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University of Alaska Fairbanks |
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Updated 8-17-2026 Contact: jwkeller/at/alaska.edu |
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More Details |
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WebMO compute servers:
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Use B3LYP-D3(BJ) for research grade
calculations. We have used and recommended the world's most
popular DFT method B3LYP for years, however, this functional has a
serious shortcoming in not properly taking into account London
dispersion forces. This is an issue for larger molecules and noncovalent
complexes, but not so much for small molecules. This option is available
in Gaussian by selecting "D3(BJ)" in the Empirical Dispersion dropdown
menu in the WebMO Advanced tab as shown below. (D3 is the third
dispersion correction introduced by Stephan Grimme some years ago; BJ
stands for Becke-Johnson damping, which is a "correction on the
correction.") |
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WebMO Demo tutorial - H2O. |
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How do you
interpret the thermochemistry section in the output of a
Gaussian frequency job?
That is, what are ZPE,
Internal Energy, Enthalpy, and how does Gaussian derive these
values?
An explanation, including an example, is available
here.
(While rather long, it's shorter than the authoritative
whitepaper on thermochemistry
by Joseph Ochterski of Gaussian, Inc.) |
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What are Natural Bond
Orbitals
(NBOs)?
NBOs are localized orbitals derived mathematically from
the normal MOs. They reflect the molecule's bonding as suggested by a valence
bond model or a Lewis formula. That is, NBOs correspond to isolated sigma (σ) bonds, pi (π) bonds,
or lone pairs. For example, propene: |
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| How do you get
a 3D-rotatable structure from a 2D formula? In WebMO, use
the Line Editor under the Build menu. For example, "pulegone" is show
below. Or, go to the MolView website:
https://molview.org/ |
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| How does the WebMO job queue work? For ORCA, for example, the number of cores assigned by default per job is 8. Thus, if the Select Server box is set at "First Available", WebMO can schedule three "8-core" ORCA jobs on Antec12 if they are submitted at the same time. Then, if there is a fourth job, it would be assigned to the next server down the list. For a large job (bigger molecule), 12, 16, or 20 cores may be requested. In that case, the job will be sent to the next server down the list with that many cores unused. | ||||||||||||||||||||||||||||
| WebMO-MOPAC interface. The Theory drop-down menu for MOPAC now contains an additional term: PM6-D3H4. This method was developed by Hozba et al. to better describe hydrogen-bonded complexes. Literature references concerning this and other "PM" theories can be found here. | ||||||||||||||||||||||||||||
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User's guide for organic chemistry (PDF). This briefly explains theory
and basis sets, and how to optimize a molecule's geometry and predict
its infrared and NMR
spectra. An example calculation for pulegone C10H16O
is shown. Gaussian version. ORCA version. |
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GaussView5 error with
Gaussian16 freq output. It turns out that GV5 - Windows or Linux
version - throws an error when it tries to open a G16 output.log file
for a freq or opt+freq job. The workaround is to manually remove the
"Dipole orientation" section near the end of the file: delete the text
between the dashed lines with a text editor. Save the file as output-mod.log,
or similar. Here are example files: output.log and output-mod.log for the Cl-..CH3F complex. Why bother? Because GV5's vibration analysis and animations are way better than those of WebMO. The above workaround was published several years ago on Dr. Joaquin Barroso's computational chemistry blog (https://joaquinbarroso.com/2018/01/29/chk-files-gaussview/) |
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| For more
information, see following links: WebMO https://www.webmo.net MOPAC https://openmopac.net Gaussian https://www.gaussian.com ORCA: https://www.faccts.de/orca/ xTB: https://xtb-docs.readthedocs.io/en/latest/ |
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| Contact: jwkeller /at/ alaska.edu | ||||||||||||||||||||||||||||