Overview of Molecule Specifications
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 (usually 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. Multiple charge/spin pairs may/must be included for some calculation types.
The charge and spin line 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.
Here is the basic format for specifying atoms within the molecule specification (omitting all of the optional items):
Element-label [freeze-code] x y z
Although these examples use spaces to separate items within a line, any valid separator may be used. The position of the atom is specified in Cartesian coordinates. freeze-code is an optional parameter related to freezing atoms during optimizations using ONIOM (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. The maximum length of the element label is 4 characters.
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 is a simple molecule specification section for ethane which uses element labels for the carbon atoms and element types for the hydrogen atoms:
C1 0.00 0.00 0.00
C2 0.00 0.00 1.52
H 1.02 0.00 -0.39
H -0.51 -0.88 -0.39
H -0.51 0.88 -0.39
H -1.02 0.00 1.92
H 0.51 -0.88 1.92
H 0.51 0.88 1.92
Z-matrix molecule specifications are also accepted. See Appendix C for details.
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:
Iso=n: Isotope selection. If integers are used to specify the atomic masses, the program will automatically use the corresponding actual exact isotopic mass (e.g., 18 specifies 18O, and Gaussian uses the value 17.99916).
Spin=n: Nuclear spin, in units of 1/2.
ZEff=n: Effective charge. This parameter is used in spin orbit coupling (see CASSCF=SpinOrbit), and the ESR g tensor and the electronic spin-molecular rotation hyperfine tensor (NMR Output=Pickett).
QMom=n: Nuclear quadrupole moment.
GFac=n: Nuclear magnetic moment in nuclear magnetons.
Fragments within a molecular system may be defined using the Fragment parameter, which appears in parentheses following the atom label along with any isotope and/or nuclear parameter values. The value to Fragment is an integer; all atoms with the same fragment number are defined as a fragment. Fragments are useful for fragment guess calculation, counterpoise calculations, and so on.
For example, the following biphenyl structure is divided into two fragments by benzene ring:
0,1 0,1 0,1 Total spin & charge, followed by fragment-specific ones.
C(Fragment=1) -3.05015529 -0.24077322 0.00000698
C(Fragment=1) -1.64875545 -0.24070572 0.00067327
C(Fragment=1) -0.94811361 0.97297577 0.00020266
C(Fragment=1) -1.64887160 2.18658975 -0.00093259
C(Fragment=1) -3.05027145 2.18652225 -0.00159819
C(Fragment=1) -3.75091329 0.97284076 -0.00112735
H(Fragment=1) -3.58511088 -1.16744597 0.00036555
H(Fragment=1) -1.11371117 -1.16732692 0.00154256
H(Fragment=1) -1.11391601 3.11326250 -0.00129286
H(Fragment=1) -3.58531573 3.11314346 -0.00246648
H(Fragment=1) -4.82091317 0.97278922 -0.00163655
C(Fragment=2) 0.59188622 0.97304995 0.00093742
C(Fragment=2) 1.29252806 2.18673144 0.00046795
C(Fragment=2) 1.29264421 -0.24056403 0.00207466
C(Fragment=2) 2.69392790 2.18679894 0.00113535
C(Fragment=2) 2.69404405 -0.24049653 0.00274263
C(Fragment=2) 3.39468590 0.97318496 0.00227326
H(Fragment=2) 0.75768862 -1.16723678 0.00243403
H(Fragment=2) 0.75748378 3.11335264 -0.00040118
H(Fragment=2) 3.22888349 3.11347169 0.00077519
H(Fragment=2) 3.22908834 -1.16711773 0.00360969
H(Fragment=2) 4.46468577 0.97323650 0.00278063
This example also illustrates the use of fragment-specific charge and spin multiplicity specifications. The format of the corresponding input line in this case is:
total charge, total spin, fragment1 charge, fragment1 spin, fragment2 charge, fragment2 spin
Negative spin multiplicity values have a special meaning for Guess=Fragment calculations, indicating that the unpaired orbitals for the corresponding fragment are to become β spin orbitals in the combined set specified. Negative spin multiplicities will generate an error in any other job type.
For Guess=Fragment and Counterpoise calculations, fragment numbers must begin at 1 and run consecutively. For other calculation types, this restriction is not enforced, but violating it may result in some extraneous, empty data sections in the output (e.g., all zero fragment population analyses).
GaussView provides a graphical tool for defining fragments.
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:
PDB File Parameters
Several additional items may be defined along with the nuclear parameters and/or fragment definitions. These items are designed for use with PDB files to retain residue and other structural information they contain and as such will not be defined by the user. However, you may see them in Gaussian 09 input files created by GaussView using structures originating in PDB files.
RESNum specifies the residue in which the atom is located. The value takes the form of n[X[Y]], where n is an integer (which need not be positive), X is the optional one-character insertion code, and Y is the optional chain letter. If the chain is specified but there is no insertion code, then X can be an underscore: ResNum=-17_C for the residue with number -17 in chain C.
RESName specifies the three character residue name.
PDBName specifies the name assigned to the atom if it is not just the element name.
Specifying Ghost Atoms
An atom with mechanics type Bq (e.g., O-Bq) is set up as a ghost [Macbeth] 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.
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
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 a graphite sheet:
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
Here is the molecule specification that could be used for a three-dimensional PBC calculation on gallium arsenide:
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
Last update: 22 May 2013