Thesis(Ph.D.(Physics)) -- University of Limpopo, 2020 / Surface properties of pyrite (FeS2), chalcopyrite (CuFeS2), galena (PbS) and sphalerite (ZnS) most thermodynamically stable surfaces have been studied using first priniciples density functional theory. The most stable surfaces showed the highest surface exposure as it covered a higher percentage of the surface area on morphologies. The interaction of water with such sulphide surfaces was also investigated; the structures of sulphide minerals surfaces were changed in the presence H2O molecules. The surfaces of FeS2 and ZnS relax most while those of CuFeS2 and PbS surfaces change slightly in the presence of H2O molecules. The results on the effect of chain length of DTPs and DTCs on the enthalpies of adsorption on pyrite, galena, chalcopyrite and sphalerite have shown that an increase in chain length of the DTPs resulted in an increase in the enthalpies of adsorption trend for pyrite, galena and sphalerite. This is an important observation since the ligand is the same in all cases and therefore the effect is due to the role of the alkyl group Moreover, we noted a decrease of enthalpies of adsorption with an increase of DTCs chain lengths on pyrite, galena, chalcopyrite and sphalerite. The effect of the branching of the hydrocarbon chain length of the dithiocarbamates on the enthalpy of adsorption of pyrite was investigated. The results show that the configuration of the alkyl chain length of the same carbon number has an influence on the enthalpy of adsorption. Furthermore, the results indicate that there was minimal enthalpy of adsorption when DeDTP was dosed to galena, chalcopyrite and sphalerite minerals as compared to DeDTC and ethyl xanthate. On the other hand, the enthalpies of adsorption of DeDTP on pyrite were very high which represented a greater exothermic reaction than for any of the DeDTC and ethyl xanthate. The bond distance between thiol collector and the surface is consistent with the corresponding calculated adsorption energies. The Mulliken population of S-Fe/S-Pb/S-Zn bond for the adsorption of eX on CuFeS2 surface are high compared to PbS and ZnS surfaces, which indicated that there is a strong covalent bond between S and Fe atoms as compared to S-Pb and Pb-Zn bonds. Such observations are consistent with results of other thiol collectors. It was seen that the Mulliken atomic charges populations of CuFeS2, PbS and ZnS surface layers are different before and after DTPs adsorption. The charges of Fe atom reduce, which indicates that the Zn and Pb atoms become more positive and the Fe atom becomes more negative. In addition, there are changes in the charges of S atoms in ZnS and PbS surface layers before and after H2O absorption, suggesting that the presence of water would affect the adsorption of thiol collector. The densities of states (DOS) of the thiol collectors on surfaces of sulphide minerals have shown a strong hybridisation between the S 3p-orbital HOMO, metals (Fe, Pb, Zn) 3d-orbital for pyrite and chalcopyrite, 6p-orbital for galena and (3d and 4s)-orbitals for sphalerite. The collector S 3p-orbital reduces to zero states on the surfaces of Fe, Pb and Zn atoms. The Fe-S bond population for DeDTP is lower than that of DispDTP and DbDTP in pyrite, respectively. For chalcopyrite the DeDTP Fe-S population is higher than both DispDTP and DbDTP: similar trends were observed for Pb-S and Zn-S, however, the Pb-S bonding was less covalent as compared to the Fe S in chalcopyrite. The DTPs Fe-S bond population is generally higher in chalcopyrite than in pyrite. Mulliken charges analysis indicated that the DTPs S atoms lost charges and the metals gained with a decreasing DTPs chain length for pyrite: a similar trend was observed for chalcopyrite. The DTPs gained electrons from galena and sphalerite surface. For DTCs pyrite and chalcopyrite surface Fe atoms gain more electrons in the presence of DeDTP than other DTPs, while galena and sphalerite lost most electrons in the presence of DbDTC than other DTCs. As for xanthate, the Mulliken bond charges indicated that the S atoms and the metals lost charges, suggesting that some charges reside at the internuclear region between the metals and sulphurs (M– S). These show that electron charges are collector and mineral dependent; collector would be an electron acceptor or donor depending on the mineral makeup. A comparison of the computational results, isothermal titration calorimetry (ITC) and microfloatation experiments for the interaction of DeDTP, DeDTC and eX with pyrite and galena was made. The calculated adsorption energies between thiol collectors and mineral surfaces were always more exothermic than the experimentally determined ones. In computational calulations, water adsorption was found to reduce the reactivity of Fe and Pb atom for the interaction with thiol collectors and bring the adsorption energies closer to the magnitude of the experimental values. FeS2 (100) surface heat of adsorption depict similar trends to experimental recoveries from microfloation for DeDTP, DeDTC and eX, while FeS2 (111) heats of adsorptions for DeDTP and DeDTC are consistent with ITC experimental results. Lastly, calculated DeDTP and DeDTC adsorptions on the PbS (100) are also consistent with experimental recoveries. / National Research Foundation (NRF), South African Minerals of Metal Institution (SAMMRI) and University of Limpopo (UL)

El objetivo de esta tesis se centra en el estudio de la transferencia de electrones (ET), una de las reacciones más simples y cruciales en bioquímica. Para dichos procesos, obtener información directa de los factores que lo promueves, asi como del camino de transferencia electronica, no es una tarea trivial. Dicha información a un nivel de conocimiento detallado atómico y electrónico, sin embargo, es muy valiosa en términos de una mejor comprensión del ciclo enzimático, que podría conducir, por ejemplo, a un diseño más eficaz de inhibidores. El objetivo principal de esta tesis es el desarrollo de una metodología para el estudio cuantitativo de la ET en los sistemas biológicos. En este sentido, hemos desarrollado un nuevo método para obtener el camino de transferencia electrónico, llamado QM/MM e-­‐ Pathway, que se puede aplicar en sistemas complejos con ET de largo alcance. El método se basa en una búsqueda sucesiva de residuos importantes para la ET, utilizando la modificación de la región quantica en métodos mixtos QM/MM, y siguiendo la evolución de la densidad de espín dentro de la zona de transferencia. Hemos demostrado la utilidad y la aplicabilidad del algoritmo en el complejo P450cam/Pdx, identificando el papel clave de la Arg112 (en P450cam) y del Asp48 (en Pdx), ambos conocidos en la literatura. Además de obtener caminos de ET, hemos cuantificado su importancia en términos del acoplamiento electrónico entre el dador y aceptor para los diferentes caminos. En este sentido, se realizaron dos estudios de la influencia del solvente y de la temperatura en el acoplamiento electrónico para sistemas modelo oligopéptidos. Ambos estudios revelaron que los valores del acoplamiento electrónico fluctúan fuertemente a lo largo de las trayectorias de dinámica molecular obtenidas, y el mecanismo de transferencia de electrones se ve ampliamente afectado por el espacio conformacional del sistema. La combinación del QM/MM e-­‐pathway y de los cálculos de acoplamiento electronico fueron utilizados finalmente para investigar la ET en el complejo CCP/Cytc. Nuestros hallazgos indican el papel fundamental del Trp191 en localizar un estadio intermedio para la transferencia electronica, así como el camino ET principal que incluye Ala194, Ala193, Gly192 y Trp191. Ambos hallazgos fueron confirmados a través de la literatura. Los resultados obtenidos para el muestro de manios de ET, junto con su evaluación a través de cálculos de acoplamiento electrónico, sugieren un enfoque sencillo y prometedor para investigar ET de largo alcance en proteínas. / The focus of this PhD thesis lies on electron transfer (ET) processes, belonging to the simplest but most crucial reactions in biochemistry. Getting direct information of the forces driving the process and the actual electron pathway is not a trivial task. Such atomic and electronic detailed information, however, is very valuable in terms of a better understanding of the enzymatic cycle, which might lead, for example, to more efficient protein inhibitor design. The main objective of this thesis was the development of a methodology for the quantitative study of ET in biological systems. In this regard, we developed a novel approach to map long-­‐range electron transfer pathways, called QM/MM e-­‐Pathway. The method is based on a successive search for important ET residues in terms of modifying the QM region following the evolution of the spin density of the electron (hole) within a given transfer region. We proved the usefulness and applicability of the algorithm on the P450cam/Pdx complex, indicating the key role of Arg112 of P450cam and Asp48 of Pdx for its ET pathway, both being known to be important from the literature. Besides only identifying the ET pathways, we further quantified their importance in terms of electronic coupling of donor and acceptor incorporating the particular pathway residues. Within this regard, we performed two systematic evaluations of the underlying reasons for the influence of solvent and temperature onto electronic coupling in oligopeptide model systems. Both studies revealed that electronic coupling values strongly fluctuate throughout the molecular dynamics trajectories obtained, and the mechanism of electron transfer is affected by the conformational space the system is able to occupy. Combining both ET mapping and electronic coupling calculations, we finally investigated the electron transfer in the CcP/Cytc complex. Our findings indicate the key role of Trp191 being the bridge-­‐localized state of the ET as well as the main pathway consisting of Ala194, Ala193, Gly192 and Trp191 between CcP and Cytc. Both findings were confirmed through the literature. Moreover, our calculations on several snapshots state a nongated ET mechanism in this protein complex. The methodology developed along this thesis, mapping ET pathways together with their evaluation through electronic coupling calculations, suggests a straightforward and promising approach to investigate long-­‐range ET in proteins.

Living cells accumulate compensatory solutes for protection against the harmful effects of extreme environmental conditions such as high salinity, temperature and desiccation. Even at high concentrations these solutes do not disrupt the normal cellular functions and at times counteract by stabilizing the cellular components. These properties of compensatory solutes have been exploited for stabilizing proteins and cells in vitro. Betaines are widespread natural compensatory solutes that have also been used in other applications such as therapeutic agents and polymerase chain reaction (PCR) enhancers. Some biomedical applications of novel synthetic analogues of natural betaines were investigated. Natural compensatory solutes are either dipolar zwitterionic compounds or polyhydroxyl compounds, and the physical basis of compensation may differ between these, so one focus was on synthetic betaines with hydroxyl substituents. The majority of the synthetic solutes stabilized different model proteins against stress factors such as high and low temperatures. The presence of hydroxyl groups improved protection against desiccation. The observed stabilization effect is not just on the catalytic activity of the enzyme, but also on its structural conformation. Synthetic compensatory solutes have a potential application as protein stabilizers. Dimethylthetin was evaluated as a therapeutic agent and found to be harmful in a sheep model. However, from the study we were able to generate a large-animal continuous ambulatory peritoneal dialysis (CAPD) model and showed that glycine betaine could be added to the dialysis fluid in chronic renal failure. Some synthetic compensatory solutes reduce the melting temperatures of DNA better than most natural solutes. Synthetic solutes were identified that have potential to enhance PCR and could replace some reagents marketed by commercial suppliers. Density, viscosity and molecular model data on the solutes showed correlations with the biochemical effects of the solutes, but no physical measurements were found that reliably predicted their potential for biotechnological applications.