Modeling Ab Initio Quantum Dynamics in Complex Systems through Multi-Scale Embedding

Abstract

Quantum dynamics underpin almost all methods that chemists have to interrogate molecules - spectroscopy is inherently time-dependent, and reactions occur with nuclear motion. At the same time, the environment surrounding a molecule can have drastic impacts on its properties, and understanding these impacts is a central goal in almost all fields of chemistry, from biochemistry to materials science. More often than not, the actual system of interest is in contact with a system that is of less interest, whether that be a solvent, a protein backbone, or a substrate, and this interaction can drastically modify the observed molecular behavior. Treating the whole system as accurately as possible requires an excess of computational power, since the cost of accurate quantum chemical calculations scale quickly with system size. Classical embedding approaches can circumvent this high computational cost by describing the environment with an approximate, coarser model. The goal of this dissertation is to develop time-dependent quantum chemical methods that interface with classical embedding approaches in a dynamic way. The first chapter sets up the theoretical preliminaries of single Slater determinant wavefunctions and their corresponding Hamiltonians. The second chapter details the classical embedding theories and their time independent interfaces to the Hamiltonians from chapter one. The third chapter describes the development of a time-dependent mixed quantum mechanical and molecular mechanical method and its application. The fourth chapter extends this development to include nonequilibrium propagation of degrees of freedom in the molecular mechanics environment. The fifth chapter discusses the development of a quantum nuclear dynamics method using the nuclear electronic orbital approach and the same real-time formalism as presented in chapter 1. The sixth chapter embeds this real-time nuclear electronic orbital approach inside a classical polarizable continuum model and investigates the change on the predicted time independent and time dependent properties.