Dissertation/Thesis Abstract

Quantum wavepacket ab initio molecular dynamics: Simulating quantum nuclear effects in complex systems
by Sumner, Isaiah, Ph.D., Indiana University, 2010, 251; 3397483
Abstract (Summary)

A methodology, Quantum Wavepacket Ab Initio Molecular Dynamics (QWAIMD), for the efficient, simultaneous dynamics of electrons and nuclei is presented. This approach allows for the quantum-dynamical treatment of a subset of nuclei in complex, molecular systems while treating the remaining nuclei and electrons within in the ab initio molecular dynamics (AIMD) paradigm. Developments of QWAIMD discussed within include: (a) a novel sampling algorithm dubbed Time-Dependent Deterministic Sampling (TDDS), which increases the computational efficiency by several orders of magnitude; (b) generalizations to hybrid QM/QM and QM/MM electronic structure methods via a combination of the ONIOM and empirical valence bond approaches, which may allow for the accurate simulation of large molecules; and (c) a novel velocity-flux autocorrelation function to calculate the vibrational density-of-states of quantum-classical systems. These techniques are benchmarked on calculations of small, hydrogen-bound clusters. Furthermore, since many chemical processes occur over time-scales inaccessible to computation, a scheme is discussed and benchmarked here which can bias both QWAIMD and classical-AIMD dynamics to sample these long time-scale events, like proton transfer in enzyme catalysis. Finally, hydrogen tunneling in an enzyme, soybean lipoxygenase-1 (SLO-1) is examined by calculating the orbitals (eigenstates) of the transferring proton along the reaction coordinate. This orbital analysis is then supplemented by using quantum measurement theory to reexamine the transfer.

Indexing (document details)
Advisor: Iyengar, Srinivasan S.
Commitee: Gottlieb, Steven A., Raghavachari, Krishnan, de Souza, Romualdo
School: Indiana University
Department: Chemistry
School Location: United States -- Indiana
Source: DAI-B 71/04, Dissertation Abstracts International
Subjects: Biochemistry, Physical chemistry, Molecular physics
Keywords: Enzyme kinetics, Hydrogen transfer, Molecular dynamics, Quantum nuclear effects, Vibrational spectroscopy, Wavepackets
Publication Number: 3397483
ISBN: 978-1-109-69379-9
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