Great game! (even though I don't know chemistry). I think it would be a great practice / teaching tool with a few refinements, like drill-based levels (for instance, 10 puzzles with 2-3 connecting components for Level 1; another 10 puzzles with slightly more complicated connections in Level 2, etc.) I also think it would be interesting to add challenges. For instance, perhaps there is a partially formed connection with an objective at the bottom instead of the substance to make. Maybe the formed substance is an acid and the object is to create the correct connection to dilute it (with only one valid connection out of the three on the board). I could even see two games, with the first being drill-based for learning and memorising connections while the sequel is challenge-based and designed for understanding chemical reactions in context.
*You might already have these later in the game. I didn't play very far.
** As I said, I'm horrible at chemistry so my suggestions might not make sense for actually learning chemistry. That was written with a completely novice POV :)