weasel damn you we asked for physics games not chemistry games.
On a related note, if it wasn't so "this is a physics game with chemistry remotely linked" it's be like every other basic flash game.
Pop in the different bond types, and using your ELECTRON BEAM to break some bonds, or your UV BLASTER to make them vibrate more and cause things to change...

The game isn't really bad conceptually, it's unique and stylish, it just fails hard at capturing said concept.

And that background music is awesome. It's so catchy.