Until we received that email, I've never given much thought about the "Chemical X" that I add to bring my characters to life. It's obviously something that I do because flat characters are horribly boring but I've only done it subconsciously.
My "Chemical X" is very similar to Laina's - it's the imperfections in the characters, whether it's a major thing that makes up their personalities, like an abusive relationship or a bad childhood or a temper, or a little quirk, like being overly sarcastic or awkward or even the little habits they have, like blasting a certain band when they're angry.
If you're unsure of how to add Chemical X to your story, my suggestion is to watch others - what quirks do they have? Things that they do when they're nervous or angry or any annoying habits they have. What things do you do? Think of your character like a real person and give them quirks and habits that will make them that much more realistic.