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University of Alaska Fairbanks
Department of Chemistry and Biochemistry

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Updated 8-17-2026                                                          Contact: jwkeller/at/alaska.edu

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 WebMO compute servers:
Server Cores/
Threads
Cores (=processors) available Memory (GB) Processor
Antec12
(default)
16/32 24 64 AMD 9950X
Trx40 24/48 24 128 AMD threadripper 3960X
Corsair 16/32 24 64 AMD 7950X
Merlin 16/32 24 64 Intel i9-13900X

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.")


In ORCA, one must enter the dispersion correction manually in the input file. Also note that MP2 and CCSD(T) already correct for dispersion; do not attempt to apply D3(BJ) with these methods. Two references with further documentation are the ORCA manual and a 2025 paper on drug molecule calculations.

WebMO Demo tutorial - H2O.

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.)

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:


NBO version 7 is accessed through Gaussian or ORCA. In WebMO's  "Configure Job Options" page, select a "Natural Bond Orbitals" calculation. Both MOs and NBOs will be shown on the Results page. View the NBO 7 MANUAL here.

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/
 
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.
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.
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/)
 
 
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/
Contact: jwkeller /at/ alaska.edu