The boxes and spheres to represent the particles? I just made some primitives in the free 3d animation program called Blender (blender.org). You can edit the models with this exporter:
http://winggamepak.com/3dgs_export.zip (it goes in the .blender/scripts)
I made this subatomic particle simulator, but I haven't accurately placed the atoms in each molecule yet, you may be interested...enjoy!
http://www.winggamepak.com/stuff/atombuilder.exe
Here's a picture of it:
http://www.winggamepak.com/stuff/atombuilder.jpg
plus there are other...