Date of Award

Spring 1-1-2013

Document Type


Degree Name

Doctor of Philosophy (PhD)


Chemistry & Biochemistry

First Advisor

Rex T. Skodje

Second Advisor

Robert Parson

Third Advisor

Veronica Vaida

Fourth Advisor

Joel D. Eaves

Fifth Advisor

J. Will Medlin


Several problems concerning both the dynamics and kinetics of a selection of small organic molecules in different environments are considered. Chapters 2 and 3 concern the photochemistry of the hydrated clusters of the fluoromethanol, CH2(OH)F, and methanediol, CH2(OH)2, molecules upon vibrational overtone excitation of an OH chromophore in the cluster. Ab initio calculations unambiguously predict a dramatic drop in the barrier height of the reaction CH2OHX · (H2O)n → CH2O + HX · (H2O)n (X=F,OH). However, analysis of "on-the-fly" trajectory simulations shows a pronounced delayed threshold in the quantum yield for the reaction. This phenomenon originates from a competition between the reaction and the evaporation of water molecules from the cluster, which can quench the possibility of reaction by removing energy from the activated complex. The conclusion of this work is that quantum chemistry calculations at stationary points on the potential energy surface can be insufficient to establish water catalysis in photochemical reactions where the dynamical details are important due to the non-statistical nature of the excitation. In the second part of this work, an adiabatic semiclassical treatment is proposed for incorporating low frequency torsional motions into molecular state sums. In this treatment, "fast" internal degrees of freedom, often well represented in the harmonic, free, or hindered rotor approximations, can be incorporated quantum mechanically into a local state sum that is a function of the "slow" coordinate. The slow torsional states can then be included using a classical phase space integral over the local state sum. This method is applied to a simple model problem of coupled harmonic oscillators and to the hydrogen peroxide molecule and its isotopomer HOOD. The method is compared to simpler, commonly used state count algorithms. In the last section, the catalyzed decomposition of methanol on the metal surfaces of Pd(111), Pt(111), and Ni(111) is considered. These reactions are used to construct a microkinetics model composed of surface symmetry consistent rate coefficients to simulate the relevant surface kinetics. Global sensitivity and stochastic pathway analyses are used to identify reactions to which the model output shows the greatest sensitivity. Due to its modest size, this mechanism is considered as a model problem on which to compare the ability of global sensitivity and stochastic pathway analyses methods to identify and understand competing pathways within a chemical mechanism.

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