COMPUTATIONAL CHEMISTRY METHODS
The categories of computational methods are:
Aragon S’04
1) Semi-Empirical
Experimental data are used to give values to the few molecular integrals that are
not taken to be zero. HF like equations are solved via SCF methods.
2) Ab-Initio
The Schroedinger equation is solved starting only from the values of fundamental
constants. No empirical information is used. All molecular integrals are
computed.
3) Molecular Mechanics
A classical force field method suitable for the study of conformations of large or
small molecules. Empirical parameters to describe bond stretching, bending,
torsion, electrostatic interactions and Van der Waals interactions are used to
generate effective forces. The energy is minimized to obtain a stable
conformation.
A schematic of the various methods under these categories follows.
Method
1) Semi-Empirical
MNDO
AM1
PM3 and PM3/TM
2) Ab-Initio
HF
Computer Packages
MOPAC
AMPAC
MP2, MP4
CI, MRCI
Coupled Cluster
Gaussian
Spartan
HyperCube
GAMESS
SVWN
BP
BLYP
B3LYP
Gaussian
Spartan
DMOL
DGauss
Amsterdam DFT
DFT
3) Molecular Mechanics
MM2, MM3
MMFF
UFF, Dreiding
Charm
Gaussian
Sybyl
Quanta
Cerius2
EXCHANGING FILES BETWEEN COMPUTATIONAL CHEMISTRY
PACKAGES
Aragon S’07
Package Availability
At SFSU we have two main commercial computational chemistry packages available to
all students: Spartan and Gaussian . Spartan has been designed with teaching applications
in mind, while Gaussian is a professional level program. The main location to access and
work with these programs is the Computational Chemistry & Visualization Laboratory
(CCV Lab, TH 408). Please see your instructor if you wish to request access to the CCV
Lab in order to use these packages. [There are other packages in private use such as
Jaguar, Titan, and MolPro.]
Spartan Pro 1.07 is installed on the Windows PC’s. A general class account is used on
the PC’s. Please see your instructor for the account parameters.
Gaussian is available in two implementations, G98 and G03, with G03 being the most
recent. GaussView 2.1, the graphical user interface, G98W, and G03W are installed on
the Windows PC’s in the CCV Lab. Gaussian 03 is also available within certain courses
(Chem 850) and the research groups of Aragon and Ichimura on Unix/Linux
environments. For Chem 850, G03 may be run in the Aragon Group AMD cluster
(castalia); inquire with your instructor.
File Exchange
The graphical molecule builder in Spartan is one of the most intuitive available. Many of
you may wish to generate your molecules in Spartan and read them into GaussView to do
advanced calculations in Gaussian. A quick check of the file formats shown below tells
us that the easiest way to do this is to export your molecule file made in Spartan in the
Brookhaven format, “pdb”. In the “Save As” menu option in Spartan, look for the “.pdb”
before you execute the save. The file will be molecule.pdb, where molecule is the name
that you chose. Next, exit Spartan and Start GaussView and under the “File /Open”
menu, select “.pdb”. Now you can continue to work and generate an input file for
Gaussian within this program and submit the calculation, as well as review the results.
The natural format choices provide no equivalent solution to go from GaussView to
Spartan, but it is possible to edit a .gjf file written with the “Write Cartesian Coordinates”
box checked in GaussView, and transform it into a .mol file format with the aid of a text
editor. However, a general file conversion utility exists, called NewZmat.
NewZmat:
This program is available within G98W (the Windows version, under utilities), or as a
separate executable in the Unix/Linux system. This is a general file format conversion
utility. The list of available formats shows that the only common format to produce a
Spartan readable file externally is the Brookhaven (.pdb) format.
NewZmat File Formats
Open/Save: Biograph (.BGF); Brookhaven (.pdb); Cartesian.s; Cache(CAC); Checkpoint
(.chk); Mopac (.inp); Macromodel; PC-Model (.PCM)
Unix/Linux installations often do not run a graphical user interface for molecule building,
but are much faster and have more memory than the PC’s and thus attractive for large
jobs. While simple molecular structures allow a .gjf file to be written by hand, for
complex molecules, an easy solution is to build it in either Spartan or GaussView, and
then ftp the .gjf file to the larger machine. In order to do this, you must use an ftp
program on the PC to access the relevant Unix/Linux machine where gaussian is installed
and you have an account. Request instructions from your instructor.
Spartan Pro 1.07 Formats
Open/Save:
Binary: .spartan .sxf
Text: .pdb .mol .mol2 .mac
Output file: *.txt [Only for output of a calculation]
GaussView 2.1 Formats (Graphical Interface to Gaussian 98)
Open: .com .out .log .gjf .ent .chk .fch .pdb .cub
Save: .gjf [option: save cartesian coordinates]
Sample Gaussian Input files (.gjf)
Cartesian Coordinate Style:
%mem=6MW
%nproc=1
%chk=CO.chk
# rhf geom=connectivity
Title Card Required
0
1
C
O
1
2
0.000000
0.000000
2 3.0
Z Matrix Style:
%mem=6MW
0.654857
-0.491143
0.000000
0.000000
%nproc=1
%chk=CH3.chk
# opt ub3lyp/3-21g* geom=connectivity
CH3
0
2
C
H
H
H
D1
1
1
1
B1
B2
B3
A1
A2
D1
1
2
3
4
2 1.0
B1
B2
B3
2
2
A1
A2
1.070000
1.070000
1.070000
120.000000
120.000000
180.000000
3 1.0
4 1.0
Sample PDB file (.pdb)
HEADER
REMARK PC Spartan Pro exported Molecule001
HETATM
1 C
UNK 0001
0.000
0.000
HETATM
2 O
UNK 0001
0.000
0.000
CONECT
1
2
CONECT
2
1
END
0.573
-0.573
3
Generating Surfaces in GaussView
Unlike Spartan, GaussView requires that a computation already exist before a request for
the generation of a surface can be entered. When a computation is about to be done, one
must enter the name for a checkpoint file in the beginning of the Gaussian input file, for
example:
%chk: c:\home\pchem\methane.chk
The checkpoint file stores the information about the basis set used and the variational
coefficients determined during the run. When the calculation completes, load the
checkpoint file using the File/Open menu. The file will be opened in a new view
window. Select this window and now select the Results/Surfaces menu. On the window
that opens, press the “Generate” button. A new small, self explanatory, window opens,
similar to the one in Spartan, for selecting the different surfaces. As each surface is
selected, the CubeGen utility generates the surface in the background. When the
generation is completed, then the surface name is added to the list of Available “cubes”.
Wait for this to happen before generating the next surface (it takes only a few seconds).
To display a given surface, select it from the list of Available Cubes, press the “Apply”
button, and a new window will pop-up with the 3-D surface display.