The characterization of reactions which occur during the oxidation of highly oriented pyrolytic graphite (HOPG) was performed using high-resolution electron energy loss spectroscopy (HREELS). temperature programmed desorption (TPD), and scanning tunneling microscopy (STM). The results of this investigation provide spectroscopic evidence for the presence of semi-quinone functionalities on sputtered and oxidized HOPG. STM images are presented to quantify the increase in defect sites after oxygen ion sputtering, and to correlate defect site density with reactivity.