It will strongly depend on the sub-field within chemistry. If your work is very high impact, and your PI will know if it is, then Science or Nature is the way to go. You could also aim for other general science journals such as PNAS or PLoS. After that, general chemistry journals like Angewandte Chemie and JACS are certainly good choices. If you can't get into these journals, you will have to go more subspecialized. Impact factors drop like a stone as you get more and more specialized, however this will be more or less important depending on your field. In general, the more quantitative and basic your work, the less impact factor will matter. For example, the introduction of scanning tunneling microscopy, which led to a Nobel Prize, was published in Surface Science, a journal with an impact factor of only 2.01. This is not the case with more biological projects however. There aren't any Nobel Prizes awarded for biological work published in journals with an impact factor of 2. This type of work is published in Nature or Science. Basically, this is a long winded way of saying that it depends on your field. You should ask your PI. The good thing for you is that it won't much matter for med school apps. Having anything published at all will put you way ahead of the curve. Good luck!