Access Type

Open Access Dissertation

Date of Award

January 2017

Degree Type

Dissertation

Degree Name

Ph.D.

Department

Chemistry

First Advisor

H. Bernhard Schlegel

Abstract

This dissertation includes three topics: molecular dynamics in strong laser fields, pKa’s and redox potential calculations of bio–organic molecules, and oxidative damage of the nucleobases. Electronic structure calculations are used to provide a deeper understanding of experimental observations as well as to predict new results.

Chapters 2, 3 and 4 investigate the fragmentation and isomerization reactions of small monocations in the presence of strong laser fields. In the presence of intense laser pulses with 800 nm wavelengths, Born-Oppenheimer classical trajectory simulations were performed to investigate the dynamics of methanol monocation on the ground state potential energy surface (Chapter 2). With initially added 75-125 kcal/mol energy and the applied laser fields, 79-81% of the trajectories were seen to produce H atom. H2 loss was found to be the second most frequent dissociation channel (9-13%) and isomerization of CH3OH+ to CH2OH2+ was the third most abundant reaction path (1-3%). Chapter 3 compares the difference in dynamics of the methanol monocation in the presence of 800 nm and 7 µm laser pulses. Randomly oriented methanol cations gained an average of 42 and 81 kcal/mol for 4 cycle 7 µm pulses with intensities of 0.88 × 1014 Wcm-2 and 1.7 × 1014 Wcm-2 respectively, but only 0.5 and 2.0 kcal/mol from 4 cycle 800 nm pulses with the same intensity. Chapter 4 explores the effect of changes in potential energy surface on the isomerization and dissociation reactions driven by the laser field for CH3NH2+, CH3OH+, and CH3F+. The amount of energy absorbed nearly doubled when the laser field was aligned along the C−X axis (X=NH2, OH, and F) and, also when the field intensity was increased from of 0.88 × 1014 to 1.7 ×1014 Wcm-2. Dissociation after isomerization was observed only in CH3F+ (0−6%). The amount of CH3+ + X dissociation for all three molecules increased when the laser field was aligned along C-X bond.

Chapters 5-8 detail the development of a computational protocol for computing accurate pKa’s and redox potentials of various bio–organic compounds in aqueous solution. Chapter 5 investigates the effect of explicit water molecules with implicit solvation on the calculated pKa’s and redox potential of nucleobases. Using a few explicit water molecules and an implicit solvation model, the pKa’s and redox potentials of the nucleobases were found to be in good agreement with the experimentally measured values. The methodology is then expanded to calculate the pKa’s of larger sets of organic molecules such as thiols (Chapter 6), selenols (Chapter 7), alcohols, phenols and hydroperoxides (Chapter 8). A survey of a wide range of DFT functionals and basis sets with varying numbers of explicit waters were performed in each of those studies to determine the appropriate computational method and the number of explicit waters needed. At least one explicit water molecule was needed in all cases to reduce some of the errors in implicit solvation model while three explicit waters were required to obtain the chemical accuracy. B97XD/6-31+G(d,p) with three explicit waters in SMD implicit solvation predicted the pKa’s of organic substituted thiols and selenols within 1 pKa units of the experimentally measured values. When three explicit waters were included along with SMD solvation, B3LYP/6-311++G(d,p) was found to perform the best for the alcohols, phenols, and hydroperoxides with very good agreement with the experimentally known pKa values.

Chapters 9, 10 and 11 explore some of the pathways of guanine-lysine crosslink formation in aqueous solution in the presence of different oxidizing agents such as benzophenone photosenzetizer, singlet oxygen, and sulfate radical. Various reaction pathways in aqueous solution were investigated by DFT calculations with the SMD solvation model. In some cases, high level quantum chemistry calculations such as CCSD(T), BD(T), and CASSCF calculations were also used to achieve greater accuracy. The barrier heights, enthalpies, pKa’s and reduction potentials were calculated for intermediates to find the lowest energy paths. These chapters provide insight into some of the experimental findings, such as product distributions, the effect of pH, etc.

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