Gaussian 03 Online ManualLast update: 2 October 2006 | |

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
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:
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):
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
In the first form, the remaining items on each line are Cartesian
coordinates specifying the position of that nucleus. In the second form, 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 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: Variables: 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., ## Specifying Periodic SystemsPeriodic 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 The final line specifies
the translation vector. Note that it specifies 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 ParametersIsotopes 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 **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^{18}O, 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 g-factor.
## Molecular Mechanics Atom TypesMolecule specifications for molecular mechanics calculations may also include atom typing and partial charge information. Here are some examples: C-CT 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) ## Specifying Ghost AtomsAn atom with mechanics type Click here to go on to the next section. |