Gaussian

1. Input structure

A Gaussian input contains Link 0 commands, route section, title, charge and multiplicity, and molecular coordinates. Blank lines are part of the syntax.

%chk=acetone.chk
%mem=4GB
%nprocshared=4
#p wB97XD/def2SVP Opt Freq Int=UltraFine SCF=Tight

Acetone optimization and frequency

0 1
...

2. SCF

Hartree-Fock and Kohn-Sham DFT iteratively build a matrix from the current density, solve for orbitals, and update the density. Check convergence, the intended electronic state, spin contamination for unrestricted references, and wavefunction stability when relevant.

For difficult convergence, diagnose the cause before changing algorithms: poor geometry, an inappropriate charge or multiplicity, near-degenerate orbitals, or an unstable reference can all produce similar symptoms. Report any nondefault convergence procedure.

3. Geometry optimization

Opt searches for a stationary point using energy gradients. Confirm the reported force and displacement convergence rather than relying only on normal termination.

An optimization finds a nearby stationary point, not necessarily the intended conformer or global minimum. Monitor connectivity and compare alternative starting structures.

#p wB97XD/def2SVP Opt=(CalcFC,Tight) Int=UltraFine SCF=Tight

4. Frequency analysis

A minimum normally has no imaginary frequencies and a first-order saddle point has one mode along the reaction coordinate. Visualize the mode. Low-frequency torsions and the harmonic approximation can strongly affect entropies and free energies.

Thermal corrections depend on temperature, pressure, standard state, and the harmonic approximation. State whether low-frequency or quasi-harmonic corrections were applied.

5. Transition states and IRC

Use Opt=TS, QST2, or QST3 as appropriate, verify the imaginary mode, follow both IRC directions, and reoptimize endpoints to establish connectivity.

#p B3LYP/def2SVP Opt=(TS,CalcFC,NoEigenTest) Freq
#p B3LYP/def2SVP IRC=(CalcFC,Forward,MaxPoints=50)

6. Solvent and theory level

For small selectivity differences, assess functional, basis, dispersion, integration grid, solvation, conformer ensemble, and standard-state dependence. State exactly which geometry each single-point energy uses.

Do not combine electronic energies, thermal corrections, and solvation contributions from incompatible geometries or levels without describing the composite protocol explicitly.

7. Checkpoint and downstream analysis

Convert a binary checkpoint with formchk. The resulting fchk contains coordinates, basis information, and orbital coefficients for Multiwfn and cube generation.

formchk acetone.chk acetone.fchk
Multiwfn acetone.fchk

8. Validation checklist

1. Confirm charge, multiplicity, atom order, and geometry.
2. Confirm SCF and geometry convergence.
3. Inspect spin contamination or stability when relevant.
4. Use frequencies to classify the stationary point.
5. Visualize the transition vector and verify IRC connectivity for a TS.
6. Record method, basis, grid, solvent, temperature, standard state, and software revision.

9. References

• Gaussian 16
• SCF keyword
• Opt keyword
• Freq keyword
• Gaussian IRC keyword