Exploring Molecular Systems From Chemical Physics To Biochemistry Using Classical And Quantum Mechanics

Six topic are considered in this dissertation. Chapter 2 is an investigation into the role of ultra-fast hydrogen dynamics in determining fragmentation products of C3H4 following exposure to intense laser fields. Classical dynamics simulations were performed starting from C3H4 isomers with 190 - 240 kcal/mol excess energy distributed randomly as nuclear momenta. Deprotonation events were seen in ca. 50 - 75 % of all trajectories. Roughly one third of all trajectories showed fragmentation involving internal isomerization prior to dissociation. Chapter 3 is a survey of currently popular density functional methods and their ability to calculate accurate excitation energies and intensities of some organic molecules and simple first row transition metal complexes. Choice of a reasonable basis set seemed to have little effect on the calculated electronic spectra of the inorganic complexes. Long-range corrected functionals and hybrid density functionals seemed to perform relatively well with only slight underestimations in either energies or intensities. Chapters 4 and 5 probe the structural and aromatic properties for a novel class of second row transition metal metallapyrimidine compounds. Aromaticity was gauged using Nucleus Independent Chemical Shift calculations and Natural Chemical Shielding analysis by obtaining ring π orbital contributions to the calculated chemical shift. The paramagnetic contribution to the chemical shift was used as an enhanced metric for determining aromaticity in metallacycle compounds. Metallapyrimidines containing metals with no valence d orbitals were found to be no better than weakly aromatic, while metals with valence d orbitals can be quite aromatic. Chapter 6 documents the force field parameterization for 50 modified DNA and 107 naturally occurring modified RNA nucleosides. Hartree-Fock calculations were used with a restraining procedure to generate atom-centered partial charges for use in molecular dynamics simulations using the AMBER force field. The parameters will allow AMBER and other similar force fields method users to incorporate modified nucleosides into their classical simulations. Chapters 7 and 8 detail the development of a computational method for computing accurate acid dissociation constants and solution phase oxidation potentials of canonical nucleic acid residues in addition to intermediates and products of guanine oxidation. Using implicit solvent modeling and accounting for relevant tautomers and protonation states present in aqueous solution, the trends in the calculated oxidation potentials were found to be in relatively good agreement with the trends in experimentally measured potentials. The methodology was then used to map out the pKa\u27s and redox potentials of pathways for guanine oxidation