Date of Award

Fall 2023

Document Type

Open Access Dissertation

Department

Chemistry and Biochemistry

First Advisor

Sophya Garashchuk

Abstract

This dissertation describes our research in theory and applications of reactive molecular dynamics. Quantum dynamics provides the foundation for understanding chemical processes. However, the computational cost of describing a general quantum system scales exponentially with the system size. Thus, an efficient basis representation of wavefunctions is essential. Time-dependent Gaussian bases are often employed to describe the large-amplitude motion of high-dimensional systems. The time dependence of such bases is typically determined by (i) the variational principle or by (ii) classical dynamics. But those approaches have shortcomings due to intrinsic singularity of the variational equations in the full basis limit or due to inadeqaute coverage of the configuration space relevant to quantum dynamics, respectively. Here we describe the Quantum Trajectory-guided Adaptable Gaussian (QTAG) bases where the basis function position, phase, and width are coupled to the wavefunction evolution via the continuity of the probability density in the course of the quantum trajectory dynamics. Thus, an efficient basis is generated to represent the evolving wavefunction in many dimensions, bypassing the variational equations on the parameters of the Gaussians. We also present a time-sliced propagation with basis projections, which lends generality, efficiency and stability to the QTAG dynamics, as illustrated on model systems. Turning to experimentally-relevant systemd, we have studied the hydroxide diffusion in cobaltocenium-containing anion-exchange membranes (AEM) at the atomistic level. We have employed molecular dynamic simulations for molecular representations of AEMs consisting of the hydroxide and cobaltocenium cations in an aqueous environment, constrained in one dimension to mimic the AEM channels. In order to describe the proton hopping mechanism, the forces are obtained from the electronic structure computed at the Density Functional Tight Binding level. We find that the hydroxide diffusion depends on the modulation of the electrostatic interactions by the solvation shell, and its rearrangement ability controlled by the channel size and hydration level. The hydroxide diffusion proceeds via both vehicular and structural diffusion mechanisms, with the latter playing a larger role at low diffusion coefficients. The highest diffusion coefficient is observed under moderate water densities (around half the density of liquid water) when there are enough water molecules to form the solvation shell reducing the electrostatic interaction between ions, yet there is enough space for the water rearrangements during the proton hopping. The effects of the cobaltocenium separation, orientation, chemical modifications, and the role of the nuclear quantum effects – each modulaitng the diffusion coefficient by a factor of 2 -- are also discussed.

Rights

© 2024, Mohottige Sachith Prasanga Wickramasinghe

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