What chemical compound is shown in episode 17 of Monogatari Second Season?
The first image is the structural formula of epinephrine (or adrenaline, depending on where you live). 



Epinephrine is a neurotransmitter that plays a significant role in the fight-or-flight response, and so its appearance here makes sense - Koyomi is certainly about to take flight upon seeing the "darkness".



The second image contains the following compounds:


dopamine
serotonin
α-Neoendorphin
epinephrine (again)
(Leu-)enkephalin
norepinephrine (or noradrenaline)


All of these are neurotransmitters, as well, though none of them are as localized to the fight-or-flight response as epinephrine is.