with the power gle around a set of points to select them or zoom in to see
and flexibility of a data catalog-driven mining program. them more closely.
CHEMICAL
Inventory, Registration,
Chemical and Biological Inventory, Freezer Management,
Chemicals and Biologicals

• Register and Track Chemicals & Biologicals
Inventory is an application designed to manage the chemical and throughout the enterprise
biological reagent tracking needs of laboratories and research cen-
ters in multiple contexts: lab reagents, freezers/racks, plate man-
• Freezer/Rack/Plate Handling--Targeting, Workflow
agement, proprietary compounds and stockroom are just some of
and HTS Support
the areas where Inventory has been deployed.
• Supports Barcoding, Report Generation & Audit Trails
The system manages data associated with both commercially pro-
cured and internally produced chemical substances from procure-
ment or initial production through depletion and disposal.
Inventory Enterprise is an Oracle-based ChemOffice Enterprise
Registration Enterprise
product and can be used with other modules, such as E-Notebook,
to track batch records in manufacturing, or to look up reagents Registration Enterprise is built around robust data model for pure
from stockroom when planning a synthesis, BioAssay when sup- compounds, batches, salt management, automatic duplicate
porting a high throughput screening environment, Registration for checking and unique ID assignments. Built on the Oracle
tracking proprietary compounds, DocManager for linking certifi- Cartridge, it handles stereochemistry (including advances in rela-
cates of analyzes, analytical reports, or other documents associat- tive stereochemistry), tautomerization and structure normaliza-
ed with samples, and ChemACX available chemicals database for tion for duplicate checking. Using ChemScript, it also can enforce
sourcing new compounds. drawing business rules, such as orientation around a scaffold and
functional group normalization. Compounds may be entered
Inventory Enterprise includes plate handling and interfaces to
individually through a user-friendly web form, through the use of
liquid handlers for HTS environments, freezer/rack layout and
targeting for managing biologicals, full chain of custody, audit a batch loader, from Inventory, or directly from E-Notebook.
trails for GxP compliance, request/disbursement workflow for use
in both manufacturing and pre-clinical settings, and features As compounds are registered, regardless of whether through the
tailored to specific material domains. web user interface, E-Notebook, or from a batch file, they are com-
pared for uniqueness via a configurable, stereoselective duplicate
• Reagent handling and stockroom reporting check, and assigned a registry number. All information about the
• Request/disbursement workflow for stockroom and compound, including its test data and other syntheses, is tracked
GxP environments by the registry number, and this is used to link data throughout
• EH&S module, and links for MSDS data sheets ChemOffice Enterprise. Registration Enterprise is the only true
• Freezer/rack layout for biological materials n-tiered application of its kind that is designed around thin clients
• Extensive plate handling for HTS and uHTS settings
and thin servers, with interfaces directly to Inventory, batch file
Inventory is also available in two other editions: Workgroup and registration and E-Notebook. Oracle is supported on a variety of
Desktop. Inventory Workgroup is a rich-client SQL Server-based platforms and operating systems. Using Oracle secures your pro-
product geared at managing stockrooms and reagents. Inventory prietary data through the use of Oracle’s role-based security and
Ultra is a desktop edition based on the Workgroup product, and allows all chemical and non-chemical data to be stored directly in
includes the ChemACX database. the Oracle tables.
DocManager & ChemFinder

GxP, Registration and Enterprise Infrastructure
Formulations & Mixtures

• DocManager parses Word, Excel and PowerPoint
Formulation scientists face different challenges from those work-
documents, including free text and structures
ing with individual molecules, yet many of the tools they are
forced to use emerge from the drug discovery world, where single-
• ChemFinder is tightly integrated with BioSAR, BioViz
molecule research is the norm. Take an essential task such as com-
and Oracle
pound registration and you will find that most systems are
designed for registration of single molecules, with little thought
for the world of formulations and mixtures. CambridgeSoft has • Support for advanced form layout and design
developed a system specifically designed for this registration need

called Formulations & Mixtures. DocManager Enterprise
ChemFinder Enterprise • DocManager parses Microsoft Word, Excel and PowerPoint

documents, including free text and structures.
ChemFinder Enterprise is a multiple-user system designed for sites • DocManager has a web based interface and a file drop
with comprehensive chemical and biological data needs. folder for quick submissions.
ChemFinder Enterprise contains its own engine for working with • Oracle Cartridge is compatible with Linux, Solaris, AIX
local and shared databases, and it is also delivered with the and Windows and includes structure searching, property
CambridgeSoft Oracle Cartridge, the powerful Oracle-hosted predictions and nomenclature.
structure engine based on ChemFinder search technology. The face
of ChemFinder Enterprise is the same friendly form-oriented inter- Web browser based, DocManager Enterprise extends the capability
face as the desktop version, but underneath is a fast direct connec- of standard search engines to include full free text searching and
tion to Oracle and the robust, scalable Oracle Cartridge running chemically intelligent structure searching of electronic documents
on the server. including Text, Microsoft Word, Excel, PowerPoint, and Adobe
PDF. The DocManager Enterprise interface allows users to easily
submit documents through a series of simple-to-navigate web
Index Documents forms. When a new document is submitted, DocManager builds a
free text index of the document, and extracts chemical informa-
tion into a chemically-aware, substructure searchable database.
Chemical information can originate from either ChemDraw or
ISIS Draw.
DocManager Enterprise includes a batch loading utility for admin-

istration level users to load multiple documents at one time. The
system can be configured to submit a batch of documents as one
Manage your event, or as a reoccurring submission to be executed daily. The
Inventory
administrator specifies a time for the submission to take place and
the location of the files. DocManager Enterprise utilizes the search-
ing intelligence of the ChemOffice Enterprise suite.
M A N U FA C T U R I N G
Reference Standards,
Regulated Materials Management,
Inventory Enterprise
• Request/Dispense/Reference Standard Materials
CambridgeSoft’s Inventory Enterprise application is designed to from Central Group to Sites
manage the chemical, reagent, sample and compound tracking
needs of large multi-site chemical and pharmaceutical laboratories.
• Certification/Expiration/Certificate of Analysis of
Inventory Enterprise is an Oracle-based, ChemOffice Enterprise Containers and Aliquots
product that is designed for multiple users with diverse container
types, racks and multi-well plate formats.
• Create/Manage Container History and Genealogy
Entities in the Inventory system include locations, containers and

substances. A location is defined as any physical location where a Searching
container, plate or another location can be stored. An inventory
container represents a container capable of storing chemical sub- Every field in a record is searchable. The application includes a
stances. An inventory substance represents a chemical compound, number of specially designed inventory search forms. Search
mixture, sample, etc. Inventory Enterprise manages an unlimited results are returned in list form and can be exported into a docu-
number of diverse locations, containers and substances. ment (PDF, RTF, HTML) via the report engine.
Containers are created to represent the actual storage vessels used Workflow Support
by the organization. Each container is assigned a unique barcode Supported user transactions include the ability to request,
identifier which can be printed, using customizable report tem- dispense, modify, duplicate, dispose, etc. entities throughout the
plates, from the Inventory interface. Updating the inventory system. These and other transactions are an integral part of
becomes as easy as scanning barcodes into the system and adjust- Inventory workflows.
ing parameters for one or multiple containers. Users are able to
order, check-in/out, move, split and merge containers at will. For example: a user logs-on, finds the substance(s) they’d like to
Typicalcontainers include: ttles, vials, tubes, cylinders, boxes, request and makes a request entry in the system; the request is ful-
racks, multi-well plates, etc. filled directly by changing the location the substance or by taking
an aliquot and creating a new container of the substance. The new
Multi-well Plates substance/container is also tracked in the system and inherits all
Inventory Enterprise manages multi-well plate information. In of the critical properties of its parent container. If a quality con-
addition to creating, storing, moving and deleting plates, the trol test is run on the parent, then the results are viewable in the
application allows users to create daughter plates, reformat plates daughter’s properties.
and utilize plate maps. Inventory also supports user-interfaces or
machine-interfaces for these operations (including reading files The multi-select capability allows the user to select several con-
from liquid handler robots). Inventory Enterprise has the capabili- tainers and perform a transaction on all of the selected containers
ty to import datafiles from other computer systems such as liquid simultaneously, including check-in/out, move, retire, delete and
dispensers/handlers, Microsoft Excel spreadsheets, etc. to accom- update. For instance, if a request is made of the system that is
modate automated updating of information in the Inventory fulfilled by another user (such as dispensing), the requester can
database. automatically receive e-mail notification of the progress. Likewise,
users can be alerted to pending requests in the system.
Inventory & GxP

Document Storage, Batch Records
Conflict Resolution
• Validated for GxP Environments with Audit Trails,
The Conflict Resolution processes flags and corrects Container History
duplicates in the system automatically. You may also search for
duplicates at any time. If a conflict is found, the screen
• Store Datafiles with Samples such as Batch and
identifies the conflicting field(s) by highlighting it in red. The user
Certificates of Analysis
has the option to select the existing substance and edit the con-
flicting substance or create a duplicate substance and resolve the
conflict later. • Allows for Flexible Reporting
Printed Reports & Labels

The Inventory interface allows for printing labels and can generate Electronic Data Files
elaborate reports. Inventory Desktop and Workgroup use a report
engine that incorporates wizards that allow for the quick creation In addition to storing, moving and disposing containers, the
of simple report/label templates that can be shared across an application allows users to reformat plates and create daughter
organization. A user has the ability to design a label based on templates as well as integrate with liquid dispensers/ handlers for plate
plates for a number of commercially available label sheets (e.g. reformatting from pipette log files.
Avery Dennison). The Inventory manager makes extensive use of
barcodes and web-based user interfaces to speed use, but substan- Compliance
tial gains come in the automated reporting and alerting. Examples Handling FDA regulations in an organization is an area that lends
include notifying all users of samples derived from a single stan- itself to automation. Thus, systems must be carefully implement-
dard of some change in status, such as different analytical results ed in order to meet the letter and spirit of FDA guidelines.
or failure to recertify. Underlying the system are the controls expected by systems in reg-
Inventory Enterprise ulated environments: audit tables, security and validated develop-
ment methods. All transactions on all containers in the system are
tracked and audits are customizable for simple presentation.
Document Management
To manage the myriad of documents that get generated in research
and regulated environments, CambridgeSoft stores documents
securely in Oracle where they are indexed (by chemistry and text)
and managed by database security. Storing the associated docu-
ments in Oracle preserves system integrity such that you can back-
up to a known point, and be assured that the documents and data
are entirely in sync with each other. It also provides tight docu-
ment security, reduces IT overhead associated with file shares and
attaches directly to Inventory containers.
DESKTOP
S O F T WA R E
Chem & Bio Office

Software Standard for Scientists
The ultimate Chem & Bio Office is a powerful suite of software, consisting of ChemDraw, Chem3D, ChemFinder and ChemACX
software suite for chemists, BioDraw, BioAssay and BioViz for biologists and Inventory and E-Notebook for all types of scientists. Chem &
for scientists Bio Office is available for Microsoft Windows.
The standard Chem & Bio Draw includes Struct=Name, ChemDraw/Excel and ChemNMR, BioDraw, a biological sequence tool,
achieves the hotlinks to 3D structures, Stoichiometry grid, live linked chemical property calculations, a TLC plate tool and more. The
ultimate ChemDraw ActiveX/Plugin adds chemical intelligence to your browser for querying databases and displaying information.
Computational ChemBio3D provides state-of-the art visualization and display of protein structures, molecular surfaces, molecular
chemistry made easy orbitals, electrostatic potentials, charge densities and spin densities. Chem3D provides basic computational tools such as 3D
Molecular Overlay and Dihedral Driver and utilizes MOPAC, Jaguar, Gaussian, GAMESS and extended Hückel to com-
pute molecular properties. ChemProp computes Connolly surface areas, molecular volumes and properties, including ClogP,
molar refractivity, critical temperature and pressure.
Desktop to ChemFinder is a chemically intelligent database manager and search engine. ChemFinder provides support for a database
enterprise searching searching, compound profiling, R-Group Analysis, subforms, tight integration with ChemDraw/Excel and Combichem/Excel,
statistical analysis and visualization through BioViz all in a friendly form-based environment. ChemFinder/Office searches
documents, spreadsheets, and files for chemical structures and references. ChemFinder/Oracle provides enterprise solution
integration.
Ultimate suite BioOffice is the ultimate suite for management, analysis and visualization of biological data using BioDraw for drawing
for biologists pathways and BioAssay, BioFinder and BioViz for data analysis. Includes Bio3D, Draw/Excel, CombiChem/Excel, Inventory and
E-Notebook.
Draw pathways BioDraw provides support for biological pathway drawing and annotation. A wide variety of customizable drawing tools
are available, including membranes, DNA, enzymes, receptors, tRNA, ribosomes, and a plasmid map tool.
Screening data BioAssay manages both high and low throughput biological screening data. Designed for complex lead optimization
experiments, the software supports the quick set-up of biological models.
Visualize data BioViz offers automated statistical analysis, curve fitting, and customized structure activity reports, including a user-friendly
interface for importing, viewing, validating and plotting chemical and biological data.
Handle reagent Inventory manages your reagent and biological tracking needs. Using MSDE as the desktop database, you organize, store
racking and search over your inventory. Inventory integrates with the ChemACX database of available chemicals and ChemMSDX
safety data providing chemical sourcing and purchasing.
Efficient notebook E-Notebook is an efficient, accurate way to write notebooks. It stores Microsoft Office documents, ChemDraw
keeping structures and reaction drawings, and related data in a notebook searchable by text or chemical structure. Organize pages by
project, experiment or in your own style. Use CombiChem/Excel to build libraries.
Access info Databases include ChemINDEX, including the NCI and AIDS databases. The ChemACX database contains nearly 400
with ease catalogs from leading suppliers and ChemMSDX Database contains over 20,000 material safety data sheets for commonly
used laboratory chemicals.
DESKTOP
ChemDraw, Chem3D,
Structure Drawing and Molecular Modeling
ChemBioDraw Ultra adds BioDraw, ChemFinder, BioViz

and E-Notebook to ChemDraw Ultra. Easily draw and annotate • ChemDraw’s improved Struct=Name feature produces
publication quality biological pathway illustrations with the names for more types of compounds
BioDraw tools. The combination of the BioDraw tools with
ChemDraw and E-Notebook creates an excellent environment for • Live ChemDraw window embedded in Chem3D application
smooth communication between Chemists and Biologists. allows simultaneous 2D and 3D editing
ChemDraw Ultra adds Struct=Name, ChemDraw/ Excel, • Chem3D brings workstation-quality molecular graphics and
ChemNMR, Stoichiometry Grid, CLogP, tPSA as well as the added rigorous computational methods to your desktop
capabilities of Chem3D Pro and ChemFinder Std to the
ChemDraw Pro application. With rich polymer notation, gener-
ic structure expansion, fragmentation tools, and a modern user
interface, ChemDraw is more powerful than ever before. Create
tables of structures, identify and label stereochemistry, estimate ChemNMR can be used to accurately estimate 13C and 1H
NMR spectra from ChemDraw structures, obtain structures from chemical shifts. The structure and the spectrum appear with the
chemical names, assign names from structures, and create multi- chemical shifts displayed on the molecule and the spectrum is
page documents and posters. linked to the structure so that clicking on a peak in the spectrum
highlights the corresponding fragment on the molecule.
ChemDraw Pro will boost your productivity more than ever.
Draw quality publications with structures, reactions, chemical ChemBio3D Ultra includes visualization and molecular mod-
queries, polymers, relative stereochemistry, generic structures, eling capabilities for both small molecules and protein structures
TLC plate depictions and a biological sequence tool. Publish on designed for the bench chemist. Small molecule computational
the web using the ChemDraw Plug-in. Create precise database methods include Molecular Overlay and Dihedral Driver. It also
queries by specifying atom and bond properties and stereochem- includes interfaces to the MOPAC, Jaguar, Gaussian and
istry. Display spectra, structures and annotations on the same page GAMESS semi-empirical and ab initio computational packages.
High quality Chem3D graphics can be viewed on the web using
Struct=Name contains the leading comprehensive
the Chem3D ActiveX.
methods for converting chemical structures into chemical names
and names to structures. It can be used for many types of com-
Chem3D Pro brings workstation quality molecular visualiza-
pounds, including charged compounds and salts, highly symmet-
tion and display to your desktop. Convert ChemDraw and
ric structures and many other types of inorganic and
organometallics. Struct=Name is available in two forms: a batch ISIS/Draw sketches into 3D models. View molecular surfaces,
application, and an interactive version that is also available in orbitals, electrostatic potentials, charge densities and spin densi-
ChemDraw Ultra. ties. Use built-in extended Hückel to compute partial atomic
charges. Use MM2 to perform rapid energy minimization and
ChemDraw/Excel allows the user to create chemically molecular dynamics simulations. Chem3D can also be used to
knowledgeable spreadsheets within the familiar Microsoft Excel estimate physical properties such as logP, boiling point, melting
environment. You can build and manipulate chemical structures, point and more. Visualize Connolly surface areas and
compute chemical properties and perform database searches. molecular volumes.
S O F T WA R E
ChemFinder & ChemInfo

Structure Searching and Scientific Databases
ChemFinder Ultra is a chemically intelligent database man-

agement and search system designed for chemical and biological • ChemFinder offers improved searching and hit list management,
data. ChemFinder Ultra can be used with local (MSDE) or shared along with new property generation
(Oracle) databases. Either way, the face of ChemFinder is the
same friendly form-oriented interface. BioViz, included in • ChemFinder is tightly integrated with CambridgeSoft's
ChemFinder Ultra, provides data visualization features to help Oracle Cartridge
the user understand relationships between biological data and
chemical structures. These features allow you to plot structural • Search ChemACX and other CambridgeSoft
and biological data in a variety of styles, perform statistical analy-
sis, filter plots based on your criteria, highlight intersecting sets on
plots, generate histograms of data distributions, and more. ChemACX Database includes over 1 million chemical
products available for purchase from 472 supplier catalogs, search-
BioViz, included in ChemFinder Ultra, provides statistical analysis able with a single query by structure, substructure, name, syonym,
and visualization tools for structural and biological data. BioViz partial name, and other text and numeric criteria.
transforms ChemFinder database information into easy to under-
stand graphics, allowing users to discern structure-activity rela- ChemMSDX Database provides material safety datasheets
tionships more easily. With BioViz it is easy to retrieve a set of and is integrated into ChemACX, and contains over 23,000
compounds using filters or searching capabilities; and generate an Material Safety Data Sheets (MSDS) in PDF format.
interactive window showing a wide variety of useful graphical
information. ChemINDEX Database includes 100,000 chemicals, public
NCI compounds, AIDS data and more.
ChemFinder Pro is a fast, chemically intelligent, relational
database search engine for the Desktop. The integration with NCI Database contains over 200,000 compounds with anti-
Microsoft Excel and Word adds chemical searching and database cancer drug dose-response data.
capability to spreadsheets and documents. Compatibility with
MDL ISIS databases is provided by SDfile and RDfile AIDS Database is an NCI compiled database for AIDS anti-
import/export. viral compounds.
ChemRXN Database is a collection of 30,000 fully atom-

Molecular Modeling mapped reactions selected and refined from chemical literature. It
also includes reactions from InfoChem’s ChemSelect database and
ISI’s ChemPrep database.
ChemBioFinder.Com is the award-winning web site with-

in formation and WWW links for over 100,000
chemicals. Users can search by name or partial name, view struc-
Estimate Spectra
ture drawings, or use the ChemDraw ActiveX/Plugin for structure
and substructure searches.
DESKTOP
BioAssay, BioViz, BioDraw,

Biological Assay, Visualization and Pathways
BioAssay Ultra
BioAssay Ultra, the cornerstone of BioOffice, provides flexible • BioAssay offers flexible storage, retrieval and analysis of
storge, retrieval and analysis of biological data. BioAssay biological data

easily manages both high and low throughput biological screening
data. • BioViz provides statistical analysis and graphical representations
of the data loaded into a ChemFinder form
Designed for complex lead optimization experiments, the soft-
ware supports quick set-up of biological protocols, automated • BioDraw allows for quick and easy drawing and annotation
calculations and curve fitting, and the creation of customized of biological pathway depictions.
structure activity reports. BioAssay brings all of this functionality
to your desktop. BioAssay Ultra, compatible with the MSDE
database, offers a user-friendly interface for importing, viewing, many elements that are difficult to draw with the standard presen-
validating and plotting your biological assay data. tation and word processing software. Common pathway elements
such as membranes, enzymes, receptors, DNA, tRNA and plas-
BioViz mid maps are built into the BioDraw toolbar. BioDraw is built
Combining biological data with chemical structures is of the into the same backbone as ChemDraw, allowing users to take
utmost importance in any drug discovery environment. BioViz advantage of the wide variety of the publishing capabilities avail-
allows you to visually analyze and perform statistical analysis on able in ChemDraw such as the ability to import and export images
structure-related data combined with biological data in in GIF, PNG or JPEG formats. In addition, the integration of
ChemFinder. ChemDraw and BioDraw in Chem & Bio Draw application pro-
vides a great communication mechanism between chemists and
Users can search over structural and biological data and biologists.
Notebook Pages
construct various plots such as scatterplots or histograms. The
plots are interactive; allowing you to select subsets of your data,
perform statistical analysis, filter plots based on your criteria,
highlight lists and intersecting sets on plots, generate histograms
of data distributions and more.
BioDraw
Reporting on and presenting findings is a task familiar to every
biologist. Making this process easier and more effective benefits
everyone involved. BioDraw is doing for biologists what
ChemDraw has done for chemists for years—saving time, and
resulting in a more professional representation of the science.
unmatched. Typical drawings of biological pathways include
Data Visualization
S O F T WA R E
Inventory & E-Notebook

Materials Management and Electronic Journal
Inventory Ultra
• Inventory manages the chemical and reagent tracking needs
Inventory Ultra allows users to manage the tracking needs of of laboratories and research centers
chemical and non-chemical inventory data for laboratories and
research centers. The system manages data associated with both
• Inventory maintains its own internal chemical structure database
commercially procured and internally produced chemical sub-
with advanced duplicate checking
stances from their procurement or initial production through
their depletion and disposal. Inventory Ultra is an MSDE based
product and includes the ChemACX database with over 450 cat- • E-Notebook stores Microsoft Office documents, ChemDraw
alogs of chemical reagents. structures, reaction drawings and related data in a convenient,
searchable format
The three primary entities in an Inventory system are
locations, containers and substances. Users or administrators con-
figure a network of locations, which represent locations within an E-Notebook Ultra
organization. Containers are created to represent actual containers E-Notebook Ultra is an efficient, accurate way to store lab note-
in your facility. Each container is assigned a unique barcode, book information. It stores Microsoft Office documents,
which can be printed using a customized template from the ChemDraw structures, reaction drawings and related data in an
Inventory interface. electronic notebook that is searchable by text or chemical struc-
ture. You can organize pages by project, experiment or in your
Each container stores a substance. Additional text fields are avail- own style with the MSDE database. CombiChem/Excel builds
able to track other chemical contents such as the solvent. Custom combinatorial libraries. E-Notebook is configured exactly like a
fields may also be defined. To keep track of substances the system chemist would like his or her own notebook to be. Reactions can
maintains its own internal chemical structure database containing be easily drawn into the reaction template by either selecting from
unique substances that can be associated with inventory contain- the generous list of preloaded reagents or by entering or drawing
ers. Advanced duplicate checking is incorporated in the system. one’s own chemicals. Commonly used reagents can be stored in a
Every field in a record, including the chemical structure, molecu- separate folder for easy access. Another fantastic feature is the pro-
lar formula and molecular weight are searchable. cedural section. This section contains pre-written procedural sen-
tences with the ability to easily drop in the specific names of
The application includes a number of specially designed invento- reagent chemicals present in the reaction. One can also easily add
ry search forms. Search results are returned in list form and can be other data to the notebook page such as spectra and Microsoft
exported into a document (PDF, RTF, HTML) using the report Word or Excel documents.
engine. The Inventory interface allows for printing labels as well as
generating reports. Inventory uses a report application that incor- CombiChem/Excel
porates wizards that allow for the quick creation of simple reports CambridgeSoft provides you with the tools to effectively plan
and label templates that can be shared across an organization. combinatorial chemistry experiments in Excel. The
CombiChem/Excel add-in introduces additional functionality for
Inventory Pro handling combinatorial chemistry. Users can generate products
Inventory Pro contains the same features as CambridgeSoft’s from a reaction and lists of reagents, you can view all the products
Inventory Ultra application, except without CambridgeSoft’s arising from a given reagent or all the reagents of a given product,
ChemACX database. and you can lay out reagent and reaction plates.
SCIENTIFIC
The Merck Index, NCI, AIDS,

Scientific Reference, Chemical Reactions and Patents
ChemBioFinder Gateway
• The Merck Index offers encyclopedic reference for over 10,000
ChemBioFinder Gateway allows searching of the complete chemicals, drugs and biological agents
CambridgeSoft reference collection of databases with a
• R&D Insight for Chemists has information on more than 20,000
single query. Search such databases as The Merck Index, R&D drug products in various stages of development world-wide
Insight for Chemists and Traditional Chinese Medicines with only from over 1,700 sources.
one click of a search button. All results federate back to the spe-
cific databases for complete information. • All databases are updated, contain information unavailable in
print, and are searchable by structure, as well as text and
numeric range by structure, as well as text and numeric range
The Merck Index
Known for its integrity, detail, and longevity, The Merck Index Traditional Chinese Medicines
contains over 10,000 monographs on drugs, chemicals and other
biologically active molecules. Each monograph contains informa- Access to this wealth of knowledge is now available with the
tion on the compound and its derivatives; common, trade, and Traditional Chinese Medicines database. The database consists of
systematic names; trademarks and associated companies; CAS monographs for 10,458 chemicals isolated from 4,625 natural
Registry Numbers, physical and toxicity data, therapeutic and sources used in traditional Chinese remedies. The monographs
commercial uses, literature citations, as well as chemical strucures, feature bio-activity data for many of the compounds, effects and
formulas andmolecular weights. The electronic versions include indications of the medicines, English, Latin, and Chinese names
archived monographs from previous editions and is updated twice a year. for the natural sources, and over 2,000 references.
R&D Insight/Chemists ChemINDEX, NCI AIDS & Cancer
Information on current drug products under development is Scientists have used the award-winning ChemFinder.Com database
essential for those working in research and development, licensing since 1995. Now, the data on ChemFinder.Com is integrated into
and marketing at pharmaceutical and healthcare institutions. ChemOffice as ChemINDEX. ChemINDEX contains data from
R&D Insight for Chemists, a collaborative product from Wolters over 75,000 compounds including structures, names and
Kluwer Health and CambridgeSoft, combines the power of chem- synonyms, physical properties and Internet links. Additionally,
ical structure searching with a wealth of drug development data to three informative databases have been integrated into one power-
give subscribers a competitive edge when making decisions rele- ful application with the NCI and AIDS database, a collection of
vant to the direction of their research. Updated weekly, users can over 200,000 molecules studied by the National Cancer Institute.
search the collection of over 20,000 compounds by structure,
substructure, names, partial names and synonyms. ChemReact and ChemSynth
These reaction database collections from InfoChem GmbH com-
Patent Database prising essential information on chemical reactions published in
Researchers, chemists and patent analysts are now able to easily the literature between 1974 and 2001. The largest is
search full text patents for chemical structures using ChemReact500, with almost 500,000 reactions selected with an
CambridgeSoft's powerful search and analysis tools. The new eye toward synthetic utility. ChemSynth is a subset of the reac-
CambridgeSoft Patent Database portal, co-developed by tions found in ChemReact500 chosen because they have greater
CambridgeSoft and Reel Two, will give users access to all the than 50% yield and have been sited in leading journals more than
chemical compounds named in a patent, and enable them to once. ChemReact68 has 68,000 reactions that have greater than
search by structure, keyword or chemical name. 50% yield and have appeared in more than five example reactions.
D ATA B A S E S
ChemACX & Sigma-Aldrich MSDS

Available Chemicals and Material Safety Data Sheets
ChemACX Database
• ChemACX is fully structure searchable with more than 1
Sifting through chemical catalogs is a poor use of time for any million products from nearly 500 catalogs
researcher. ChemACX database solves this problem by offering a
• ChemACX and the Sigma-Aldrich MSDS are updated
complete tool for research chemical sourcing and purchasing. semi-annually to meet the needs of scientists
With an emphasis on up-to-date information of high quality,
ChemACX allows you to purchase chemicals fast, efficiently and • Search by name, synonym, partial name, formula, and
without worry or cumbersome paper catalogs. The database can other criteria
be accessed from both desktop and enterprise environments and
boasts nearly 500 catalogs from major suppliers, from Alfa Aesar to be aware of their proper handling, storage, disposal and emer-
and Aldrich, to TCI and Zeneca, with hundreds in between. gency procedures. Helping to fulfill these diverse needs is the
Sigma-Aldrich MSDS collection. The database contains over
Sigma-Aldrich MSDS 130,000 MSDSs for the products of the Sigma-Aldrich family of
Environmental, Heath and Safety (EH&S) is an important com- catalogs (Sigma, Aldrich, Fluka, Supelco, Riedel-de Haën) in
ponent of today’s research institutions. A key document that aids HTML format. With a click of a hyperlink, users will be able to
in the management of EH&S tasks is the Material Safety Data view the Sigma-Aldrich MSDS in their preferred browser. This
Sheet, also commonly referred to as MSDS. In every organization, information is smoothly integrated with the ChemACX
there are several groups of personnel who require access to database and other enterprise applications.
MSDSs. Everyone who comes into contact with chemicals needs
Drugs: Synonyms and Properties
Drugs: Synonyms and Properties from Ashgate, provides compre-
hensive coverage of the 8,000 drugs currently in common use
worldwide. A key component of this reference is the extensive cov-
erage given to synonyms. The electronic version adds almost
70,000 synonyms and trade names that did not fit into the print
version. This information is also available as an SD file to
facilitate in silico research.
Nanogen Index
The Nanogen Index contains data on over 1,000 pesticides and
other environmental contaminants. The database is the up-to-date
and authoritative source for information on all pesticides and agri-
cultural chemicals in world wide use, those which are currently
under development in R&D pipelines, and compounds which
were once marketed or reached a development status. Data fields
include chemical structures and SMILES strings, names (CAS,
IUPAC, trade), the various registration codes assigned to the com-
pounds (RTECS, EINECS/ELINCS, CAS, US EPA, CA DPR,
Tarrifs, etc.), Hazard and Safety codes, the developing company
and use.
PROFESSIONAL
Development, Deployment,
Custom Development and System Deployment
When processes and technologies are disjointed, organizations lose

efficiency and decision making capability. Our Professional With custom development, CambridgeSoft works collaboratively
Services use technology to bring business processes together, with your team to create a system that meets your needs while
integrate systems and assist with strategic informatics planning. executing our quality driven software development process. We
deliver what you need, on time and within budget, without surprises.
Informatics Planning
Strategic and Operational Planning
A formal review of the discovery and development process and Product Development
human/system interfaces is mapped to form the basis of a Development Consulting
roadmap for successful technology utilization.
• Analysis of the current laboratory and technology workflows With custom development, CambridgeSoft works collaboratively with
• An analysis of the current state of the science technology your team to create a system that meets your needs, while execut-
ing our quality driven software development process. We meet
environment, including architecture/operational processes
your needs, on time and within budget, without surprises.
• A view of strategic goals and the barriers to achievement
Systems Integration
• The delivery of a phased technology transition plan
Requirements Analysis & Proof of Concept Process improvement often requires integrating systems designed
for focused areas of work. CambridgeSoft has integrated various
With years of experience meeting the needs of the scientific com- E-Notebook, registration, inventory, and biological assay systems
munity, CambridgeSoft understands the user. The prototyping in a variety of settings. Whether these are CambridgeSoft, a third-
process allows definition and testing of the functional and techni- party product or an in-house developed solution. CambridgeSoft
cal feasibility of potential technology solutions. The process pro- has the expertise to unite these systems in order to they improve
vides a baseline for the future development and deployment of a business processes, laboratory efficiency and decision making.
tailored solution. Users gain valuable first-hand knowledge in Application Configuration
experiencing how the system can help achieve individual and
Your organization will see the benefit from implementing a
workgroup goals.
CambridgeSoft application, but would like to customize it for a
Legacy System Migration
unique environment. Our professional services teams provide
Legacy systems, with private data structures and architecture, can those specific features by developing market add-ins, or other
be barriers for migrating systems to new technologies. Our con- modifications that are supported in the future.
sultants have significant experience with these systems and can
successfully migrate chemical and biologial data, business work- Systems Deployment
flow, and other aspects of legacy informatics technologies.
Installation and Configuration
21 CFR Part 11 Compliance and GxP Validation
CambridgeSoft has a tested methodology for system
As an integral part in creating 21 CFR Part 11 and GxP deployment that consists of an IT architectural review, a business
validated applications, CambridgeSoft offers services to: workflow and process review as relates to specific scientific areas,
• Audit the software and process a process integration review, and maintenance guidelines. By care-
• Create conforming systems design specifications fully following this proven methodology, CambridgeSoft installs
• Create IQ/OQ/PQ documentation and configures systems that are easy to maintain and have the flex-
• Generate test plans and validation matrices ibility to accommodate variations in the science or business work-
• Insure systems compliance with functional guidelines flow that come from extensive experience in these areas.
SERVICES
Training & Support

Educational Training and Technical Support
Systems Optimization
CambridgeSoft’s systems deployment team will work with you to Managed Informatics allows your organization to focus on science,
make sure that your computing environment has been optimized while CambridgeSoft plans, implements and manages your
for high performance. Your systems,networks, applications and technology environment.
databases are assessed and designed to deliver maximum achieve-
ment.
Beta and Pre-Release Programs
Committed to maximizing your productivity through the use of Systems Management
our products, as well as exposing you to the newest technologies, Managed Informatics
our beta and pre-release programs provide you with first-hand Informatics outsourcing provides the people, processes and tech-
product knowledge and allows CambridgeSoft to improve appli- nology to develop a unique level of service for your organization.
cations with your feedback. For a monthly fee, CambridgeSoft will deliver the informatics
Pilot Software Evaluations applications and the technology staff required to maximize pro-
It makes sense to pilot an application before a major commitment ductivity. This service allows your organization to focus on sci-
to an enterprise-wide implementation is made. CambridgeSoft ence, while CambridgeSoft plans, implements and manages your
will work closely with you to plan the evaluation, deploy the technology environment.
application, and gather feedback regarding systems design, API’s Systems Hosting
and technology specifications. A hosting service that allows customers to use our state-of-the-art
Training enterprise applications over the extranet from any location 24
Effective user, administrator and help desk training is often an hours a day, seven days a week is available. With this hosting serv-
afterthought in many systems deployments. However, the produc- ice, our customers can shift the responsibilities of application devel-
tivity returns generated by an investment in systems training can opment and IT infrastructure management to CambridgeSoft,
be dramatic. CambridgeSoft offers a complete array of powerful, allowing more time to focus on core science, research, discovery
user-focused training services. and development functions.
Ultra Services
The Ultra Services program is CambridgeSoft’s personalized, pre-
mium service for supporting our customers. Organizations can
take advantage of both telephone and electronic access to
CambridgeSoft’s support scientists who can address:
• Usage and installation questions
• Product compatibility and interoperability questions
• Diagnostic review to help isolate the cause of a problem
• Configuration assistance
• Planning information for software updates and upgrades
• Assistance with problem resolution
Technical Support & Remote DBA Services

Technical Support and Remote DBA Services for Oracle and SQL
Server are also available.
Chem & Bio Office
Desktop Software to Enterprise Solutions
Research, Discovery, Development, T rials & Manufacturing

Enterprise Solutions include Chem & Bio Office with Oracle Cartridge and Chem & Bio Office Workgroup, based on SQL Server
to help organizations from small workgroups to large enterprises collaborate and share information more effectively.
Knowledge Management with E-Notebook, including Reaction Explorer, CombiChem, E-Signatures for intellectual property
protection and 21CFR11 Compliance, streamlines daily record-keeping with rigorous security and efficient archiving.
Laboratory Informatics includes Workflow LIMs for instrumentation automation and Compliant DB for storage of your data.
Biological Informatics scientists use BioDraw, BioAssay, BioSAR and BioViz to set up biological models and visualize
information, generate spreadsheets correlating structure and activity, search by structure, and draw and annotate pathways.
Chemical Informatics, including Registration, organizes new compound information. Inventory provides complete management of
chemical and biological inventories including GxP Validation. DocManager indexes chemical structures in documents.
Manufacturing Informatics include Inventory to meet the chemical, reagent, sample and compound tracking needs of large
multi-site chemical and pharmaceutical laboratories and E-Notebook for manufacturing compliance management.
Desktop Software includes Chem & Bio Office, a powerful suite of software, consisting of ChemBioDraw, ChemBio3D,
ChemFinder and ChemACX for chemists, BioDraw, BioAssay, and BioViz and for biologists, and Inventory and E-Notebook for all.
Scientific Databases include the ChemACX Database of commercially available chemicals and Sigma-Aldrich MSDS. The Merck
Index and other scientific databases provide information about chemicals, their properties, and reactions.
Professional Services include custom development, system deployment, educational training, and technical support for
pharmaceutical, biotechnology, and chemical customers, including government and academia, by experienced staff.
Web www.cambridgesoft.com Email info@cambridgesoft.com

America 1 800 315-7300 United Kingdom +44 1223 464900
Europe 00 800 875 20000 Germany +49 69 2222 2280
Japan 0120 146 700 France +33 1 70 71 98 80
Chem & Bio Office
SDMS
Research, Discovery, Development, Trials & Manufacturing

Laboratory Informatics includes Workflow LIMs for instrumentation automation and Compliant SDMS for storage of your data.
Europe 00 800 875 20000 Germany +49 69 2222 2280
Japan 0120 146 700 France +33 1 70 71 98 80
MAE 04980 0902
CambridgeSoft
Solutions
featuring
E-Notebook
D ESKTOP S OFTWARE
E NTERPRISE S OLUTIONS
C HEMICAL & B IOLOGICAL

R ESEARCH I NFORMATICS
L ABORATORY, D EVELOPMENT &

M ANUFACTURING I NFORMATICS
K NOWLEDGE M ANAGEMENT
S CIENTIFIC D ATABASES
CAMBRIDGESOFT
Vision, Passion
Research, Discovery, Development,
CambridgeSoft Software, Solutions and Databases

SOLUTIONS
& Innovation
Motivated by Vision
Innovation is an organizational must in pharmaceutical, biotechnology, and chemical industries.
Effective new ideas, developed through collaboration and communication, free from organizational
boundaries, will determine your long-term success. In today’s connected world, information flow
within organization can be overwhelming. Large amounts of data—some structured and some
unstructured—can cloud an R&D organization’s ability to focus on what is important. Since 1986,
CambridgeSoft has been solving the problem of electronic storage and communication of chemical structures, models, and informa-
tion. Starting with ChemDraw, then broadening to ChemOffice in 1992 and BioOffice in 2004, CambridgeSoft extended its software to
include enterprise wide solutions with ChemOffice Enterprise in 1998, E-Notebook in 2000 and biology with BioAssay in 2001. Today,
CambridgeSoft products are used by hundreds of thousands of chemists, biologists, scientists, and engineers who work in pharmaceutical,
biotechnology, and chemical industries, including government and academic research. These systems work within your research, discov-
ery, development, trials and manufacturing, and information technology to help you capitalize on your organization’s intellectual assets. By
turning information into explicit knowledge, you accelerate innovation and drive organizations forward.
Created with Passion

Chemists, biologists, scientists, and engineers need timely, convenient access to critical information,
whether structured or unrefined. CambridgeSoft, which began by helping scientists manage desktop
chemical and biological information with Chem & Bio Draw, now addresses enterprise-wide scientific
information problems with Chem & Bio Office Enterprise and Workgroup. These solutions are flexible
and powerful to deal with today’s complex projects which span functional organizations and geographi-
cal boundaries. Eliminating data barriers and bringing information to all—in the form they need to interpret it—aligns all of the mem-
bers of your teams, focusing their collective knowledge and diverse skills toward the common goals of problem solving and innovation.
The results can be dramatic:
· Information transparency and group collaboration improve productivity and reduce costs.
· Faster and smarter research decisions cut time to market and increase productive efforts.
· Empowered employees contribute increased value to the research, discovery, development, trials and manufacturing organization.
Advanced through Innovation

When your research, discovery, development, trials and manufacturing organization is
able to respond swiftly and effectively to opportunities and market changes, promote innovation and
accelerate product delivery, you are working smarter to outpace your competitors. As the speed of busi-
ness continues to accelerate, leading organizations constantly seek faster and better informed decision
making as well as new business efficiencies. For the individual chemist, biologist, scientist, and engi-
neer who needs to capture, organize, and communicate chemical and biological data, through the complex and widespread workgroup
and enterprise scientific information systems needs, CambridgeSoft Solutions can help.
CAMBRIDGESOFT
Chem & Bio Office Desktop

KNOWLEDGE CHEMICAL,
MANAGEMENT BIOLOGICAL
Desktop
Chemistry Biology BioAssay &

E-Notebook E-Notebook ChemBioViz
Process Workflow BioSAR

E-Notebook LIMS Enterprise
Enterprise
Compliance DocManager
E-Notebook Enterprise
Chem & Bio Office KNOWLEDGE MANAGEMENT

Enterprise
Research organizations thrive when information is easily captured, well organized and readily avail-
E-Notebook Enterprise able. E-Notebook Enterprise streamlines record keeping with rigorous security and efficient archiv-
Chemistry & Biology ing, and facilitates text and structure searching. E-Notebook provides organizations with a powerful
mechanism to transfer mission criticalwork product from shared drives to a well-organized, compli-
Analytical Services ant and searchable Oracle application. MS Office, chemical structures and workflow support
modules are provided for the full range of research and development activities.
Sample Management
Workflow LIMS LABORATORY INFORMATICS

Compliant DB Laboratory Informatics includes Workflow LIMS for instrumentation automation, Compliant DB for stor-
age of your data and the Oracle Cartridge which is the industry’s only enterprise content manage-
Oracle Cartridge ment system developed by a large pharmaceutical company.
BioAssay Enterprise BIOLOGICAL INFORMATICS

BioDraw Finding structural determinants of biological activity requires processing masses of biological
assay data. Scientists use BioAssay Enterprise and BioSAR Enterprise to set up biological models
BioSAR & BioViz and visualize information. The BioViz application allows you to create graphical representations
of data.
Registration Enterprise CHEMICAL INFORMATICS

ChemBioFinder Managing huge data streams is a key challenge. Registration Enterprise organizes information
Enterprise about new compounds according to an organization's business rules.
SOLUTIONS
to Enterprise Solutions
LABORATORY & SCIENTIFIC
MANUFACTURING DATABASES
Inventory ChemACX The Merck

Enterprise Database Index
Registration GxP Sigma-Aldrich

Enterprise Validation MSDS
Compliant ChemBioFinder
Oracle Cartridge
or SQL DB SDMS Gateway
MANUFACTURING INFORMATICS
Inventory Enterprise CambridgeSoft’s Inventory Enterprise application is designed to manage the
chemical, reagent, sample and compound tracking needs of large multi-site
Materials Management
chemical and pharmaceutical laboratories. Inventory Enterprise is an Oracle-based,
Compliance Management ChemOffice Enterprise product that is designed for multiple users with diverse
container types, racks, and multi-well plate formats.
ChemDraw & Chem3D DESKTOP SOFTWARE

ChemFinder & ChemInfo Success begins at the desktop, where scientists use ChemOffice, ChemDraw, BioOffice and
BioDraw to pursue ideas and communicate with the natural language of chemical structures,
BioDraw, BioAssay & biological pathways, and models. Scientists organize information and manage data with E-
BioViz Notebook and Inventory. ChemBio3D provides modeling, ChemBioFinder aids searching, while
BioOffice adds BioDraw, BioAssay and BioViz. All are integrated with Microsoft Office to speed
Inventory & E-Notebook research tasks.
ChemBioFinder Gateway SCIENTIFIC DATABASES

Good research depends on reference information, starting with the structure-searchable
The Merck Index
ChemACX Database of commercially available chemicals and Sigma-Aldrich MSDS. The Merck
ChemACX Database Index and other scientific databases provide necessary background about chemicals, their prop-
erties, and reactions.
Development PROFESSIONAL SERVICES

Training & Support CambridgeSoft's scientific staff has the industry experience and the chemical and biological
knowledge to maximize the effectiveness of your information systems.
ENTERPRISE &
Chem & Bio Office Enterprise

Integrated Research, Discovery, Development,
Desktop to Enterprise Development and Testing
Since the company's founding, CambridgeSoft's desktop soft- Building on productivity software, CambridgeSoft created enter-
ware, starting with its industry-leading Chem & Bio Draw, has prise applications to meet the needs of an everexpanding research
been the cornerstone application for scientists who draw and and development community that relies on data sharing across sci-
annotate molecules, reactions, and pathways. This suite of enter- entific disciplines, research campuses, and even oceans as global-
prise applications has developed and now provides solutions in all ization has increased demands. Since the software takes advantage
areas of discovery. of the latest web based technologies, it is deployed readily
throughout a research and development organization. Using the
Research and Discovery integrated suite, scientific teams are well armed to solve the daily
challenges of development. These teams include scientists who
Researchers can record and share their experimental
scale up and design manufacturing procedures,toxicologists who
information using E-Notebook, while protecting intellectual prop-
determine the metabolic fate of drugcandidates, formulation sci-
erty with digital signatures and 21 CFR Part 11 compliance. They
entists who determine drugdosing and delivery systems, as well as
can design both single experiments or design combinatorial
many others.
libraries of compounds. They can find and purchase reagents in
ChemACX database, store and use them from Inventory, record
Trials
newly made compounds within a proprietary Registration system,
record the results in BioAssay, analyze the results with BioViz, and A suitable drug candidate is one that has the desired activity to
generate reports linking activity and structure with BioSAR. provide disease therapy while meeting drug safety requirements,
can be manufactured in a cost effective and reproducible fashion
Virtually every aspect of discovery, from synthesis planning, under 21 CFR Part 11 and Good Manufacturing Processes
library enumeration, reagent selection, primary and secondary (GMP) guidelines, and is stable under normal formulation and
screening, in vivo testing, through to analysis of results and report- storage conditions. With a drug candidate in hand, the final chal-
ing is covered by this integrated application suite. lenge is to determine safety and efficacy in a patient population.
All specifications subject to change without notice.
WORKGROUP
and Workgroup Solutions

Trials and Manufacturing Workflow
Manufacturing management and informatics solution, covering electronic note-
books, biological screening and chemical registration over your
Manufacturing requires the transfer of data and batch process
intranet. ChemBioOffice Enterprise Ultra includes E-Notebook for
records from the pilot plant studies using Inventory, E-Notebook,
record keeping, BioAssay for low and high throughput screening
and Registration systems under Good Laboratory and
with integrated plate inventory, BioSAR for SAR reports,
Manufacturing Processes (GxP).
Registration System, Inventory for reagents and biologicals, and
ChemACX database of available chemicals. Technologies include
The handling of materials, including chain of custody require-
ChemDraw ActiveX and Oracle Cartridge.
ments, material documentation, material workflow, such as avail-
ability states and recertification dates, are tracked and handled by
the system.
Chem & Bio Office Workgroup
Chem & Bio Office Workgroup Ultra is a comprehensive knowl-
These systems meet the requirements and provide the basis to edge management and informatics solution, covering electronic
manage materials and records during clinical trials. Clinicians can notebooks, biological screening and more over your intranet.
design and record results from protocols, and all of these web
based software systems provide the access required by clinicians Chem & Bio Office Workgroup Ultra includes E-Notebook
who are removed from the sponsoring company. for record keeping, BioAssay for low and high-throughput screen-
ing, BioViz for visualization, Inventory for reagents and ChemACX
Chem & Bio Office Enterprise database of available chemicals. Technologies also include SQL
Chem & Bio Office Enterprise is a comprehensive knowledge- Server for affordability and ease of administration.
KNOWLEDGE
Overview &
E-Notebook’s Flexible Architecture
E-Notebook E-Notebook Architecture

Used for collaboration and knowledge sharing, regulatory compli- E-Notebook Enterprise edition is a globally-deployable, Oracle-
ance, intellectual property protection, LIMS,document manage- based application designed for everyone from small research
ment, project management, and workflow support, E-Notebook is groups to global organizations. Oracle Cartridge manages chemical
the leader in a new class ofapplications. Configurable, multi-pur- structures and reactions in a common data repository, layered with
detailed security and is 21CFR Part 11 Compliant (audit trails,
pose, and enterprise-scalable, it provides a solution to a large set of
digital signatures). The enterprise edition works with procurement
requirements across R&D and manufacturing. E-Notebook's foun- databases and services including ChemACX database and Inventory
dation layer of features includes support for 21 CFR Part 11, 37 management systems to save time locating chemicals and entering
CFR and GxP compliance, on top of which a widely configurable structures.
design interface provides support for specific scientific and regula-
tory workflows. Because this diverse portfolio of requirements is Flexible and Configurable Architecture
met in a single applicationplatform, E-Notebook both lowers the The E-Notebook architecture is designed to provide organizations
total investment required to meet these needs, and provides a sub- with an unparalleled level of flexibility. A powerful configuration
stantial increase in productivity due to a far more integratedenvi- layer is provided to make it possible to modify substantially the
ronment for scientists and technical staff. look and feel of the application in order to meet very diverse work-
flows. Detailed workflow support in the same application is pro-
E-Notebook Architecture vided for researchers in early stage discovery through early clinical
development even though the requirements for these groups are
CambridgeSoft’s E-Notebook provides a comprehensive, easy-to- totallydifferent. Beyond configuration, a rich API is provided for
use interface designed to replace paper laboratorynotebooks in a custom development and system integration.
variety of settings. Underneath is a fullyconfigurable, secure sys-
tem for organizing the flow ofinformation generated by your E-Notebook is also in production with integrated inventory sys-
organization. Scientists can enter chemical reactions, Microsoft tems including CambridgeSoft’s Inventory manager, as well as
documents (Word, Excel, PowerPoint), spectra, biological data in-house systems, analytical data capturing systems, and com-
and images, and other types of information and documents. It also pound registration systems. E-Notebook supports limiting access to
allows you to search by text, chemical substructure, metadata tags, certain information at the project or group level if desired, as secu-
organizational hierarchy, or other keys. rity is granular. Information can be shared or secured as desired
throughout the framework.
MANAGEMENT
General R&D
IP Protection and Regulatory Compliance
General R&D
• Replace Shared Drives with Oracle
CambridgeSoft’s E-Notebook is a solution that enables
pharmaceutical and biotechnology companies to improve the
efficiency of the process from diseased target identification to prod- • DMPK, Screening Biology, Genetics, and Microscopy
uct launch. Its core Oracle database manages the workflow to be
compliant with Good Laboratory Practices (GLP), Good
• LIMS, Method Execution, 21 CFR Part 11, GxP
Manufacturing Processes (GMP), and the FDA’s 21 CFR Part
11; while the client interface is highly configurable and flexible.
Anywhere a shared drive is used, E-Notebook can offer a better
Development and Testing
solution.
CambridgeSoft’s Enterprise E-Notebook meets the needs of ever
Through the R&D process, using CambridgeSoft’s E-Notebook in expanding research and development communities that rely on
each subsequent stage adds increasing scientific and economic data sharing across scientific disciplines and campuses as globaliza-
value by providing workflow automation and knowledge sharing. tion has increased demands.
Research and Discovery E-Notebook allows custom integration of a large array of modules,
in-house applications, lab instruments, and back-end data storage
E-Notebook Enterprise is capable of providing knowledge manage-
to provide a true end-to-end solution for development and testing.
ment, chemical- and biological-focused solutions in virtually all
Designing workflows and calculations is much faster and requires
areas of discovery. Researchers can record and share their experi-
far less programming using the E-Notebook than existing lab infor-
mental information, while protecting intellectual property with
mation systems. End users include scientists and process chemists
digital signatures and 21CFR Part 11 and 37 CFR compliance.
who scale up and design manufacturing procedures, toxicologists
who determine the metabolic fate of drug candidates,
• Chem & Bio Draw—draw and annotate molecules,
formulation scientists who determine drug dosing and
reactions, and biological pathways
delivery systems, as well as many others.
• ChemACX—find and purchase reagents
• Inventory—store and track reagents and samples
• Registration—record newly made compounds
• BioAssay—model complex protocols and record results A suitable drug candidate has the desired activity to provide dis-
from biological testing ease therapy while still meeting safety requirements, can be man-
• BioSAR—generate reports linking activity with structure ufactured in a cost effective fashion under 21 CFR Part 11 and
• BioViz—analyze biological results GMP guidelines, and is stable under normal
formulation and storage conditions. The handling of
Virtually every aspect of discovery process—from synthesis materials, including chain of custody requirements, material
planning, library enumeration, reagent selection, primary and documentation, material workflow, such as availability states and
secondary screening, in vivo testing, through to analysis of results recertification dates, are tracked and handled by the
and the reporting of data—is covered by the integrated E-Notebook application. CambrideSoft’s E-Notebook meets these
E-Notebook solution. requirements under Good Laboratory and Manufacturing
Processes (GxP) and provides the basis to manage materials and
records during clinical trials.
KNOWLEDGE
Chemistry &
Electronic Journal and Record Keeping,
Chemistry
Under the R&D value chain, chemistry can be further
divided into three separate stages: synthetic chemistry
(research/discovery), analytical chemistry (pre-clinical) and • 37 CFR Electronic Signatures
process chemistry (development). The flexibility and configura-
bility of E-Notebook enables a successful data repository, analysis, • Service Requests and Discovery Workflow
sharing, reporting, and searching efficiently and paper-free.
Process Chemistry
Synthetic Chemistry
The objective of process research is to identify efficient processes
Synthetic Chemists take advantage of many features tied into a
for the synthesis of active pharmaceutical agents at the scale
smooth interface within CambridgeSoft’s Enterprise E-Notebook. required for clinical trials and commercial use. It is necessary to
Reactions are drawn with in-place editing; a stoichiometry grid provide precise descriptions of these processes so that they can be
dynamically fills with the formulas, molecular weights, and chem- executed by different groups in different locations. It is also
ical names. Reagents can also be imported from other systems, required that such processes be compliant with Good Laboratory
such as available chemicals from the ChemACX database or Practices (GLP), Good Manufacturing Processes (GMP) and the
Registration system. FDA's 21 CFR Part 11 regulation. E-Notebook's process chemistry
modules are designed to support these dual workflow and
CombiChem is one important aspect of library generation for regulatory compliance needs of process chemists.
Synthetic Chemists. For some, E-Notebook serves as the complete Reaction Properties
CombiChem solution, taking advantage of features such as the
enumeration of products from a virtual library on a flexible plate
layout, a multiple reaction site checker, and multiple step parallel
synthesis. Others simply import a list of compounds from an
external source or SDFile so that they can record and calculate
data on a library-wide stoichiometric table.
Analytical Chemistry
E-Notebook serves as a repository for analytical data, and it also
acts as a communication portal with which scientists and analysts
communicate with each other. Scientists can create and send
service requests directly to an analyst with the click of a button.
Paper is eliminated: when results are obtained, the analyst can
send the images and chromatograms directly back to the scientist's
E-Notebook.
PowerPoint Integration
MANAGEMENT
Biology
DMPK, Screening Biology, Microscopy
Discovery Biology
These scientists are involved at the very start of the drug
discovery process, as genomics and genetics are essential
disciplines used when identifying a disease target. This work is • DMPK, Screening Biology, Genetics, and Microscopy
methodical but unscripted, and so requires an electronic note-
book pallet that is as free form as its paper predecessor. This is
• LIMS, Method Execution, 21 CFR Part 11, and GxP
where the benefit of E-Notebook's flexibility is unmistakable.
While the system can be set up with rigid form based data entry
appropriate for later stage research and development, discovery Assay & Screening Biology
biology configurations are typically open and boundless. Genomic One of E-Notebook's strengths is its ability to integrate with exist-
map and DNA, RNA and protein sequence files can be dragged- ing electronic methods of data capture, including using it with
and-dropped into E-Notebook, sequencing results can be sent CambridgeSoft’s BioAssay module to provide full screening exper-
directly from instruments to electronic experiments, and protocols imental support. In addition to this, Microsoft Word and Excel
and data can be managed with familiar tools such as Microsoft are also embedded directly in E-Notebook, as is image and movie
Word and Excel. capture. Scientists benefit from the functionality of these tools
implanted in a rich, searchable environment. Biological experi-
The beauty of capturing data in E-Notebook is that ments can be managed and organized in a way that is not possi-
information can be compiled and viewed in a meaningful way. For ble with a traditional file system.
example, the creation of a new biological strain entails many steps,
potentially involving nonconsecutive workdays of various individ- In vivo Experiments/Animal Management
uals. E-Notebook can generate customized reports that meaning- In vivo experiments are important aspects of target discovery and
fully summarize the process in real time. These reports are validation, and are critical paths to determine the
navigable—clicking on each step will bring you to the efficacy of selective therapeutic candidates. CambridgeSoft’s E-
corresponding experiment. Notebook becomes the centralized location to collect, store and
Database Structure interpret in vivo experiment results. Again, when used with
BioAssay, the full end-to-end experimental workflow is supported,
from creation, to data analysis and quality control, to summary
and reporting. In conjunction with in vivo experiments, animal
housing and breeding can also be tracked. Traditionally, the work-
flow consists of paper-based record keeping across the animal
facility, lab bench, and researchers desktop. With E-Notebook,
paper tracking and recording is eliminated. Instead, form tools can
be designed to:
• Track animal status

• Track animal pedigree
• Record Genotype
• Create mating records
• Create litter records
KNOWLEDGE
Analytical Services &

Electronic Journal and Record Keeping
Formulation and Validation

• Service Request Workflow
E-Notebook's formulation module is designed to support the dual
workflows and regulatory compliance needs of formulation engi-
neers. The flexibility allows any number of formulations to be • Sample Management
created, and security allows only designated administrators to
create a new formulation.
• Method Execution Framework
Analytical & Quality Control
Analytical and Quality Control Laboratories must execute defined
procedures to test material that may be administered during pre- Pharmacokinetics (DMPK)
clinical and clinical trials. This work must also be compliant with
There is a holistic approach to Drug Metabolism and
both GxP and 21 CFR Part 11. Templates for standard analytical
Pharmacokinetics. No single study describes the behavior of a
tests are provided and analytical procedures are implemented as
compound; it is the combination of data from disparate experi-
E-Notebook forms, which are easily designed and controlled.
ments that represents the pharmacological profile for a com-
Equally important, E-Notebook provides workflow enforcement
pound. It is here where E-Notebook reveals one of its most signifi-
that monitors data entry and ensures that the forms are complet-
cant capabilities: the reporting feature. E-Notebook reports are
ed in sequence for proper method execution.
flexible: any field (e.g. compound ID, study type, etc.) can be used
to query the system and any field (e.g. conclusion, dose, etc.) or
For example, rules can be configured such that the 'Day 3' form
field aggregate (e.g. average radioactivity) can be displayed in the
of a multi-day process will not accept any entries unless all
report. Reports are dynamic and navigable: results are displayed
required fields on the 'Day 2' form are first completed. The forms
with links that provide quick access to experiments.
can contain automatic calculations to compute totals, averages,
differences, and much more. E-Notebook can further streamline
Reports are viewed directly in the E-Notebook interface, but they
the procedure by allowing for electronic management of solutions,
can also be exported to Microsoft Word or PDF to share with
equipment, and other resources that are needed for experiments.
those who do not have E-Notebook access.
Drug Metabolism Inventory Enterprise
E-Notebook supports the DMPK laboratories in testing the metab-

olism and longevity of compounds in various in vitro and in vivo
models. DMPK data capture needs can vary significantly, and the
flexibility of the E-Notebook solution addresses this. For example,
an in vivo enzyme induction test may create relatively small
amounts of data for which scientists utilize E-Notebook integra-
tion with Microsoft Excel. Conversely, large quantities of data,
such as those generated by in vitro enzyme inhibition studies, are
often collected and analyzed by applications such as BioAssay.
Therefore, integration with BioAssay and Excel are fundamental to
DMPK E-Notebook usage.
MANAGEMENT
Sample Management
Compliance Execution and Sample Tracking
Drug Safety / Toxicology

• Track & Barcode Samples
Paper notebooks have traditionally been considered to be the
record source for the entirety of an experiment, but they often
miss non-experimental information generated shortly after con- • Create Any Report from Database
ception. For example, toxicology studies are often initiated not
by the scientist who ultimately runs the experiment, but instead • Full Audit Trail
by a manager or coordinator who assigns the study to the scien-
tist. Important material related to this first step in the process,
such as ideas, emails, and other communications are often left out Sample Login
of traditional paper notebooks. The E-Notebook toxicology work-
E-Notebook is able to easily configure sample logins (registration of
flow addresses this concern: studies are first created by a manager,
sample, assignment of barcode label, and initiation of sample
and subsequently assigned to the scientist for execution.
tracking) by incorporating CambridgeSoft’s Inventory application.
Through E-Notebook, forms can be created to keep track of newly
Compliance Execution
synthesized or acquired compounds, tracking their physical prop-
E-Notebook is also useful for capturing the Standard Operating erties and tests, and assigning unique identifiers. New compounds
Procedure (SOP) corresponding to the experiment. These docu- are entered directly via the E-Notebook form, and chemical, along
ments are often stored separately from the actual data, leading to with non-chemical, data is kept alongside the sample. When a
error and confusion, thus causing risk to the validity of the data. proprietary compound is registered, if desired, it is compared for
Storing and displaying procedures and other related documents in uniqueness via a configurable, stereoselective duplicate check and
concert with the data eliminates this risk and helps build perspec- assigned a registry number.
tive on the study.
Sample Tracking
Sample Lifecycle Management
Tracking samples, requesting analysis and establishing chain of
E-Notebook can manage the entire sample lifecycle through tight custody can all be simply managed within the E-Notebook inter-
integration with Inventory. Sample lifecycle management is essen- face. E-Notebook serves as a repository for analytical data and
tial for the registration, testing, evaluation, and reporting in vari- experiments, linking such data directly to the sample ID, and it
ous analytical and manufacturing stages. Manual tracking of sam- acts as a communication portal with which scientists and analysts
ples and test results is labor-intensive and time-consuming; and communicate with each other during the service request lifecycle.
compliance with GxP guidelines requires expensive manual Scientists create and send service requests directly to an analyst
audits. with the click of a button. Paper is eliminated: when results are
obtained, the analyst can send the images and chromatograms
The controlled flexibility of CambridgeSoft’s E-Notebook is well directly back to the scientist's E-Notebook (which appear in the
suited for these detail and compliance-oriented environments. person's E-Notebook inbox, and are then accepted into the experi-
E-Notebook’s Sample Lifecycle Management module is compliant ment if desired). To establish chain of custody, each step of sam-
with Good Laboratory Practices (GLP), Good Manufacturing ple ownership is tracked, recorded and made compliant with
Processes (GMP) and 21 CFR Part 11. FDA's 21 CFR Part 11.
L A B O R AT O RY
Workflow LIMS,
Visual LIMS, Lab Automation,
Workflow LIMS Automation • Service Request Workflow allows scientists to

CambridgeSoft’s Workflow LIMS is a scientific data and communicate as they work
workflow management tool for lab automation and in silico
experimentation. Workflow LIMS eliminates the need for custom • Direct Communication from E-Notebook to create
programming by providing a visual experiment design and work-
tasks and send results
flow layout with built-in laboratory automation and analytics.
By using Workflow LIMS, researchers can connect their • Method Execution Framework to enable standard
laboratory processes, instruments, and decision points in a operation procedures and compliance
conceptual manner that directly couples to instrumentation— for
both automation and data gathering—and provide
Applied Technologies and Benefits
real-time results. The Workflow LIMS solution enables a
scientific team to design procedures, execute those procedures, Workflow management enables discovery teams to rapidly trial
capture the results and integrate lab equipment to automate part new procedures, capture best practices and scale successful designs
or all of the process. Procedures typically revolve around lab activ- from a manual prototype right up to a fully automated high-
ities, but may also draw in decision support tools on a scientist's throughput lab. But discovery and research, by its very nature,
desktop, and queries/updates to databases. demands that processes be flexible and that workflow execution
rapidly adapt to new techniques and equipment.
Interactivity and Integrity
1. The modeling environment, Workshop Configuration Editor, Conventional laboratory information workflow applications can-
in which the scientific team models the capabilities of the lab - for not meet this requirement because of their heavyweight configu-
example, the kind of basic processes which are available in the lab, ration needs, their lack of adaptability and the cost and complex-
and their inputs and outputs. ity of integrating them with rapidly changing lab technology.
2. The design environment, Workbench, in which researchers Workflow LIMS addresses these problems by providing a visual,
create workflows from these basic processes. easy-to-use environment for describing processes and building
3. The runtime Operations Manager, which manages the assign- workflows out of those processes, enabling scientists to rapidly
ment of tasks to agents, tracks the progress of tasks and workflows, trial new procedures, and by offering a rapid development tool kit
and manages the storage of captured data. for equipment integration which supports gradual automation to
4. The agent tier, made up of a number of applications that han- minimize up-front costs and ongoing risk.
dle specific types of task, either manually (through a user inter-
face), or automatically (by driving equipment through a control CambridgeSoft’s Workflow LIMS simplifies even manual lab pro-
interface or performing automated data processing). cedures by managing the breakdown of a procedure into tasks, and
5. The monitoring tier consists of a reporting tool that by automating the majority of data capture and transfer tasks; but
provides historical utilization information, and a live activity by capturing process as well as data, Pathways reduces the costs
viewer that allows scientists to drill into individual workflows and risks of implementing discovery techniques, and enables
and samples. companies to accelerate the entire discovery process.
Compliant DB & Oracle Cartridge

Compliant Storage and Chemical Data Management
Compliant DB
• Develop Centralized Validated Storage and
CambridgeSoft’s Compliant DB is the industry's enterprise GxP Compliant Storage
content management system developed by a large pharmaceutical
company. It serves as an electronic library that collects, organizes,
• Store Documents, Machine Files & Chemical Objects
warehouses, indexes and safely archives all your structured and
unstructured electronic records. From raw data and laboratory
reports to compliance records, Compliant DB also will support any • Oracle Cartridge is compatible with Linux, Solaris,
of CambridgeSoft’s workflow solutions, including E-Notebook, AIX and Windows and includes structure searching,
BioAssay, and Inventory. As its name implies, Compliant DB is fully property predictions and nomenclature
compliant with the requirements of 21 CFR Part 11 for
electronic records and electronic signatures.
Oracle Cartridge
Compliant DB can be used directly over your company's intranet, The CambridgeSoft Oracle Cartridge is used by all ChemOffice
extranet, or over the Internet with a simple web browser. Enterprise applications for storing, searching, and analyzing chem-
Complaint DB gives your organization a secure, 21 CFR Part 11 ical data. It can also be used in the development of your custom
compliant centralized electronic library for all electronic data files. Oracle applications. Chemical structure and reaction data is diffi-
Not only can machine-readable instrument data files be stored,
cult to manipulate without utilizing special software, and Oracle
but also images, multimedia files, presentations, human-readable
data cartridges define new, recognized data types. CambridgeSoft’s
word processing and Adobe PDF documents, spreadsheets and
hundreds of other formats. This data can serve as source data Oracle Cartridge utilizes this technology, making it possible to
(instrument data to BioAssay), and also repository. Although manipulate chemical structure and reaction data from within
Compliant DB can operate as a stand-alone application, only Oracle, improving portability and consistency in applications.
CambridgeSoft provides fully-integrated Knowledge Management Since the Oracle Cartridge is accessed through native Oracle SQL,
and Enterprise Informatics applications integrated with compliant programmers can interact with chemical structure data directly in
storage. Compliant DB makes this possible. the database.
Workbench Sample
The CambridgeSoft Oracle Cartridge supports CDX, CDXML,
MolFile, MolFile v.3000, RXN and SMILES formats, making it
flexible enough to be included with both new and legacy data
applications, without the need for file conversion. Chemical infor-
mation can originate from either ChemDraw or ISIS Draw, E-
Notebook, Inventory, or Registration. Oracle Cartridge has extensive
support for stereochemistry, relative stereochemistry, tautomers
and structure normalization. There is also a built-in structure enu-
merator (for nonspecific structures), basic property predictors,
nomenclature algorithms (name=struct), and dynamic utilities for
molecular file format conversions.
BIOLOGICAL
BioAssay, BioViz,
Assay Screening and Visualization
BioAssay
• Effectively manage data from complex biological
For modeling complicated in vivo experiments, or
assays involved with lead optimization
supporting an ultra-HTS platform, BioAssay has become the lead-
ing choice for managing biological experimental data. It is the
• Scalable HTS & HTTS
only application of its kind to provide a best-of-breed solution for
both ultra-high volume laboratories and lower-throughput set-
tings. BioAssay includes support for laboratory automation, calcu- • Use BioDraw to document cellular pathways
lation, and statistics, and also complicated low and medium
throughput assays such as animal models and in vivo experiments.
BioDraw
BioAssay is designed to tackle the needs of high and low through-
Diagramming and presenting cellular pathways is made easier and
put screening biologists alike by providing an application flexible
more effective with BioDraw. Formerly called Pathworks,
enough to model any assay, regardless of complexity, through an
BioDraw does for biologists what ChemDraw has done for
easy-to-use interface for importing, storing and analyzing the data.
chemists—saving time and producing a more professional
The software supports the quick set-up of biological models, auto-
representation of the science.
mated calculations and curve fitting, data validation, and the cre-
ation of customized structure activity reports.
BioAssay Extends E-Notebook
unmatched. Common pathway elements such as membranes,
BioAssay Enterprise is a scalable, flexible biological screening solu- enzymes, receptors, DNA and reaction arrows are built into the
tion utilizing Oracle’s role based security and the Oracle Cartridge. BioDraw toolbar. BioDraw also allows the import of images in
When used as part of ChemOffice Enterprise, BioAssay is integrat- GIF, PNG or JPEG formats. BioDraw offers many ways to share
ed with E-Notebook for experimental data, Inventory Enterprise for your drawings and accompanying data. Users can export data to
plate tracking and management, Registration Enterprise for the reg- Microsoft Office applications for inclusion in presentations and
istration of new compounds and BioSAR Enterprise for customized grant proposals or save data as an image file for use in journal
reporting. article submission.
BioAssay Ultra is designed to deliver much of the functionality of our

enterprise level applications, without a widespread roll-out.
BioAssay Ultra, coupled with BioViz, offers a user friendly inter- Draw Biological
Pathways
face for importing, viewing, validating, and plotting your biolog-
ical assay data from your desktop.
• BioAssay effectively manages data from complex biological assays

involved with lead optimization.
• BioViz integrates with BioSAR for one step in-depth data Plot Assay Data
analysis from a BioSAR report.
BioSAR & BioDraw

Data Mining and Pathway Drawing
BioSAR
• BioSAR is a catalog driven mining and structure-
BioSAR Enterprise, a strategic must for any discovery
activity analysis program
organization interested in serious data mining, is a data dictionary
driven structure-activity analysis program. Users may choose
among assays registered in the dictionary or search for assays • BioSAR provides both form and table views within
of interest. a simple and powerful web interface
The power of BioSAR lies in the researcher’s freedom from • BioViz provides one-step in-depth analysis of
dependence on IT support for dynamically working with all avail- several variables
able scientific data. For example, once an assay is registered into
the data-dictionary, it is automatically included in the powerful
analysis framework. By reducing the time between question and
answer, BioSAR gives researchers the ability to explore new ideas
• BioSAR is a catalog driven data-mining and structure
and avoids this issue by placing SAR report creation in the
activity analysis program.
researcher’s control.
• BioSAR provides both form and table views within a
simple and powerful web interface.
BioSAR Enterprise allows the researcher to create custom reports
• BioDraw makes it easy to draw and annotate
and views of their data. You decide what is displayed, and BioSAR
biological pathways including common elements such as mem-
takes care of the rest.
branes, enzymes, receptors and DNA.
While most SAR tools provide only a table-based interface,
BioViz
BioSAR provides both a form view and table view, and connects to
BioViz for high-dimensional analysis. BioSAR merges the sophisti- BioViz with ChemFinder transforms the numbers in your database
cation of a powerful data catalog technique with knowledge into graphics on your screen. Retrieve or search for a set of com-
gained through years of working closely with scientist users. The pounds, choose the data you want to see, whether it is biological
result is a SAR application that is as intuitive as it is powerful. test results in Oracle tables, physical property values calculated
Security within BioSAR Enterprise is highly granular; different automatically or prices in a catalog, and BioViz will generate an
roles exist for administrators, publishers, and browsers. interactive window showing a scatterplot, histogram, or other
useful data graphic.
Administrators may add assays to the data catalog engine, publish-
ers may create reports and publish them, and browsers may use The Plot Window, the key to data visualization in BioViz, is able
data query and analysis. Most data mining tools provide a mech- to show two variables plotted against each other in a scatterplot
anism to store queries, but the interface for creating queries is too with each point representing a structure from the current hit list.
complex. With BioSAR, each set of assays is a complete report If you, for example, modify the list by performing a search, the
with a query form, a view form, and a table view, combining the plot updates to show the new set of points. You can drag a rectan-
convenience of a ChemFinder or ISIS application with the power gle around a set of points to select them or zoom in to see
and flexibility of a data catalog-driven mining program. them more closely.
CHEMICAL
Inventory, Registration,
Chemical and Biological Inventory, Freezer Management,
Chemicals and Biologicals

• Register and Track Chemicals & Biologicals
Inventory is an application designed to manage the chemical and throughout the enterprise
biological reagent tracking needs of laboratories and research cen-
ters in multiple contexts: lab reagents, freezers/racks, plate man-
• Freezer/Rack/Plate Handling--Targeting, Workflow
agement, proprietary compounds and stockroom are just some of
and HTS Support
the areas where Inventory has been deployed.
• Supports Barcoding, Report Generation & Audit Trails
The system manages data associated with both commercially pro-
cured and internally produced chemical substances from procure-
ment or initial production through depletion and disposal.
Inventory Enterprise is an Oracle-based ChemOffice Enterprise
Registration Enterprise
product and can be used with other modules, such as E-Notebook,
to track batch records in manufacturing, or to look up reagents Registration Enterprise is built around robust data model for pure
from stockroom when planning a synthesis, BioAssay when sup- compounds, batches, salt management, automatic duplicate
porting a high throughput screening environment, Registration for checking and unique ID assignments. Built on the Oracle
tracking proprietary compounds, DocManager for linking certifi- Cartridge, it handles stereochemistry (including advances in rela-
cates of analyzes, analytical reports, or other documents associat- tive stereochemistry), tautomerization and structure normaliza-
ed with samples, and ChemACX available chemicals database for tion for duplicate checking. Using ChemScript, it also can enforce
sourcing new compounds. drawing business rules, such as orientation around a scaffold and
functional group normalization. Compounds may be entered
Inventory Enterprise includes plate handling and interfaces to
individually through a user-friendly web form, through the use of
liquid handlers for HTS environments, freezer/rack layout and
targeting for managing biologicals, full chain of custody, audit a batch loader, from Inventory, or directly from E-Notebook.
trails for GxP compliance, request/disbursement workflow for use
in both manufacturing and pre-clinical settings, and features As compounds are registered, regardless of whether through the
tailored to specific material domains. web user interface, E-Notebook, or from a batch file, they are com-
pared for uniqueness via a configurable, stereoselective duplicate
• Reagent handling and stockroom reporting check, and assigned a registry number. All information about the
• Request/disbursement workflow for stockroom and compound, including its test data and other syntheses, is tracked
GxP environments by the registry number, and this is used to link data throughout
• EH&S module, and links for MSDS data sheets ChemOffice Enterprise. Registration Enterprise is the only true
• Freezer/rack layout for biological materials n-tiered application of its kind that is designed around thin clients
• Extensive plate handling for HTS and uHTS settings
and thin servers, with interfaces directly to Inventory, batch file
Inventory is also available in two other editions: Workgroup and registration and E-Notebook. Oracle is supported on a variety of
Desktop. Inventory Workgroup is a rich-client SQL Server-based platforms and operating systems. Using Oracle secures your pro-
product geared at managing stockrooms and reagents. Inventory prietary data through the use of Oracle’s role-based security and
Ultra is a desktop edition based on the Workgroup product, and allows all chemical and non-chemical data to be stored directly in
includes the ChemACX database. the Oracle tables.
DocManager & ChemFinder

GxP, Registration and Enterprise Infrastructure
Formulations & Mixtures

• DocManager parses Word, Excel and PowerPoint
Formulation scientists face different challenges from those work-
documents, including free text and structures
ing with individual molecules, yet many of the tools they are
forced to use emerge from the drug discovery world, where single-
• ChemFinder is tightly integrated with BioSAR, BioViz
molecule research is the norm. Take an essential task such as com-
and Oracle
pound registration and you will find that most systems are
designed for registration of single molecules, with little thought
for the world of formulations and mixtures. CambridgeSoft has • Support for advanced form layout and design
developed a system specifically designed for this registration need

called Formulations & Mixtures. DocManager Enterprise
ChemFinder Enterprise • DocManager parses Microsoft Word, Excel and PowerPoint

documents, including free text and structures.
ChemFinder Enterprise is a multiple-user system designed for sites • DocManager has a web based interface and a file drop
with comprehensive chemical and biological data needs. folder for quick submissions.
ChemFinder Enterprise contains its own engine for working with • Oracle Cartridge is compatible with Linux, Solaris, AIX
local and shared databases, and it is also delivered with the and Windows and includes structure searching, property
CambridgeSoft Oracle Cartridge, the powerful Oracle-hosted predictions and nomenclature.
structure engine based on ChemFinder search technology. The face
of ChemFinder Enterprise is the same friendly form-oriented inter- Web browser based, DocManager Enterprise extends the capability
face as the desktop version, but underneath is a fast direct connec- of standard search engines to include full free text searching and
tion to Oracle and the robust, scalable Oracle Cartridge running chemically intelligent structure searching of electronic documents
on the server. including Text, Microsoft Word, Excel, PowerPoint, and Adobe
PDF. The DocManager Enterprise interface allows users to easily
submit documents through a series of simple-to-navigate web
Index Documents forms. When a new document is submitted, DocManager builds a
free text index of the document, and extracts chemical informa-
tion into a chemically-aware, substructure searchable database.
Chemical information can originate from either ChemDraw or
ISIS Draw.
DocManager Enterprise includes a batch loading utility for admin-

istration level users to load multiple documents at one time. The
system can be configured to submit a batch of documents as one
Manage your event, or as a reoccurring submission to be executed daily. The
Inventory
administrator specifies a time for the submission to take place and
the location of the files. DocManager Enterprise utilizes the search-
ing intelligence of the ChemOffice Enterprise suite.
M A N U FA C T U R I N G
Reference Standards,
Regulated Materials Management,
Inventory Enterprise
• Request/Dispense/Reference Standard Materials
CambridgeSoft’s Inventory Enterprise application is designed to from Central Group to Sites
manage the chemical, reagent, sample and compound tracking
needs of large multi-site chemical and pharmaceutical laboratories.
• Certification/Expiration/Certificate of Analysis of
Inventory Enterprise is an Oracle-based, ChemOffice Enterprise Containers and Aliquots
product that is designed for multiple users with diverse container
types, racks and multi-well plate formats.
• Create/Manage Container History and Genealogy
Entities in the Inventory system include locations, containers and

substances. A location is defined as any physical location where a Searching
container, plate or another location can be stored. An inventory
container represents a container capable of storing chemical sub- Every field in a record is searchable. The application includes a
stances. An inventory substance represents a chemical compound, number of specially designed inventory search forms. Search
mixture, sample, etc. Inventory Enterprise manages an unlimited results are returned in list form and can be exported into a docu-
number of diverse locations, containers and substances. ment (PDF, RTF, HTML) via the report engine.
Containers are created to represent the actual storage vessels used Workflow Support
by the organization. Each container is assigned a unique barcode Supported user transactions include the ability to request,
identifier which can be printed, using customizable report tem- dispense, modify, duplicate, dispose, etc. entities throughout the
plates, from the Inventory interface. Updating the inventory system. These and other transactions are an integral part of
becomes as easy as scanning barcodes into the system and adjust- Inventory workflows.
ing parameters for one or multiple containers. Users are able to
order, check-in/out, move, split and merge containers at will. For example: a user logs-on, finds the substance(s) they’d like to
Typicalcontainers include: ttles, vials, tubes, cylinders, boxes, request and makes a request entry in the system; the request is ful-
racks, multi-well plates, etc. filled directly by changing the location the substance or by taking
an aliquot and creating a new container of the substance. The new
Multi-well Plates substance/container is also tracked in the system and inherits all
Inventory Enterprise manages multi-well plate information. In of the critical properties of its parent container. If a quality con-
addition to creating, storing, moving and deleting plates, the trol test is run on the parent, then the results are viewable in the
application allows users to create daughter plates, reformat plates daughter’s properties.
and utilize plate maps. Inventory also supports user-interfaces or
machine-interfaces for these operations (including reading files The multi-select capability allows the user to select several con-
from liquid handler robots). Inventory Enterprise has the capabili- tainers and perform a transaction on all of the selected containers
ty to import datafiles from other computer systems such as liquid simultaneously, including check-in/out, move, retire, delete and
dispensers/handlers, Microsoft Excel spreadsheets, etc. to accom- update. For instance, if a request is made of the system that is
modate automated updating of information in the Inventory fulfilled by another user (such as dispensing), the requester can
database. automatically receive e-mail notification of the progress. Likewise,
users can be alerted to pending requests in the system.
Inventory & GxP

Document Storage, Batch Records
Conflict Resolution
• Validated for GxP Environments with Audit Trails,
The Conflict Resolution processes flags and corrects Container History
duplicates in the system automatically. You may also search for
duplicates at any time. If a conflict is found, the screen
• Store Datafiles with Samples such as Batch and
identifies the conflicting field(s) by highlighting it in red. The user
Certificates of Analysis
has the option to select the existing substance and edit the con-
flicting substance or create a duplicate substance and resolve the
conflict later. • Allows for Flexible Reporting
Printed Reports & Labels

The Inventory interface allows for printing labels and can generate Electronic Data Files
elaborate reports. Inventory Desktop and Workgroup use a report
engine that incorporates wizards that allow for the quick creation In addition to storing, moving and disposing containers, the
of simple report/label templates that can be shared across an application allows users to reformat plates and create daughter
organization. A user has the ability to design a label based on templates as well as integrate with liquid dispensers/ handlers for plate
plates for a number of commercially available label sheets (e.g. reformatting from pipette log files.
Avery Dennison). The Inventory manager makes extensive use of
barcodes and web-based user interfaces to speed use, but substan- Compliance
tial gains come in the automated reporting and alerting. Examples Handling FDA regulations in an organization is an area that lends
include notifying all users of samples derived from a single stan- itself to automation. Thus, systems must be carefully implement-
dard of some change in status, such as different analytical results ed in order to meet the letter and spirit of FDA guidelines.
or failure to recertify. Underlying the system are the controls expected by systems in reg-
Inventory Enterprise ulated environments: audit tables, security and validated develop-
ment methods. All transactions on all containers in the system are
tracked and audits are customizable for simple presentation.
Document Management
To manage the myriad of documents that get generated in research
and regulated environments, CambridgeSoft stores documents
securely in Oracle where they are indexed (by chemistry and text)
and managed by database security. Storing the associated docu-
ments in Oracle preserves system integrity such that you can back-
up to a known point, and be assured that the documents and data
are entirely in sync with each other. It also provides tight docu-
ment security, reduces IT overhead associated with file shares and
attaches directly to Inventory containers.
DESKTOP
S O F T WA R E
Chem & Bio Office

Software Standard for Scientists
The ultimate Chem & Bio Office is a powerful suite of software, consisting of ChemDraw, Chem3D, ChemFinder and ChemACX
software suite for chemists, BioDraw, BioAssay and BioViz for biologists and Inventory and E-Notebook for all types of scientists. Chem &
for scientists Bio Office is available for Microsoft Windows.
The standard Chem & Bio Draw includes Struct=Name, ChemDraw/Excel and ChemNMR, BioDraw, a biological sequence tool,
achieves the hotlinks to 3D structures, Stoichiometry grid, live linked chemical property calculations, a TLC plate tool and more. The
ultimate ChemDraw ActiveX/Plugin adds chemical intelligence to your browser for querying databases and displaying information.
Computational ChemBio3D provides state-of-the art visualization and display of protein structures, molecular surfaces, molecular
chemistry made easy orbitals, electrostatic potentials, charge densities and spin densities. Chem3D provides basic computational tools such as 3D
Molecular Overlay and Dihedral Driver and utilizes MOPAC, Jaguar, Gaussian, GAMESS and extended Hückel to com-
pute molecular properties. ChemProp computes Connolly surface areas, molecular volumes and properties, including ClogP,
molar refractivity, critical temperature and pressure.
Desktop to ChemFinder is a chemically intelligent database manager and search engine. ChemFinder provides support for a database
enterprise searching searching, compound profiling, R-Group Analysis, subforms, tight integration with ChemDraw/Excel and Combichem/Excel,
statistical analysis and visualization through BioViz all in a friendly form-based environment. ChemFinder/Office searches
documents, spreadsheets, and files for chemical structures and references. ChemFinder/Oracle provides enterprise solution
integration.
Ultimate suite BioOffice is the ultimate suite for management, analysis and visualization of biological data using BioDraw for drawing
for biologists pathways and BioAssay, BioFinder and BioViz for data analysis. Includes Bio3D, Draw/Excel, CombiChem/Excel, Inventory and
E-Notebook.
Draw pathways BioDraw provides support for biological pathway drawing and annotation. A wide variety of customizable drawing tools
are available, including membranes, DNA, enzymes, receptors, tRNA, ribosomes, and a plasmid map tool.
Screening data BioAssay manages both high and low throughput biological screening data. Designed for complex lead optimization
experiments, the software supports the quick set-up of biological models.
Visualize data BioViz offers automated statistical analysis, curve fitting, and customized structure activity reports, including a user-friendly
interface for importing, viewing, validating and plotting chemical and biological data.
Handle reagent Inventory manages your reagent and biological tracking needs. Using MSDE as the desktop database, you organize, store
racking and search over your inventory. Inventory integrates with the ChemACX database of available chemicals and ChemMSDX
safety data providing chemical sourcing and purchasing.
Efficient notebook E-Notebook is an efficient, accurate way to write notebooks. It stores Microsoft Office documents, ChemDraw
keeping structures and reaction drawings, and related data in a notebook searchable by text or chemical structure. Organize pages by
project, experiment or in your own style. Use CombiChem/Excel to build libraries.
Access info Databases include ChemINDEX, including the NCI and AIDS databases. The ChemACX database contains nearly 400
with ease catalogs from leading suppliers and ChemMSDX Database contains over 20,000 material safety data sheets for commonly
used laboratory chemicals.
DESKTOP
ChemDraw, Chem3D,
Structure Drawing and Molecular Modeling
ChemBioDraw Ultra adds BioDraw, ChemFinder, BioViz

and E-Notebook to ChemDraw Ultra. Easily draw and annotate • ChemDraw’s improved Struct=Name feature produces
publication quality biological pathway illustrations with the names for more types of compounds
BioDraw tools. The combination of the BioDraw tools with
ChemDraw and E-Notebook creates an excellent environment for • Live ChemDraw window embedded in Chem3D application
smooth communication between Chemists and Biologists. allows simultaneous 2D and 3D editing
ChemDraw Ultra adds Struct=Name, ChemDraw/ Excel, • Chem3D brings workstation-quality molecular graphics and
ChemNMR, Stoichiometry Grid, CLogP, tPSA as well as the added rigorous computational methods to your desktop
capabilities of Chem3D Pro and ChemFinder Std to the
ChemDraw Pro application. With rich polymer notation, gener-
ic structure expansion, fragmentation tools, and a modern user
interface, ChemDraw is more powerful than ever before. Create
tables of structures, identify and label stereochemistry, estimate ChemNMR can be used to accurately estimate 13C and 1H
NMR spectra from ChemDraw structures, obtain structures from chemical shifts. The structure and the spectrum appear with the
chemical names, assign names from structures, and create multi- chemical shifts displayed on the molecule and the spectrum is
page documents and posters. linked to the structure so that clicking on a peak in the spectrum
highlights the corresponding fragment on the molecule.
ChemDraw Pro will boost your productivity more than ever.
Draw quality publications with structures, reactions, chemical ChemBio3D Ultra includes visualization and molecular mod-
queries, polymers, relative stereochemistry, generic structures, eling capabilities for both small molecules and protein structures
TLC plate depictions and a biological sequence tool. Publish on designed for the bench chemist. Small molecule computational
the web using the ChemDraw Plug-in. Create precise database methods include Molecular Overlay and Dihedral Driver. It also
queries by specifying atom and bond properties and stereochem- includes interfaces to the MOPAC, Jaguar, Gaussian and
istry. Display spectra, structures and annotations on the same page GAMESS semi-empirical and ab initio computational packages.
High quality Chem3D graphics can be viewed on the web using
Struct=Name contains the leading comprehensive
the Chem3D ActiveX.
methods for converting chemical structures into chemical names
and names to structures. It can be used for many types of com-
Chem3D Pro brings workstation quality molecular visualiza-
pounds, including charged compounds and salts, highly symmet-
tion and display to your desktop. Convert ChemDraw and
ric structures and many other types of inorganic and
organometallics. Struct=Name is available in two forms: a batch ISIS/Draw sketches into 3D models. View molecular surfaces,
application, and an interactive version that is also available in orbitals, electrostatic potentials, charge densities and spin densi-
ChemDraw Ultra. ties. Use built-in extended Hückel to compute partial atomic
charges. Use MM2 to perform rapid energy minimization and
ChemDraw/Excel allows the user to create chemically molecular dynamics simulations. Chem3D can also be used to
knowledgeable spreadsheets within the familiar Microsoft Excel estimate physical properties such as logP, boiling point, melting
environment. You can build and manipulate chemical structures, point and more. Visualize Connolly surface areas and
compute chemical properties and perform database searches. molecular volumes.
S O F T WA R E
ChemFinder & ChemInfo

Structure Searching and Scientific Databases
ChemFinder Ultra is a chemically intelligent database man-

agement and search system designed for chemical and biological • ChemFinder offers improved searching and hit list management,
data. ChemFinder Ultra can be used with local (MSDE) or shared along with new property generation
(Oracle) databases. Either way, the face of ChemFinder is the
same friendly form-oriented interface. BioViz, included in • ChemFinder is tightly integrated with CambridgeSoft's
ChemFinder Ultra, provides data visualization features to help Oracle Cartridge
the user understand relationships between biological data and
chemical structures. These features allow you to plot structural • Search ChemACX and other CambridgeSoft
and biological data in a variety of styles, perform statistical analy-
sis, filter plots based on your criteria, highlight intersecting sets on
plots, generate histograms of data distributions, and more. ChemACX Database includes over 1 million chemical
products available for purchase from 472 supplier catalogs, search-
BioViz, included in ChemFinder Ultra, provides statistical analysis able with a single query by structure, substructure, name, syonym,
and visualization tools for structural and biological data. BioViz partial name, and other text and numeric criteria.
transforms ChemFinder database information into easy to under-
stand graphics, allowing users to discern structure-activity rela- ChemMSDX Database provides material safety datasheets
tionships more easily. With BioViz it is easy to retrieve a set of and is integrated into ChemACX, and contains over 23,000
compounds using filters or searching capabilities; and generate an Material Safety Data Sheets (MSDS) in PDF format.
interactive window showing a wide variety of useful graphical
information. ChemINDEX Database includes 100,000 chemicals, public
NCI compounds, AIDS data and more.
ChemFinder Pro is a fast, chemically intelligent, relational
database search engine for the Desktop. The integration with NCI Database contains over 200,000 compounds with anti-
Microsoft Excel and Word adds chemical searching and database cancer drug dose-response data.
capability to spreadsheets and documents. Compatibility with
MDL ISIS databases is provided by SDfile and RDfile AIDS Database is an NCI compiled database for AIDS anti-
import/export. viral compounds.
ChemRXN Database is a collection of 30,000 fully atom-

Molecular Modeling mapped reactions selected and refined from chemical literature. It
also includes reactions from InfoChem’s ChemSelect database and
ISI’s ChemPrep database.
ChemBioFinder.Com is the award-winning web site with-

in formation and WWW links for over 100,000
chemicals. Users can search by name or partial name, view struc-
Estimate Spectra
ture drawings, or use the ChemDraw ActiveX/Plugin for structure
and substructure searches.
DESKTOP
BioAssay, BioViz, BioDraw,

Biological Assay, Visualization and Pathways
BioAssay Ultra
BioAssay Ultra, the cornerstone of BioOffice, provides flexible • BioAssay offers flexible storage, retrieval and analysis of
storge, retrieval and analysis of biological data. BioAssay biological data

easily manages both high and low throughput biological screening
data. • BioViz provides statistical analysis and graphical representations
of the data loaded into a ChemFinder form
Designed for complex lead optimization experiments, the soft-
ware supports quick set-up of biological protocols, automated • BioDraw allows for quick and easy drawing and annotation
calculations and curve fitting, and the creation of customized of biological pathway depictions.
structure activity reports. BioAssay brings all of this functionality
to your desktop. BioAssay Ultra, compatible with the MSDE
database, offers a user-friendly interface for importing, viewing, many elements that are difficult to draw with the standard presen-
validating and plotting your biological assay data. tation and word processing software. Common pathway elements
such as membranes, enzymes, receptors, DNA, tRNA and plas-
BioViz mid maps are built into the BioDraw toolbar. BioDraw is built
Combining biological data with chemical structures is of the into the same backbone as ChemDraw, allowing users to take
utmost importance in any drug discovery environment. BioViz advantage of the wide variety of the publishing capabilities avail-
allows you to visually analyze and perform statistical analysis on able in ChemDraw such as the ability to import and export images
structure-related data combined with biological data in in GIF, PNG or JPEG formats. In addition, the integration of
ChemFinder. ChemDraw and BioDraw in Chem & Bio Draw application pro-
vides a great communication mechanism between chemists and
Users can search over structural and biological data and biologists.
Notebook Pages
construct various plots such as scatterplots or histograms. The
plots are interactive; allowing you to select subsets of your data,
perform statistical analysis, filter plots based on your criteria,
highlight lists and intersecting sets on plots, generate histograms
of data distributions and more.
BioDraw
Reporting on and presenting findings is a task familiar to every
biologist. Making this process easier and more effective benefits
everyone involved. BioDraw is doing for biologists what
ChemDraw has done for chemists for years—saving time, and
resulting in a more professional representation of the science.
unmatched. Typical drawings of biological pathways include
Data Visualization
S O F T WA R E
Inventory & E-Notebook

Materials Management and Electronic Journal
Inventory Ultra
• Inventory manages the chemical and reagent tracking needs
Inventory Ultra allows users to manage the tracking needs of of laboratories and research centers
chemical and non-chemical inventory data for laboratories and
research centers. The system manages data associated with both
• Inventory maintains its own internal chemical structure database
commercially procured and internally produced chemical sub-
with advanced duplicate checking
stances from their procurement or initial production through
their depletion and disposal. Inventory Ultra is an MSDE based
product and includes the ChemACX database with over 450 cat- • E-Notebook stores Microsoft Office documents, ChemDraw
alogs of chemical reagents. structures, reaction drawings and related data in a convenient,
searchable format
The three primary entities in an Inventory system are
locations, containers and substances. Users or administrators con-
figure a network of locations, which represent locations within an E-Notebook Ultra
organization. Containers are created to represent actual containers E-Notebook Ultra is an efficient, accurate way to store lab note-
in your facility. Each container is assigned a unique barcode, book information. It stores Microsoft Office documents,
which can be printed using a customized template from the ChemDraw structures, reaction drawings and related data in an
Inventory interface. electronic notebook that is searchable by text or chemical struc-
ture. You can organize pages by project, experiment or in your
Each container stores a substance. Additional text fields are avail- own style with the MSDE database. CombiChem/Excel builds
able to track other chemical contents such as the solvent. Custom combinatorial libraries. E-Notebook is configured exactly like a
fields may also be defined. To keep track of substances the system chemist would like his or her own notebook to be. Reactions can
maintains its own internal chemical structure database containing be easily drawn into the reaction template by either selecting from
unique substances that can be associated with inventory contain- the generous list of preloaded reagents or by entering or drawing
ers. Advanced duplicate checking is incorporated in the system. one’s own chemicals. Commonly used reagents can be stored in a
Every field in a record, including the chemical structure, molecu- separate folder for easy access. Another fantastic feature is the pro-
lar formula and molecular weight are searchable. cedural section. This section contains pre-written procedural sen-
tences with the ability to easily drop in the specific names of
The application includes a number of specially designed invento- reagent chemicals present in the reaction. One can also easily add
ry search forms. Search results are returned in list form and can be other data to the notebook page such as spectra and Microsoft
exported into a document (PDF, RTF, HTML) using the report Word or Excel documents.
engine. The Inventory interface allows for printing labels as well as
generating reports. Inventory uses a report application that incor- CombiChem/Excel
porates wizards that allow for the quick creation of simple reports CambridgeSoft provides you with the tools to effectively plan
and label templates that can be shared across an organization. combinatorial chemistry experiments in Excel. The
CombiChem/Excel add-in introduces additional functionality for
Inventory Pro handling combinatorial chemistry. Users can generate products
Inventory Pro contains the same features as CambridgeSoft’s from a reaction and lists of reagents, you can view all the products
Inventory Ultra application, except without CambridgeSoft’s arising from a given reagent or all the reagents of a given product,
ChemACX database. and you can lay out reagent and reaction plates.
SCIENTIFIC
The Merck Index, NCI, AIDS,

Scientific Reference, Chemical Reactions and Patents
ChemBioFinder Gateway
• The Merck Index offers encyclopedic reference for over 10,000
ChemBioFinder Gateway allows searching of the complete chemicals, drugs and biological agents
CambridgeSoft reference collection of databases with a
• R&D Insight for Chemists has information on more than 20,000
single query. Search such databases as The Merck Index, R&D drug products in various stages of development world-wide
Insight for Chemists and Traditional Chinese Medicines with only from over 1,700 sources.
one click of a search button. All results federate back to the spe-
cific databases for complete information. • All databases are updated, contain information unavailable in
print, and are searchable by structure, as well as text and
numeric range by structure, as well as text and numeric range
The Merck Index
Known for its integrity, detail, and longevity, The Merck Index Traditional Chinese Medicines
contains over 10,000 monographs on drugs, chemicals and other
biologically active molecules. Each monograph contains informa- Access to this wealth of knowledge is now available with the
tion on the compound and its derivatives; common, trade, and Traditional Chinese Medicines database. The database consists of
systematic names; trademarks and associated companies; CAS monographs for 10,458 chemicals isolated from 4,625 natural
Registry Numbers, physical and toxicity data, therapeutic and sources used in traditional Chinese remedies. The monographs
commercial uses, literature citations, as well as chemical strucures, feature bio-activity data for many of the compounds, effects and
formulas andmolecular weights. The electronic versions include indications of the medicines, English, Latin, and Chinese names
archived monographs from previous editions and is updated twice a year. for the natural sources, and over 2,000 references.
R&D Insight/Chemists ChemINDEX, NCI AIDS & Cancer
Information on current drug products under development is Scientists have used the award-winning ChemFinder.Com database
essential for those working in research and development, licensing since 1995. Now, the data on ChemFinder.Com is integrated into
and marketing at pharmaceutical and healthcare institutions. ChemOffice as ChemINDEX. ChemINDEX contains data from
R&D Insight for Chemists, a collaborative product from Wolters over 75,000 compounds including structures, names and
Kluwer Health and CambridgeSoft, combines the power of chem- synonyms, physical properties and Internet links. Additionally,
ical structure searching with a wealth of drug development data to three informative databases have been integrated into one power-
give subscribers a competitive edge when making decisions rele- ful application with the NCI and AIDS database, a collection of
vant to the direction of their research. Updated weekly, users can over 200,000 molecules studied by the National Cancer Institute.
search the collection of over 20,000 compounds by structure,
substructure, names, partial names and synonyms. ChemReact and ChemSynth
These reaction database collections from InfoChem GmbH com-
Patent Database prising essential information on chemical reactions published in
Researchers, chemists and patent analysts are now able to easily the literature between 1974 and 2001. The largest is
search full text patents for chemical structures using ChemReact500, with almost 500,000 reactions selected with an
CambridgeSoft's powerful search and analysis tools. The new eye toward synthetic utility. ChemSynth is a subset of the reac-
CambridgeSoft Patent Database portal, co-developed by tions found in ChemReact500 chosen because they have greater
CambridgeSoft and Reel Two, will give users access to all the than 50% yield and have been sited in leading journals more than
chemical compounds named in a patent, and enable them to once. ChemReact68 has 68,000 reactions that have greater than
search by structure, keyword or chemical name. 50% yield and have appeared in more than five example reactions.
D ATA B A S E S
ChemACX & Sigma-Aldrich MSDS

Available Chemicals and Material Safety Data Sheets
ChemACX Database
• ChemACX is fully structure searchable with more than 1
Sifting through chemical catalogs is a poor use of time for any million products from nearly 500 catalogs
researcher. ChemACX database solves this problem by offering a
• ChemACX and the Sigma-Aldrich MSDS are updated
complete tool for research chemical sourcing and purchasing. semi-annually to meet the needs of scientists
With an emphasis on up-to-date information of high quality,
ChemACX allows you to purchase chemicals fast, efficiently and • Search by name, synonym, partial name, formula, and
without worry or cumbersome paper catalogs. The database can other criteria
be accessed from both desktop and enterprise environments and
boasts nearly 500 catalogs from major suppliers, from Alfa Aesar to be aware of their proper handling, storage, disposal and emer-
and Aldrich, to TCI and Zeneca, with hundreds in between. gency procedures. Helping to fulfill these diverse needs is the
Sigma-Aldrich MSDS collection. The database contains over
Sigma-Aldrich MSDS 130,000 MSDSs for the products of the Sigma-Aldrich family of
Environmental, Heath and Safety (EH&S) is an important com- catalogs (Sigma, Aldrich, Fluka, Supelco, Riedel-de Haën) in
ponent of today’s research institutions. A key document that aids HTML format. With a click of a hyperlink, users will be able to
in the management of EH&S tasks is the Material Safety Data view the Sigma-Aldrich MSDS in their preferred browser. This
Sheet, also commonly referred to as MSDS. In every organization, information is smoothly integrated with the ChemACX
there are several groups of personnel who require access to database and other enterprise applications.
MSDSs. Everyone who comes into contact with chemicals needs
Drugs: Synonyms and Properties
Drugs: Synonyms and Properties from Ashgate, provides compre-
hensive coverage of the 8,000 drugs currently in common use
worldwide. A key component of this reference is the extensive cov-
erage given to synonyms. The electronic version adds almost
70,000 synonyms and trade names that did not fit into the print
version. This information is also available as an SD file to
facilitate in silico research.
Nanogen Index
The Nanogen Index contains data on over 1,000 pesticides and
other environmental contaminants. The database is the up-to-date
and authoritative source for information on all pesticides and agri-
cultural chemicals in world wide use, those which are currently
under development in R&D pipelines, and compounds which
were once marketed or reached a development status. Data fields
include chemical structures and SMILES strings, names (CAS,
IUPAC, trade), the various registration codes assigned to the com-
pounds (RTECS, EINECS/ELINCS, CAS, US EPA, CA DPR,
Tarrifs, etc.), Hazard and Safety codes, the developing company
and use.
PROFESSIONAL
Development, Deployment,
Custom Development and System Deployment
When processes and technologies are disjointed, organizations lose

efficiency and decision making capability. Our Professional With custom development, CambridgeSoft works collaboratively
Services use technology to bring business processes together, with your team to create a system that meets your needs while
integrate systems and assist with strategic informatics planning. executing our quality driven software development process. We
deliver what you need, on time and within budget, without surprises.
Informatics Planning
Strategic and Operational Planning
A formal review of the discovery and development process and Product Development
human/system interfaces is mapped to form the basis of a Development Consulting
roadmap for successful technology utilization.
• Analysis of the current laboratory and technology workflows With custom development, CambridgeSoft works collaboratively with
• An analysis of the current state of the science technology your team to create a system that meets your needs, while execut-
ing our quality driven software development process. We meet
environment, including architecture/operational processes
your needs, on time and within budget, without surprises.
• A view of strategic goals and the barriers to achievement
Systems Integration
• The delivery of a phased technology transition plan
Requirements Analysis & Proof of Concept Process improvement often requires integrating systems designed
for focused areas of work. CambridgeSoft has integrated various
With years of experience meeting the needs of the scientific com- E-Notebook, registration, inventory, and biological assay systems
munity, CambridgeSoft understands the user. The prototyping in a variety of settings. Whether these are CambridgeSoft, a third-
process allows definition and testing of the functional and techni- party product or an in-house developed solution. CambridgeSoft
cal feasibility of potential technology solutions. The process pro- has the expertise to unite these systems in order to they improve
vides a baseline for the future development and deployment of a business processes, laboratory efficiency and decision making.
tailored solution. Users gain valuable first-hand knowledge in Application Configuration
experiencing how the system can help achieve individual and
Your organization will see the benefit from implementing a
workgroup goals.
CambridgeSoft application, but would like to customize it for a
Legacy System Migration
unique environment. Our professional services teams provide
Legacy systems, with private data structures and architecture, can those specific features by developing market add-ins, or other
be barriers for migrating systems to new technologies. Our con- modifications that are supported in the future.
sultants have significant experience with these systems and can
successfully migrate chemical and biologial data, business work- Systems Deployment
flow, and other aspects of legacy informatics technologies.
Installation and Configuration
21 CFR Part 11 Compliance and GxP Validation
CambridgeSoft has a tested methodology for system
As an integral part in creating 21 CFR Part 11 and GxP deployment that consists of an IT architectural review, a business
validated applications, CambridgeSoft offers services to: workflow and process review as relates to specific scientific areas,
• Audit the software and process a process integration review, and maintenance guidelines. By care-
• Create conforming systems design specifications fully following this proven methodology, CambridgeSoft installs
• Create IQ/OQ/PQ documentation and configures systems that are easy to maintain and have the flex-
• Generate test plans and validation matrices ibility to accommodate variations in the science or business work-
• Insure systems compliance with functional guidelines flow that come from extensive experience in these areas.
SERVICES
Training & Support

Educational Training and Technical Support
Systems Optimization
CambridgeSoft’s systems deployment team will work with you to Managed Informatics allows your organization to focus on science,
make sure that your computing environment has been optimized while CambridgeSoft plans, implements and manages your
for high performance. Your systems,networks, applications and technology environment.
databases are assessed and designed to deliver maximum achieve-
ment.
Beta and Pre-Release Programs
Committed to maximizing your productivity through the use of Systems Management
our products, as well as exposing you to the newest technologies, Managed Informatics
our beta and pre-release programs provide you with first-hand Informatics outsourcing provides the people, processes and tech-
product knowledge and allows CambridgeSoft to improve appli- nology to develop a unique level of service for your organization.
cations with your feedback. For a monthly fee, CambridgeSoft will deliver the informatics
Pilot Software Evaluations applications and the technology staff required to maximize pro-
It makes sense to pilot an application before a major commitment ductivity. This service allows your organization to focus on sci-
to an enterprise-wide implementation is made. CambridgeSoft ence, while CambridgeSoft plans, implements and manages your
will work closely with you to plan the evaluation, deploy the technology environment.
application, and gather feedback regarding systems design, API’s Systems Hosting
and technology specifications. A hosting service that allows customers to use our state-of-the-art
Training enterprise applications over the extranet from any location 24
Effective user, administrator and help desk training is often an hours a day, seven days a week is available. With this hosting serv-
afterthought in many systems deployments. However, the produc- ice, our customers can shift the responsibilities of application devel-
tivity returns generated by an investment in systems training can opment and IT infrastructure management to CambridgeSoft,
be dramatic. CambridgeSoft offers a complete array of powerful, allowing more time to focus on core science, research, discovery
user-focused training services. and development functions.
Ultra Services
The Ultra Services program is CambridgeSoft’s personalized, pre-
mium service for supporting our customers. Organizations can
take advantage of both telephone and electronic access to
CambridgeSoft’s support scientists who can address:
• Usage and installation questions
• Product compatibility and interoperability questions
• Diagnostic review to help isolate the cause of a problem
• Configuration assistance
• Planning information for software updates and upgrades
• Assistance with problem resolution
Technical Support & Remote DBA Services

Technical Support and Remote DBA Services for Oracle and SQL
Server are also available.
Chem & Bio Office
Research, Discovery, Development, T rials & Manufacturing

Laboratory Informatics includes Workflow LIMs for instrumentation automation and Compliant DB for storage of your data.

Europe 00 800 875 20000 Germany +49 69 2222 2280
Japan 0120 146 700 France +33 1 70 71 98 80
Chem & Bio Office
SDMS
Research, Discovery, Development, Trials & Manufacturing

Laboratory Informatics includes Workflow LIMs for instrumentation automation and Compliant SDMS for storage of your data.
Europe 00 800 875 20000 Germany +49 69 2222 2280
Japan 0120 146 700 France +33 1 70 71 98 80
MAE 04980 0902

ChemBioDraw PDF

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ChemBioDraw PDF

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ChemBioOffice.

Chem & Bio Draw

 ystem running CS software (check one):

Thank You! Enjoy your software!

US 1 617 588-9300 FAX 1 617 588–9390 Web www.cambridgesoft.com

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CambridgeSoft Software and Database License

Database Product License

A: That’s correct. Other than copying the software you

A: Yes. Bulletin boards and user groups are bound by the

A: The Copyright Act allows a copyright owner to

Chem & Bio 3D ■

Chem & Bio Finder ■

MOPAC, GAMESS, MM2 ■

CS Gaussian, Jaguar Interface ■

Formulations & Mixtures ■

The Merck Index ■

ChemINDEX Database, NCI, AIDS & Cancer ■

Traditional Chinese Medicines ■

Drugs: Synonyms & Properties ■

Nanogens Index; Medicinal Chemistry ■

ChemACX, ChemMSDS Database ■

ChemReact500, ChemReact68 & ChemSynth ■

Chem & Bio Draw 12.0 i

Chem & Bio Draw 12.0 iii

Chem & Bio Draw 12.0 v

Chem & Bio Draw 12.0 1

Just a few of the BioDraw templates that are new in

Chem & Bio Draw 12.0 3

Chem & Bio Draw 12.0 5

Chem & Bio Draw 12.0 7

a. title bar e. document window

Toolbars Tearing Off Toolbars

Chem & Bio Draw 12.0 9

Chem & Bio Draw 12.0 11

Chem & Bio Draw 12.0 13

3. 1. Select the Bold, Dashed, or Solid Bond

NOTE: Chem & Bio Draw 12.0 treats hashed

Chem & Bio Draw 12.0 15

Chem & Bio Draw 12.0 17

4. Click OK. After you expand the nicknames, you can

NOTE: Nicknames are tokens and do not flip

Chem & Bio Draw 12.0 19

Chem & Bio Draw 12.0 21

Figure 3.4 Reversing chain direction

NOTE: If Fixed Lengths is off, use Ctrl+Alt or

Chem & Bio Draw 12.0 23

For example, to draw a new arrow starting at

Click a modified arrow (with the same arrow

NOTE: Click an unmodified arrow, or one that

Chem & Bio Draw 12.0 25

Chem & Bio Draw 12.0 27

NOTE: If an atom is unselected when a struc-

To rotate a selected object by a specified angle:

Chem & Bio Draw 12.0 29

Chem & Bio Draw 12.0 31

Scaling Objects NOTE: Objects are aligned with the selected

Chem & Bio Draw 12.0 33

ystem running CS software (check one):