Computer simulations can be used in parallel with experimental techniques to gain valuable insights into physical systems, test theoretical models or predict new be- haviour of molecular materials. Long time and large length scales, in combination with problems of phase space sampling, present a grand challenge for simulations of self-organising molecular materials. In the work presented in this thesis, the aim has been to develop and apply new or recent simulation models and methods to address these issues, with the aim of producing improved simulations of molecular materials. A new anisotropic model for simulating mesogenic systems has been developed, based on a soft core spherocylinder potential. This model is tested for single site systems and a multipedal liquid crystalline molecule, using conventional molecular dynamics simulations. It is used also to map out an approximate phase diagram for a main chain liquid crystalline polymer as a function of the volume fraction of the mesogenic unit; and to study the effects of a chiral medium on flexible achiral dopant molecules. Results here, show a preferential selection of conformations of similar chirality to the solvent. Later in the thesis, this new soft core spherocylinder model, is combined with a recently developed simulation methdology, Statistical Temperature Molecular Dynamics, to study the isotropic-nematic phase transition of a single site mesogen and the isotropic-lamellar phase transition of a model rod- coil diblock copolymer, using a single simulation to span the temperature window corresponding to the phase transition. Additional simulations combine a mesoscopic simulation method, Stochastic Ro- tational Dynamics, with a coarse grained surfactant model. This allows a computa- tionally efficient solvent description while maintaining correct hydrodynamics. Re- sults presented here include the formation of a bilayer, via spontaneous self-assembly of surfactant molecules, and information on the pathways of micelle formation. In the final result chapter of this thesis, Hamiltonian replica exchange simulations are performed employing soft-core replicas for a Gay-Berne system. The simulation results show an order of magnitude increase in equilibration speed of the ordered phase when compared to conventional simulations of a Gay-Berne fluid.

A range of new tertiary diallylalkylammonium (t-DAAA) based Ionic Liquids (ILs) were successfully synthesised in good yields with cation alkyl substituent lengths of 5, 6, 9, 10, 11, 12 and 14 carbons. The counter anions used were [Cl]¯, [HSO4]¯, [H2PO4]¯, [BF4]¯, [PF6]¯, [TFSI]¯ and [TFA]¯. The ILs physico- and electro-chemical properties were evaluated in order to draw structure-property relationships between them. The thermal stability of the t-DAAA ILs depended heavily on the nature of the anion. The t-DAAA [TFSI]¯ ILs were the most stable reported in this work with decomposition temperatures of over 300°C. The thermal stability of the t-DAAA ILs generally increases in the order [H2PO4]¯ < [Cl]¯ ≈ [TFA]¯ < [PF6]¯ < [HSO4]¯ ≈ [BF4]¯ < [TFSI]¯. The majority of the t-DAAA ILs were solid or very viscous at ambient temperature. However, the [TFSI]¯ and [TFA]¯ based ILs displayed some very low viscosities with the lowest of 58 cP reported for diallylhexylammonium [TFA]¯. The electrochemical windows of the less viscous t-DAAA ILs compared well with those reported in literature for protic ammonium and aprotic imidazolium ILs. The most stable t-DAAA ILs were those based on the [TFSI]¯ anion which demonstrated electrochemical windows of between 4.9 and 5.2 V. ii Acyclic diene metathesis (ADMET) polymerisation produced cyclic products rather than the desired polymeric materials. Diallylhexylammonium [BF4]¯ and [PF6]¯ gave 100% conversion to cyclic products, whilst the conversion decreased to 46 and 25% for the diallyhexylammonium [TFSI]¯ and [HSO4]¯; 4% for [TFA]¯ and [Cl]¯ and 0% for [H2PO4]¯. Ring closing metathesis (RCM) reactions were performed in order to improve on the conversions obtained in the ADMET reactions. However, only moderate conversions (74-54%) to cyclic products were obtained for the diallylhexylammonium [BF4]¯, [PF6]¯ and [HSO4]¯ ILs, while [Cl]¯, [H2PO4]¯ and [TFA]¯ did not undergo any reaction.

A review has been given of molecular orbital theory and of its application of calculations of ground and excited state properties of substituted aromatic hydrocar bons .The nitrations of ortho, meta and para-xylsnes and naphthalene have been studied, alone and in competitive reactions with benzene, using, nitric acid/acetic acid as the nitrating medium. Partial rate factors have been determined relative to benzene. Competitive nitrations have been carried out between: naphthalene and 2-flucro-6-mathylnaphthalene, naphthalene and 2-acetamido-6-methylnaphthalene, 2-methylnaphthalene and 2, 6-dimethylnaphthalene, 2-methoxy-6-methylnaphthalene and 2,6-dimethylnaphthalene. Partial rate factors have been determined relative to naphthalene. Proton magnetic resonance studies at 60, 100 and 220 Mc/s have been made of a series of 2, 6-disubstituted naphthalenes. An attempt has been made to interpret the experimental data by detailed Parlser-Parr-Pople self-consistent field molecular orbital calculations.

This thesis describes the preparation and properties of some new organonitrogen derivatives of silicon, germanium, and tin. The structural implications of their I.R., (^1)H-NMR. , and mass spectra are discussed with X-ray crystal structures in some cases. A survey of species containing tin-nitrogen bonds, and a discussion of the stereochemistry of tin are also presented. New methyleneamine derivatives of the type (R(_2)CN)(_n)Sn(^IV)C1(_4-n)(n = 2-4), (Ph(_2)CN)(_2)GeC1(_2), [(R(_2)CN)(_2)Sn(^11)](_n),(Ph(_2) CNSn(^11)c1)(_2), and Li(^t)Bu(_2)CN)(_3)Sn(^11) were prepared from the metal chlorides and N-lithioketimines. The adducts Ph(_2)CNH.Sn(^11)Cl(_2), ((^t)Bu(_2)CNH)(_n)Sn(^IV)Cl(_4) (n = 1,2), Ph(_2)CNH. (Ph(_2)CNSn(^11)Cl)(_2). C(_7)H(_8), and (^t)Bu(_2)CNH. (^t)Bu(_2)CNSn(^11)(_2)C1(_3) are described. Attempts to prepare (^t)Bu(_2)CNSn(^IV) led to (^t)BuCN and Sn(^11)Cl(_2). Similar decomposition of ((^t)Bu(_2)CN)(_n)Sn(^IV)c1(_4-n) (n = 2,3) 2,3) led to the imino-tin(II) complexes (^t)Bu(_2)CNH. (^t)Bu(_2)CNSn(_2)(^11)Cl(_3) and (^t)Bu(_2)CNH(_2)(^+). ((^t)Bu(_2)Sn(_3)(^11)C1(_5)(^-). The new M(^IV) derivatives are monomeric, except for the iminotin chlorides [(ph(_2)CN)(_n)Sn(^IV)C1(_4-n)](_m)(n = 2,3; m ≥ 2). The Sn(^11) derivatives are mostly di- or oligomeric, containing three-coordinate tin. Association appears to involve bridging methyleneamino groups. The adducts R(_2)CNH. (R(_2)CN)(_n)Sn(_2)(^11)C1(_4-n) to contain one three-coordinate and one four- coordinate tin atom. The C=N-M skeletons of those compounds containing terminal methyleneamino groups are probably bent with little or no N→M (p→d) π-bonding.

The use of CO2 as an alternative to traditional organic solvents has been an extensive area of research over the last several decades with research focusing mainly on supercritical applications. Gas eXpanded Liquids (GXLs) combine the advantages of liquid CO2 and co-solvents. Much like its supercritical counterpart, the solvent power of GXLs can be tuned by varying the liquid phase concentration as a function of pressure. Determination of solvent-solute interactions is key to the understanding of solvent properties in liquids and expanded solvents. Spectroscopic measurements of a range of binary mixtures of organic solvent with carbon dioxide have been recorded to calculate solvatochromic parameters for gas expanded liquids. Data obtained for gas expanded solvents showed a significant change in local polarity upon addition of CO2, modifying the properties of traditional organic solvents. Protic solvents were found to behave anomalously to conventional aprotic solvents. Density, relative permittivity, and CO2 solubility at 25 °C and 50 bar pressure for a range of CO2-expanded solvents are reported for the first time. The dissolution of CO2 into liquid organic solvents to generate expanded liquids has resulted in significant changes in bulk solvent properties. Collation of relative permittivity data and solvatochromism data of the expanded liquids has given an insight into the structural changes occurring in the local and bulk regions of the solvent, resulting in the occurrence of preferential solvation. Variation in these solvent properties are understood by the determination of molar free volumes which was correlated with the Hildebrand solubility parameter showing that the expansion of molecular solvents is controlled by the thermodynamics of cavity formation. A range of applications have been probed using gas expanded liquids as replacement solvents. One of the most prominent advantages of GXLs for chemical synthesis is their adjustable solvating power. Areas such as biphasic chemistry, selective reactions, solubility, and phase behaviour studies have been explored. It was found that in each application the CO2 expanded solvent had a varied ‘role’.

Unlike the familiar “ring-stain" formed when spilt coffee drops are left to dry, liquids containing high molecular weight polymer molecules leave a range of other deposit pat terns. In this thesis I observe that aqueous solutions of the polymer poly(ethylene oxide) (PEO) dries to form either the common coffee-ring stain, flat uniform “pancakes", or tall central “pillars". To investigate this phenomenon, I varied experimental factors including: atmospheric temperature, humidity and pressure; polymer molecular weight and concentration; water-ethanol solvent ratios; droplet volume, contact angle and inclination. These factors indicate a region in parameter-space in which central pillars form, favouring fast drying, low temperature, high contact angle, high concentration, high or low (but not intermediate) water-ethanol ratio, and intermediate molecular weight. I identify four stages in the pillar forming drying process, including a pseudo-dewetting liquid stage which appears to be driven by the formation of a contracting spherulite collar around the droplet's 3-phase contact line. If the liquid base radius recedes quickly enough compared with the height reducing effects of the evaporation, the growing solid deposit eventually lifts the droplet from the surface, resulting in the final central pillars. This is characterised by a minimum droplet volume when precipitation begins, above which the receding radius vanishes before the volume is lost to evaporation, resulting in tall central structures. Conversely, if the volume at the precipitation time is below this value, the height will reach zero during the pseudo-dewetting stage and the common coffee-ring stain is the result. I show that the dimensionless Péclet number Pe, which compares the relative effects of evaporation and diffusion on the polymer motion, successfully predicts the precipitation time and thus the final deposit shape. To incorporate the effect of molecular weight into our understanding, a further parameter of liquid phase resistance to the contracting collar at high viscosities is introduced.

This study has contributed to the developing understanding of fundamental principles through which interactions at peptide-inorganic interfaces occur. The inorganic materials; crystalline zinc oxide (ZnO) and platinum (Pt) together with specific binding peptides identified using the phage display technique and alanine scanning for mutant sequences selected on the basis of peptide stability calculated in silico were synthesized, extensively characterized and the mechanisms of their interaction and the effects thereof studied. Firstly ZnO growth was monitored during solution synthesis from precursors using two different ZnO methods in the absence and presence of ZnO binding peptides (ZnO-BPs); G-12 (GLHVMHKVAPPR), its mutants (G-12A6, G-12A11, G-12A12) and GT-16 (GLHVMHKVAPPR-GGGC). Secondly, adsorption characteristics and thermodynamics of interaction of ZnO with ZnO-BPs and Pt with platinum binding peptides (Pt-BPs) were studied using biophysical tools; quartz crystal microbalance with dissipation monitoring (QCM-D) and isothermal titration calorimetry (ITC). The outcomes of the ZnO synthesis studies demonstrated that peptides are smart, versatile tools possessing different mechanisms through which material formation processes and resultant morphologies can be modulated. Biphasic isotherms were observed in the adsorption of the ZnO-BPs on ZnO consisting of an endothermic and an exothermic event with ΔG values between -6 and -8.5 kcal/mol and high adsorption affinity values indicating the occurrence of favourable interactions. Among the examined ZnO-BPs, G-12 had the highest affinity for ZnO. QCM-D studies of Pt and Pt-BPs revealed that peptides TLHVSSY and SSFPQPN adsorbed strongly to the predominantly Pt (111) surface whereas TLTTLTN had a weak reversible interaction with the surface. Information from QCM-D studies was instrumental for experimental design and data interpretation of ITC experiments for the same counterparts. Differences in isothermal profiles of the Pt-BPs with Pt nanoparticles show their unique adsorption behaviours. The adsorption of peptides on inorganic surfaces is driven by kinetic and thermodynamic factors and varies depending on inherent properties of the peptide, physico-chemical properties of the inorganic surface and reaction conditions. ITC has shown great potential for use as a standard technique to monitor peptide-inorganic interactions and for possible application in peptide design.

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This thesis is concerned with the design, preparation and structural characterisation of several molecular dyads. The molecular dyads were synthesized for the study of energy/electron/charge transfer processes to advance our understanding of artificial photosynthesis. We were hoping to enhance our ability in mimicking natural photosynthesis through our discoveries. Chapter 1 introduces the field of artificial photosynthesis. The working principles and the highest efficiency dye sensitized solar cells (DSSCs) to date are highlighted. Molecular units working as photo-active switches for fabrication of light-driven molecular scale machines are emphasized. Finally, previous work on the acridinium-, naphthalimde-, viologen- and 1,1'-bi-2-naphthol-based derivatives are reviewed. Chapter 2 is the experimental section, it describes the techniques used for characterisation, and details of synthetic procedures used to obtain molecular dyads discussed in chapters 3 to 6. Chapter 3 discusses the synthesis and properties of expanded acridinium dyads, and their application as sensitizers for DSSCs. Coupling of N,N-dimethylaniline and an expanded acridinium unit afforded a purple dyad, DMA. The charge transfer property of DMA was studied by solvent polarity dependent UV-Visible absorption spectroscopy. The fluorescence of DMA was almost totally quenched by the charge transfer state. The quenching of fluorescence was also found in BODAC, which couples a bodipy unit with the expanded acridinium unit through an acetylene bridge. No long-lived species were found from a transient absorption study of DMA and a decay model was proposed to explain the relaxation process. We demonstrated for the first time that acridinium based dyads can be used as sensitizers for DSSCs by testing results of two dyads on p-and/ or n-type semiconductors. Chapter 4 demonstrates the synthesis of donor-acceptor systems based on naphthalimide and phthalimide derivatives for a solid state charge transfer fluorescence study. The fluorescence images of the dyads were obtained through confocal microscopy. UV-Vis absorption spectra also revealed their charge transfer properties. X-ray crystal structures of several compounds were obtained. The existence of two polymorphs of one dyad enabled us to compare their solid state fluorescence properties more closely. The polymorphs displayed different properties such as colours, melting points and the emission lifetimes. Chapter 5 concerns the synthesis of a disulfide-strapped methyl viologen derivative DSV, which can work as a molecular switch. The viologen derivative is capable of storing up to four electrons as revealed by reversible reduction peaks for a cyclic voltammogram. DSV is one of the easiest to reduce viologen derivatives to date. Molecular orbital calculations were used to model the “spring opening” of the disulfide-strapped six membered ring. Chapter 6 continues our further work into bridging units for donor acceptor assemblies and focuses on the synthesis of 1,1'-bi-2-naphthol based molecular dyads. The length of alkyl chain to link the diol group was varied to control the conformation of the chiral bridges. The aim was to study chirality effects on energy/electron transfer processes. Different synthetic routes were tried to achieve the target molecular dyads. Primary photophysical properties and results on attaching the dyad to fullerene are presented.