Towards reverse engineering of Photosystem II: Synergistic Computational and Experimental Approaches

ABSTRACT Photosystem II (PSII) of oxygenic photosynthesis has the unique ability to photochemically oxidize water, extracting electrons from water to result in the evolution of oxygen gas while depositing these electrons to the rest of the photosynthetic machinery which in turn reduces CO2 to carbohydrate molecules acting as fuel for the cell. Unfortunately, native PSII is unstable and not suitable to be used in industrial applications. Consequently, there is a need to reverse-engineer the water oxidation photochemical reactions of PSII using solution-stable proteins. But what does it take to reverse-engineer PSII’s reactions? PSII has the pigment with the highest oxidation potential in nature known as P680. The high oxidation of P680 is in fact the driving force for water oxidation. P680 is made up of a chlorophyll a dimer embedded inside the relatively hydrophobic transmembrane environment of PSII. In this thesis, the electrostatic factors contributing to the high oxidation potential of P680 are described. PSII oxidizes water in a specialized metal cluster known as the Oxygen Evolving Complex (OEC). The pathways that water can take to enter the relatively hydrophobic region of PSII are described as well. A previous attempt to reverse engineer PSII’s reactions using the protein scaffold of E. coli’s Bacterioferritin (BFR) existed. The oxidation potential of the pigment used for the BFR ‘reaction centre’ was measured and the protein effects calculated in a similar fashion to how P680 potentials were calculated in PSII. The BFR-RC’s pigment oxidation potential was found to be 0.57 V, too low to oxidize water or tyrosine like PSII. We suggest that the observed tyrosine oxidation in BRF-RC could be driven by the ZnCe6 di-cation. In order to increase the efficiency of iii tyrosine oxidation, and ultimately oxidize water, the first potential of ZnCe6 would have to attain a value in excess of 0.8 V. The results were used to develop a second generation of BFR-RC using a high oxidation pigment. The hypervalent phosphorous porphyrin forms a radical pair that can be observed using Transient Electron Paramagnetic Resonance (TR-EPR). Finally, the results from this thesis are discussed in light of the development of solar fuel producing systems.

Thermodynamic properties and Debye-Waller factor of fee materials

We have calculated the equation of state and the various thermodynamic properties of monatomic fcc crystals by minimizing the Helmholtz free energy derived in the high temperature limit for the quasiharmonic theory, QH, and the lowest-order (cubic and quartic), 'A2, anharmonic terms of the perturbation theory, PT. The total energy in each case is obtained by adding the static energy. The calculation of the thermal properties was carried out for a nearest-neighbour central-force model of the fcc lattice by means of the appropriate thermodynamic relations. We have calculated the lattice constant, the thermal expansion, the coefficient of volume expansion, the specific heat at constant volume and at constant pressure, the isothermal and adiabatic bulk moduli, and the Griineisen parameter, for the rare-gas solids Kr and Xe, and gold. Morse potential and modified Morse potential were each used to represent the atomic interaction for the three fcc materials. For most of the calculated thermodynamic properties from the QH theory, the results for Kr and Xe with the modified Morse potential show an improvement over the results for the Morse potential when compared with the experimental data. However, the results of the 'A 2 equation of state with the modified Morse potential are in good agreement with experiment only in the case of the specific heat at constant volume and at constant pressure. For Au we have calculated the lattice contribution from the QH and 'A 2 PT and the electronic contribution to the thermal properties. The electronic contribution was taken into account by using the free electron model. The results of the thermodynamic properties calculated with the modified Morse potential were similar to those obtained with the Morse potential. U sing the minimized equation of state we also calculated the Mossbauer recoilless fraction for Kr and Xe and the Debye-Waller factor (DWF) for Pb, AI, eu, Ag, and Au. The Mossbauer recoilless fraction was obtained for the above two potentials and Lennard-Jones potential. The L-J potential gives the best agreement with experiment for Kr. No experimental data exists for Xe. At low temperature the calculated DWF results for Pb, AI, and eu show a good agreement with experimental values, but at high temperature the experimental DWF results increase very rapidly. For Ag the computed values were below the expected results at all temperatures. The DWF results of the modified Morse potential for Pb, AI, eu and Ag were slightly better than those of the Morse potential. In the case of Au the calculated values were in poor agreement with experimental results. We have calculated the quasiharmonic phonon dispersion curves for Kr, Xe, eu, Ag, and Au. The calculated and experimental results of the frequencies agree quite well for all the materials except for Au where the longitudinal modes show serious discrepancies with the experimental results. In addition, the two lowest-order anharmonic contributions to the phonon frequency were derived using the Green's function method. The A 2 phonon dispersion curves have been calculated only for eu, and the results were similar to those of the QH dispersion curves. Finally, an expression for the Griineisen parameter "( has been derived from the anharmonic frequencies, and calculated for these materials. The "( results are comparable with those obtained from the thermodynamic definition.