Molecule Specifications

Nuclei Properties

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.
• NMagM=n: Nuclear magnetic moment in nuclear magnetons.
• ZNuc=n: Modifies nuclear charge.
• RadNuclear=radius: Specifies the radius to use when finite (non-point) nuclei are used. radius is a floating point value in atomic units.

Fragments

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.

MM Types

Molecule specifications for molecular mechanics calculations may also include atom typing and partial charge information. Here are some examples:

Atom types and optional partial charges can be specified for each atom. Nuclear parameters can also be defined, as in these examples:

C-CT(Iso=13)
C-CT--0.1(Spin=3)

PDB 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 16 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.

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.