It's absolutely not necessary for your research to be related to medicine. I would describe my undergraduate research as "physical organic chemistry for environmental science applications". I never touched or saw PCR/cells/mice at my college. I didn't even have publications like you do and managed to do very well in my application cycle regardless. The most important thing is to demonstrate that you want to and are able to do scientific research, regardless of the field.
That said, most people in MD-PhD admissions are in the biomedical sciences and don't remember what an SN2 reaction is. You should tailor your explanations as if they were directed to an educated layperson, making sure to carefully introduce anything that could be perceived as jargon, no matter how basic it may seem to you as a chemist.
In general, you should be able to pursue a Chemistry PhD at a medical school's associated university. But remember that the research you will do will depend on the mentor you choose to do research with, so don't limit your options to those medical schools with nearby undergraduate campuses. Medical schools themselves generally have at least some chemist/physicist PI's. Just because your PhD doesn't say "Chemistry" doesn't mean that you didn't do research in chemistry!
Good luck, fellow chemist!
