Molecular dynamics simulations of motion in organic molecular crystals

Alexandra Nemkevich

Research output: ThesisDoctoral Thesis

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Abstract

The subject of this thesis is the application of molecular dynamics (MD) techniques to study motion in organic molecular crystals. MD can provide a higher level of detail compared to experimental methods used to study molecular motion, such as crystallography and solid state NMR spectroscopy. However, due to the many simplifications and approximations involved, the results of MD simulations have uncertain reliability. The aim of this work was to assess the reliability of MD in simulating the structure and dynamics of simple organic crystals, and to explore the potential of using MD for understanding dynamics in more complicated crystalline systems. The range of possible applications of MD simulations of organic molecular crystals is very wide. They could include, for example, refinement of disordered crystal structures (including large biomolecules), obtaining anisotropic atomic displacement parameters (ADPs) for weakly scattering hydrogens in Xray structure determination, providing insight into some interesting physical phenomena that involve molecular motion and aiding the design of materials showing these phenomena, better understanding of drug-receptor interactions and reactivity in the solid state and helping to design molecular motors. This thesis is organised as a series of papers that have been published or prepared for publication and contains eight Chapters. Chapters 1 and 2 give a general introduction into the topics of molecular motion and computational chemistry. Chapter 1 contains an overview of the types of dynamical processes taking place in organic molecular crystals known from experiment and their relevance to crystal properties. Chapter 2 introduces molecular dynamics and related techniques and reviews their applications to date in studying motion in crystals. Chapter 3 provides an introduction into the experimental work presented in Chapters 4 to 7, which are written as journal articles.
Original languageEnglish
QualificationDoctor of Philosophy
Publication statusUnpublished - 2012

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