eprintid: 6286
rev_number: 5
userid: 6
dir: disk0/00/00/62/86
datestamp: 2011-11-10 19:31:02
lastmod: 2016-11-15 13:36:03
status_changed: 2011-11-10 19:31:02
type: thesis_degree
metadata_visibility: show
contact_email: vam2@pitt.edu
item_issues_count: 0
eprint_status: archive
creators_name: McCarthy, Valerie Nicole
creators_email: vam2@pitt.edu
creators_id: VAM2
title: COMPUTATIONAL STUDIES OF CHEMICAL SYSTEMS: I. A THEORETICAL INVESTIGATION OF CLATHRATE HYDRATESII. CONFORMATIONAL POTENTIAL ENERGY SURFACE OF TRYPTAMINE
ispublished: unpub
divisions: sch_as_chemistry
full_text_status: public
keywords: clathrate; molecular dynamics; tryptamine
abstract: 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.
date: 2008-06-16
date_type: completed
institution: University of Pittsburgh
refereed: TRUE
etdcommittee_type: committee_chair
etdcommittee_type: committee_member
etdcommittee_type: committee_member
etdcommittee_type: committee_member
etdcommittee_name: Jordan, Kenneth D.
etdcommittee_name: Pratt, David 
etdcommittee_name: Madura, Jeffry 
etdcommittee_name: Siska, Peter
etdcommittee_email: jordan@pitt.edu
etdcommittee_email: pratt@pitt.edu
etdcommittee_email: madura@duq.edu
etdcommittee_email: pes@pitt.edu
etdcommittee_id: JORDAN
etdcommittee_id: PRATT
etdcommittee_id: 
etdcommittee_id: PES
etd_defense_date: 2008-01-10
etd_approval_date: 2008-06-16
etd_submission_date: 2008-01-14
etd_access_restriction: immediate
etd_patent_pending: FALSE
assigned_doi: doi:10.5195/pitt.etd.2011.6286
thesis_type: dissertation
degree: PhD
committee: Kenneth D. Jordan (jordan@pitt.edu) - Committee Chair
committee: David Pratt (pratt@pitt.edu) - Committee Member
committee: Jeffry Madura (madura@duq.edu) - Committee Member
committee: Peter Siska (pes@pitt.edu) - Committee Member
etdurn: etd-01142008-181522
other_id: http://etd.library.pitt.edu/ETD/available/etd-01142008-181522/
other_id: etd-01142008-181522
citation:   McCarthy, Valerie Nicole  (2008) COMPUTATIONAL STUDIES OF CHEMICAL SYSTEMS: I. A THEORETICAL INVESTIGATION OF CLATHRATE HYDRATESII. CONFORMATIONAL POTENTIAL ENERGY SURFACE OF TRYPTAMINE.  Doctoral Dissertation, University of Pittsburgh.    (Unpublished)  
document_url: http://d-scholarship-dev.library.pitt.edu/6286/1/mccarthy.pdf