I'm a chemistry student, and I just use superscript and subscript, and MS Equation 3.0. If you want to draw structures, I'd recommend ISIS Draw 2.4 (free if you're a student). You can embed them into word, but as pictures. It's more suited to drawing structures, but if you write something like C6H12O6 it'll subscript the numbers automatically, and it has all sorts of arrows and other stuff you can use. If you can't download it because you're not a student at university, the alternative is ACD ChemSketch, which is shareware but the free demo has more than what you'll need (the fee is to access databases). Hope this helps.