Andrew Lang has created a script to generate 3D structures of molecules and shown how to represent the docking of a molecule in the receptor site of a protein (this is important for demonstrating how drugs can interfere with infectious agents like the parasite that causes malaria). I have also described how these molecules can be indexed by common search engines, like Google, so that people can discover locations in Second Life where chemistry is displayed.
Now, with the help of Andrew and my students Jessica and Khalid, we can demonstrate a chemical reaction. Andrew came up with an elegant solution for controlling animation in Second Life. Simply by saying "back" or "next" in regular chat next to the molecules, the reaction will proceed to the next step. (see video below) Jessica minimized the conformation of each intermediate in ChemSketch so that its 3D structure is probably fairly close to what it actually looks like.
This should provide an additional perspective to use in the teaching of organic chemistry reaction mechanisms. Walking around a giant molecule with a student is certainly a contrast to looking at a 2D representation in a textbook, especially with the control of animation. This is actually just the first step in the Ugi reaction that Jessica and Khalid are performing in my lab for the synthesis of anti-malarial compounds.
This example starts with the reaction of benzaldehyde with 5-methylfurfurylamine to form an imine. (Note: we generally form the imine without adding an acid catalyst and so the mechanism under basic conditions is displayed).
For the full Ugi reaction keep climbing the staircase on Drexel Island that starts with imine formation here: slurl. (These reactions are also going to be indexed on the SL molecule wiki)