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Theoretical Studies of Chemical Kinetics and Dynamics in Condensed Phases and Gases
Theoretical models have brought unprecedented views of chemical kinetics and dynamics. This dissertation presents the results of theoretical and computational studies on several molecular systems: enzyme reactions in aqueous solution and charged molecules (ions) mobility in He and N2 gases. Zinc ions are required for the catalytic activity of a large number of metalloproteinases that participate in important biological functions. In this dissertation, highly accurate QM/MM style MP2 calculations have been performed to determine the catalytic mechanisms of three zinc enzymes: Amyloid-? peptide hydrolysis catalyzed by human insulin degrading enzyme (IDE), the hydroxylation of ampicillin catalyzed by New Delhi metallo-beta-lactamase-1 (NDM-1) and the deacetylation reaction catalyzed by human histone deacetylase 8 (HDAC8). New catalytic mechanisms have been identified for these enzyme reactions. For example, different from the catalytic mechanisms reported in the literature, QM/MM style MP2 calculations show that the rate-determining step of the hydroxylation by NDM-1 is a proton transfer reaction, which successfully explains the solvent kinetic isotope effect observed in experiments. These mechanisms can provide the basis for the design of biochemical methods to modulate the catalytic activity of these enzymes. A force field molecular dynamics method is developed to directly simulate the drift of charged molecules (ions) in buffer gases driven by an electric field. With the fully consideration of intermolecular interactions and the dynamic motions of ion atoms in buffer gases, this method is more realistic than traditional methods, such as projection approximation and trajectory methods. The ion mobility and collision cross sections (CCS) with relevance to ion mobility spectrometry can be calculated via the Mason- Schamp equation by using the simulated drift velocity in high-density buffer gases (pressure ∼50 bar) and high electric fields (∼107 V per m). The simulated CCS values are consistent with experimental values. The sensitivity of the simulated CCS values to random diffusion, drift velocity, electric field strength, temperature and buffer gas density is examined.
Lai, Rui, "Theoretical Studies of Chemical Kinetics and Dynamics in Condensed Phases and Gases" (2018). ETD collection for University of Nebraska - Lincoln. AAI10791697.