Maybe a community contribution board/service could have people suggest chemical bonds (maybe starting with 2 atom bonds) and have it so if multiple people agree that a chemical is accurate it will get added. Since this does not seem to be a program for scientific purposes, inaccuracies should not be a big deal with my current understanding of this project.
While it may be too complex currently, adding a system that handles chemical reactions + a library of every chemical reaction could allow people to update the chemical reactions without needing to redownload the game, also potentially allowing for a simple online program that checks a server for the latest version of the library upon startup.