Wednesday, December 9, 2009

Electron density and steric strain

Figure 3.2. (a) RHF/6-31G(d) 0.002 au isodensity surface and (b) van der Waals surface of cis-CH3(H)C=C(H)CH3 (click on the picture for a bigger version).
From Molecular Modeling Basics CRC Press, May 2010.

This figure shows how the electron density and van der Waals surfaces can be used to visualize steric strain. See this post on how to make such pictures and this post on how to make an interactive version such as the one shown below.

Figure 3.2. The RHF/6-31G(d) electron density of cis-CH3(H)C=C(H)CH3.
Click on the picture for an interactive version


JONATHAN said...


Great Blog, Great work!

Question, where do you have jmol hosted so you can post jmol scipts in your blog post or web page? Do you host it locally or are you using something like google app engine to run it?


Jan said...

Jonathan - thank you!

I host Jmol locally, together with the necessary coordinate files.

Have a look at the page source for this page, which I made as a test before using it in the blog. Everything in the header is put in a gadget on the blog.

Felix said...

do you know if that completely planar structure is a minimum or does it have an imaginary torsion frequency?

Jan said...

it's a minimum - no imaginary frequencies.