I haven't used Mathematica 9.0 and its chemistry-related functions, but from the presentations, they look like practically useless toys for dabbles.

Can Mathematica do raytracing, display secondary structure, semi-transparent molecular surface and allow you to select coloring patterns? Is it easy to predict protonation states of molecules at different pH levels and electrostatic potentials? Can it do molecular dynamics?

Who cares that they have built-in access to the melting point of caffeine?!