Exploration and characterisation of the energy landscapes of biomolecules and hydrated ions

• Main Author: Smeeton, Lewis Conrad
• Published: University of Birmingham 2015
• Subjects: 540; QD Chemistry
• Online Access: https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.675795

This study is primarily concerned with the application of energy landscape theory to problems in molecular science. Due to the diverse nature of the research undertaken, the thesis is divided into two parts. In the first part, the energy landscapes of the BLN-69 and G\={o}-69 model proteins are investigated using metric disconnectivity graph analysis, which incorporates both the kinetic and geometric structure of an energy landscape. Results are presented which demonstrate the effectiveness with which metric disconnectivity graphs can elucidate the connection between structures in the energy landscape, such as funnels and barriers, with certain structural motifs of the protein, including chain slips and twists in the turn regions. The second part of the thesis focuses on the energy landscape exploration of micro-hydrated ions. A combination of global optimisation and discrete path sampling is used to study the energy landscapes of five anionic species; sulfate, thiocyanate, perchlorate, ferricyanide and ferrocyanide. For the hydrated sulfate and ferricyanide ions, rigid-body modelling of the clusters is capable of replicating the physical chemistry of these systems, with both exhibiting a size-dependent suppression of dangling OH bonds, provisionally consistent with infrared photodissociation spectroscopy of size selected hydrated ions. For all the systems studied, it is demonstrated that ions and water molecules modelled as rigid-bodies interacting via pair-wise empirical potentials are capable of exhibiting a wide range of water structure morphologies.