BICOL UNIVERSITY

College of Science
Department of Chemistry

Z MATRICES

NAME: ________________________________________________
SECTION: _____________________________________________
PROF: _________________________________________________

Z Matrices
In chemistry, the Z-matrix is a way to represent a
system built of atoms.
It is also known as an internal coordinate
representation.
It provides a description of each atom in a molecule
in terms of its atomic number, bond length, bond
angle, and dihedral angle.
A symbolic reference to the degree of freedom. This is
composed of one of the following letters to signify the position in
the zmatrix of the relevant degree of freedom, followed by the
index of the atom concerned.
r
a
t
x
y
z

a bond length
a bond angle
a torsion angle
an x-co-ordinate
a y-co-ordinate
a z-co-ordinate

Procedure to Construct Z matrices

Step 1: Draw a water molecule on the screen
Step2: Go to setup and chose Periodic box with
the box size 12x12x12 A.
Step 3: Do the geometry optimization.
Step 4: Go to select and choose Atoms and Name
selection Repeat this operation several (four) times
each time assigning a new name. Try to select a
possibly broader range of distances (shown at the
bottom of the screen).

 Step 5: Go to Molecular dynamics simulations and

chose to graph the four choices. Chose a name for a
snapshot file and
Step 6. Take the distances from a .cvs file and
analyze them using Mathematica as shown in
Lab3.nb notebook.

Constructing Z matrices

This section presents a brief overview of traditional Zmatrix descriptions of molecular systems. There are
restrictions on the size of a Z-matrix: the maximum
number of variables and the maximum number of atoms
within a calculation. These are set consistently for a
maximum of 250,000 real atoms (including ghost but not
dummy atoms), and a maximum of 250,000 Z-matrix
centers (atoms, ghost atoms, and dummy atoms).

Using Internal
Coordinates

Each line of a Z-matrix gives the internal coordinates for one

of the atoms within the molecule. The most-used Z-matrix
format uses the following syntax:
a)
b)
c)
d)
e)
f)
g)

Element-label atom 1
bond-length
atom 2
bond-angle
atom 3,
dihedral-angle
[format-code]

Element-label is a character string consisting of either the

chemical symbol for the atom or its atomic number. If the
elemental symbol is used, it may be optionally followed by other
alphanumeric characters to create an identifying label for that
atom. A common practice is to follow the element name with a
secondary identifying integer: C1, C2, etc.

Atom1, atom2, atom3 are the labels for previouslyspecified atoms and are used to define the current atoms
position. Alternatively, the other atoms line numbers within the
molecule specification section may be used for the values of
variables, where the charge and spin multiplicity line is line 0.
The position of the current atom is then specified by giving
the length of the bond joining it to atom1, the angle formed by
this bond and the bond joining atom1 and atom2, and the
dihedral (torsion) angle formed by the plane
containing atom1, atom2 and atom3 with the plane containing
the current atom, atom1 and atom2.
Note: Bond angles must be in the range 0 < angle < 180.
Dihedral angles may take on any value.
The optional format-code parameter specifies the format of the
Z-matrix input. For the syntax being described here, this code is
always 0. This code is needed only when additional parameters
follow the normal Z-matrix specification data, as in
an ONIOM calculation.
As an initial example, consider hydrogen peroxide. A Zmatrix for this structure would be:
1.
2.
3.
4.

H
1 0.9
2 1.4 1 105.0
H 3 0.9 2 105.0 1 120.0

The first line of the Z-matrix simply specifies a hydrogen.

The second line lists an oxygen atom and specifies the

internuclear distance between it and the hydrogen as 0.9
Angstroms.
The third line defines another oxygen with an O-O
distance of 1.4 Angstroms (i.e., from atom 2, the other oxygen)
and having an O-O-H angle (with atoms 2 and 1) of 105 degrees.
The fourth and final line is the only one for which all three
internal coordinates need be given. It defines the other
hydrogen as bonded to the second oxygen with an H-O distance
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of 0.9 Angstroms, an H-O-O angle of 105 degrees and a H-O-O-H

dihedral angle of 120 degrees.

Variables may be used to specify some or all of the values

within the Z-matrix. Here is another version of the previous Zmatrix:
H
O 1 R1
O 2 R2 1 A
H 3 R1 2 A 1 D
Variables:
R1 0.9
R2 1.4
A 105.0
D 120.0

Symmetry constraints on the molecule are reflected in the

internal coordinates.
When such a Z-matrix is used for a geometry
optimization in internal coordinates (Opt=Zmatrix), the values of the variables will be
optimized to locate the lowest energy structure.
For a full optimization (FOpt), the variables are
required to be linearly independent and include all
degrees of freedom in the molecule.
For a partial optimization (POpt), variables in a
second section (often labeled Constants:) are held
fixed in value while those in the first section are
optimized:

Mixing Internal and Cartesian

Coordinates
Cartesian coordinates are actually a special case of the Z-matrix,
as in this example:
C
C

0.00
0.00

0.00
0.00

0.00
1.52

H
H
H
H
H
H

1.02
-0.51
-0.51
-1.02
0.51
0.51

0.00
-0.88
0.88
0.00
-0.88
0.88

-0.39
-0.39
-0.39
1.92
1.92
1.92

It is also possible to use both internal and Cartesian

coordinates within the same Z-matrix, as in this example:
O
C
C
N
H
H
H
H
H

0
0
0
0
2
2
3
3
4

xo
0.
0.
xn
r1
r2
r1
r2
r3

0.
yc
-yc
0.
3 a1
3 a2
2 a1
2 a2
2 a3

zo
0.
0.
0.
1 b1
1 b2
1 -b1
1 -b2
3 d3

Variables:
xo
zo
yc
xn
r1
r2
r3
a1
a2
d3
b1
b2

-1.
0.
1.
1.
1.08
1.08
1.02
125.
125.
160.
90.
-90.

This Z-matrix has several features worth noting:

The variable names for the Cartesian coordinates are

given symbolically in the same manner as for internal

coordinate variables.
The integer 0 after the atomic symbol indicates symbolic

Cartesian coordinates to follow.

Computational Chemistry

Cartesian coordinates can be related by a sign

change just as dihedral angles can.

Alternate Z Matrix Format

An alternative Z-matrix format allows nuclear positions to
be specified using two bond angles rather than a bond angle and
a dihedral angle. This is indicated by a 1 in an additional field
following the second angle (this field defaults to 0, which
indicates a dihedral angle as the third component):
C4 O1 0.9 C2 120.3 O2 180.0 0
C5 O1 1.0 C2 110.4 C4 105.4 1
C6 O1 R C2 A1 C3 A2 1

The first line uses a dihedral angle while the latter two use a
second bond angle.

Using DUMMY ATOMS

This section will illustrate the use of dummy atoms within
Z-matrices, which are represented by the pseudo atomic
symbol X. The following example illustrates the use of a dummy
atom to fix the three-fold axis in C3v ammonia:
N
X
H
H
H

1
1
1
1

1.
nh 2 hnx
nh 2 hnx 3 120.0
nh 2 hnx 3 -120.0

nh 1.0
hnx 70.0

The position of the dummy on the axis is irrelevant, and

the distance 1.0 used could have been replaced by any other
positive number. hnx is the angle between an N-H bond and the
threefold axis.

Here is a Z-matrix for oxirane:

X
C1
O
C2
H1
H2
H3
H4

X halfcc
X
ox C1 90.
X halfcc O 90. C1 180.0
C1
ch X hcc O hcco
C1
ch X hcc O -hcco
C2
ch X hcc O hcco
C2
ch X hcc O -hcco

halfcc
0.75
ox
1.0
ch
1.08
hcc
130.0
hcco
130.0

This example illustrates two points. First, a dummy atom

is placed at the center of the C-C bond to help constrain
the cco triangle to be isosceles. ox is then the perpendicular
distance from O to the C-C bond, and the angles oxc are held at
90 degrees. Second, some of the entries in the Z-matrix are
represented by the negative of the dihedral angle variable hcco.
The following examples illustrate the use of dummy atoms
for specifying linear bonds. Geometry optimizations in internal
coordinates are unable to handle bond angles of l80 degrees
which occur in linear molecular fragments, such as acetylene or
the C4 chain in butatriene. Difficulties may also be encountered
in nearly linear situations such as ethynyl groups in
asymmetrical molecules. These situations can be avoided by
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Computational Chemistry

introducing dummy atoms along the angle bisector and using

the half-angle as the variable or constant:
N
C 1 cn
X 2 1. 1 90.
H 2 ch 3 90. 1 180.
cn 1.20
ch 1.06

Similarly, in this Z-matrix intended for a geometry

optimization, half represents half of the N-C-O angle which is
expected to be close to linear. Note that a value of half less
than 90 degrees corresponds to a cis arrangement:
N
C
X
O
H

1
2
2
4

cn
1. 1 half
co 3 half 1 180.0
oh 2 coh 3
0.0

cn 1.20
co 1.3
oh 1.0
half 80.0
coh 105.

Model Builder Geometry

The model builder is another facility within Gaussian for

Specifications
quickly specifying certain sorts of molecular systems.It is
requested with the ModelA or ModelB options to
the Geom keyword, and it requires additional input in a separate
section within the job file.
The basic input to the model builder is called a short
formula matrix, a collection of lines, each of which defines an
atom (by atomic symbol) and its connectivity, by up to six more
entries. Each of these can be either an integer, which is the
number of the line defining another explicitly specified atom to
which the current atom is bonded, or an atomic symbol (e.g. H,
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F) to which the current atom is connected by a terminal bond, or

a symbol for a terminal functional group which is bonded to the
current atom. The functional groups currently available are OH,
NH2, Me, Et, NPr, IPr, NBu, IBu, and TBu.
The short formula matrix also implicitly defines the
rotational geometry about each bond in the following manner.
Suppose atoms X and Y are explicitly specified. Then X will
appear in row Y and Y will appear in row X. Let I be the atom to
the right of X in row Y and J be the atom to the right of Y in row
X. Then atoms I and J are put in the trans orientation about the
X-Y bond. The short formula matrix may be followed by optional
lines modifying the generated structure. There are zero or more
of each of the following lines, which must be grouped together in
the order given here:

AtomGeom,I, Geom
Normally the local geometry about an atom is defined by
the number and types of bond about the atom (e.g., carbon in
methane is tetrahedral, in ethylene is trigonal, etc.). All bond
angles at one center must be are equal.
The AtomGeom line changes the value of the bonds at
center I. Geom may be the angle as a floating point number, or
one of the strings Tetr, Pyra, Trig, Bent, or Line.

BondRot,I,J,K,L,Geom
This changes the orientations of the I-J and K-L bonds
about the J-K bond. Geom is either the dihedral angle or one of
the strings Cis (0), Trans (180), Gaup (+60), or Gaum (
60).

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BondLen,I,J,NewLen
This sets the length of the I-J bond to NewLen (a floating
point value).
The model builder can only build structures with atoms in
their normal valencies. If a radical is desired, its extra valence
can be effectively tied down using dummy atoms, which are
specified by a minus sign before the atomic symbol (e.g., H).
Only terminal atoms can be dummy atoms.
The two available models (A and B) differ in that model A
takes into account the type (single, double, triple, etc.) of a bond
in assigning bond lengths, while model B bond lengths depend
only on the types of the atoms involved. Model B is available for
all atoms from H to Cl except He and Ne. If Model A is requested
and an atom is used for which no Model A bond length is
defined, the appropriate Model B bond length is used instead.

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Examples of Z matrices

A. Water

H
O 1 OH
H 2 OH 1 OHO
OH = 1.08
OHO = 107.5

For water, all we need is a bond distance and an angle.

We start with the first atom, hydrogen, on a line of its own. The
next line begins with the second atom, oxygen, and then states
with which atom to measure the bond distance OH from, in this
case, atom one. On the next line, the third atom, hydrogen, is
OH distance away from atom two and has a bond angle of OHO
in relation to atom one.

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B. Acetylene

H
C
X
C
X
H
HC
XL
CC
A1
D1
D2

1
2
2
3
4

HC
XL
CC
XL
HC
=
=
=
=
=
=

1
3
2
5

A1
A1 1 D1
A1 4 D2
A1 2 D1

1.08
1.0
1.2
90.0
180.0
0.0

For acetylene, it is necessary to use dummy atoms. This is

because the Z-matrix does not accept bond angles equal to 180
degrees. With these dummy atoms, one can define acceptable
bond angles. When the input is read into a computer code, these
dummy atoms are just used as reference points, and do not
enter into any calculation. Judicious use of dummy atoms can
simplify a problem hundred-fold.
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C. Benzene

X
X
C
C
C
C
C
C
X
H
H
H
H
H
H
A1
A2
XC
HC

1
2
2
2
2
2
2
3
3
4
5
6
7
8

1.0
XC 1 A1
XC 1 A1 3 60.0
XC 1 A1 4 60.0
XC 1 A1 5 60.0
XC 1 A1 6 60.0
XC 1 A1 7 60.0
1.0 2 A1 1 0.0
HC 9 A1 2 180.0
HC 3 A2 2 180.0
HC 4 A2 2 180.0
HC 5 A2 2 180.0
HC 6 A2 2 180.0
HC 7 A2 2 180.0
=
=
=
=

90.0
120.0
1.3
1.08

One would find it very difficult to get the C6-C1 bond

distance to work out to be exact. As one can see here, a much
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Computational Chemistry

better way is to use dummy atoms. By using three dummy

atoms, the input is much easier to write, and a minimum
number of variables are required. Notice that it is possible to put
numbers directly into the Z-matrix.

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https://en.wikipedia.org/wiki/Z-matrix_(chemistry)

http://www.gaussian.com/g_tech/g_ur/c_zmat.htm
http://iopenshell.usc.edu/howto/zmatrix/

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