Even if you have not studied quantum chemistry in detail, you probably have realized that a typical molecular mechanics problem is a many-body problem in which several nuclei and many electrons interact while moving. As there is no known analytical, closed form solutions to such many-body problems, one has to rely on approximate methods when solving molecular quantum mechanics problems. The large number of different quantum mechanics programs is partially a result of different researchers focusing effort on different approximate solutions or trying to describe different aspects of molecular behaviour. Thus, each popular quantum mechanics program has some set of strengths that sets it apart from other programs.
In addition to providing unique strengths in a specific area, computer programs developers also aim to broaden capabilities of the program by implementing additional computational methods. As a result, there is a significant overlap between different computational chemistry programs in terms of capabilities. This makes it often difficult to choose which computational chemistry program best serves the goal. Factors such as program cost, performance, avaliability on multiple platforms, ease of use, and available support play a significant role. Oftentimes, programs that are more powerful in terms of performance or feature set may be the ones that are most difficut to install and use. Below is a list of some computational chemistry programs along with brief descriptions of their unique strengths.
Programs that perform quantum chemistry calculations typically require an input file that specifies the molecular geometry and contains keyword that tell the program what type of calculation is requested. The format of the molecular structure input section is fairly similar in different programs: the geometry is either specified as a Z-matrix or as XYZ atomic coordinates. Furthermore, programs such as babel can interconvert between different structure file formats. The keyword section is rather unique for each program and one has to learn what keywords and options are most appropriate for performing a given task with a particular program. Click on the program names in the table on the right to see how the input for a calculation that requests coupled-cluster energy evaluation of a water looks with Gaussian, Gamess, Q-Chem, Dalton, DIRCCR-12, Psi3, and MolPro.
|
|
You will be using a computational chemistry program Gaussian03 to perform the semiempirical calculations. Gaussian is one of the most commonly used computational chemistry programs and it is important that you learn well how to use it. One valuable resource is their on-line technical documentation.
The input structure for Gaussian can be either in the Z-matrix format or in XYZ format. In the XYZ format, the positions of atoms are defined by their Cartesian ccordinates. Oftentimes, the origin of the coordinate system is at the first atom or at the center-of-mass. The units can be either angstroms or bohrs; make sure that you use units expected by your program. Gaussian expects angstroms by default. The geometry of water can be specified in the Gaussian XYZ format as follows:
O 0.000000 0.000000 0.117613 H 0.000000 0.757348 -0.470450 H 0.000000 -0.757348 -0.470450
You can use MOLDEN to create XYZ coordinates for Gaussian or use the program OpenBabel to convert existing molecular structures from various sources into appropriate XYZ format. For example, you can use the Maestro Builder on the workstation to create an input structure for butane and save the XYZ coordinates in MOL2 format as butane.mol2, then use command babel -imol2 butane.mol2 -ocom butane.com to create structure that Gaussian can process.
In the Z-matrix notation, the position of each atom in the molecule is defined by a bond length to one of the preceding atoms, by a bond angle made to two preceding atoms and by a dihedral angle made to three preceding atoms. The geometry of water can be specified in the Gaussian Z-matrix format as follows:
O
H 1 rOH
H 1 rOH 2 aHOH
Variables:
rOH = 0.95885
aHOH = 104.343
You can use MOLDEN to create a Z-matrix input for Gaussian. For simple molecules, one can easily write Z-matrixes by hand. There are several ways to specify a Z-matrix for a molecule. For example, consider conformational analysis of methanol via scanning the H-O-C-H torsion in 20 degree increments. One way to define the Z-matrix for this task is:
C
O 1 oc2
H 2 ho3 1 hoc3
H 1 hc4 2 hco4 3 dih4
H 1 hc5 2 hco5 3 dih5
H 1 hc5 2 hco5 3 -dih5
Variables:
oc2 1.400
ho3 0.950
hoc3 109.471
hc4 1.089
hco4 109.471
hc5 1.089
hco5 109.471
dih5 120.000
dih4 0.000 S 2 30.0
Another way to define the Z-matrix for this task is:
C
O 1 oc2
H 2 ho3 1 hoc3
H 1 hc4 2 hco4 3 dih4
H 1 hc5 2 hco5 4 dih5
H 1 hc5 2 hco5 4 -dih5
Variables:
oc2 1.400
ho3 0.950
hoc3 109.471
hc4 1.089
hco4 109.471
hc5 1.089
hco5 109.471
dih5 120.000
dih4 0.000 S 2 30.0
Notice that in the first case, the last two methyl hydrogen positions are defined via normal dihedrals and that in the second case, these hydrogen positions are defined using improper dihedrals. These two ways are more or less equivalent when calculationg the first point (H-O-C-H) of the torsional profile. However, these two methods are not equivalent for the second point of the scan. When the scanning algorithm changes the first methyl hydrogen dihedral by 30 degrees, the positions of the remaining two methyl hydrogens do not change if the first Z-matrix definition is used. This results in a distorted methyl group (image on the right) and the geometry optimization will spend lots of time bringing the two hydrogens in their equilbrium positions. The second definition avoids this by making the -CH3 group rotate as one tetrahedral unit.