However, there is no package that gives us a simple solution to draw Ball-and-Stick diagrams of molecules that give a 3d impression. This does not mean it is impossible to do. It can be done with TikZ (of course, one is tempted to add). You want some proof? Well, look here.
Who knows — the blog entry I just linked to might lead to a new package. If you feel up to that challenge: go ahead! (I’d be happy to beta test :) ).