Investigating the influence of the sulfur oxidation state on solid state conformation

Design, synthesis and structural characterization of a series of diphenylacetylene derivatives bearing organosulfur, amide and amine moieties has been achieved in which the molecular conformation is controlled through variation of the hydrogen bond properties on alteration of the oxidisation level of sulfur.

Crystal engineering: exploiting variation of sulfur oxidation for the control of the solid state structure of organosulfur compounds

This thesis is focused on the design and synthesis of a diverse range of novel organosulfur compounds (sulfides, sulfoxides and sulfones), with the objective of studying their solid state properties and thereby developing an understanding of how the molecular structure of the compounds impacts upon their solid state crystalline structure. In particular, robust intermolecular interactions which determine the overall structure were investigated. These synthons were then exploited in the development of a molecular switch. Chapter One provides a brief overview of crystal engineering, the key hydrogen bonding interactions utilized in this work and also a general insight into “molecular machines” reported in the literature of relevance to this work. Chapter Two outlines the design and synthetic strategies for the development of two scaffolds suitable for incorporation of terminal alkynes, organosulfur and ether functionalities, in order to investigate the robustness and predictability of the S=O•••H-C≡C- and S=O•••H-C(α) supramolecular synthons. Crystal structures and a detailed analysis of the hydrogen bond interactions observed in these compounds are included in this chapter. Also the biological activities of four novel tertiary amines are discussed. Chapter Three focuses on the design and synthesis of diphenylacetylene compounds bearing amide and sulfur functionalities, and the exploitation of the N-H•••O=S interactions to develop a “molecular switch”. The crystal structures, hydrogen bonding patterns observed, NMR variable temperature studies and computer modelling studies are discussed in detail. Chapter Four provides the overall conclusions from chapter two and chapter three and also gives an indication of how the results of this work may be developed in the future. Chapter Five contains the full experimental details and spectral characterisation of all novel compounds synthesised in this project, while details of the NCI (National Cancer Institute) biological test results are included in the appendix.

Cocrystallisation involving the thioamide, amide and imide functional groups

The work presented in this dissertation focused on the development and characterisation of novel cocrystals that incorporated the thioamide, amide and imide functional groups. A particular emphasis was placed on the characterisation of these cocrystals by single crystal X-ray diffraction methods. In Chapter One a summary of the intermolecular interactions utilised in this work and a short review of the solid state and multicomponent systems is provided. A brief introduction to the ways in which different multicomponent systems can be distinguished, crystal engineering strategies and a number of cocrystal applications highlights the importance the understanding of intermolecular interactions can have on the physical and chemical properties of crystalline materials. Chapter Two is the first Results and Discussion chapter and includes an introduction that is specific to the chapter. The main body of this work focuses on the primary aromatic thioamide functional group and its propensity to cocrystallise with a number of sulfoxides. Unlike the amide functional group, thioamides are not commonly employed in cocrystallisation studies. This chapter presents the first direct comparison between the cocrystallisation abilities of these two functional groups and the intermolecular hydrogen bonding interactions present in the cocrystal structures are examined. Chapter Three describes the crystal landscape of a short series of secondary aromatic amides and their analogous thioamides. Building on the results obtained in Chapter Two, a cocrystal screen of the secondary thioamides with the sulfoxide functional group was carried out in order to determine the effect removing a hydrogen bond had on the supramolecular synthons observed in the cocrystals. These secondary thioamides are also utilised in Chapter Four, which examines their halogen bonding capabilities with two organoiodine coformers: 1,2- and 1,4-diiodotetrafluorobenzene. Chapter Five explores the cocrystallisation abilities of three related cyclic imides as coformers for cocrystallisation with a range of commonly used coformers. Chapter Six is an overall conclusions chapter that highlights the findings of the results presented in Chapters Two to Five. Chapter Seven details the instrument and experimental data for the compounds and cocrystals discussed in the Results and Discussion Chapters. The accompanying CD contains all of the crystallographic data in .cif format for the novel single crystal structures characterised in this work.

Ab initio calculations of group 4 metallocene reaction mechanisms: atomic layer deposition and bond activation catalysis

Thin film dielectrics based on titanium, zirconium or hafnium oxides are being introduced to increase the permittivity of insulating layers in transistors for micro/nanoelectronics and memory devices. Atomic layer deposition (ALD) is the process of choice for fabricating these films, as it allows for high control of composition and thickness in thin, conformal films which can be deposited on substrates with high aspect-ratio features. The success of this method depends crucially on the chemical properties of the precursor molecules. A successful ALD precursor should be volatile, stable in the gas-phase, but reactive on the substrate and growing surface, leading to inert by-products. In recent years, many different ALD precursors for metal oxides have been developed, but many of them suffer from low thermal stability. Much promise is shown by group 4 metal precursors that contain cyclopentadienyl (Cp = C5H5-xRx) ligands. One of the main advantages of Cp precursors is their thermal stability. In this work ab initio calculations were carried out at the level of density functional theory (DFT) on a range of heteroleptic metallocenes [M(Cp)4-n(L)n], M = Hf/Zr/Ti, L = Me and OMe, in order to find mechanistic reasons for their observed behaviour during ALD. Based on optimized monomer structures, reactivity is analyzed with respect to ligand elimination. The order in which different ligands are eliminated during ALD follows their energetics which was in agreement with experimental measurements. Titanocene-derived precursors, TiCp*(OMe)3, do not yield TiO2 films in atomic layer deposition (ALD) with water, while Ti(OMe)4 does. DFT was used to model the ALD reaction sequence and find the reason for the difference in growth behaviour. Both precursors adsorb initially via hydrogen-bonding. The simulations reveal that the Cp* ligand of TiCp*(OMe)3 lowers the Lewis acidity of the Ti centre and prevents its coordination to surface O (densification) during both of the ALD pulses. Blocking this step hindered further ALD reactions and for that reason no ALD growth is observed from TiCp*(OMe)3 and water. The thermal stability in the gas phase of Ti, Zr and Hf precursors that contain cyclopentadienyl ligands was also considered. The reaction that was found using DFT is an intramolecular α-H transfer that produces an alkylidene complex. The analysis shows that thermal stabilities of complexes of the type MCp2(CH3)2 increase down group 4 (M = Ti, Zr and Hf) due to an increase in the HOMO-LUMO band gap of the reactants, which itself increases with the electrophilicity of the metal. The reverse reaction of α-hydrogen abstraction in ZrCp2Me2 is 1,2-addition reaction of a C-H bond to a Zr=C bond. The same mechanism is investigated to determine if it operates for 1,2 addition of the tBu C-H across Hf=N in a corresponding Hf dimer complex. The aim of this work is to understand orbital interactions, how bonds break and how new bonds form, and in what state hydrogen is transferred during the reaction. Calculations reveal two synchronous and concerted electron transfers within a four-membered cyclic transition state in the plane between the cyclopentadienyl rings, one π(M=X)-to-σ(M-C) involving metal d orbitals and the other σ(C-H)-to-σ(X-H) mediating the transfer of neutral H, where X = C or N. The reaction of the hafnium dimer complex with CO that was studied for the purpose of understanding C-H bond activation has another interesting application, namely the cleavage of an N-N bond and resulting N-C bond formation. Analysis of the orbital plots reveals repulsion between the occupied orbitals on CO and the N-N unit where CO approaches along the N-N axis. The repulsions along the N-N axis are minimized by instead forming an asymmetrical intermediate in which CO first coordinates to one Hf and then to N. This breaks the symmetry of the N-N unit and the resultant mixing of MOs allows σ(NN) to be polarized, localizing electrons on the more distant N. This allowed σ(CO) and π(CO) donation to N and back-donation of π*(Hf2N2) to CO. Improved understanding of the chemistry of metal complexes can be gained from atomic-scale modelling and this provides valuable information for the design of new ALD precursors. The information gained from the model decomposition pathway can be additionally used to understand the chemistry of molecules in the ALD process as well as in catalytic systems.

A first principles analysis of the effect of hydrogen concentration in hydrogenated amorphous silicon on the formation of strained Si-Si bonds and the optical and mobility gaps

In this paper, we use a model of hydrogenated amorphous silicon generated from molecular dynamics with density functional theory calculations to examine how the atomic geometry and the optical and mobility gaps are influenced by mild hydrogen oversaturation. The optical and mobility gaps show a volcano curve as the hydrogen content varies from undersaturation to mild oversaturation, with largest gaps obtained at the saturation hydrogen concentration. At the same time, mid-gap states associated with dangling bonds and strained Si-Si bonds disappear at saturation but reappear at mild oversaturation, which is consistent with the evolution of optical gap. The distribution of Si-Si bond distances provides the key to the change in electronic properties. In the undersaturation regime, the new electronic states in the gap arise from the presence of dangling bonds and strained Si-Si bonds, which are longer than the equilibrium Si-Si distance. Increasing hydrogen concentration up to saturation reduces the strained bonds and removes dangling bonds. In the case of mild oversaturation, the mid-gap states arise exclusively from an increase in the density of strained Si-Si bonds. Analysis of our structure shows that the extra hydrogen atoms form a bridge between neighbouring silicon atoms, thus increasing the Si-Si distance and increasing disorder in the sample.