Sunday, September 13, 2009

The Computational Chemistry Movie

Last week I presented the Computational Chemistry group to the new graduate students, and made the above movie for the occasion. As I mentioned in previous posts (here and here) I think molecular animation is a powerful but overlooked recruiting tool.

Most of the movie is one long Jmol script, but it took some post-editing of the resulting recording to smooth the transitions, i.e. remove the lag time when Jmol is computing the surfaces. The coordinates of the reaction and the large nanostructure is taken from Chemtube3D and this site, respectively. I have described how to extract the coordinates from a site using Jmol in a previous post. The orbitals and vibrational modes were computed using GAMESS and RHF/STO-3G.

The molecular dynamics animation towards the end is done with Molecular Workbench. You can find the simulation here, but you need to install Molecular Workbench to see it.

The equation animation and final credits are done with Powerpoint.

I hope you find the movie entertaining and useful, and feel free to use it (i.e. link to it, embed it, use in a Powerpoint presentation, etc.) if you do. Here is the page in where you can find the link and the source file in .mov and .flv formats.


philip said...

The pictures, animation and music were all nice. Too bad you muffed the methyl ester geometry.

Sorry, but these types of things bother me.

Anonymous said...


Marcelo Lima (UFMT-Brasil)

Jan said...

Thank you both. Glad you liked it!

Steve W said...

Great movie, I think I'll show it to my Organic Class tomorrow.

Jan said...

Steve W. Thank you, and thanks for mentioning the movie on your blog.

Btw, i really enjoyed the special effects movie you posted earlier.

Eduardo L. Schilling said...

Really nice!

I am a undergraduate student and my dream is to make the molecular cinema. The power of Jmol is impressive and your skill to create this video too.

Thank you.

Jan said...

Thank you very much. I'm glad you liked it.

I look forward to seeing your movies. Do leave a comment here when you have something or if you have any questions along the way.