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Title: Density Functional Theory Studies on the Active Site of the Multicopper Oxidases
Author: Zhekova, Hristina Rumenova
Advisor: Ziegler, Tom
Keywords: Biochemistry;Chemistry--Inorganic;Physics--Molecular
Issue Date: 4-Dec-2013
Abstract: Multicopper oxidases (MCO) feature a complex active site which contains a T1 copper center and a trinuclear center responsible for the binding and reduction of oxygen to water. In this thesis we apply novel methods based on density functional theory (DFT) for studies of the copper centers found in MCO. The absorption, circular dichroism, magnetic circular dichroism (MCD) and electron paramagnetic resonance parameters of models of the T1 copper site were calculated and compared to experimentally measured values. The observed deviations of the calculated excitation energies were discussed as a result of deficiencies in the used computational method (time dependent DFT). The spin-spin coupling interactions in some binuclear copper models which resemble the T3 site of the trinuclear copper center, as well as two synthetic models of the native intermediate (NI) of MCO were studied successfully with the second order spin-flip constricted variational DFT (SF-CV(2)-DFT). In addition, the MCD spectrum of one of the NI models was simulated in the presence of zero-field splitting and alternative assignments have been suggested for some of the spectral bands. Finally, the orientation of the oxygen moiety in the peroxide intermediate (PI) of MCO relative to the trinuclear copper center has been studied with SF-CV(2)-DFT, conventional DFT and hybrid quantum mechanics/molecular mechanics. It was determined that the formation of a fully bridged structure arises due to coordination unsaturation of the three copper atoms, rather than the influence of the second coordination sphere. Studies with the extended transition state - natural orbitals for chemical valence method of the spin density redistribution in the trinuclear center upon oxygen binding revealed that all copper atoms participate in the reduction of O2 and are partially oxidized in the PI.
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