Viewing electrostatic potential and dipole moment vector

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cfmark
Posts: 2
Joined: Sun Jan 22, 2023 3:36 pm
Full Name: Mark McGuire
Organization: Eastern Illinois University
Subdiscipline: Chemistry

Viewing electrostatic potential and dipole moment vector

Post by cfmark »

I would like to be able to be able to overlay the dipole moment vector on top of the electrostatic potential of a molecule. I can display the dipole moment vector on the molecule OR the electrostatic potential, but not both at the same time. Ideally (to maximize student comprehension), I would like to show them the electrostatic potential and then overlay the dipole moment vector, in that order.

schmidt
Posts: 76
Joined: Sat May 30, 2020 3:00 pm
Full Name: JR Schmidt
Organization: WebMO, LLC

Re: Viewing electrostatic potential and dipole moment vector

Post by schmidt »

This is an interesting idea, but not possible as of right now. The philosophy has been one property at a time, for simplicity. As we move toward a Python-based implementation for analysis, it may be possible to generate such images in the near future.

cfmark
Posts: 2
Joined: Sun Jan 22, 2023 3:36 pm
Full Name: Mark McGuire
Organization: Eastern Illinois University
Subdiscipline: Chemistry

Re: Viewing electrostatic potential and dipole moment vector

Post by cfmark »

Thanks for the reply - much appreciated. For now, my alternative plan will be to simply show the two separate images side-by-side (and most likely add an image showing partial charge assignments to the side-by-side arrangement.)

jwk
Posts: 67
Joined: Sat Jun 20, 2020 3:37 am
Full Name: John Keller
Organization: University of Alaska Fairbanks
Subdiscipline: Chemistry

Re: Viewing electrostatic potential and dipole moment vector

Post by jwk »

Hi Mark,
Jmol can display various surfaces, molecules, and graphic items simultaneously.
First you need to do a Molecular Orbital calculation in WebMO. Do File, Export molecule as .mol. Display the electron density, and do File, Export Molecule, as .cub. Then display the electrostatic potential, and again File, Export Molecule, as .cub. For example, for water this would be wat.mol, wat-dens.cub, and wat-esp.cub. Move or copy these files to c:/docs (or where ever you'd prefer.)
Then open Jmol and the Jmol console, and copy and paste the following script:

cd c:/docs;
load wat.mol;
zoom 90;
background white;
dipole dip1 width 0.1 {0 0 -2.0} {0 0 2.0};
color dipole yellow;
isosurface esp cutoff 0.02 wat-dens.cub color absolute -0.15 0.2 wat-esp.cub;
isosurface esp translucent 95;
isosurface fullylit;
water-dipole-Jmol.jpg
water-dipole-Jmol.jpg (42.17 KiB) Viewed 55182 times
The Jmol commands are documented at https://chemapps.stolaf.edu/jmol/docs/

Jmol can be run live in class. Just alt-tab to the running instance of Jmol from PowerPoint if that's what you use.
Or, the web version of Jmol (Jsmol) can be used. The benefit of that is the programmable buttons make changing the image quick and easy during class. I have done this for water . See
https://chem4.cns.uaf.edu/orbitals/jmol ... 2o-esp.htm

Let me know by email if you want some more details.
John Keller
University of Alaska Fairbanks

jwk
Posts: 67
Joined: Sat Jun 20, 2020 3:37 am
Full Name: John Keller
Organization: University of Alaska Fairbanks
Subdiscipline: Chemistry

Re: Viewing electrostatic potential and dipole moment vector

Post by jwk »

An updated version of a "dipole+esp surface" display in Jmol and Jsmol is given at the following URL: https://tinyurl.com/2vsksdbp .
This example uses a less-symmetric molecule otimized in ORCA. In the example given above, the water dipole moment just happens to align with the default dipole produced by Jmol, which is not usually the case. Therefore, the dipole coordinates must be adjusted (most easily in Excel) before being used in Jmol, as explained in the webpage.

jwk
Posts: 67
Joined: Sat Jun 20, 2020 3:37 am
Full Name: John Keller
Organization: University of Alaska Fairbanks
Subdiscipline: Chemistry

Re: Viewing electrostatic potential and dipole moment vector

Post by jwk »

The above web pages are no longer online. Contact jwkeller@alaska.edu for more information.

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