Despite comprehensive studies addressing the chemical kinetics of butanol isomers, relevant uncertainties associated with the emissions of relevant pollutants persists. Also, a lack of chemistry knowledge of processes designed to produce biofuels limits their implementation at industrial scales. Therefore, the first objective of this thesis was to use cutting-edge kinetic theories to calculate rate constants of propen-2-ol, 1-pronenol, and vinyl alcohol keto-enol tautomerizations, which account for the production of the harmful carbonyl species. The second objective was to use the predictive capabilities of dynamic theories to reveal new chemistry of syngas oxy-combustion in supercritical CO2 and complexities of the zeolite dealumination, two processes involved in coal and biomass conversion. Rate constants computations considered transition state theory with variational effects, tunneling correction, and multistructural torsional anharmonicity. The study also included pressure effects by using and improving the system-specific quantum Rice-Ramsperger-Kassel/modified strong collision model. The atomistic simulations used ReaxFF force fields in hydrogen/oxygen/carbon monoxide/ carbon dioxide mixtures to represent the syngas system and an MFI zeolite with different water loading to model the dealumination. The results show that the studied assisted tautomerizations have much lower energy barriers than the unimolecular process. However, the “catalytic” effect is efficient only if the partner molecule is at high concentrations. Pressure effects are pronounced in the chemically activated tautomerizations, and the improved algorithm to compute pressure-dependent rate constants overcomes the initial difficulties associated with its application to C3 or larger molecules at temperatures above 800-1000 K. Reactive molecular dynamics simulations revealed the role of CO2 as an initiator in the syngas oxy-combustion and a new step involving the formation of formic acid. Those simulations for the zeolite dealumination process also showed that proton transfer, framework flexibility, and aluminum dislodging mediated by silicon reactions are complex dynamic phenomena determining the process. These aspects complement the dealumination theory uncovered so far and establish new paths in the study of water-zeolite interactions. Overall, the rate constants computed in this work reduce relevant uncertainties in the chemical kinetic mechanisms of alcohol oxidation, and the molecular dynamics simulations broaden the chemical knowledge of processes aimed at the utilization of alternative energy resources.

In the thesis work we investigate four problems connected with dynamical processes in condensed medium, using different techniques of equilibrium and non-equilibrium statistical mechanics. Biology is rich in dynamical events ranging from processes involving single molecule [1] to collective phenomena [2]. In cell biology, translocation and transport processes of biological molecules constitute an important class of dynamical phenomena occurring in condensed phase. Examples include protein transport through membrane channels, gene transfer between bacteria, injection of DNA from virus head to the host cell, protein transport thorough the nuclear pores etc. We present a theoretical description of the problem of protein transport across the nuclear pore complex [3]. These nuclear pore complexes (NPCs) [4] are very selective filters that monitor the transport between the cytoplasm and the nucleoplasm. Two models have been suggested for the plug of the NPC. The first suggests that the plug is a reversible hydrogel while the other suggests that it is a polymer brush. In the thesis, we propose a model for the transport of a protein through the plug, which is treated as elastic continuum, which is general enough to cover both the models. The protein stretches the plug and creates a local deformation, which together with the protein is referred to as the bubble. The relevant coordinate describing the transport is the center of the bubble. We write down an expression for the energy of the system, which is used to analyze the motion. It shows that the bubble executes a random walk, within the gel. We find that for faster relaxation of the gel, the diffusion of the bubble is greater. Further, on adopting the same kind of free energy for the brush too, one finds that though the energy cost for the entry of the particle is small but the diffusion coefficient is much lower and hence, explanation of the rapid diffusion of the particle across the nuclear pore complex is easier within the gel model. In chemical physics, processes occurring in condensed phases like liquid or solid often involve barrier crossing. Simplest possible description of rate for such barrier crossing phenomena is given by the transition state theory [5]. One can go one step further by introducing the effect of the environment by incorporating phenomenological friction as is done in Kramer’s theory [6]. The “method of reactive flux” [7, 8] in chemical physics allows one to calculate the time dependent rate constant for a process involving large barrier by expressing the rate as an ensemble average of an infinite number of trajectories starting at the barrier top and ending on the product side at a specified later time. We compute the time dependent transmission coefficient using this method for a structureless particle surmounting a one dimensional inverted parabolic barrier. The work shows an elegant way of combining the traditional system plus reservoir model [9] and the method of reactive flux [7] and the normal mode analysis approach by Pollak [10] to calculate the time dependent transmission coefficient [11]. As expected our formula for the time dependent rate constant becomes equal to the transition state rate constant when one takes the zero time limit. Similarly Kramers rate constant is obtained by taking infinite time limit. Finally we conclude by noting that the method of analyzing the coupled Hamiltonian, introduced by Pollak is very powerful and it enables us to obtain analytical expressions for the time dependent reaction rate in case of Ohmic dissipation, even in underdamped case. The theory of first passage time [12] is one of the most important topics of research in chemical physics. As a model problem we consider a particle executing Brownian motion in full phase space with an absorbing boundary condition at a point in the position space we derive a very general expression of the survival probability and the first passage time distribution, irrespective of the statistical nature of the dynamics. Also using the prescription adopted elsewhere [13] we define a bound to the actual survival probability and an approximate first passage time distribution which are expressed in terms of the position-position, velocity-velocity and position-velocity variances. Knowledge of these variances enables one to compute the survival probability and consequently the first passage distribution function. We compute both the quantities for gaussian Markovian process and also for non-Markovian dynamics. Our analysis shows that the survival probability decays exponentially at the long time, irrespective of the nature of the dynamics with an exponent equal to the transition state rate constant [14]. Although the field of equilibrium thermodynamics and equilibrium statistical mechanics are well explored, there existed almost no theory for systems arbitrarily far from equilibrium until the advent of fluctuation theorems (FTs)[15] in mid 90�s. In general, these fluctuation theorems have provided a general prescription on energy exchanges that take place between a system and its surroundings under general nonequilibrium conditions and explain how macroscopic irreversibility appears naturally in systems that obey time reversible microscopic dynamics. Based on a Hamiltonian description we present a rigorous derivation [16] of the transient state work fluctuation theorem and the Jarzynski equality [17] for a classical harmonic oscillator linearly coupled to a harmonic heat bath, which is dragged by an external agent. Coupling with the bath makes the dynamics dissipative. Since we do not assume anything about the spectral nature of the harmonic bath the derivation is valid for a general non-Ohmic bath.

Despite numerous advances in experimental methodologies capable of addressing the various phenomenon occurring on metal surfaces, atomic scale resolution of the microscopic dynamics remains elusive for most systems. Computational models of the processes may serve as an alternative tool to fill this void. To this end, parallel molecular dynamics simulations of self-diffusion on metal surfaces have been developed and employed to address microscopic details of the system. However these simulations are not without their limitations and prove to be computationally impractical for a variety of chemically relevant systems, particularly for diffusive events occurring in the low temperature regime. To circumvent this difficulty, a corresponding coarse-grained representation of the surface is also developed resulting in a reduction of the required computational effort by several orders of magnitude, and this description becomes all the more advantageous with increasing system size and complexity. This representation provides a convenient framework to address fundamental aspects of diffusion in nonequilibrium environments and an interesting mechanism for directing diffusive motion along the surface is explored. In the ensuing discussion, additional topics including transition state theory in noisy systems and the construction of a checking function for protein structure validation are outlined. For decades the former has served as a cornerstone for estimates of chemical reaction rates. However, in complex environments transition state theory most always provides only an upper bound for the true rate. An alternative approach is described that may alleviate some of the difficulties associated with this problem. Finally, one of the grand challenges facing the computational sciences is to develop methods capable of reconstructing protein structure based solely on readily-available sequence information. Herein a checking function is developed that may prove useful for addressing whether a particular proposed structure is a viable possibility.

A time-delayed response of individual living organisms to information exchanged within flocks or swarms leads to the emergence of complex collective behaviors. A recent experimental setup by (Khadka et al 2018 Nat. Commun. 9 3864), employing synthetic microswimmers, allows to emulate and study such behavior in a controlled way, in the lab. Motivated by these experiments, we study a system of N Brownian particles interacting via a retarded harmonic interaction. For N 3 , we characterize its collective behavior analytically, by solving the pertinent stochastic delay-differential equations, and for N>3 by Brownian dynamics simulations. The particles form molecule-like non-equilibrium structures which become unstable with increasing number of particles, delay time, and interaction strength. We evaluate the entropy and information fluxes maintaining these structures and, to quantitatively characterize their stability, develop an approximate time-dependent transition-state theory to characterize transitions between different isomers of the molecules. For completeness, we include a comprehensive discussion of the analytical solution procedure for systems of linear stochastic delay differential equations in finite dimension, and new results for covariance and time-correlation matrices

In this work, experimental and theoretical approaches are applied to the study of chemical reaction dynamics. In Chapter 2, two applications of transition state theory are presented: (1) Application of microcanonical transition state theory to determine the rate constant of dissociation of C2F3I after π∗ ← π excitation. It was found that this reaction has a very fast rate constant and thus is a promising system for testing the statistical assumption of molecular reaction dynamics. (2) A general rate constant expression for the reaction of atoms and molecules at surfaces was derived within the statistical framework of flexible transition state theory. In Chapter 4, a computationally efficient TDDFT approach was found to produce useful potential energy surface landscapes for application to non-adiabatic predissociative dynamics of the molecule CS2 after excitation from the ground state to the singlet C-state. In Chapter 5, ultrafast experimental results of excitation of CS2 to the predissociative neutral singlet C-state is presented. The bandwidth of the excitation laser was carefully tuned to span a two-component scattering resonance with each component differently evolving electronically with respect to excited state character during the quasi-bound oscillation. Scalar time-resolved photoelectron spectra (TRPES) and vector time-resolved photoelectron angular distribution (TRPAD) observables were recorded during the predissociation. The TRPES yield of photoelectrons was found to oscillate with a quantum beat pattern for the photoelectrons corresponding to ionization to the vibrationless cation ground state; this beat pattern was obscured for photoelectron energies corresponding to ionization from the vibrationally excited CS2 cation. The TRPAD data was recorded for two general molecular ensemble cases: with and without a pre-excitation alignment laser pulse. It was found that in the case of ensemble alignment (Chapter 6), the “molecular frame” TRPAD (i.e. TRMFPAD) was able to image the purely valence electronic dynamics of the evolving CS2 C-state. The unaligned ensemble TRPAD observable suffers from excessive orientational averaging and was unable to observe the quantum beat. Engineering efforts were also undertaken to eliminate scattered light background signal (Chapter 7, Appendix A) and improve laser stability as a function of ambient pressure (Appendix B) for TRMFPAD experiments. / Thesis (Ph.D, Chemistry) -- Queen's University, 2012-09-11 22:18:20.89

Les alliages à haute entropie forment une nouvelle classe de matériaux découverts récemment et démontrant des propriétés physiques et mécaniques très prometteuses. Ces solutions solides à phase unique présentent une grande dureté, une haute résistance à la corrosion, une bonne résistance aux dommages causés par l’irradiation ionique et une phase stable même à température élevée. Pour ces raisons, ils ont attiré l’attention pour plusieurs utilisations potentielles, notamment dans la prochaine génération de réacteurs nucléaires. Dans ce mémoire, nous étudierons la diffusion de défauts ponctuels dans l’alliage de 55Fe-28Ni-17Cr. Ces défauts sont très fréquemment créés par l’irradiation par ion ayant lieu dans les cuves des réacteurs nucléaires. Nous profiterons de l’occasion d’étudier un alliage ayant une microstructure complexe afin d’introduire et de tester une méthode du calcul du taux de transition global et local se basant sur le calcul du facteur pré-exponentiel de la théorie de l’état de transition harmonique (hTST). Ces méthodes sont implantées dans la technique d’activation-relaxation cinétique, une méthode de Monte Carlo cinétique, que nous utiliserons pour réaliser la diffusion de défauts ponctuels dans l’alliage. Nous démontrons une différence importante entre le taux de transition calculé avec et sans hTST qui peut mener à une erreur dans les propriétés calculées de diffusion des défauts. Nous démontrons également que le facteur pré-exponentiel obéit à une anti-loi de compensation de Meyer-Neldel. Le calcul local du facteur pré-exponentiel est étudié et nous démontrons qu’il est capable de reproduire le taux global pour plusieurs événements. / High-entropy alloys are a novel class of materials discovered recently and demonstrating promising physical and mechanical properties. These single-phase solid solutions present a high hardness, a great resistance to corrosion, a good resistance to ion radiation damages and a stable phase even at high temperature. For these reasons they have attracted the attention for numerous potential uses, notably in the next generation of nuclear reactors. In this thesis, we study the diffusion of point defects in the 55Fe-28Ni-17Cr alloy. This kind of defect being very frequently created by irradiation in nuclear reactors. We will also use the occasion of having an alloy with a complex microstructure to add and test a method of computing the transition rate globally and locally based on the computation of the prefactor of the harmonic Transition State Theory (hTST). These additions will be made in the kinetic Activation-Relaxation Technique, a kinetic Monte Carlo method that will be used to study the diffusion of point defects in the alloy. We demonstrate that there is an important discrepancy between the rate computed with and without the hTST that can lead to an error in the computed diffusion properties of defects. We also show that the prefactor obeys an anti Meyer-Neldel compensation law. The local method to compute the prefactor is then studied and proven to be able to reproduce the global rate for a large number of events.