Although I didn't participate in the jam, I also had a vague idea of doing something with chemistry, so I was glad to see someone else actually did it! It was a nice little puzzler, definitely has potential for more complex mechanics and levels. I do think that if you go with the chemistry theme you should take more advantage of it, though. Other than the fact that you're using the number of bonds, it wouldn't matter that much if it were any kind of things being bonded. Have a think about the effects certain combinations would have in real life, that might lead to more interesting mechanics and/or levels!