Strong electron density for a peroxide type dioxygen species bridging the Fe-a3 and CUB dinuclear center (DNC) was observed in the high-resolution (1.8 angstrom) X-ray crystal structures (PDB entries 3S8G and 3S8F) of ba(3) cytochrome c oxidase (CcO) from Thermus thermophilus. The crystals represent the as-isolated X-ray photoreduced CcO structures. The bridging peroxide was proposed to arise from the recombination of two radiation-produced HO center dot radicals formed either very near to or even in the space between the two metals of the DNC. It is unclear whether this peroxide species is in the O-2(2-), O-2(center dot-), HO2-, or the H2O2 form and what is the detailed electronic structure and binding geometry including the DNC. In order to answer what form of this dioxygen species was observed in the DNC of the 1.8 angstrom X-ray CcO crystal structure (3S8G), we have applied broken-symmetry density functional theory (BS-DFT) geometric and energetic calculations (using OLYP potential) on large DNC cluster models with different Fe-a3-Cu-B oxidation and spin states and with O-2(2-), O-2(center dot-), HO2-, or H2O2 in the bridging position. By comparing the DFT optimized geometries with the X-ray crystal structure (3S8G), we propose that the bridging peroxide is HO2-. The X-ray crystal structure is likely to represent the superposition of the Fe-a3(2+)-(HO2-)-Cu-B(+) DNC's in different states (Fe2+ in low spin (LS), intermediate spin (IS), or high spin (HS)) with the majority species having the proton of the HO2- residing on the oxygen atom (O1) which is closer to the Fe-a3(2+) site in the Fe-a3(2+)-(HO-O)(-)-Cu-B(+) conformation. Our calculations show that the side chain of Tyr237 is likely trapped in the deprotonated Tyr237(-) anion form in the 3S8G X-ray crystal structure.