First, let me point out that you do have a competitive profile; however, as has been said many times on this forum, Letters of Recommendation are often a very substantial portion of the application. How do you think your letters of rec were? Were they from research advisors who could truly comment on your ability to do graduate level research? Were they from professors who have had you in high level chemistry courses? These are important factors that may sway an admissions committee's mind in selecting you for a Ph.D. program.
How much did your Statement of Purpose stress the leadership positions and teaching positions you have attained? Focusing on this would be a very strong part of your application.
Also, do you have any publications throughout your research? Many individuals on this forum do, but a good number (myself included) do not. Having one may be helpful to your application.
Other points that are of note - your 720 on the Quantitative section of the GRE is somewhat low for an individual trying to apply for a science based degree at the schools you are talking about. 720 is below the 80th percentile, yet you are applying to many of the top 10 programs in the country (Stanford, MIT, Scripps) and many of the next 10 to 15 or so. This is something to keep in mind when you start hearing back from schools. With a 3.83, 720Q, 440V, 760Chem, your stats are somewhat below (on a pure numbers basis) many of the people on this forum who have received acceptance letters to the schools you are talking about. This is not to discourage you, just an assessment of what can be attained from reading this board. Perhaps applying to some middle tier programs would be a good next move (even though many deadlines have passed, speaking to the graduate coordinator at other schools you may be interested in could prove fruitful).
In the meantime, my advice would be to contact the programs you are waiting to hear from and ask them if they have received all of your application materials. Normally, they would have e-mailed you if there were an issue, but it doesn't hurt to follow up! If, in the next couple of weeks, you have not heard back successfully, I would strongly consider searching for an internship (or full time position) in the industry you wish to pursue after your Ph.D. This will then allow you to make new contacts who can comment on your potential to do research, confirm your own reasoning for pursuing a Ph.D., and likely strengthen your application for next year!
Good luck! Hopefully you will hear back soon!