# Farmamol Wiki

### Site Tools

geometry_optimization_and_molecular_orbitals_mos_calculation

## General setup

• Firstly, generate a Z-matrix using OpenBabel, Molden, …
• Then, paste the next lines at the beginning of the document, according to your needs:
• NOTE: This is not a Gaussian tutorial; it is only a (very brief) summary of some input possibilities.
• GEOMETRY OPTIMIZATION

`%chk=your_file_name`
`%nproc=1` Number of processor(s) that are going to be used.
`#p B3LYP/6-311+G(d,p) opt=Z-matrix scf=tight/direct scrf=(iefpcm,solvent=m-xylene)` Quantum method and basis set. Use scrf if you want to take into account the solvent effect.
(space)
`molecule geometry optimization` Describe here what you are working on.
(space)
`-1 1` Total charge of the quantum system and spin multiplicity (unpaired electrons = 1; 1 unpaired electron = 2 (singlet); 2 unpaired electrons = 3 (doublet), …

• TRANSITION STATE SEEKING

`%chk=your_file_name`
`%nproc=1` Number of processor(s) that are going to be used.
`#p B3LYP/6-311+G(d,p) opt=(TS,CalcFc,NoEigenTest) Freq` Now, keyword opt has TS as the argument. If the TS geometry is unknown, you can use QST2/QST3 instead of TS. The former implies that the reactant and final product geometries (in this order) need to be specified. The latter requires, in addition, a guess of the TS geometry at the end of the input.
(space)
`TS geometry seeking` !Describe here what you are working on.
(space)
`-1 1` Total charge of the quantum system and spin multiplicity (unpaired electrons = 1; 1 unpaired electron = 2 (singlet); 2 unpaired electrons = 3 (doublet), …

• MOLECULAR ORBITALS (MOs) CALCULATION

`%chk=your_file_name`
`%nproc=1` Number of processor(s) that are going to be used.
`#p B3LYP/6-311+G(d,p) pop=full iop(6/7=3) GFinput` Quantum method and basis set. We specify GFinput because we usually visualize the results in Molden or gmolden.
(space)
`1attack MO visualization` Describe here what you are working on.
(space)
`-1 1` Total charge of the quantum system and spin multiplicity (unpaired electrons = 1; 1 unpaired electron = 2 (singlet); 2 unpaired electrons = 3 (doublet), … 