Cytochrome c oxidase couples the reduction of dioxygen to proton pumping against an electrochemical gradient. The D-channel provides the principal uptake pathway for protons. A water chain is thought to mediate the relay of protons through the D-channel, but it is interrupted at N139 in all crystallographic structures. Here, free energy simulations are used to examine the proton uptake pathway in the wild type and in single-point mutants N139V and N139A, where reduction and pumping is compromised. A general approach for the calculation of water occupancy in protein cavities is presented and demonstrates that combining efficient sampling algorithms with long simulation times is required to achieve statistical convergence of equilibrium properties in the protein interior. The relative population of conformational and hydration states of the D-channel is characterized. Results shed light onto the role of N139 in the mechanism of proton uptake and clarify the physical basis for inactive phenotypes.

Cytochrome c oxidase couples the reduction of dioxygen to proton pumping against an electrochemical gradient. The D-channel provides the principal uptake pathway for protons. A water chain is thought to mediate the relay of protons through the D-channel, but it is interrupted at N139 in all crystallographic structures. Here, free energy simulations are used to examine the proton uptake pathway in the wild type and in single-point mutants N139V and N139A, where reduction and pumping is compromised. A general approach for the calculation of water occupancy in protein cavities is presented and demonstrates that combining efficient sampling algorithms with long simulation times is required to achieve statistical convergence of equilibrium properties in the protein interior. The relative population of conformational and hydration states of the D-channel is characterized. Results shed light onto the role of N139 in the mechanism of proton uptake and clarify the physical basis for inactive phenotypes.

Computer-aided drug discovery involves the application of computer science and programming to solve chemical and biological problems. Specifically, the QSAR (Quantitative Structure Activity Relationships) methodology is used in drug development to provide a rational basis of drug synthesis, rather than a trial and error approach. Molecular dynamics (MD) studies focus on investigating the details of drug-target interactions to elucidate various biophysical characteristics of interest. Infectious diseases like Trypanosoma brucei rhodesiense (TBR) and P. falciparum (malaria) are responsible for millions of deaths annually around the globe. This necessitates an immediate need to design and develop new drugs that efficiently battle these diseases. As a part of the initiatives to improve drug efficacy QSAR studies accomplished the formulation of chemical hypothesis to assist development of drugs against TBR. Results show that CoMSIA 3D QSAR models, with a Pearson’s correlation coefficient of 0.95, predict a compound with meta nitrogens on the phenyl groups, in the combinatorial space based on a biphenyl-furan diamidine design template, to have higher activity against TBR relative to the existing compound set within the same space. Molecular dynamics study, conducted on a linear benzimidazole-biphenyl diamidine that has non-classical structural similarity to earlier known paradigms of minor groove binders, gave insights into the unique water mediated interactions between the DNA minor groove and this ligand. Earlier experiments suggested the interfacial water molecules near the terminal ends of the ligand to be responsible for the exceptianlly high binding constant of the ligand. Results from MD studies show two other modes of binding. The first conformation has a single water molecule with a residency time of 6ns (average) that is closer to the central part of the ligand, which stabilizes the structure in addition to the terminal water. The second conformation that was detected had the ligand completely away from the floor of the minor groove, and hydrogen bonded to the sugar oxygens.

The discovery and mechanistic investigation of a new class of photochemical reactions of benzophenones and related compounds is documented in this Thesis. Their photobehaviour in aqueous solvent media varied dramatically from their well-known behaviour in organic solvents and suggests unique and unprecedented mechanistic pathways. The aqueous photoredox chemistry of various substituted benzophenones was initially explored. Particular attention was paid to 3-(hydroxymethyl)benzophenone (47), which upon photolysis in acidic aqueous media undergoes an intramolecular photoredox reaction to produce 3-formylbenzhydrol (61). Extensive investigation into the mechanistic behaviour of 3-(hydroxymethyl)benzophenone (47) produced evidence of a unique solvent-mediated, acid catalysed photoreaction. A mechanism has been proposed for the intramolecular photoredox reaction that proceeds via the protonated triplet state. This protonated triplet state subsequently promotes the deprotonation of the benzylic carbon before rearranging to form the redox product. The modification of the benzylic carbon with an alkyl group or with a phenyl group resulted in only slight changes in the photobehaviour. In both cases intramolecular photoredox reactions were observed although significantly more oligomeric side products were observed in some cases. To more fully elucidate the photobehaviour and to test the generality of the photoredox reaction, a variety of structurally related hydroxyalkyl aromatic carbonyls were synthesized and studied. Alternative chromophores were explored using xanthone and fluorenone derivatives. Both types of derivative compounds underwent an intramolecular photoredox reaction, supporting the assertion that the intramolecular photoredox reaction could be considered a general feature of aromatic carbonyls under aqueous conditions. However, significant differences in photoreactivity were also observed. It was found that 2-(hydroxymethyl)xanthone (53) exhibited sufficient photoactivity that the intramolecular photoredox reaction was observable even under neutral conditions whereas 2-(hydroxymethyl)fluorenone (54) was nearly photoinert. The last topic focuses on the extension of the electronic transmission from the carbonyl functional group to the benzylic alcohol by insertion of an additional phenyl group. The addition of the phenyl group also provided a bichromophoric molecule, rather than the monochromophoric substrates studied to this point. The substituent’s position played an important role in the photobehaviour, in that both of the meta- and ortho- substituted compounds underwent intramolecular photoredox reaction, while the para- substituted compound primarily exhibited photobehaviour indicative of hydrogen abstraction.