To further understand the structure of graphene oxide, several structures of graphene oxide were systematically investigated using density functional theory (DFT). Our models consisted of a hexagonal in-plane structure of graphene with epoxy groups, and different oxidation levels. We found that different arrangements of these units yielded a range of vibrational spectra. Raman positions of the D and G bands depend sensitively on the local atomic configurations. Both structure energy and spectra computations indicate that the oxidation functional groups are energetically favorable to aggregate together and to be close to one another on the opposite side of graphene surface.