Some things you should consider:
1) A sub-3.0 GPA doesn't bar you from Ph.D programs, but it does bar you from the top tier ones. That being said, some good research experience and a real good GRE score will compensate for some of your GPA.
2) I'm guessing your plan is to get a MS in chem to increase your GPA, then apply to a better school for your Ph.D. If this is your sole reason for doing a Master's, I suppose I can understand. Just be aware that the first 2 years of a Ph.D program are identical to a Master's program, and that once you have your MS you don't get to just bypass this requirement at your next school. You start back at the bottom with everyone else. If any of the schools you listed are ones that you'd be happy getting a Ph.D at, then just apply to the Ph.D program there.
3) Go to the best school you can. It'll help when you're looking for jobs. Ultimately though, if you get a Ph.D at a middle of the road school and then do a great postdoc at an awesome school, it won't matter as much.
4) I don't know of any schools that have rolling admission and allow students to start in the spring. Just FYI, if those programs were available somewhere, I'd guess that you're running late or are already too late to apply. The deadline for Fall 2012 programs are going to be due in Nov/Dec, so you're already approaching that deadline.