Modeling cytochrome oxidase:: A quantum chemical study of the O-O bond cleavage mechanism

The mechanism of O-O bond cleavage at the binuclear center in cytochrome oxidase has been investigated by using hybrid density functional theory (B3LYP). A potential energy surface for the reaction step from compound A, with the O-2 molecule coordinated to heme a(3), to the bond-cleaved compound P is constructed. The features of the calculated potential surface agree well with experimental information on this reaction step. First, a free energy of activation of 15 kcal/mol is obtained, reasonably close to the value of 12 kcal/mol corresponding to the observed lifetime of compound A. Second, the calculations give a large entropy effect on the reaction rate, which explains the weak temperature dependence observed for the P formation reaction. Third, the calculated potential surface has no stable intermediate between A and P, in agreement with the experimental observation that compound A decays with the same rate as compound P forms. Fourth, the calculations show that the oxo-ferryl compound P together with a tyrosyl radical and a cupric-hydroxyl can be formed in a close to thermoneutral reaction, which gives support to the suggestion that the source of the fourth electron in the O-O bond cleavage reaction is the cross-linked tyrosine residue near the binuclear center. The calculations indicate, however, that a direct hydrogen-atom transfer from the tyrosine to the iron-coordinated Or molecule produces too high an energy barrier. We attribute this to weak electronic coupling between the tyrosine and the iron center. Instead, our work suggests that the rate-limiting step involves a hydrogen-atom transfer from a water molecule in the vicinity of the copper center, and that the actual O-O bond cleavage step requires an extra proton to be available in the vicinity of the tyrosine residue, possibly on the hydroxyl group of the heme a(3) farnesyl side chain. The reason the additional proton is needed fur the O-O bond cleavage is discussed.