Thanks for playing and for your feedback!
The atoms form bonds by looping over neighbours counter-clockwise starting from above, creating one bond at a time until either the new atom or all neighbours cannot accept more bonds. I was trying to avoid overwhelming the player with text at the beginning and ended up leaving this out as I could not think of a good way to phrase it and demonstrate all the possibilities, but it is an important part of the rules so I agree it should have been included. Maybe showing it through an animation would have been an option to make it clearer.