The work presented in this thesis details the structural and chemical flexibility of water layers on a selection of plane and templated metallic surfaces. The water layers are found to adapt their structure to achieve a compromise between optimising its surface and intermolecular interactions differently in each system investigated. This compromise often results in water layers which do not stay in strict registry with the substrate, instead forming complex structures. Modifying the substrate by introducing a secondary metal affects the adsorption of water, the structure and species formed, indicating the sensitivity of water to the exact geometric and electronic structure of the substrate. Initially focussing on plane (non-templated) surfaces, we find an intact water layer on Pd(111), with a (root3 x root3)R30 LEED pattern but a disordered helium atom scattering signal. Using a combination of techniques we propose that the water layer comprises of regions of flat lying water, tightly bound atop Pd(111), separated by anti-phase domain boundaries. Water in the domain boundaries forms from H-bonded rings of water, oriented mostly H-down, interacting weakly with the surface. The disorder in the layer is likely to be in the H-down network and hampers attempts to achieve a complete picture of the detailed water structure. On Ni(110), a preliminary STM study into the structure and dissociation of water reveals that water forms a mixture of diffuse and more rigidly held hexagonal structures at low temperature. We assign the diffuse structures to chains of intact water which are labile under the influence of the tip, with the more rigidly held structures being a mixture of OH/H2O. The proportion of dissociated water increases with dose temperature, and is associated with loss of the labile structure associated with intact water by 200 K. Further study is required in order to establish if water adsorbs intact to Ni(110) at temperatures below 100 K. Creating a Pt skin alloy on a Ni(111) substrate allows us to investigate how a change in the Pt environment perturbs water adsorption. Water dissociates spontaneously on this surface, in a marked departure from its behaviour on the pure Ni or Pt surfaces. Pre-dosing the Pt/Ni(111) surface with oxygen has a negligible effect on the water desorption behaviour, confirming that the mixed OH/H2O phase is less stable on the Pt/Ni(111) surface than on Pt(111). We suggest that the reduced stability of OH(ads) groups on the Pt/Ni surface leads to the improved oxygen reduction reaction efficiency reported for this alloy, making OH less likely to act as a poison, as it is believed to on Pt(111). Based on our understanding of the optimum water adsorption site, we created a r3 Sn/Pt(111) alloy, designed to stabilise a traditional "ice-like" bilayer water structure. The water layer was investigated using HAS, LEED-IV and DFT modelling, which confirm that the water structure is indeed a simple commensurate root3 bilayer. Based on LEED-IV measurements we report the first quantitative structural study of monolayer water adsorbed at a metal surface and compare this to DFT predictions. Maintaining the (root3 x root3)R30 symmetry and altering the host metal from Pt to root3 Sn/M (M = Rh, Cu and Ni) resulted in no stable wetting structures. Alloying Sn with these metals appears to reduce the ability of Sn to accept electron density from the O of water, reducing the water-Sn interaction and leading to water forming clusters.

An extensive amount of literature can be found containing experimental and theoretical studies of water adsorption on metal surfaces, yet an understanding of the water – metal interface remains far from complete. The binding energy of the water – metal interface determines whether water wets a metal surface to form a complete hydrogen bonded network, forms 3-dimensional ice clusters on a non-wetting surface or dissociates to form hydroxyl, hydrogen and sometimes oxygen on the surface. All of these structures are seen depending on the growth conditions and reactivity of the metal surface. In this thesis it is shown that submonolayer water adsorbs intact on Pd(111) to form a structure with (√3×√3)R30° periodicity. As the first layer saturates the spots in the √3 position split due to the formation of dense domain boundaries. Although the first layer of water covers the Pd surface, subsequent layer-by-layer growth does not occur. Instead, an extended superstructure forms by attaching 3D clusters of ice and areas of bare monolayer remain exposed. The formation of an ordered oxygen network results in detection of an intense LEED pattern, even at a coverage of 80 layers. As the first layer of water compresses, it stabilises the growth of the larger superstructure. Further investigation shows the hydrogen network formed during multilayer growth is weakly bonded and helium atom scattering shows that there is disorder on a local scale. Co-adsorption of oxygen alters the structure and stability of water overlayers and on Pd(111) a stable mixed (OH + H2O) layer forms with (√3×√3)R30° periodicity but is unreactive towards hydrogen, therefore the low temperature reaction between hydrogen and oxygen cannot be catalysed.

Chapter 1 begins with a general introduction to the main aspects of this work: Firstly, a species of electrogenic bacteria, Geobacter sulfurreducens is introduced. Their ability to take part in extracellular electron transfer, the mechanisms by which this happens, and their involvement in electricity generation and bioremediation when applied in microbial fuel cells is discussed; Secondly, microbial fuel cells (MFCs) as an alternative method of electricity generation to fossil fuels, their methods of operation and their potential for use in the treatment of wastewater is briefly reviewed; Finally, antimalarial drugs (including their semi-synthetic and synthetic analogues) and their mechanisms of action are presented. The possibility of exploiting them as a template for bi-functional molecular wires that are capable of tethering bacteria to carbon and/or gold electrode surfaces is discussed in detail. Chapter 2 outlines our efforts towards novel analogues of synthetic antimalarials, dispiro-1,2,4-trioxolanes, for use as bi-functional molecular wires. These are shown to be capable of immobilising heme on carbon and gold surfaces via appropriate functional groups. Chapter 3 discusses our efforts towards novel analogues of synthetic antimalarials, dispiro-1,2,4,5-tetraoxanes for use as bi-functional molecular wires. The syntheses of many novel precursors; namely functionalised adamantanone derivatives and their corresponding tetraoxanes are presented. Synthetic routes towards bi-functional tetraoxane molecular wires have been extensively optimised and the incorporation of functional groups that are compatible with carbon/gold surfaces has been attempted. Chapter 4 briefly introduces the design and synthesis of β-turn mimetics and the synthesis of chiral enamine N-oxides. Chapter 5 details the experimental procedures.

The methanolic atom transfer radical polymerisation (ATRP) of 2-hydroxypropyl methacrylate (HPMA) to controllably form the hydrophobic polymer p(HPMA) using a one-pot methodology at ambient temperature has been demonstrated, where polymerisations were shown to reach >99 % conversion. By simple variation of initiator:monomer feed ratio, polymers of varying chain length were synthesised. Using identical polymerisation conditions, addition of a small amount of ethylene glycol dimethacrylate (EGDMA) divinyl brancher resulted in the generation of high molecular weight branched copolymers without any modification of reaction kinetics. This approach was extended to include the first synthesis of linear and branched amphiphilic A-B block copolymers using polyethylene oxide (PEG) macroinitiators without loss of the ATRP controlled polymerisation. A series of systematically varying copolymers, containing variation in PEG length and/or variation in p(HPMA) primary chain length, have been synthesised to allow direct comparison of the impact of architectural variation on polymer properties. Nanopreciptation approaches were investigated for the linear and branched copolymers and extremely stable hydrophobic nanoparticles were produced using copolymers with branched architecture. Moreover, it has been shown that nanoparticle z-average diameter can be controlled using extremely facile methods. The loading capacity of amphiphilic branched A-B block copolymer nanoparticles with various guest-molecules has been systematically investigated. The world leading HIV/AIDS antiretroviral drug Lopinavir (LPV) was used in a preliminary loading screen and shown to produce candidate LPV/drug nanocarrier options for future studies and optimisation.

This study aimed to prepare, characterise and test the performance of heterogeneous catalysts in the conversion of biomass-derived molecules including deoxygenation of propionic acid in the gas phase and the Prins condensation of β-pinene with paraformaldehyde in the liquid phase. The surface area and porosity of catalysts were characterised by BET, water content and thermal stability by TGA, crystallinity by XRD and composition by ICP. The acidity of oxide catalysts was characterised using NH3 adsorption calorimetry and FTIR of adsorbed pyridine. High purity amorphous silicas and crystalline silicalite (MFI structure) were found to be active catalysts of the deoxygenation of propionic acid. Silicalite was prepared by the hydrothermal method. Silica and silicalite were treated with aqueous acidic (HCl) and basic (NH3+NH4NO3 (aq) or NH3 (aq)) solutions in a Teflon-lined autoclave. The reaction was carried out in a fixed-bed continuous flow reactor in the gas phase at 400-500 °C. A preliminary blank reaction showed a small contribution of homogeneous catalysis at 500 °C, with 12% of propionic acid converted to form 3-pentanone. The chemical treatment did not affect silica activity; it showed only 85% selectivity with 39% conversion at 500 °C. HZSM-S zeolite (Si/Al = 180) possessing strong acid sites showed low catalytic activity at 400-500 °C and the main product was ethane. Silicalite had higher activity and selectivity of 3-pentanone than silica. Acidic treatment had little effect on catalyst activity, whereas basic treated silicalite was the most active catalyst in the deoxygenation of propionic acid at 500 °C, because silanol nests formed on the silicalite surface, acting as catalytically active sites for the reaction. Catalyst activity increased with increasing reaction temperature from 400-500 °C. Silicalite performance was stable for at least 28 h time on stream at 500 °C, with 84-92% of 3 pentanone selectivity at 93-80% conversion of acid. Bulk Zn(II)-Cr(III) mixed oxides with a Zn/Cr atomic ratio of 1:1 – 20:1 were found to be active catalysts for the gas-phase ketonisation of carboxylic acids (acetic and propionic) to form acetone and 3-pentanone, respectively, at 300 – 400 oC and ambient pressure. Zn-Cr (10:1) oxide showed the best performance, significantly exceeding that of the parent oxides ZnO and Cr2O3. The catalytic activity was further enhanced by supporting Zn-Cr (10:1) oxide on TiO2 and γ-Al2O3. With 20%Zn-Cr/Al2O3, ketonisation of propionic acid occurred with 97% selectivity to 3-pentanone at 99% conversion at 380 oC, without catalyst deactivation observed during at least 24 h time on stream. Zn-Cr oxides were characterised by BET, XRD, DRIFTS of pyridine and acetic acid adsorption and microcalorimetry of ammonia adsorption. From DRIFTS, carboxylic acid adsorbed dissociatively on Zn-Cr oxide to form a surface metal carboxylate in bidentate bridging bonding mode. A mechanism for ketonisation of carboxylic acids via -ketoacid intermediate route was proposed. Metal oxides such as Nb2O5, Cr2O3, and especially a Zn(II)-Cr(III) mixed oxide were demonstrated to be highly active and recyclable heterogeneous catalysts for Prins condensation, which provides a clean, high-yielding route for the synthesis of nopol through the condensation of biorenewable β-pinene with paraformaldehyde. Zn-Cr mixed oxide with an optimum Zn/Cr atomic ratio of 1:6 gave 100% nopol selectivity at 97% β-pinene conversion, with the catalyst easily recovered and recycled. The acid properties of Nb2O5 and Zn-Cr mixed oxide were characterized by the diffuse reflectance IR Fourier transform spectroscopy of adsorbed pyridine and ammonia adsorption microcalorimetry. An appropriate combination of acid– base properties of Zn-Cr mixed oxide is believed to be responsible for its efficiency.

Microporous organic polymers (MOPs) are materials made from organic monomers that have a pore width smaller than 2 nm. Due to their high porosity and diversity of functional group, MOPs have potential in broad ranges of applications. As well as absolute surface area, the functional groups also play an important role in the design and synthesis of materials for desired utilisations. In this work, we demonstrate strategies to synthesise functionalised networks to be utilised as sorbents. The focus is on hypercross-linked polymers (HCPs) and conjugated microporous polymers (CMPs), which are amorphous networks and subclasses of MOPs. Different strategies including copolymerisation, post-cross-linking of functionalised linear polymer chains, and post-synthetic modification (PSM) were found able to incorporate different functional groups into the networks. The structures and properties of the networks could be fine tuned. The networks were investigated for applications in CO2 capture and separations as well as molecular imprinting polymers (MIPs).

The dynamics of protein folding has become a major area of research interest today, particularly in biophysical chemistry. The first steps of protein folding have been reported to occur on the 100-ns time scale, made possible by with the development of several experimental techniques. For this research, laser induced temperature jumps coupled to infrared spectroscopy were used for observing the fast folding dynamics of a small protein and a peptide on the nanosecond time scale by probing changes in the amide I band, which is sensitive to secondary structure. This research project also describes the development and demonstration of a new photochemical triggering technique for protein folding. Peptide and poly-ethylene glycol-capped gold nanoparticles were tested and used as heat transducers for inducing temperature jumps in protein and peptide samples. The results demonstrate that, for the typical concentration used in our temperature jump measurements, the nanoparticles do not affect the helix-coil transition of proteins and peptides. We also describe a new method for subtracting the pressure relief artifact observed after a ns-temperature jump. Application of this method allows us to identify a hidden phase on the nanosecond time scale in the temperature jump induced dynamics of a small protein. The effect of pD and temperature on the fast folding dynamics of a small protein (BBL) was studied. The results show, for the first time, that the protein exhibits three distinct phases; two nanosecond phases and a microsecond phase. However, we found that the nanosecond components are not easily distinguished due to similarities in the time constants. Finally, this research project also describes the development of a new photo-triggering method which is based on a photocleavage reaction that generates the desired functional group from an inactive caged one upon photolysis, namely the photocleavage reaction of a peptide that is covalently bonded to 4,5-dimethoxy-2-nitrobenzyl. Our experimental results show, that cleavage of the backbone peptide is very fast, so that the photo-triggering technique is valid for observing the fast dynamics of peptides and proteins on the nanosecond/microsecond timescale.

Diastereoselective Synthesis of syn-1,3-Polyols The stereoselective construction of polyacetate 1,3-diols has attracted considerable attention due to the ubiquity of this motif in complex biologically active polyene macrolides (amphotericin B, RK-397, mycoticin, candidin). We have developed a highly stereoselective bismuth(III)-mediated two-component hemiacetal/oxa-conjugate addition reaction, which directly provides syn-1,3-diols in the form of cyclic acetals having an adjacent electron-withdrawing group in the form of aldehydes and ketones. The scope and limitations of this transformation were examined and culminated with the synthesis of the C18-C28 fragment of antibiotic RK-397. Studies towards the C1-C31 and C32-C52 Fragments of Amphidinol 3 Temporary-tethered reactions provide an important strategy for target- directed synthesis, since they circumvent the problems encountered with entropically unfavorable reactions. The temporary silicon-tethered ring-closing metathesis (TST- RCM) allows for the highly (Z)-selective coupling of mixed silaketals in the formation of the medium sized rings. The latter compounds can undergo a substrate controlled stereoselective electrophilic functionalisation, for example, hydroboration, dihydroxylation or epoxidation, and produce polyoxygenated motifs that are present in many biologically important natural products. In the course of these studies we have developed a highly convergent asymmetric synthesis of the C1-C31 polyol fragment of amphidinol 3, where the TST-RCM/hydroboration reaction is successfully employed for the efficient coupling ii of the C16-C23 and C24-C30 units of the natural product with concomitant introduction of the crucial propionate-type C23-C24 stereocentres. In the final part of thesis the investigation of the stereoselective dihydroxylation reaction of mixed syn and anti eight-membered cyclic silaketals was carried out. The resulting oxygenated products can be efficiently transformed via an intramolecular cyclisation of δ-hydroxy epoxides into the highly substituted syn- and anti-tetrahydropyrans (THPs), a strategy that could also have application in related natural products, for example, ladder polyether polyketides. The merit of the developed methodology was highlighted in the asymmetric synthesis of the common C31(52)-C39(44) THP fragment of amphidinol 3, which could be ultimately used in the bidirectional route towards the bis-THP segment of the natural product.

The local structure investigation by Reverse Monte Carlo modeling and comparison to average crystallographic structure of Bi-based perovskite materials are presented in this thesis. This novel technique using neutron total scattering is applied in search of possible short-range correlations between atoms to understand complex structure of these materials. Chapter One gives an introduction into perovskite structure and its properties. Chapter Two describes the difference between periodic and aperiodic crystals, which average crystallographic structure has been adopted by materials presented in this thesis. It also describes the total scattering and Pair Distribution Functions used in Reverse Monte Carlo modeling. The next chapters describe the local and average structure investigated during this thesis. Chapter Three describes the local and average perovskite structure of BiTi3/8Fe1/4Mg3/8O3 at various temperatures, where local structure analysis revealed particular displacements and correlations of A site and B site cations not captured by average crystallographic structure. Chapter Four compares local structure derived from RMC modeling and average incommensurate and commensurate crystallographic structures of Bi2Mn4/3Ni2/3O6 at room and high temperatures respectively, demonstrating importance of recognizing the length-scale of the probe used for structural characterization. Chapter Five describes the work on BiFe0.6Mn0.4O3 perovskite which was investigated by traditional crystallography to determine the modulated behavior and distorted structure of this material. The last Chapter 6 contains main conclusions from all experimental chapters.

In this thesis a range of phenomena related to molecular adsorption on silicon surfaces is investigated. The majority of the studies are performed in response to experimental results, where, using newly developed methods within the framework of density functional theory, we aim to elucidate some of the underlying physics as well as test the performance of the chosen methodology. The studies cover a range of subjects such as molecularly mediated pinning of surface geometry, single molecular adsorptions, molecule migration via exited states and finally an analysis of coverage dependent adsorption phenomena, where interactions between molecules are mediated by the surface or enacted via dipole interactions. The main molecules of our simulations were water, ethylene, acetylene, and benzene, as well as halogenated hydrocarbons. We studied processes at two different surfaces, the Si(111)-7 x 7 surface, and the Si(100)-c(4 x 2) surface. Finally we simulated and characterized one type of grain boundary observed experimentally for a set of photovoltaic absorbers (CuInSe_{2}) and kesterite and stannite(Cu_{2}ZnSnSe_{4} or Cu_{2}ZnSnS_{4}) in order to resolve the open question of how these grain boundaries influence efficiencies of the photovoltaic device.