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Title: The hydrated torsions method : incremental solvation of amino acids
Author: Alexandersson, Kristján Friðrik
Awarding Body: University of Oxford
Current Institution: University of Oxford
Date of Award: 2013
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In this thesis, the development and applications of the Hydrated Torsions (HT) method are discussed. The method is designed to study the incremental solvation of biomolecules and thus is ideal for the study of zwitterion formation. A reduced dimensionality approach, torsional path integral Monte Carlo, is used to explicitly treat the torsional motion of the biomolecules to provide anharmonic and quantum corrections of the torsional free energy. Four amino acids are treated with the HT method in this work; glycine, alanine, proline and serine. The initial development was performed using glycine. Microsolvated amino acid clusters were studied, with the number of solvent molecules ranging from one to six. The low energy structures identified in the work using density functional theory are in good agreement with structures found in the literature. The hydrogen bond networks formed in the structures were found to resemble hydrogen bond networks found in analogous water clusters. The incremental addition of water molecules to glycine and alanine reduced the electronic ,energy difference between the zwitterionic and neutral systems by a linear amount, up until the fourth water molecule due to stabilization of the more polar zwitterion. After four water molecules the stabilization is diminished and the make-up of the hydrogen bond network becomes more important. This change in electronic energy difference after four water molecules was not observed for proline and serine. Water molecules added to the systems beyond four water molecules do not affect the free energy difference as much as when one to four water molecules are added. Calculations indicate that the zwitterionic systems are not been fully stabilized at four, five or six water molecules, so this change in free energy behaviour must be due to the vibrational characteristics of the systems. Frequency analysis of the systems reveals that the difference in frequency of the torsional vibrational modes is not enough to cause this, so other low frequency modes are likely to be affecting the free energy.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available