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 blip.com where you can find the link and the source file in .mov and .flv formats.