Abstract
Cytochrome c oxidase is a mitochondrial membrane bounded enzyme which is the fourth complex of the respiratory electron transport chain. Cytochrome c oxidase catalyzes the respiratory reduction reaction of O2 to water. Reduction of O2 takes places at the metallic center of the cytochrome c oxidase. This thesis intensively studies the oxygen reduction reaction using the first principles calculations based on the time-independent density functional theory (TI-DFT) with the B3LYP /6-31G (d, p) method in the Gaussian09 program. It is generally agreed that DFT methods give accurate results for the geometries and vibrational frequencies of transition metals. In this study, the functional model of the metallic active site in the respiratory enzyme cytochrome c oxidase is simulated and the output data are used to analyze the bond length, band gaps, molecular orbitals, IR spectra, the structure energy and the reaction energy of the oxygen reduction reaction (ORR). The metallic active center was calculated with three different multiplicities, which are singlet, triplet, and quintet. According to the results of geometric energy of different multiplicities, we can sum up the reaction center of cytochrome c oxidase to be quintet. Finally, the total energy of the reaction product is calculated and the reaction energy of the ORR is discussed in this thesis.