I love the idea! This would also have fit quite well with the "out of control" theme as it gets a bit chaotic when the molecule is so big you're picking up every atom that goes across the screen. I'm sure I'm not the first person to say this but it would be nice if it was a bit easier to break off branches (although having everything done by hitting atoms is a good concept in my opinion). Also it would be nice if the game wasn't quite so pedantic about which way up your molecule has to be for it to count as correct, there were some times when I had the correct shape but the molecule I was meant to be copying was a different way up, which was quite annoying. Overall great though! I was able to get a score of 144 before giving up.
Edit: I forgot to mention that just making the biggest molecule possible was really fun, maybe that could be a goal or a different game mode?