DFT Fea3–O/O–O Vibrational Frequency Calculations over Catalytic Reaction Cycle States in the Dinuclear Center of Cytochrome c Oxidase

Density functional vibrational frequency calculations have been performed on eight geometry optimized cytochrome c oxidase (C c O) dinuclear center (DNC) reaction cycle intermediates and on the oxymyoglobin (oxyMb) active site. The calculated Fe-O and O-O stretching modes and their frequency shifts along the reaction cycle have been compared with the available resonance Raman (rR) measurements. The calculations support the proposal that in state A [Fe a3 3+ -O 2 -• ···Cu B + ] of C c O, O 2 binds with Fe a3 2+ in a similar bent end-on geometry to that in oxyMb. The calculations show that the observed 20 cm -1 shift of the Fe a3 -O stretching mode from the P R to F state is caused by the protonation of the OH - ligand on Cu B 2+ ( P R [Fe a3 4+ ═O 2 - ···HO - -Cu B 2+ ] → F [Fe a3 4+ ═O 2 - ···H 2 O-Cu B 2+ ]), and that the H 2 O ligand is still on the Cu B 2+ site in the rR identified F [Fe a3 4+ ═O 2 - ···H 2 O-Cu B 2+ ] state. Further, the observed rR band at 356 cm -1 between states P R and F is likely an O-Fe a3 -porphyrin bending mode. The observed 450 cm -1 low Fe a3 -O frequency mode for the O H active oxidized state has been reproduced by our calculations on a nearly symmetrically bridged Fe a3 3+ -OH-Cu B 2+ structure with a relatively long Fe a3 -O distance near 2 Å. Based on Badger's rule, the calculated Fe a3 -O distances correlate well with the calculated ν Fe-O - 2/3 ( ν Fe-O is the Fe a3 -O stretching frequency) with correlation coefficient R = 0.973.