This thesis explores the picosecond dynamics of aqueous solvent and the low frequency modes of biomolecular systems. These dynamics are probed with a combination of experimental THz spectroscopy and theoretical models from molecular dynamic simulations. The dynamics of the water are first measured in a polar liquid concentration series, with an attenuated total reflectance method to reduce absorption from the highly absorbing solvent. Reverse micelle systems are also investigated using a transmission method to reduce the non-essential bulk water around the sugar trehalose. The THz spectrum and molecular dynamic simulations of both these experiments show increasingly sterically hindered waters in the presence of a perturbed hydrogen bond network. Classical computational models of condensed phased water do not reproduce a broad spectral feature at 200 cm-l (6 THz). A region associated with the bending and stretching motions of hydrogen bonding. Three methods of explicit polarisation are tested on classical water models to improve modelling of this bending and stretching dynamic, but each method fails to replicate a 200 cm-l peak. It was concluded quantum mechanical effects of the hydrogen bond are not adequately accounted for, which may significantly impact the 200 cm-l frequency region. The low frequency modes of proteins are also investigated using the Gprotein coupled receptor bovine rhodopsin . Rhodopsin is activated by light illumination, which causes a conformational shift in the protein structure. This was detected as a change in the proteins low frequency dynamics that were stabilised by the presence of membrane. Normal mode analysis of the inactive and active bovine rhodopsin crystal structure confirmed these results. Furthermore, part of this thesis explores a novel THz spectrometer design, based on the principles of polarisation modulation infrared reflection absorption spectroscopy. This spectrometer has advantages over traditional methods, principally being able to perform real time referencing without the need of a separate optical path.
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:617016 |
| Date | January 2014 |
| Creators | Crompton, D. L. |
| Publisher | University of Essex |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
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