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The surfaces of highly oriented pyrolytic graphite (HOPG) samples were treated using two different methods, exposure to an energetic oxygen ion beam and immersion in an oxygen ion plasma, and the reactions which occur during treatment were characterized using high-resolution electron energy loss spectroscopy (HREELS), temperature programmed desorption (TPD), and scanning tunneling microscopy (STM). Both surface treatments result in similar oxidation species. The results of this investigation provide spectroscopic evidence for the presence of semiquinone 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.