Computational Chemistry: A Practical Guide for Applying Techniques to Real-World Problems.

David C. Young
Copyright ( 2001 John Wiley & Sons, Inc.
ISBNs: 0-471-33368-9 (Hardback); 0-471-22065-5 (Electronic)

9 Constructing a Z-Matrix

The previous chapter discussed the merits of specifying the molecular geometry
using a Z-matrix versus Cartesian coordinates. This chapter describes the con-
struction of a Z-matrix. The use of a Z-matrix geometry speci®cation is slowly
declining with the increasing availability of graphic user input programs and
the increasing availability of redundant internal coordinate algorithms. How-
ever, Z-matrix geometry speci®cation is a skill still necessary for using some
software programs and it remains the best way of incorporating symmetry
constraints. Furthermore, a well-constructed Z-matrix can often help a pro-
gram run more e½ciently, thus allowing more work to be done in a given
amount of time. The examples in this chapter show the construction of a
Z-matrix in the format used by the Gaussian program. Other programs may
require slightly di¨erent formats.

9.1 Z-MATRIX FOR A DIATOMIC MOLECULE

Here is a Z-matrix for a carbon monoxide molecule:

line 1 C
line 2 O 1 R
line 3
line 4 R 0.955

Line 1: ``C'' speci®es that the ®rst atom is a carbon atom.

Line 2: ``O 1 R'' speci®es that an oxygen atom occurs at a distance R from
the ®rst atom (the carbon).
Line 3: There must be a blank line between the list of atoms and the list of
variables.
Line 4: R is de®ned (in Angstroms or A Ê ).

9.2 Z-MATRIX FOR A POLYATOMIC MOLECULE

Here is a Z-matrix for a formaldehyde molecule:

line 1 C
line 2 O 1 OC
line 3 H 1 HC 2 A
73
74 9 CONSTRUCTING A Z-MATRIX

O2
OC O2
180o
A
C1 H4 C1 H3

(b)
HC
H3
(a)
FIGURE 9.1 Illustration of the formaldehyde Z-matrix example. (a) First three atoms
and associated variables. (b) Dihedral angle.

line 4 H 1 HC 2 A 3 180.0
line 5
line 6 OC 1.2
line 7 A 120.0
line 8
line 9 HC 1.08

Line 1: ``C'' indicates that the ®rst atom is a carbon.

Line 2: ``O 1 OC'' indicates that the second atom is an oxygen with a dis-
tance of OC to the ®rst atom.
Line 3: ``H 1 HC 2 A'' indicates that the third atom is a hydrogen with a
distance of HC to the ®rst atom and an angle between the third, ®rst, and
second atoms of A (in degrees).
Line 4: ``H 1 HC 2 A 3 180.0'' indicates that the fourth atom is a hydrogen
with a distance of HC to the ®rst atom and an angle between the third,
®rst, and second atoms of A. The dihedral angle between the ®rst, second,
third, and fourth atoms is 180 (see Figure 9.1).
Line 5: There must be a blank line between the list of atoms and the list of
variables.
Line 8: The second blank line sets aside variables that are not to be opti-
mized in the geometry optimization.
If an optimization were being done, the parameters OC and A would be
optimized, but HC would be held ®xed and the molecule would be kept planar.
Note that parameters can be used more than once in the Z-matrix. This makes
the geometry optimization run more quickly because fewer parameters are being
optimized. Additional atoms are added by appending lines like line 4 consisting
of distance, angle, and dihedral angle speci®cations.

9.3 LINEAR MOLECULES

A linear molecule, such as CO2 , presents an additional di½culty. If an angle of
180 is speci®ed, then the dihedral angle referenced to that angle will be math-
 9.4 RING SYSTEMS 75

X2

1.0

OC OC
O4 C1 O5

1.0
X3
FIGURE 9.2 Illustration of the geometry formed from the CO2 Z-matrix example.

ematically unde®ned. This is avoided by using a dummy atom, denoted by an

element of X type. A dummy atom is not an atom at all. It is a way of de®ning
a point in space from which geometry can be speci®ed. A dummy atom does
not have any associated nucleus or basis functions. Here is a carbon dioxide
input with two dummy atoms, which is also shown in Figure 9.2:

C
X 1 1.0
X 1 1.0 2 90.0
O 1 OC 2 90.0 3 90.0
O 1 OC 2 90.0 3 -90.0
OC 1.2

Note that the distance to the dummy atoms is held ®xed at 1.0 A Ê . This value
was chosen arbitrarily. The calculation would likely fail if told to optimize this
distance because there is no energy associated with it.
Enforcing the molecular symmetry will also help orbital-based calculations
run more quickly. This is because some of the integrals are equivalent by sym-
metry and thus need be computed only once and used several times.

9.4 RING SYSTEMS

It is possible to specify a ring system by specifying the atoms sequentially. Each

atom can be referenced to the previous atom. In this case, a small change in
angle between, say, the 3rd and 4th atoms speci®ed would result in a signi®cant
change in the distance between the ®rst and last atoms speci®ed. This makes the
calculation run ine½ciently if it is successful at all.
Molecules with rings should always be given a dummy atom in the center of
the ring. The atoms in the ring should then be referenced to the central dummy
atom rather than each other. Here is a Z-matrix for a benzene molecule enforcing
D6h symmetry:
76 9 CONSTRUCTING A Z-MATRIX

H9

HX

C3 H10
H14

CX C4
C8

o
X1 60

C7 C5
X2
H13 H11
C6

H12
FIGURE 9.3 Illustration of the geometry formed from the benzene Z-matrix example.

X
X 1 1.0
C 1 CX 2 90.0
C 1 CX 2 90.0 3 60.0
C 1 CX 2 90.0 4 60.0
C 1 CX 2 90.0 5 60.0
C 1 CX 2 90.0 6 60.0
C 1 CX 2 90.0 7 60.0
H 1 HX 2 90.0 3 0.0
H 1 HX 2 90.0 4 0.0
H 1 HX 2 90.0 5 0.0
H 1 HX 2 90.0 6 0.0
H 1 HX 2 90.0 7 0.0
H 1 HX 2 90.0 8 0.0
CX 1.3
HX 2.3

It is often convenient to use two dummy atoms: one in the center of the ring
and one perpendicular to the ring as shown here and in Figure 9.3. Even if the
actual optimization is being done in redundant internal coordinates, the pres-
ence of a dummy atom in the center of the ring can give the redundant internals
a better point from which to reference bond lengths and angles. Note that only
two parameters need be optimized when the symmetry is used correctly.
 BIBLIOGRAPHY 77

BIBLIOGRAPHY

Geometry speci®cation is usually addressed in the software manual as well as

the following books
A. R. Leach, Molecular Modeling Principles and Applications Longman, Essex (1996).
J. B. Foresman, á. Frisch, Exploring Chemistry with Electronic Structure Methods
Gaussian, Pittsburgh (1996).
T. Clark, A Handbook of Computational Chemistry John Wiley & Sons, New York
(1985).