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COMPUTATIONAL STUDIES OF CHEMICAL SYSTEMS: I. A THEORETICAL INVESTIGATION OF CLATHRATE HYDRATES II. CONFORMATIONAL POTENTIAL ENERGY SURFACE OF TRYPTAMINE

by McCarthy, Valerie Nicole

Abstract (Summary)
Hydrogen clathrates have recently been discovered and considered as storage medium for H2. Hydrogen forms a Type II clathrate structure, with a small and large cage. Multiple guest hydrogen molecules can occupy both cages (up to two in the small cage and four in the large cage), although the number of hydrogen molecules occupying the small cage has been a source of debate in the literature. The goal of this work has been to develop a polarizable force field for use in molecular dynamics simulations of hydrogen clathrates. The resulting force field has been coded in the DLPOLY package and simulations of the system as a function of the number of guest hydrogen molecules have been performed. The development of the force field, and the results of the simulations are discussed. In order for a clathrate structure to form, a 'guest' molecule must be present under ideal conditions. That is, water does not form a so-called 'self' hydrate. In order to elucidate the factors responsible for clathrate formation, emph{ab initio} calculations were performed on (H2O)$_{21}$ and (H2O)$_{20}$*H2S clusters. The results of these calculations have provided insight into why water does not form a self hydrate. Stimulated emission pumping experiments done by the Zwier group have established bounds on the low energy isomerization barriers between specific minima of tryptamine. In order to identify the low energy isomerization pathways, the Becke3LYP and RI-MP2 methods were used to characterize the low-energy minima and the transition states of tryptamine. In general there is good agreement between theory and experiment, but for a subset of the isomerization processes, the calculations give significantly higher barriers than deduced from experiment. Possible causes of this discrepancy are discussed.
Bibliographical Information:

Advisor:David Pratt; Jeffry Madura; Peter Siska; Kenneth D. Jordan

School:University of Pittsburgh

School Location:USA - Pennsylvania

Source Type:Master's Thesis

Keywords:chemistry

ISBN:

Date of Publication:06/16/2008

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