This page is meant as an introduction and tutorial to using the Gaussian software - not as an all inclusive guide. You may follow this link to connect to GAUSSIAN, Inc. www.gaussian.com for the definitive guide on the net to using the software. It also contains a listing of ALL the keywords and their implementation.
If you are a :
and you need
additional assistance, e-mail
Dr. Robert Bohn (the author) or call at X-4731.
A Gaussian 94/98 input file has the following syntax:
A basic GAUSSIAN input file has several different sections described
below. Lines marked with a red asterisk (*)
are required in every input file. Click on
a link to get a more detailed explanation of a section.
INPUT | BRIEF EXPLANATION |
Link 0 Commands | Defines the location of scratch files and job resource limits. Begins with a % sign. Used in SF_{6} example. |
*Route Section | Specifies the job type and model chemistry. Begins with a # sign in the first column. |
*blank line | Separates the route section from the title section. |
*Title Section | Describes the job for the output and archive entry. |
*blank line | Separates the title section from the molecule section. |
*Molecule Specification | Charge, spin and structure of the molecule to be studied. |
*blank line | Separates the molecule section from the variable section OR End Of File. |
Variables Section | Specifies values for the variables used in the molecule specification. |
blank line | End of File if you use a variable section. |
The first line of the Route Section begins with a pound sign (#) in the first column. This line details the theoretical procedure you want to use, the basis set and the type of calculation. This is usually accomplished via two separate keywords within the route section of the input file, although a few method keywords imply a choice of basis set.
Some procedures are: HF (Hartree-Fock), RHF (Restricted Hartree-Fock), UHF (Unrestricted Hartree-Fock), and Density Functional Theory (DFT). The most commonly used standard basis sets are STO-3G, 3-21G, 3-21G*, 4-31G, 6-31G, 6-31G*, 6-31G**, 6-311G*, 6-311G** and 6-31G(d).
This card also determines the way the output will be presented at the end of the run. There are 3 options for this.
#T | Terse option which is essential information and results. |
#P | Additional output is generated. Includes messages at the beginning and end of each link giving machine dependent information as well as convergence information. |
#N or # | Normal print level. This is the default. |
A few examples are of ROUTE cards are:
# HF/STO-3G SP | A single point (fixed geometry) Hartree-Fock energy calculation using an STO-3G basis set. The default if NO route card is given. |
#T RHF/6-31G | A single point (fixed geometry) Restricted Hartree-Fock using the 6-31G basis set. RHF is used for closed shell restricted wavefunctions only. (multiplicity = 1) (terse output) |
# UHF/6-31G** | A single point (fixed geometry) Unrestricted Hartree-Fock using the 6-31G** basis set. UHF is used for unrestricted open-shell wavefunctions. (multiplicity > 1) (normal output) |
#P RHF/6-31G(d) Opt Freq | Geometry Optimization and vibrational frequency calculation using a Restricted Hartree-Fock with a 6-31G(d) basis set. (full output) |
#P B3LYP/6-31G(d) Opt Freq | Geometry Optimization and vibrational frequency calculation using DFT with a 6-31G(d) basis set. The keyword for DFT is B3LYP for closed shell. For open-shell calculations use UB3LYP. |
TITLE section
This section is required in the input, but is not interpreted in any
way by the Gaussian program. It appears in the output for purposes of identification
and description. Typically, this section might contain the compound name,
its symmetry, the electronic state, and any other relevant information.
The title section cannot exceed five lines and must be followed by a terminating
blank line.
The following characters should be avoided in the title section: @ # ! - _ \ and all control characters.
This section contains specifics on the molecule namely its charge, multiplicity and initial geometry.
The charge and multiplicity are on the same line and separated by a white space.
Remember multiplicity = 2S+1 where S is the total spin. Alpha and Beta
electrons have spins of +½ and -½, respectively. Equal numbers of
each completely cancel and the total spin in that case is 0 and the
multiplicity = 1 (singlet). An odd number of electrons gives at least spin = +½
and multiplicity = 2 (doublet).
The entry for a neutral molecule in the singlet state is: 0 1
The entry for a doublet anion (charge=-1) is: -1 2
Defining a starting geometry for a molecule can be done in 2 ways; either in Cartesian coordinates or Z-matrix format. As you get more proficient in Gaussian, you will find that both formats have their pros and cons. Simple geometries tend to work well with Z matrices. With more complex geometries, you might find that Cartesian coordinates are more useful. You will just have try them out and then make up your own mind.
In Cartesian format, the atom is defined in the following way:
Element-label, x, y, z
In Z-matrix format, the atom is defined in the following way:
Element-label, atom 1, bond-length ,atom 2, bond-angle, atom 3, dihedral-angle
The label is usually the elemental abbreviation with a secondary identifying integer: eg C1, C2 etc..
Please note the following:
The complete molecular specification for H_{2}
(neutral,singlet) in Cartesian coordinates
is :
0 1
H1 0.0 0.0 0.0
H2 0.0 0.0 0.74
The complete molecular specification for H_{2}
(neutral,singlet) using the Z-matrix format is :
0 1
H1
H2 1 0.74
The value "1" in the last line denotes that the second atom, H2, is bonded
(connected) to the first atom in the list.
Input files for larger molecules (using Cartesian and Z-matrices) will be discussed in the section on Sample Gaussian Input Files.
One can use variable names for bond lengths, bond angles and dihedral angles as well.
Going back to our example for H_{2} and use r=0.74 Å, we get a molecular
specification that looks like:
0 1
H1
H2 1 r1
r1 0.74
We know that this is a neutral molecule (charge=0) and has 1+1+8=10 electrons (5 alpha and 5 beta). Since the number of alpha and beta spin electrons are equal, this means the total spin = 0 and the multiplicity = 1.
The complete structure of H_{2}O can be determined by 2 equivalent OH bonds and the H-O-H bond angle. The experimentally determined structure yields r(OH) = 0.957 Å and a bond angle (BA) of 104.5°. But for sake of this discussion, let's make a "bad" guess and say that r(OH) = 1.0Å and BA = 90°. But this could also be a potentially useful calculation if one is investigating the potential energy surface of water. This will give the energy at this Single Point on the surface.
Assuming the oxygen atom is located at the origin, the complete input files for both Cartesian and Z-matrix formats are:
Route Section -> | #HF/6-31G | #HF/6-31G |
blank line | ||
Title Section -> | Water with Cartesian | Water with Z-matrix |
blank line | ||
charge, multiplicity -> | 0 1 | 0 1 |
Begin Molecule specification -> | O1 0.0 0.0 0.0 | O1 |
H2 0.0 0.0 1.0 | H2 1 rOH | |
H3 is connected to atom 1 and makes an angle BA with atom 2. | H3 1.0 0.0 0.0 | H3 1 rOH 2 BA |
blank line (end for Cart) | ||
Begin Variable definitions -> | rOH 1.0 | |
BA 90.0 | ||
blank line (end for Z-matrix) |
I did this calculation using Gaussian98 on amur.nist.gov. The final SCF energy = -75.9697005 hartrees.
What can one do next? You can calculate the ground state energy and optimized geometry of H_{2}O and then make a comparison. But to get the optimized geometry, you'll have to read how to do it in the following section.
The answer to these questions can be ascertained through this calculation by seeing which one gives the lowest energy.
This molecule is neutral (charge=0). It contains 1+8+6+8 = 23
electrons. Therefore it has 1 unpaired electron which contributes to
the total spin. Using 2S+1 (S=½), multiplicity = 2. In other
words, it is a doublet and we must do a UHF calculation. The entry
for the charge and multiplicity for all 3 calculations is:
0 2
Without knowing what the structure is at first, we know that 4 atoms nominally exist in either a) cis, b) trans or c) linear arrangements. But we can create a table of initial guesses at the structures. You can get the dihedral angle from making a Newman Projection of the molecule.
The questions we want to ask here are:
The answer to these questions can be ascertained through this calculation by seeing which one gives the lowest energy.
Click Here to see the structures of all the different conformers.
Cis HOCO | Trans HOCO | Linear HOCO | |
R(O_{1}H_{3}) | 1.0 Å | 1.0 Å | 1.0 Å |
R(O_{1}C_{2}) | 1.35 Å | 1.35 Å | 1.35 Å |
R(C_{2}O_{4}) | 1.2 Å | 1.2 Å | 1.2 Å |
a(H_{3}O_{1}C_{2}) | 135° | 135° | 180° |
a(O_{1}C_{2}O_{4}) | 135° | 135° | 180° |
dihedral(H_{3}O_{1}C_{2}O_{4}) | 0° | 180° | 0° |
One can still set this molecule up in Cartesian coordinates. It's planar, so we only have to do 2-dimensional geometry to determine the proper coordinates. Click Here to see the actual set of computations you have to get the Cartesian coordinates. However, this is a case in which the Z-matrix format embarrassingly easy.
The Molecule specification section (in bold) becomes a template for all conformers of this molecule. Only the title and variable sections are altered to generate the Z-matrices for the trans and linear cases.
#UHF 6-31G OPT
Cis HOCO OPTIMIZED GEOMETRY at 6-31G
0 2
O1
C2 1 R12
H3 1 R13 2 A312
O4 2 R24 1 A124 3 DA
R12 1.35
R13 1.0
R24 1.2
A312 135.0
A124 135.0
DA 0.0
#UHF 6-31G OPT
Trans HOCO OPTIMIZED GEOMETRY at 6-31G
0 2
O1
C2 1 R12
H3 1 R13 2 A312
O4 2 R24 1 A124 3 DA
R12 1.35
R13 1.0
R24 1.2
A312 135.0
A124 135.0
DA 180.0
#UHF 6-31G OPT
Linear HOCO OPTIMIZED GEOMETRY at 6-31G
0 2
O1
C2 1 R12
H3 1 R13 2 A312
O4 2 R24 1 A124 3 DA
R12 1.35
R13 1.0
R24 1.2
A312 180.0
A124 180.0
DA 0.0
The final values for the variables and the final energy for each conformer is tabulated below:
Cis HOCO | Trans HOCO | Linear HOCO | |
R(O_{1}C_{2}) | 1.33024227 Å | 1.34262179 Å | 1.59856636 Å |
R(O_{1}H_{3}) | 0.9594721 Å | 0.95159027 Å | 0.98162564 Å |
R(C_{2}O_{4}) | 1.18933877 Å | 1.1808501 Å | 1.13782256 Å |
a(H_{3}O_{1}C_{2}) | 117.18485661° | 115.49871545° | 180.0° |
a(O_{1}C_{2}O_{4}) | 131.10877893° | 128.65088481° | 180.0° |
dihedral(H_{3}O_{1}C_{2}O_{4}) | 0° | 180° | 0° |
Final Energy (hartree) | -188.027641 | -188.0291609 | -187.9079994 |
From this data, we can see that the Trans conformer of HOCO is the most stable. It lies (-188.0291609 + 188.027641 ) = -0.0015199 hartree lower than the cis form. Converting this to kcal/mole (1 hartree = 1.0987E4 kcal/mol) yields a difference of ~17 kcal/mole.
Again this molecule is a neutral, singlet. You should verify this yourself and determine the number of alpha and beta electrons this molecule has.
The molecule has O_{h} symmetry and need only be defined by a single S-F bond (rSF) of 1.6Å and all the single F-S-F bond angles (aFSF) equal 90°.
Click Here to get a view of the structure of SF_{6}, the numbering system and how each line of the following Z-matrix is determined. Click on the Atom X link to get a description of how each line was generated.
This is an excellent example of using a Link 0 command. We will use as the first line of the file a command which save the checkpoint file for future calculations.
This file will keep copies of data that pertain to the calculation, like force constants. They will be useful starting points for future calculations. Remember that the force constants are related to the vibrational wavefunction and not the electronic wavefunction. Therefore using the results of a force constant calculation at a STO-3G level is a good place for starting a force constant calculation at a higher level of theory.
%chk=sf6.chk | Link 0 command to save the checkpoint file as "sf6.chk" |
#P HF/6-31G* OPT=CALCFC FREQ | |
SF6 HF/6-31G* geom opt with IR frequencies | |
0 1 | Charge Multiplicity |
S | Atom 1 |
F 1 r | Atom 2 |
F 1 r 2 90.0 | Atom 3 |
F 1 r 2 90.0 3 90.0 | Atom 4 |
F 1 r 2 90.0 3 180.0 | Atom 5 |
F 1 r 2 90.0 3 -90.0 | Atom 6 |
F 1 r 3 90.0 2 180.0 | Atom 7 |
r 1.6 | Variables |
Alternatively, we can use the Cartesian coordinates for SF_{6}. This is a case in which Cartesian coordinates are particularly easy. viz ...
%chk = sf6.chk
#P HF/6-31G* OPT=CALCFC FREQ
SF6 HF/6-31G* geom opt with IR frequencies
0 1
S1 0.0 0.0 0.0
F2 1.6 0.0 0.0
F3 0.0 1.6 0.0
F4 0.0 0.0 1.6
F5 0.0 -1.6 0.0
F6 0.0 0.0 -1.6
F7 -1.6 0.0 0.0
The results of this calculation are:
HF Energy (hartrees) = -993.9902203
R = 1.554035 Å
The results of the IR portion of the calculation yield 2 IR active bands at 644.7179 (T_{1u}) and 1100.1456 (T_{1u}) cm^{-1}, respectively with relative intensity ratios of 1:27.27. Experimentally, the strongest absorption appears at 939 cm^{-1}.
The essence of this calculation shows that we calculated about 160 cm^{-1} too high. One could expect a better result by adding in d- and f-type or polarization functions by starting at a higher level of theory. In any event, we can still use the checkpoint file "sf6.chk".
To use it in the next calculation, one would change the option on the OPT keyword. Above we calculated the force constants and now we need to read them. The new cards for calculation #2 would be:
%chk = sf6.chk
#P HF/6-311G** OPT=READFC FREQ
SF6 HF/6-31G* geom opt w IR freqs. Second try.
followed by the rest of the Molecular Specs.
Again, we start by knowing the charge here is 0 (a neutral). Then start counting the number electrons. But a-priori, we can tell that there is an even number because there are an equal number of atoms present. Therefore, the ground state is a singlet with multiplicity = 1.
Now, I introduce the concept of "ghost" or "dummy" atoms. They are not involved in the calculation in any way. They are only there to use as an anchor for constructing a Z-matrix. It is labeled "X".
For benzene, a good place to put the dummy atom is at the inversion center. Click here to see the molecule and it's numbering scheme. Here is the complete input file for running this job.
%chk=ben.chk | Link 0 command to save the checkpoint file as "ben.chk" |
#P B3LYP/6-31(d) OPT=(CALCFC,z-matrix) | |
C6H6 HF/6-31G(d) | |
0 1 | Charge Multiplicity |
X | Atom 1 |
C2 1 rCC | Atom 2 |
C3 1 rCC 2 60.0 | Atom 3 |
C4 1 rCC 3 60.0 2 180.0 | Atom 4 |
C5 1 rCC 4 60.0 3 180.0 | Atom 5 |
C6 1 rCC 5 60.0 4 180.0 | Atom 6 |
C7 1 rCC 6 60.0 5 180.0 | Atom 7 |
H8 2 rCH 3 60.0 1 180.0 | Atom 8 |
H9 3 rCH 4 60.0 1 180.0 | Atom 9 |
H10 4 rCH 5 60.0 1 180.0 | |
H11 5 rCH 6 60.0 1 180.0 | |
H12 6 rCH 7 60.0 1 180.0 | |
H13 7 rCH 2 60.0 1 180.0 | |
rCC 1.4 | Variables |
rCH 1.08 |
#P HF/6-31(d) OPT=z-matrix
rCC 1.4752 Å
rCH 1.1087 Å
HF=-229.8000165 hartrees
Problem 1. Create the input for NH_{3} at the
STO-3G level of theory. You may use either Z matrix or Cartesian format.
Given:
Problem 2. Create the input for a geometry optimization of
(CH_{3})_{2}CO (acetone) at the 6-31G level of theory.
You may use either Z matrix or Cartesian format.
Given:
Problem 3. Create the input for a vibrational frequency and geometry optimization of Li-cyclopentadienyl system, Li(C_{5}H_{5}). The Lithium atom lies directly over the center of the cylcopentadiene moiety. Use the 6-31G(d) level of theory.
Given:
MOLDEN is a visualization package that is installed on the machines in the Visualization Laboratory (Bldg 225, B131) and the Central Computing Facility machines (danube, arno, amur). This software is shareware which was downloaded from the Molden web site. You will find instructions there on how to use it and its features.
Some of its visualization capabilities are:
Simply, in order to use it with Gaussian, you must include this line in the ROUTE card:
#P GFINPUT IOP(6/7=3)
You may still add your other Keywords as necessary.