App for obtaining Molecular Electronic Structure (Chemistry)

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App : https://arkajitmandal.github.io/ExtendedHuckel/

This is an app that allows students to obtain molecular electronic structure, i.e. how the atomic electrons make up molecular orbitals and how the corresponding wavefunctions look like. This will allow students to understand the basic chemical theories from a quantum mechanical standpoint. This uses an approximate semi-empirical theory called the Extended Huckel Theory.

To get started, one can write the molecular geometry (in Angstroms) in the text input box on the right side of the app. These geometries are available online in a number of different databases like http://www.chemspider.com/Chemical-Structure.937.html?rid=80ddc084-3622-43c5-8e0a-39376ff102f5. For example copy paste the following geometry of a molecule called Benzene (C6H6)

H -0.21463 0.97837 0.33136
C -0.38325 0.66317 -0.70334
C -1.57552 0.03829 -1.05450
H -2.34514 -0.13834 -0.29630
C -1.78983 -0.36233 -2.36935
H -2.72799 -0.85413 -2.64566
C -0.81200 -0.13809 -3.33310
H -0.98066 -0.45335 -4.36774
C 0.38026 0.48673 -2.98192
H 1.14976 0.66307 -3.74025
C 0.59460 0.88737 -1.66708
H 1.53276 1.37906 -1.39070

After copying the above structure click Start and then the outputs will be show on the right side of the app. Click Show MO (molecular orbital) to show the molecular orbital with a molecular electronic wavefunctions.

Try this another molecule called water (H2O)

O 0.00000 0.00000 0.0
H 0.00000 0.75545 -0.47116
H 0.00000 -0.75545 -0.47116

Or alternately you can use a .xyz file (https://en.wikipedia.org/wiki/XYZ_file_format). You can find some here: http://materia.fisica.unimi.it/manini/dida/structures.html
Here’s a video of me using the app.
https://twitter.com/arkajitmandal/status/1210642826695974912

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Thanks for sharing your app here @Arkajit_Mandal! Can you explain a bit more about what it’s for and how to use it? For example, what are .xyz files and where can we find some to test?

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Hi !

I have updated the description. Apologies for the trouble.

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It is very interesting, thanks for sharing.

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Looks very cool.

Is there a reason you are using such an old version of three? It says r66, and the latest release is r112.

I tested this file:

fcc_grain_boundary.xyz (41.1 KB)

It uploads fine, but when I hit Start the tab freezes. Seems like an infinite loop is happening somewhere.

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Hi !
It will take a long time to obtain any results with the molecule you tested.

It’s too big a molecule (contains 1200 atoms) to perform a quantum mechanical calculation. This is a fundamental limitation of quantum mechanics. You should try some molecule that has less than 100 atoms. Most organic molecules contain 10-50 atoms. For such extended structure, the unit cell (for the molecule you chose the unit cell will contain only 2-4 atoms) can be taken to to compute electronic structure.

Try these instead:

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