You can see where this is going...
The red and blue waldos are about to cross over bonder tiles with a BOND + command on the bonder near the bottom left of the screen.
The problem is nothing seems to bond! Thinking it may be a bug, I've tried restarting the game and rejiggering the red path to drop the carbon atom onto the bonder, perform BOND +, then grab it again to no avail. I've also tried sending the blue waldo over a BOND + command without success. Searches online have found a couple other people in similar situations with no apparent resolution.
I love this game, but this is aggravating! Thanks for your help!