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.
|Advisor:||Iyengar, Srinivasan S.|
|Commitee:||Gottlieb, Steven A., Raghavachari, Krishnan, de Souza, Romualdo|
|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|
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