Linking Chemical Electron–Proton Transfer to Proton Pumping in Cytochrome <i>c</i> Oxidase: Broken-Symmetry DFT Exploration of Intermediates along the Catalytic Reaction Pathway of the Iron–Copper Dinuclear Complex

After a summary of the problem of coupling electron and proton transfer to proton pumping in cytochrome <i>c</i> oxidase, we present the results of our earlier and recent density functional theory calculations for the dinuclear Fe-a₃–Cu_B reaction center in this enzyme. A specific catalytic reaction wheel diagram is constructed from the calculations, based on the structures and relative energies of the intermediate states of the reaction cycle. A larger family of tautomers/protonation states is generated compared to our earlier work, and a new lowest-energy pathway is proposed. The entire reaction cycle is calculated for the new smaller model (about 185–190 atoms), and two selected arcs of the wheel are chosen for calculations using a larger model (about 205 atoms). We compare the structural and redox energetics and protonation calculations with available experimental data. The reaction cycle map that we have built is positioned for further improvement and testing against experiment