Study of Reactive and Non-Reactive Chemical Processes in Condensed Phase.

Chemical dynamics in condensed phase environments is dictated by an intricate interplay between reactive and competing non-reactive processes. This dissertation is aimed at the molecular level understanding of both types of processes in liquid solution environments within the framework of nonequilibrium statistical mechanics and using advanced molecular dynamics simulation techniques. The first part of this thesis is focused on understanding quantum effects on the rates of non-reactive vibrational energy relaxation processes in several experimentally relevant systems. The systems studied include neat liquid HCl and DCl and CN- isotopomers dissolved in H2O and D2O. The vibrational energy relaxation rate-constants for those systems were calculated within the framework of the Landau-Teller formula. Accounting for quantum effects was achieved by calculating the vibrational energy relaxation rate constants via the linearized semiclassical method. The calculated rate-constants are in excellent agreement with the experimentally measured rate constants. Comparison to the corresponding classical results suggest that quantum effects are strongly pathway dependent and that failure to account for them can lead to misinterpretation of the molecular mechanism underlying vibrational energy relaxation in liquid solution. The second part of this thesis is focused on understanding solvent effects on single-bond cZt-tZt isomerization rate constant of 1,3,5-cis-hexatriene dissolved in a series of explicit alkane and alcohol solvents. The isomerization rate constants are calculated within the framework of reactive flux theory and transition state theory, at different temperatures (275-325K), via classical molecular dynamics simulations. Our results reproduce the experimentally observed trend of slower isomerization rate constants in alcohol solvents in comparison to alkane solvents. Further analysis also reveals that the experimentally observed solvent dependence may be traced back to the fundamentally different structure of the solvation shell in alcohol and alkane solvents. More specifically, whereas in alcohol solvents, hexatriene fits inside a rigid cavity formed by the hydrogen-bonded network, which is relatively insensitive to conformational dynamics, alkane solvents form a cavity around hexatriene that adjusts to the conformational state of hexatriene, thereby increasing the entropy of transition state configurations relative to reactant configurations and giving rise to faster isomerization.PHDChemistryUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/110331/1/tsurma_1.pd

Relationship between crystalline order and melting mechanisms of solids

The mechanism for homogeneous nucleation of the liquid phase in Lennard-Jones solids is studied by combining the Landau free energy approach with some of the methodology developed to characterise transition path ensembles. The second-order bond orientational order parameter, Q 6 which indexes the overall degree of crystalline order, is shown to provide a dynamically significant collective coordinate describing the melting process. Trajectories generated from configurations sampled in the vicinity of the maximum in the Landau free energy curve, F(Q 6), are shown to have equal likelihood of teminating in either the solid or liquid-like free energy minima. It is also demonstrated that Q 6 is necessary but not sufficient as a dynamical coordinate to describe melting and it is necessary to explore possiblities for additional coordinates which are critical for initiating melting. Our sudy suggests that the additional coordinates for describing the melting process would be some type of localised defect, much smaller in spatial extent than the size of the critical nucleus predicted by classical nucleation theory