An earlier article provided some info on inputting mathematical equations. Similar issues arise when you need to input drawings of chemical structures, which use their own special "language". The basic approach is to use a separate app and then copy/paste the results as an image or pdf into your document. Links to the main OS X tools are below. I think the first two should be free. This page gives some useful general info on the topic.
BKChem
Marvin
MolWorks
ChemDraw
ChemDoodle
Chem 4-D Draw
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