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Computing
harmonic frequencies from Hessian
Chemcraft can read the Hessian (second derivatives of the energy by atomic coordinates) and compute the frequencies using it (with
the "rigid rotor - harmonic oscillator" approach). Currently the Hessian can be read from Gaussian .fch files and Orca .hess files. This utility can be convenient for predicting the vibrational spectra of isotopically-substituent molecules. Programs like Gaussian or Orca can perform same computations, but Chemcraft makes this slightly more convenient
since you don't need to restart your job.
In the latest implementation (version b758 and further), Chemcraft projects out the 6 lowest frequencies related to translational and rotational
motion (the version b748 didn't have this feature).
You can specify custom isotopes with "Tools/Set custom isotopes
for the frequencies computation" menu item. This menu item shows a windows which has three tabs:
- Isotopes for atom
types
A custom isotope can be specified for each atom type. If all checkboxes are checked for an atom type, it means that Chemcraft uses an averaged mass (calculated by averaging the masses of all isotopes existing in nature for this atom type, with their percentages);
- Isotopes for individual
atoms
The same choice is available for each individual atom in molecule;
-
Explicit masses of
atoms
With this tab, you can enter any custom mass for each atom in your molecule
in text format.
Troubleshooting
For verifying this tool, we compared the frequencies computed by it with the
values provided by other programs for some compounds. For Gaussian 09, we
got almost full match with the frequencies computed by Chemcraft and by it,
as well as with the computed Gibbs energies.
For
Orca 5.0.4, we got some small difference (e.g. 4155.59 vs 4155.51 cm-1), and currently it is difficult
for us to explain its reasons. It seems for us that Orca uses slightly
different atomic masses than it prints in the .hess file. As far as we can
see, an almost full agreement (within 0.001 cm-1) with the Orca results is obtained, if you
specify the following masses of atoms in "Explicit
masses of atoms" tab:
1.00803666900639
for H
12.0114368794449
for C
15.9995819522312
for O
35.4542904151853
for Cl
We
got these values by computing molecules like O3 in Orca, and dividing the
frequencies printed by Orca by the ones calculated by Chemcraft.
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