In the context of relationships, chemistry is a simple "emotion" that two people get when they share a special connection. It is the impulse making one think "I need to see this person again" — that feeling of "we click". It is very early in one's relationship that they can intuitively work out whether they have positive or negative chemistry.
"Twilight, I told you many times this won't work."
"Third time is a charm Dashie. I need to prove that these two substances have similar attachment and attraction with each other. Science can't be wrong. It can be proven with chemistry!"