Gaussian 03 Online Manual
This input section specifies the nuclear positions and the number of electrons of α- and β-spin. There are several ways in which the nuclear configuration can be specified: as a Z-matrix, as Cartesian coordinates, or as a mixture of the two (note that Cartesian coordinates are just a special case of the Z-matrix).
The first line of the molecule specification section specifies the net electric charge (a signed integer) and the spin multiplicity (a positive integer). Thus, for a neutral molecule in a singlet state, the entry 0 1 is appropriate. For a radical anion, -1 2 would be used. This is the only molecule specification input required if Geom=CheckPoint is used. The entire molecule specification (and title section) may be omitted by including Geom=AllCheck in the route section.
The remainder of the molecule specification gives the element type and nuclear position for each atom in the molecular system. The most general format for the line within it is the following:
Element-label[–Atom-type[–Charge]][(param=value[, ...])] Atom-position-parameters
Each line contains the element type, and possibly an optional molecular mechanics atom type and partial charge. Nuclear parameters for this atom are specified in the parenthesized list. The remainder of the line contains information about the atom's location, either as Cartesian coordinates or as a Z-matrix definition. We'll begin by considering the initial and final items, and then go on to discuss the remaining items.
The following are the basic formats for specifying atoms within the molecule specification (omitting all of the optional items):
Element-label x y z Element-label [n] atom1 bond-length atom2 bond-angle atom3 dihedral-angle [format-code]
Although these examples use spaces to separate items within a line, any valid separator may be used. The first form specifies the atom in Cartesian coordinates, while the second uses internal coordinates. Lines of both types may appear within the same molecular specification. The optional format-code parameter in the second line specifies the format of the Z-matrix input. For the syntax being described here, this code is always 0. It is needed only when additional parameters follow the normal data, as in an ONIOM calculation. n is an optional parameter related to freezing atoms during optimizations using ONIOM or (rarely) ones not performed using redundant internal coordinates (see ONIOM for details).
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, C3, and so on; this technique is useful in following conventional chemical numbering.
In the first form, the remaining items on each line are Cartesian coordinates specifying the position of that nucleus. In the second form, atom1, atom2, atom3 are the labels for previously-specified atoms which will be 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 bond joining atom2 and atom3 with the plane containing the current atom, atom1 and atom2.
Here are two molecule specification sections for ethane:
0 1 0,1 C 0.00 0.00 0.00 C1 C 0.00 0.00 1.52 C2,C1,1.5 H 1.02 0.00 -0.39 H3,C1,1.1,C2,111.2 H -0.51 -0.88 -0.39 H4,C1,1.1,C2,111.2,H3,120. H -0.51 0.88 -0.39 H5,C1,1.1,C2,111.2,H3,-120. H -1.02 0.00 1.92 H6,C2,1.1,C1,111.2,H3,180. H 0.51 -0.88 1.92 H7,C2,1.1,C1,111.2,H6,120. H 0.51 0.88 1.92 H8,C2,1.1,C1,111.2,H6,-120.
The version on the left uses Cartesian coordinates while the one on the right represents a sample Z-matrix (illustrating element labels). Note that the first three atoms within the Z-matrix do not use the full number of parameters; only at the fourth atom are there enough previously-defined atoms for all of the parameters to be specified.
Here is another Z-matrix form for this same molecule:
0 1 C1 C2 C1 RCC H3 C1 RCH C2 ACCH H4 C1 RCH C2 ACCH H3 120. H5 C1 RCH C2 ACCH H3 -120. H6 C2 RCH C1 ACCH H3 180. H7 C2 RCH C1 ACCH H6 120. H8 C2 RCH C1 ACCH H6 -120. Variables: RCH = 1.5 RCC = 1.1 ACCH = 111.2
In this Z-matrix, the literal bond lengths and angle values have been replaced with variables. The values of the variables are given in a separate section following the specification of the final atom. Variable definitions are separated from the atom position definitions by a blank line or a line like the following:
Symmetry constraints on the molecule are reflected in the internal coordinates. The C-H bond distances are all specified by the same variable, as are the C-C bond distances and the C-C-H bond angles.
This Z-matrix form may be used at any time, and it is required as the starting structure for a geometry optimization using internal coordinates (i.e., Opt=Z-matrix). In the latter case, the variables indicate the items to be optimized; see the examples for the Opt keyword for more details.
Specifying Periodic Systems
Periodic systems are specified with a normal molecule specification for the unit cell. The only additional required input are one, two or three translation vectors appended to the molecule specification (with no intervening blank line), indicating the replication direction(s). For example, the following input specifies a one-dimensional PBC single point energy calculation for neoprene:
# PBEPBE/6-31g(d,p)/Auto SCF=Tight neoprene, [-CH2-CH=C(Cl)-CH2-] optimized geometry 0 1 C,-1.9267226529,0.4060180273,0.0316702826 H,-2.3523143977,0.9206168644,0.9131400756 H,-1.8372739404,1.1548899113,-0.770750797 C,-0.5737182157,-0.1434584477,0.3762843235 H,-0.5015912465,-0.7653394047,1.2791284293 C,0.5790889876,0.0220081655,-0.3005160849 C,1.9237098673,-0.5258773194,0.0966261209 H,1.772234452,-1.2511397907,0.915962512 H,2.3627869487,-1.0792380182,-0.752511583 Cl,0.6209825739,0.9860944599,-1.7876398696 TV,4.8477468928,0.1714181332,0.5112729831
The final line specifies the translation vector. Note that it specifies TV as the atom symbol.
The following molecule specification could be used for a two-dimensional PBC calculation on BN:
0,1 5 0 -0.635463 0.000000 0.733871 7 0 -0.635463 0.000000 -0.733871 7 0 0.635463 0.000000 1.467642 5 0 0.635463 0.000000 -1.467642 TV 0 0.000000 0.000000 4.403026 TV 0 2.541855 0.000000 0.000000
Here is the molecule specification for a graphite sheet:
0 1 C 0.000000 0.000000 0.000000 C 0.000000 1.429118 0.000000 TV 2.475315 0.000000 0.000000 TV -1.219952 2.133447 0.000000
Finally, here is the molecule specification that could be used for a three-dimensional PBC calculation on gallium arsenide:
0 1 Ga 0.000000 0.000000 0.000000 Ga 0.000000 2.825000 2.825000 Ga 2.825000 0.000000 2.825000 Ga 2.825000 2.825000 0.000000 As 1.412500 1.412500 1.412500 As 1.412500 4.237500 4.237500 As 4.237500 1.412500 4.237500 As 4.237500 4.237500 1.412500 TV 5.650000 0.000000 0.000000 TV 0.000000 5.650000 0.000000 TV 0.000000 0.000000 5.650000
Specifying Isotopes and other Nuclear Parameters
Isotopes and other nuclear parameters can be specified within the atom type field using parenthesized keywords and values, as in the following example:
C(Iso=13,Spin=3) 0.0 0.0 0.0
The line specifies a 13C atom with a nuclear spin of 3/2 (3 * 1/2), located at the origin. The following items may be included in the list of parameters:
Molecular Mechanics Atom Types
Molecule specifications for molecular mechanics calculations may also include atom typing and partial charge information. Here are some examples:
C-CT Specifies an SP3 aliphatic carbon atom. C-CT-0.32 Specifies an SP3 aliphatic carbon atom with a partial charge of 0.32. O-O--0.5 Specifies a carbonyl group oxygen atom with a partial charge of -0.5.
Atom types and optional partial charges can be specified for each atom. Nuclear parameters can also be defined, as in these examples:
Specifying Ghost Atoms
An atom with mechanics type Bq (e.g.., "O-Bq") is set up as a ghost  of the corresponding atom, with its normal basis functions and numerical integration grid points but no nuclear charge or electrons. This requests a counterpoise calculation. Such calculations differ slightly from ones requested with Massage in previous versions of Gaussian in that they include the grid points from the ghost atoms in DFT XC quadrature. The new way is a more consistent superposition correction and also easier to use. Note that counterpoise calculations can also be requested with the Counterpoise keyword.
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