2023/08/01

ORC2601/ ORC221F

Organic Chemistry II

Chemistry Department

Prof VE Pakade
pakadve@unisa.ac.za
M-028 Eureka

Purpose statement
After completing this module, students will be able to categorize the
various organic functional groups (hydrocarbons, alkyl halides, alcohols,
phenols, ethers, epoxides, amines, carbonyl, carboxylic acids and
derivatives, and aromatic compounds) based on their chemical
characteristics and structures. The learner will also be able to
comprehend the fundamental concepts of organic chemistry that are
used to name organic substances and categorize acid-base processes.
Additionally, the student will be able to recognize frequent functional
groupings, explain how they respond (i.e., reactions involving such
groups), and create schematic diagrams that illustrate reaction
mechanisms.

Assignment 1 preparation

Assignment 1 covers the topics in Specific Outcomes 1 and 2.

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Specific Outcome 1
Explain and apply the basic concepts related to the structure and properties of
organic compounds
Assessment criteria
Lewis structures are correctly drawn
Various types of covalent bonding are applied to organic compounds.
Hybridization and energy level diagrams in the formation of single and multiple bonds (sigma and pi
bonds) are correctly explained and applied
Relative bond lengths, bond strengths, bond angles and bond energies in organic compounds are
correctly described.
Curved arrows are used to correctly illustrate the movement of electrons: in electron delocalization in
resonance, bond-breaking and bond-making processes (homolysis and heterolysis).
Acid-base theories, electrophiles, nucleophiles and free radicals are defined and correctly applied to
organic molecules and reactions.
Intermolecular forces are correctly illustrated and applied.
Different physical properties are predicted on the basis on intermolecular forces.
Introduction of the different classifications of organic compounds (alkanes, alkynes, alkenes, aromatic
hydrocarbon etc.)

Organic chemistry and life

• Organic chemistry – chemistry of carbon compounds.
• Compounds of carbon are central to life – Think DNA, proteins etc.
• Big bang theory - Carbon atoms, CH4, CO2, H2O, NH4, and H2
• Exposure to electric discharges (lightning) produced highly energetic pieces.
• The highly energetic pieces combined to for complex molecules like amino acids,
purines, formaldehyde, hydrogen cyanide etc.
• Sugar can be produced from formaldehyde.
• Amino acids --→ proteins
• Many other organic compounds are found in medicine, nanotechnology,
bioengineering etc.
• However, some organic compounds course harm to humans and the environment.
• Scientists – reducing the impact of toxic compounds.

Organic compounds in living organisms

Wade LG, Organic Chemistry, 8th Edition, page 2.

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Atoms
We will just review what you need to know about atomic structure.
• Atoms consist of a positive dense nucleus made of protons and neutrons. Protons and
neutrons
• Around the nucleus, we find a cloud of electrons that make the atom (nucleus)
voluminous.
• Nucleus diameter: 10–14 to 10–15 meter.
• Total atom diameter : 2 × 10–10 m or 200 picometer (pm). (1 pm = 10–12 m).
• Protons and neutrons have similar masses, about 1800 times the mass of an
electron.
• Almost all the atom’s mass is in the nucleus, but it is the electrons that take part
in chemical bonding and reactions. Cloud of electrons

Two numbers to describe atom:

The atomic number (Z) which is the number of protons.
The mass number (A) which is the number of protons plus neutrons.

Did you know?

A thin pencil line is about 3 million carbon atoms wide.

Electronic Structure of the Atom

• The electrons form bonds and determine the

structure of the resulting molecules.
• Chemical properties of elements are determined
by the number of protons in the nucleus and the
corresponding number of electrons around the
nucleus.
• Electrons that are bound to nuclei are found in
orbitals.
• An s-orbital is a sphere and a p-orbital has two lobes.
• Atomic orbitals are grouped into different “shells”
at different distances from the nucleus.
• The first electron shell contains just the 1s orbital.

Wade LG, Organic Chemistry, 8th Edition, page 4.

Electronic Structure of the Atom

Wade LG, Organic Chemistry, 8th Edition, page 5.

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Bond Formation: The Octet Rule

• Lewis proposed theories describing how atoms bond together to form molecules.
(atoms transfer or share electrons in such a way as to attain a filled shell of electrons)
• A filled shell of electrons is simply the electron configuration of a noble gas, such as He, Ne,
or Ar.: Octet Rule

Ionic Bonding
transfer of one electron gives each of these two elements a noble-gas configuration.

Covalent Bonding
Covalent bonding, in which electrons are shared rather than transferred, is the most
common type of bonding in organic compounds.

Bond Formation: The Octet Rule

The number of single electrons in the valence shell determines the number of
bonds an atom will form.

Bond Formation: The Octet Rule

Atoms can become cations when they lose an electron. The number of bonds that it can then
form is determined by the number of single electrons that remain.

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Bond Formation: The Octet Rule

Atoms can also form anions when they gain electrons. Once again the number of bonds that
they can form is determined by the number of free electrons.

Bond breaking
• In the preceding slides, we described two processes of bond formation and showed how
various atoms can bond: the ionic and covalent bonding.
• We showed how electrons are moved from one substrate to the other.
• Now we look at two processes of bond breaking, the homolytic and heterolytic cleavages.
• In heterolysis: covalent bond breaks to form reactants, intermediates and products.
• In homolysis: covalent bond breaks to form intermediates with unpaired electrons called
radicals.
• We use curved arrows with half-heads to show these reactions.

Heterolysis of bonds to carbon: Carbocations and carboanions

• The heterolysis of a bond to a carbon atom can lead to either of two ions:
• That is, an ion with a positive charge called a carbocation or an ion with a negative charge
called a carbanion.
• Carbocations are electron deficient. The have only six electrons in their valence shell. As
such the are Lewis acids. Meaning that carbocations are electron seekers. Thus,
electrophiles.
• Carboanion are Lewis bases. They seek positive centers and protons. Thus, nucleophiles.

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Lewis structures
• To symbolize the bonding in a covalent molecule we use Lewis structures.
• In a Lewis structure, each valence electron is symbolized by a dot.
• A bonding pair of electrons is symbolized by a pair of dots or by a dash (─).

(The free electron pair is not normally shown.)

Activity 1 Lewis structures

Lewis structures are the way we write organic chemistry.
Learning how to draw them quickly and correctly will help you throughout this course.

Draw Lewis and line bond structures for the following compounds and show all non-bonding
electrons.
(a) Ammonia (NH3)
(b) Nitrate ions (NO3-)
(c) Chlorate ion (ClO3-)
(d) Water (H2O)
(c) Hydronium ion (H3O+)
(d) Propane (C3H8)
(e) Dimethylamine (CH3NHCH3)
(f) diethyl ether (CH3CH2OCH2CH3)
(g) 1-chloropropane (CH3CH2CH2C1)
(h) propan-2-ol (CH3CH(OH)CH3)
(i) Borane (BH3)
(j) boron trifluoride (BF3)

Electronegativity and Bond Polarity

A bond with the electrons shared equally

between the two atoms is called a
nonpolar covalent bond.
In most bonds between two different
elements, the bonding electrons are
attracted more strongly to one of the
two nuclei.
An unequally shared pair of bonding
electrons is called a polar covalent
bond.

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Electronegativity and Bond Polarity

A more stable conjugate base and a

stronger acid are formed when a
more electronegative element
accepts a negative charge.

The sizes of anions of Group VII

increase down the group. The bigger
the anion, the more stable its negative
charge because of a larger region of
space to which the charges are spread.

Bond polarity

Wade LG, Organic Chemistry, 8th Edition, page 10.

Resonance hybrids
• Some compounds’ structures are not adequately represented by a single Lewis structure.
• When two or more valence-bond structures are possible, differing only in the placement of
electrons, the molecule will usually show characteristics of both structures.
• The different structures are called resonance structures or resonance forms because
they are not different compounds, just different ways of drawing the same compound.
• The actual molecule is said to be a resonance hybrid of its resonance forms.

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Activity 2
Draw all the equivalent resonance structures for following species. Include any non-zero formal
charges in the structures.

nitrate anion NO3-

chlorate anion ClO3– .

https://www.khanacademy.org/science/ap-chemistry-beta/x2eef969c74e0d802:molecular-and-ionic-
compound-structure-and-properties/x2eef969c74e0d802:resonance-and-formal-charge/v/introduction-
to-resonance

Practice
Draw another resonance structure based on the given one.

Practice
Draw another resonance structure based on the given one.

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Common errors for drawing resonance structures:

1. σ bond is moved
2. Atom is moved
3. More than eight electrons located around C, N or O
4. Arrows are not shown in the proper way
5. Electron pairs are moved too far away, they should only be moved
to the next position/atom.

Lewis Acids and Bases

The Brønsted–Lowry definition of acids and bases depends on the transfer of a proton from
the acid to the base.

Lewis bases are species with available electrons that can be donated to form new bonds.
Lewis acids are species that can accept these electron pairs to form new bonds.

Since a Lewis acid accepts a pair of electrons, it is called an electrophile, from the
Greek words meaning “lover of electrons.”

A Lewis base is called a nucleophile, or “lover of nuclei,” because it donates electrons to a

nucleus with an empty (or easily vacated) orbital.

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Activity 3
In the reactions shown below:
1. Identify electrophiles (acids) and nucleophiles (bases).
2. Use the curved-arrow formalism to show the movement of electron pairs in these reactions, as
well as the imaginary movement in the resonance hybrids of the products.

Solutions

Solutions

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Activity 4

Activity 5

Activity 6

Activity 7

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Activity 8

Molecular Orbitals

• The stability of a covalent bond results from

a large amount of electron density in the
bonding region, the space between the two
nuclei.
• In the bonding region, the electrons are
close to both nuclei, lowering the overall
energy.
• The bonding electrons also mask the
positive charges of the nuclei, so the nuclei
do not repel each other as much as they
would otherwise.
Wade LG, Organic Chemistry, 8th Edition, page 45.

Molecular Orbitals

Wade LG, Organic Chemistry, 8th Edition, page 46.

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Molecular Orbitals

Geometry of molecules and hybridization

sp3 sp2 sp

Hybridization and Molecular Shapes

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Molecular Orbitals

Wade LG, Organic Chemistry, 8th Edition, page 51.

Electron configuration of atoms

• The ground state electron configuration of an atom is predicted by the following rules:
• The orbitals of lowest energy are filled first in the following order:
• 1s→2s→2p→3s→3p→4s→3d→4p
• A maximum of two electrons of opposite spin can occupy an orbital.
• Electrons will only pair off once all the orbitals of a level are filled with one electron.
• The electron configurations of hydrogen, carbon and chlorine are shown below.

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Hybridization
• It appears from the hybridization of carbon that it will need to form four bonds using the 2s-
orbital and the three p-orbitals.
• That will mean that the carbon hydrogen bonds in methane will differ from one another.
• All four bonds in methane are however identical.
• It means that something is happening to the orbitals of carbon. The s-orbital and the three p-
orbitals hybridizes.

https://www.khanacademy.org/science/ap-chemistry-beta/x2eef969c74e0d802:molecular-and-ionic-compound-structure-and-
properties/x2eef969c74e0d802:bond-hybridization/v/sp3-hybrid-orbital-jay-final

Hybridization

Sp2 - Hybridization

https://www.khanacademy.org/science/ap-chemistry-
beta/x2eef969c74e0d802:molecular-and-ionic-compound-structure-and-
properties/x2eef969c74e0d802:bond-hybridization/v/sp2-hybridization-jay-
final

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Sp-Hybridization

https://www.khanacademy.org/science/ap-chemistry-beta/x2eef969c74e0d802:molecular-and-ionic-compound-
structure-and-properties/x2eef969c74e0d802:bond-hybridization/v/sp-hybridization-jay-final

Activity 9

1. What is the hybridization of each of the identified atoms?

2. Write down the geometry around each identified atom.
3. Redraw the molecule and identify all the functional groups (circle and
name each group).

(a)
(b)
(d)
O

N OH
H

(c)

Molecular Orbitals

ACTIVITY 10

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Isomerism
Isomers are different compounds with the same molecular formula.

Constitutional isomers (or structural isomers) are isomers that differ in their bonding
sequence; that is, their atoms are connected differently. C 4H10

Isomerism

Stereoisomers are different compounds that differ only in how their atoms are
oriented in space.

Similar groups on the same side of the double bond: cis.

Similar groups on opposite sides of the double bond: trans.

Activity 11 Isomerism

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Polarity of Bonds and Molecules

Bond polarities can range from nonpolar covalent, through polar covalent, to totally
ionic.

Polarity of Bonds and Molecules

A molecular dipole moment is the dipole moment of the molecule taken as a whole.
It is a good indicator of a molecule’s overall polarity.

Wade LG, Organic Chemistry, 8th Edition, page 46.

Polarity of Bonds and Molecules

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Intermolecular forces

1. the dipole–dipole forces of polar molecules;

2. the London dispersion forces that affect all molecules; and
3. the “hydrogen bonds” that link molecules having –OH or –NH groups.

Intermolecular forces

Wade LG, Organic Chemistry, 8th Edition, page 66.

Intermolecular forces
In nonpolar molecules such as carbon tetrachloride, the principal attractive force
is the London dispersion force, one of the van der Waals forces

the isomers: larger

surface areas
(and greater
potential for London
force attraction)
have higher boiling
points

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Intermolecular forces
A hydrogen bond is not a true bond but a particularly strong dipole–dipole attraction.
Hydrogen bonding influences the physical properties of organic compounds, as shown
by the boiling points of ethanol (ethyl alcohol) and dimethyl ether, two isomers of
molecular formula: C2H6O

Hydrogen bonding
increase the bp.

Intermolecular forces

Hint: To predict relative boiling points, we should look for differences in (1) hydrogen
bonding, (2) molecular weight and surface area, and (3) dipole moments.

Specific Outcome 2
Explain and apply concepts, properties and chemical reactivity related to saturated
hydrocarbons.
Assessment criteria

• The general structure of alkanes is described.

• IUPAC rules for nomenclature are used to correctly construct structural formulae, and vice
versa.
• Structural and conformational isomers are accurately constructed and their relative
energies and stabilities compared.
• The halogenation of alkanes is proposed and illustrated.

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Hydrocarbons
• The hydrocarbons are compounds composed entirely of carbon and hydrogen.
• The major classes of hydrocarbons are alkanes, alkenes, alkynes, and aromatic hydrocarbons.
• For the purpose of this brief survey, we divide organic compounds into three classes: (1)
hydrocarbons, (2) compounds containing oxygen, and (3) compounds containing nitrogen.
• Alkanes are hydrocarbons that contain only single bonds.
• Alkane names generally have the -ane suffix, and the first part of the name indicates the
number of carbon atoms.
• Alkanes undergo few reactions because they have no functional group.
• The cycloalkanes are a special class of alkanes in the form of a ring.
• An alkyl group is an alkane portion of a molecule, with one hydrogen atom removed to
allow bonding to the rest of the molecule.

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IUPAC rules for nomenclature are used to correctly construct structural

formulae, and vice versa.
Rule 1: Find the longest continuous chain of carbon atoms, and use the name of this
chain as the base name of the compound.
Rule 2: Number the longest chain, beginning with the end of the chain nearest a
substituent.

The longest chain of carbon atoms in the compound below contains six carbons, so the
compound is named as a hexane derivative.
The longest chain is rarely drawn in a straight line; look carefully to find it.

IUPAC rules for nomenclature are used to correctly construct structural

formulae, and vice versa.

• A proton from the carbons in the main chain can be replaced.

• We call the replacing groups substituents because they substitute a proton.
• When there are two longest chains of equal length, use the chain with the greater
number of substituents as the main chain.
• The compound below contains two different seven-carbon chains and is named as a
heptane.
• We choose the chain on the right as the main chain because it has more substituents
(in red) attached to the chain.

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IUPAC rules for nomenclature are used to correctly construct structural

formulae, and vice versa.
Rule 3: Name substituentst….alkyl groups

IUPAC rules for nomenclature are used to correctly construct structural

formulae, and vice versa.

Please watch the following short videos in the order that is presented here.

Video 1
https://www.khanacademy.org/science/organic-chemistry/bond-line-structures-
alkanes-cycloalkanes/naming-alkanes/v/naming-simple-alkanes

Video 2
https://www.khanacademy.org/science/organic-chemistry/bond-line-structures-
alkanes-cycloalkanes/naming-alkanes/v/naming-alkanes-with-alkyl-groups

Video 3

https://www.khanacademy.org/science/organic-chemistry/bond-line-structures-
alkanes-cycloalkanes/naming-alkanes/v/alkane-with-ethyl-groups

IUPAC rules for nomenclature are used to correctly construct structural

formulae, and vice versa.

Please watch the following short videos in the order that is presented here.

Video 4
https://www.khanacademy.org/science/organic-chemistry/bond-line-structures-
alkanes-cycloalkanes/naming-alkanes/v/naming-cycloalkane

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IUPAC rules for nomenclature are used to correctly construct structural

formulae, and vice versa.

Activity 12

Activities

Reactions of alkanes

• Alkanes are the least reactive class of organic compounds.

Reasons for low reactivity:
• The C and H have almost the same electronegativity.
• C-H bonds of alkanes are slightly polarised
• Molecules of alkanes have no unshared pairs of electrons to offer a site for attack by acids.

• Best known reactions of alkanes:

• Alkanes react vigorously with oxygen to produce carbon dioxide and water (combustion).

• Also, alkanes react with halogens (Cl2, Br2, F2, etc) Halogenation of alkanes.

Newman projections

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Newman projections

Newman projections

Please watch this video

https://www.youtube.com/watch?v=NC2LYq-nCok

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Other functional groups

Alkenes are hydrocarbons that contain carbon–carbon double bonds.

Alkene names end in the -ene suffix.

Alkynes are hydrocarbons with carbon–carbon triple bonds as their functional group.
Alkyne names generally have the -yne suffix,

Other functional groups

Aromatic hydrocarbons (also called arenes) are all derivatives of benzene,

represented by a six-membered ring with three double bonds.

Other functional groups

Activity 13

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Other functional groups : alcohol

Alcohols are organic compounds that contain the hydroxyl group as their
functional group. The general formula for an alcohol is R-OH.

R-OH

Other functional groups: ethers

Ethers are composed of two alkyl groups bonded to an oxygen atom. The general formula for
an ether is R-O-R’.

R-O-R’ R-O-R’

Other functional groups : Aldehydes and Ketones

The carbonyl group, C=O, is the functional group for both aldehydes and ketones.
A ketone has two alkyl groups bonded to the carbonyl group.
Ketone names generally have the -one suffix;

The general structure of ketones is: O

R R'
Importantly: Both R and R’ must be carbon atoms! Alkyl group

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Other functional groups : Aldehydes and Ketones

An aldehyde has one alkyl group and a hydrogen atom bonded to the carbonyl group.
aldehyde names use either the -al suffix or the -aldehyde suffix.

The general structure of an aldehyde is : O

One of the alkyl groups of ketone is replaced with a hydrogen atom.

R H
Examples:

Other functional groups : carboxylic acids

Like ketones and aldehydes, carboxylic acids contain a C=O group, but in this case the
carbon atom is linked to a hydroxyl (OH) group and we now call this functional group a
carboxyl group.
The general formula for a carboxylic acid is RCOOH or RCO2H. O
The general structure of carboxylic acids is:
R OH

Examples:

Activity 15

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Other functional groups : carboxylic acid derivatives

The hydroxyl group of the carboxylic acid can be replaced by an amine to produce
amide functional groups
Or it can be replaced by a halogen like Cl to produce acid chloride.
Lastly, by OR to produce an ester.
Carboxylic acid
Examples:
O O O

R R OH R
Cl NH2
Acid chloride
Amide

R OR'

Ester

Other functional groups : amine and amides

Amines and amides are compounds of nitrogen.
Amines are alkylated derivatives of ammonia, meaning that one, two or all the
hydrogens of ammonia are replaced as shown below.

Ammonia H
H H R +
N
N H H
R
N
.. H H .. H
Ammonium ion
1o amine

R' R'
N
N
R .. H R .. R"

2o amine 3o amine

Other functional groups : amines and amide

Amides are acid derivatives that result from a combination of an acid with ammonia or
an amine.
Proteins have the structure of long-chain, complex amides.

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Activity 15

Assignment 1 ends here

Goodluck!

Study Unit 2

• Acids, Bases and Functional groups:

• Bond polarity, dipole moment;
• Intermolecular forces such as London dispersion forces, van der Waals forces, dipole-
dipole interaction and hydrogen bonding;
• Polarity effects on physical properties, for example solubility
• Understanding the different acid-base theories
• Understanding the definition of electrophiles, nucleophiles and free radicals; Functional
groups.

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Study Unit 3
• Structure and Properties of Alkanes: Structure and nomenclature of alkanes
and cycloalkanes; Physical properties; Reactions; Mechanism for the
halogenation of alkanes; Structural isomers; Conformations (Newman and
Sawhorse projections).

Study Unit 4

• Study of chemical reactions: Understanding the mechanism of

free radical reactions of alkanes; understanding the properties
of the different type of reaction intermediates.

Study Unit 5

• Introduction to Stereochemistry:
• 3-Dimensional representations of simple organic molecules;
• Chirality and R- and S-configurations.

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Study Unit 6

• Alkyl Halides:
• Structure and nomenclature;
• Physical properties;
• Classification as primary, secondary, or tertiary alkyl halides;
• Nucleophilic substitution reactions and mechanisms: SN1 and SN2.

Study Unit 7

• Alcohols: Structure and nomenclature; Physical properties; Classification of

alcohols as primary, secondary, or tertiary; Stereochemistry:
• 3-Dimensional representations of simple organic molecules, Chirality and R-
and S-configurations; Selected Reactions of alcohols: oxidation and the
formation of alkyl halides, ethers and alkenes.
• Ethers: Structure and nomenclature; physical, synthesis and chemical
properties/reactions.

Study Unit 8

• Alkenes: Structure and nomenclature; Physical properties; Geometric

isomerism (cis/trans and E/Z configurations); Synthesis of alkenes:
Elimination reactions and mechanisms: dehydrohalogenation of alkyl
halides: E1 and E2 reactions and Dehydration of alcohols.

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Study Unit 9

• Reactions of alkenes: Reactivity of the C=C bond – reactions and mechanisms;

Electrophilic addition reactions: acid-catalyzed hydration, hydrohalogenation and
halogenation of symmetrical and unsymmetrical alkenes and the application of
Markovnikov’s rule; Mechanism of hydrohalogenation of unsymmetrical alkenes in the
presence of peroxides (anti-Markovnikov’s addition); Hydrogenation of alkenes.

Study Unit 10

• Alkynes: Structure and nomenclature; Physical properties; Acidity/

Reactivity of terminal alkynes. Reactions and mechanisms of hydration,
halogenation and hydrohalogenation of symmetrical and unsymmetrical
alkynes (Markovnikov’s rule); Hydrogenation of alkynes.

Study Unit 11

• Amines: Nomenclature, classification and structure; physical properties; reactivity and

basicity.
• Aromatic compounds: Structure and nomenclature of aromatic compounds; Huckel’s
rule
• Reactions of aromatic compounds: Electrophilic aromatic substitution; halogenation,
nitration and sulphonation of benzene; Effects of multiple substituents on electrophilic
substitution; Friedel-Crafts alkylation and acylation.

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Study Unit 12

• Carbonyl compounds and derivatives.

• Aldehydes and Ketones: Structure and nomenclature of ketones and aldehydes; Physical
properties and chemical reactivity of ketones and aldehydes.
• Carboxylic acids: Structure and nomenclature carboxylic acids; Physical properties and
acidity carboxylic acids and substituted carboxylic acid (acid-base reactions).

Thank you

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