Book Description

This thesis contains a series of density functional studies on porphyrins, surfaces and other molecules, that are of relevance to surface science and electron transfer. In chapter 1 the main concepts of the thesis and how they fit together, are outlined. Chapter 2 describes density functional theory (DFT), the principle theoretical technique used throughout. The thesis then considers two main aspects. Chapters 3, 4 and 5 look at how systems interact with surfaces and compare and contrast situations of differing interaction strengths. Chapter 3 investigates the weak interaction of a haem molecule with the Si(111):H surface and studies how this interaction can be tuned by desorbing hydrogen atoms from the surface. In chapter 4, the structure of experimentally observed Mn nanolines on the Si(001) surface is studied. How these lines self assemble and interact strongly with the surface is discussed. Elements of these two studies are then combined in chapter 5 with a study of manganese porphyrin on the Si(001) surface displaying some features common to both previous systems. In chapter 6, 7 and 8 the focus switches to electron transfer. The basics of electron transfer theory are outlined in chapter 6. Then, the difficulties faced by DFT when studying electron transfer in large systems, such as the self-interaction error and cubic scaling, are described. Chapter 7 describes the constrained DFT formalism and its implementation into the linear scaling DFT code CONQUEST. In chapter 8, this implementation is used to perform some electron transfer calculations on small organic molecules, with systems demonstrating both charge localization and charge separation investigated. Chapter 9 concludes the thesis indicating how, following this thesis, large scale electron transfer calculations of organic molecules on surfaces can be performed with some confidence and giving suggestions for future calculations.