For those of you in physical science classes or chemistry finding novels that include chemistry as a center piece might be a little challenging. I'm working on ideas for easier reading YA novels. So far I can recommend:
The House of Scorpion by Nancy Farmer (this gets into pollution). When I looked at the listing on Barnes and Nobel I discovered that Nancy Farmer was originally a high school chemistry teacher! (She's a very good writer!)
Also a book with some chemistry connections is "Flush" by Carl Hiaasen
In the NoveList search I found a series The Carbon Diaries by Saci Lloyd. These look so interesting that I am going to try and get my hands on a copy this weekend. Look for future postings.
As I searched NoveList for "eco-fiction" it appears Clive Custler is a name that appears often on the list as an author. I haven't read any of his books--it looks like I am going to be adding that to my wish list. One that came up as interesting to me was Valhalla Rising.
Of course right now forensic science is a hot theme in television. The CSI and NCIS shows all include chemistry and other sciences. Kathy Reichs and Patricia Cornwell are some of the best writers in this genre. However, I don't remember chemistry being a significant factor in their books (it does play a tangential role).
Finally, another adventure would be to return to some Sherlock Holmes short stories and see where chemistry fits in. Holmes was rather famous for his chemical experiments. These are relatively short and would fit nicely with some of the later forensic science literature.