There are two ways to say "chemistry" in Japanese, depending on the context:

化学 (kagaku) - This is the most common and general term for "chemistry" as a scientific discipline.

ケミストリー (kemisutorī) - This is a loanword from English and is used specifically to refer to the feeling of attraction or connection between two people, like "romantic chemistry".

So, if you're talking about the science of chemistry, use 化学 (kagaku). If you're talking about the attraction between people, use ケミストリー (kemisutorī).