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dc.contributor.authorFaruk, Nabil
dc.date.accessioned2014-08-18 13:15:28 (GMT)
dc.date.available2014-08-18 13:15:28 (GMT)
dc.date.issued2014-08-18
dc.date.submitted2014
dc.identifier.urihttp://hdl.handle.net/10012/8645
dc.description.abstractThis thesis presents two different approaches and applications where nuclear dynamics are treated quantum mechanically in order to obtain more accurate theoretical predictions of molecular properties. In our first application, we report a first-principles prediction of the Raman shifts of parahydrogen (pH_2) clusters of sizes N=4-19 and 33, based on path integral ground-state simulations with an ab initio potential energy surface. The Raman shifts are calculated, using perturbation theory, as the average of the difference-potential energy surface between the potential energy surfaces for vibrationally-excited and ground-state parahydrogen monomers. The radial distribution of the clusters is used as a weight function in this average. Very good overall agreement with experiment [1] is achieved for p(H_2)_{2-8,13,33}. A number of different pair potentials are employed for the calculation of the radial distribution functions. We find that the Raman shifts are sensitive to slight variations in the radial distribution functions. In our second application, we discuss the development of Path Integral Molecular Dynamics (PIMD) methodology, which our group has previously incorporated into the Molecular Modeling Toolkit (MMTK) [2] to account for nuclear quantum effects. This thesis is to provide a proof-of-concept for our software tools and PIMD method through the gas phase investigation of methyl beta-D-arabinofuranoside, which is a sugar residue in the cell wall of tuberculosis bacteria and is thought to provide bacterial resistance to drugs. We observe the effect of nuclear quantum sampling on the sugar's dihedral angle distributions at different temperatures, which we then relate to nuclear magnetic resonance proton-proton coupling constants via Karplus equations. We also determine the sugar's energy convergence with path integral sampling and the energy behaviour with temperature. We find that quantum effects are non-negligible even at biological temperatures, although some challenges remain in converging our coupling constant predictions. Finally, we discuss and benchmark our extension with the Open Molecular Mechanics (OpenMM) program [3] to enable graphics processing unit-accelerated solution phase simulations for future work.en
dc.language.isoenen
dc.publisherUniversity of Waterlooen
dc.subjectQuantum mechanicsen
dc.subjectMolecular dynamicsen
dc.subjectCarbohydrateen
dc.subjectBasis seten
dc.subjectPath integralen
dc.subjectParahydrogenen
dc.subjectRaman spectraen
dc.titleQuantum effects in molecular systemsen
dc.typeMaster Thesisen
dc.pendingfalse
dc.subject.programChemistry (Nanotechnology)en
uws-etd.degree.departmentChemistryen
uws-etd.degreeMaster of Scienceen
uws.typeOfResourceTexten
uws.peerReviewStatusUnrevieweden
uws.scholarLevelGraduateen


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