I like the game a lot. I think it would be great if you got your custom notation closer to the scientific notation as that one is dingo in my opinion. I think maybe you should focus a bit more on making players understand what they're doing rather than telling them what to do. But for 48 this is more than I would have expected. Sadly my favourite atom Radon didn't make the cut.
I think for a full game I would expect to see some variation after a while. Clicking around like this is fun for a while is fun for a bit but after even only 24 of these I got a little bored. As a stretch you could probably oven turn it into a factory style game where you develop enzymes to make the molecules for you, but that would take it into a different direction than the game is currently headed.
Well done, even the starting menu. Did you have that one lying around or did you make it during the time frame? Keep up the great work ;)