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Theoretical Investigations of Non-Covalent Interactions: From Small Water Clusters to Large DNA Quadruplexes

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dc.contributor.author Taylor, Alexis
dc.date.accessioned 2010-04-16T18:19:32Z
dc.date.available 2010-04-16T18:19:32Z
dc.date.issued 2010-04-16T18:19:32Z
dc.identifier.uri http://hdl.handle.net/10222/12736
dc.description.abstract The chemical bonds that hold molecules together are composed of electrons, and in order to study these microscopic systems, electronic structure calculations are often employed. This thesis describes the results from several studies that use computational techniques to investigate a variety of bonding interactions. The systems presented range from small water clusters to large DNA quadruplexes. High-level computational techniques, such as ab initio and density functional theory methods, were applied as well as the quantum theory of atoms in molecules (AIM). AIM uses the gradient to analyze the electron density, partitioning the molecule into atomic fragments. Once the system is partitioned, individual atomic contributions to molecular properties can be determined. Furthermore, bonding interactions can be identified by the presence of a specific type of critical point within the topology. These two facets of AIM are exploited throughout this thesis. The first project presented is a theoretical investigation of the exact electronic structure of hydrated electrons. Whether the excess electron resides within a central cavity or is smeared out over the surface of the cluster remains a contentious issue. In an attempt to investigate this dilemma from a novel viewpoint, AIM was used to analyze the electron density of small anionic water clusters up to ten water molecules. The results suggest that the preferred site of binding is dictated by the relative orientation of the non-hydrogen-bonded hydrogen atoms. At the other end of the spectrum, the largest systems investigated were several guanine quadruplexes that can form in telomeric regions of DNA. In light of the attention these structures have received as potential therapeutic agents, a clear understanding of their formation is mandatory. The study presented here is a detailed investigation of the electronic energy changes associated with the folding of the quadruplex from the single-stranded telomere. After devising a novel method to display the atomic energy data, several interesting trends in the energy changes were identified. Ultimately, the data presented could help to guide future drug development endeavours, highlighting one of the many practical applications of computational methods. en_US
dc.language.iso en en_US
dc.subject Computational chemistry, ab initio, DFT, solvated electron, guanine quadruplexes en_US
dc.title Theoretical Investigations of Non-Covalent Interactions: From Small Water Clusters to Large DNA Quadruplexes en_US
dc.date.defence 2010-03-22
dc.contributor.department Department of Chemistry en_US
dc.contributor.degree Doctor of Philosophy en_US
dc.contributor.external-examiner Dr. Stacey D. Wetmore en_US
dc.contributor.graduate-coordinator Dr. Mark Stradiotto en_US
dc.contributor.thesis-reader Dr. Axel D. Becke en_US
dc.contributor.thesis-reader Dr. T. Bruce Grindley en_US
dc.contributor.thesis-reader Dr. Donald F. Weaver en_US
dc.contributor.thesis-supervisor Dr. Russell J. Boyd en_US
dc.contributor.ethics-approval Not Applicable en_US
dc.contributor.manuscripts Yes en_US
dc.contributor.copyright-release Yes en_US

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