The vibrational entropy calculated by applying the harmonic oscillator approximation to all vibrational degrees of freedom is inherently inaccurate. One major reason is because low frequency modes such as internal rotations are not properly described by this approximation. Various techniques were developed in the past to overcome this problem. The hindered rotor potential can be approximated by a series of cosine functions, and the relevant coe cients can be determined by tting to a calculated potential energy surface. However, such a method is di cult and time consuming. Therefore, in this dissertation we propose and describe two less tedious approaches to determine entropy of internal rotational modes. The rst approximation is to express the barrier height in terms of the harmonic oscillator frequency, the local periodicity, and the reduced moment of inertia of the rotation and to approximate the torsional potential by a single cosine function. Thus, the 1D Schr odinger equation for internal rotations can be solved without nding the torsional potential, transition states, or barrier heights. We propose a further simpli cation to this approach, achieved through a simple mathematical formula, that interpolates the hindered rotor entropy between the free rotor and harmonic oscillator limits. We also propose a procedure to automatically determine the axis of rotation for any hindered rotor. The proposed methods were applied to determine the torsional entropy of n- alkanes from ethane to hexane. The entropies calculated from the proposed methods give good agreement with the experimental and accurately calculated values and have a signi cantly better accuracy than the harmonic oscillator approximation. Furthermore, we performed approximate and full hindered rotor treatments to nd the corrected vibrational entropy of bis(chromiumtricarbonyl) dibenzo[a,e]cyclooctatetraene (DBCOT). The eighth chapter of this dissertation is an independent molecular dynamics (MD) project to study how ethanol interacts with human and mouse Toll-Like- Receptor3 (TLR3) monomers and a TLR3-dsRNA complex. No major structural changes were observed during the ethanol docking and subsequent MD simulations, but the MD simulations revealed a reduction in the proportion of alpha helix present during a 1000 ns MD simulation on the h-TLR3 monomer in 0.5 percent ethanol.
| Identifer | oai:union.ndltd.org:MSSTATE/oai:scholarsjunction.msstate.edu:td-2898 |
| Date | 09 May 2015 |
| Creators | Ratnaweera, Chinthaka Nadun |
| Publisher | Scholars Junction |
| Source Sets | Mississippi State University |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | Theses and Dissertations |
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