I dig the educational angle; mad respect for games that try and make learning fun. You guys definitely succeeded btw, this was unbelievably charming. AND it's a great way to visualize molecular structures, crazy.
Only feedback would be that this game seems more suited for 2D versus 3D, since aiming is a bit tricky in this isometric perspective. But since that'd require basically scrapping everything, it's more of a pipe dream on my part lol