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This thesis describes a cheap, easily scalable and solvent-free method for doping semiconductors of group II-VI nanoparticles using melt reactions. Dithioimidodiphosphinate metal complexes of Pb, Cd and Zn were used as source of host metal sulfides while complexes of Mn, Zn and Fe were used as a source of metal dopants. Two doping regimes were obtained based on the appropriate range of mole fractions (0.02, 0.04, 0.06, 0.08, 0.10 and 0.12) of dopants which is wide enough to shed light on previously hidden regimes. Based on this, the choice of dopants in either the interstitial or substitutional positions is possible in the dithioimidodiphosphinate metal sulfide systems. The positions of the metal dopants (Mn2+, Zn2+ and Fe2+) on the host semiconductors (PbS, CdS and ZnS ) affect the microstructures and therefore, the optical properties of the doped semiconductors. The physical changes introduced to the unit cells of the host metal sulfides by the presence of metal dopants were studied using XRD, SEM, EDX, PL and Raman spectroscopy. The Debye-Scherrer and Williamson-Hall plots were used to study the contributions of crystal sizes and lattice strain on p-XRD peak broadenings. The p-XRD analysis showed that there was no phase change in any of the dithioimidodiphosphinate metal sulfide systems that were doped. We also show that Cu, Zn and Sn dithioimidodiphosphinate single source precursors can be used in tandem to produce the solar absorber material Cu2ZnSnS4 (CZTS), for potential use in type III cells.

The work contained in this thesis focusses on magnetic exchange interactions in lanthanide (Ln) dimetallic molecules, and the investigation of novel high-performance single-molecule magnets (SMMs). It combines a range of experimental techniques (Far-IR, SQUID magnetometry, and EPR and INS spectroscopies) to obtain a comprehensive picture of the magnetic properties of such molecular materials. Due to the complexity of describing exchange interactions between pairs of strongly spin-orbit coupled spin systems, the goal is to build a reliable experimental dataset before comparisons against model Hamiltonians. To this end, herein we study an asymmetric dimetallic molecule [hqH2][Dy2(hq)4(NO3)3]-MeOH (hqH = 8-hydroxyquinoline) and a symmetric molecule [Ln2(HMeQ)4(NO3)6] (HMeQ = 2-methyl-8-hydroxyquinoline). Describing the exchange interaction of two Kramer's Ln ions using an effective Seff = 1/2 model proved successful in reproducing the highly detailed experimental spectra for both systems. Therefore, the resultant exchange coupled spectrum is representative of the true exchange coupled system. These results, along with previous work within the group,1 build a data-base of spectroscopically verified exchange coupled Ln systems. As more molecules are studied in this way, it is hopeful that trends in magnetic interactions can be identified and synthetic targets can be designed with specific magnetic interactions in mind. This work also provides detailed data sets which can be used in the development of new theoretical models for complicated exchange-coupled molecules. Concurrently, work on new high-performance SMMs prepared at Manchester was undertaken, performing magnetic investigations of [Dy(DiMeQ)2(H2O)Cl3] (DiMeQ = 5,7-dimethyl-8-hydroxyquinoline) and several [Dy(SCS)2]- variants. These studies allowed the identification of trends in literature SMMs and revealed the importance of the Raman relaxation process in influencing SMM blocking temperatures. I present a detailed study of high performing literature SMMs, with the assignment of t_switch as a new parameter which correlates with SMM blocking behaviour.

Non-polar helices feature prominently in structural biology. Transmembrane alpha helix containing proteins make up around a third of all proteins, represent around 40% of drug targets, and contain some of the most critical proteins required for life as we know it. Yet they are fundamentally difficult to study experimentally. This is in part due to the very features that make them so biologically influential; their non-polar transmembrane helical regions. By leveraging large data-sets of transmembrane proteins, this thesis is focused on characterising features of transmembrane alpha helices en masse, particularly regarding their topology, membrane-protein interactions, and intramembrane protein interactions. In this study, we present statistical evidence demonstrating the `negative-outside` rule in opposition to the `positive-inside` rule. We also identify stabilising amino acid distributions in anchoring transmembrane helices compared to transmembrane helices with function beyond anchoring. Tail-anchored proteins are a group of post-translationally inserting proteins. In this thesis, we show adaptations of hydrophobicity and residue distributions through the transmembrane helices of tail-anchored proteins to different membrane environments within the cell (the mitochondria, endoplasmic reticulum, the Golgi, and the plasma membrane). However, we could not detect a hydrophobic difference between global populations of tail-anchored proteins in different species (mammals, plants, and fungi). A handful of these proteins are capable of integrating into the membrane without the need for membrane integration proteins. Structural modelling of transmembrane helices from PTP1b and cytochrome b5 reveals a 3D amphipathic arrangement of residues. This structural feature may play a role in their spontaneous membrane insertion. Finally, we find a conserved pattern of typically hydrophobic transmembrane helices neighbouring marginally hydrophobic helices in some families of transmembrane proteins. This feature corresponds to transmembrane helices that have the potential to cooperate in order to integrate the more polar, but functionally important, transmembrane helix of the pair into the membrane.

The production of H2 from the radiolysis of water in contact with spent nuclear fuel presents significant safety and engineering challenges. Anomalous gas production from adsorbed water radiolysis has the potential to generate flammable atmospheres in PuO2 storage containers residing in interim storage. Due to the nature of working with PuO2, a non-active analogue must be sought so the anomalous effects it has can be probed without the limitations associated with working with plutonium. The search for a metal oxide with a similar effect on radiolytic yields of H2 to PuO2 was undertaken by investigating the radiolysis of water adsorbed on or aqueous suspensions of ZnO. Samples were prepared humidity control it was found that the presence of ZnO enhances radiolytic H2 production, contrary to indications from literature. During the same experiments, O2 was observed in comparable quantities. Remarkably, O2 was also observed during the radiolysis of dry ZnO, previously unseen in similar experiments with other oxides. The 5.5 MeV He2+ ion beam radiolysis of aqueous ZnO suspensions was also undertaken and the results compared to the γ-ray radiolysis results. In conjunction with this, the development of a novel method by which the radiolysis of water can be evaluated is discussed. The vacuum line method was developed primarily to give much greater control over the amount of water introduced for a metal oxide sample surface for irradiation and aimed to reduce the sources of unquantifiable errors in the experiment. The method was then used to investigate the radiolysis of water adsorbed on ZrO2 with a particular focus on low water loading.

Deep Eutectic Solvents (DES) are a recently-discovered category of potentially more sustainable alternative solvents. They are liquid eutectics formed upon the combination of various precursors, normally organic halide salts and neutral species. The most common DES is a 1:2 mixture of choline chloride:urea. DES are beginning to be used as non-aqueous alternative solvents for a variety of processes, such as synthesis of small molecules and materials, and electrodeposition. For the successful development and implementation of DES as a drop-in green solvent, it is important to build a strong fundamental understanding of the structure and properties. This will aid in the realisation of DES as 'task-specific' solvents which can be rationally tuned to fit the application of interest. There are several fundamental issues presently impeding the progression of the field of DES. Firstly, due to their similar properties and designer nature, DES are often presented as a sub-category of ionic liquids (ILs) though the combination of ionic and molecular species will yield a more structurally complex system, with contributions from electrostatic forces as well as H-bonding. In this thesis the structure of various DES has been explored primarily using neutron diffraction and atomistic modelling studies. These works showed evidence for a disordered and extensive H-bond network in the liquid rather than extensive ion complexation, which has important consequences for the design of chemical processes using DES. Another issue impeding the progress of research is that pure DES are often very viscous which causes handling issues and often imposes a diffusion limitation upon processes. Moreover, being charge-dense liquids, they are hygroscopic and quickly absorb large quantities of water, and it is not known what structurally occurs to DES upon hydration. To reconcile this issue, we have studied the solvation of water by DES, and what happens to the interactions between DES components when hydrated, at known water contents, using neutron diffraction studies as well as study of the DES/solid interface using AFM. It was found that low-level water, such as that absorbed during preparation and handling, does not significantly perturb the DES structure but alters the intermolecular interaction strength. Up to a threshold concentration, the DES structure resists hydration and strong choline-water interactions are seen, but the system becomes an aqueous solution when the water volume fraction dominates. The same behaviour was observed at a Pt electrode interface, with unusually strong structure induced when water was added. These findings show the potential of using hydrated DES as replacement green solvents. Finally, it was attempted to apply DES and hydrated DES in the synthesis of nanostructured iron and cerium oxide and make use of the insights gained of the solvent structure. It was found that pure DES formed small nanoparticles whereas hydrated DES formed highly extended 1D morphologies which were active catalysts. Initially, neutron diffraction was used to understand the solvation of metal ions in the pure DES, which showed unusual structuring between reactive components. Later studies of the hydrated system revealed that this structure is not retained on addition of water, as DES ligands are substituted by water. Time-resolved studies using EXAFS and SANS respectively gave evidence for the solvent breakdown and structural rearrangement around metal ions, and the nanoparticle self-assembly process. Overall, this thesis is a coherent body of independent systematic investigations into the solvent structure and solvation behaviour of DES, and synthesis of nanoparticles with wide-reaching environmental applications. We have built further upon the fundamental understanding of DES and have drawn comparison between systematic structural observations and the performance of DES in relevant applications. It is hoped that these findings will help with the onward development of DES as alternative solvents for efficient and sustainable future industrial technologies, which can make the world a cleaner place.

The aim of this thesis was to develop new X-ray and neutron scattering techniques to investigate amyloid fibrils. Specifically, the development of techniques which can probe kinetic and structural information that can be difficult to obtain using current techniques. Lysozyme seeded aggregation kinetics was investigated at high concentrations and gave unexpected results for the dependence of initial elongation rate on monomer concentration. Briefly, a combined small angle and wide angle X-ray scattering technique was probed as a label-free method to follow lysozyme aggregation kinetics under shear. A novel contrast-matched small-angle neutron scattering technique was developed which gave kinetic elongation rates for the peptide NFGAIL and the protein α-synuclein of 1.9 ± 0.1 nm min-1 and 0.66 ± 0.09 nm min-1, respectively. In addition, the technique gave a new method for estimating fibril seed lengths, which were estimated to be 91 ± 20 nm and 1900 ± 600 nm, for NFGAIL and α-synuclein, respectively. Furthermore, this technique was sensitive to secondary kinetic pathways and reported no significant contribution to the kinetics from secondary pathways. Development of a neutron fibre diffraction technique utilising isotope-labelling allowed insight into the structural packing within TTR (105-115) fibrils. In conjunction with fibre diffraction simulations, this approach concluded the steric zipper packing within the TTR (105-115) fibrils to be that of steric zipper 3 (Parallel, face-to-face, up-down). These techniques provided extensive information on the structure and kinetics of amyloid fibrils. The methods can be employed under physiological conditions and may be useful in the study of the prevention and inhibition of amyloid aggregation.

The work presented in this thesis encompasses the crystallisation of multi-component crystalline systems, including co-crystals and salts, for solid form control, focusing on a transfer from batch to continuous crystallisation. The work forms part of the EPSRC funded Future Manufacturing Hub in Continuous Manufacturing and Advanced Crystallisation (CMAC). The opening chapters introduce the background to the project, including the broader context in which the project sits, with the move towards developing continuous crystallisation and manufacturing of pharmaceuticals. Accounts of the methodology used are given, including the importance of the solid-state, crystallisation methods, polymorphism and co-crystallisation and salt formation for multi-component molecular materials. Chapters 4-5 introduce the primary model system under investigation, urea barbituric acid (UBA), and document the work conducted on the system to further understand the polymorphism of the co-crystal system, achieve selective control of production of two of the UBA polymorphs, including the metastable form III (the relative thermodynamic stabilities of forms I and III are established, through competitive slurrying experiments) and the access of a novel polymorphic form. Chapter 5 discusses the use of seeding in batch cooling crystallisation to allow for control over the resultant solid form as well as demonstrating the transfer of UBA crystallisation, to yield metastable form III, from batch to continuous. Two continuous crystallisation platforms, the Continuous Oscillatory Baffled Crystalliser (COBC) and the Kinetically Regulated Automated Input Crystalliser (KRAIC) are described and their use investigated. Chapter 6 focuses on the crystallisation of two novel multi-component systems using the barbituric acid derivative thiobarbituric acid (TBA) as the target compound. These multi-component systems are shown to be salt systems, with hydrogen transfer occurring from the target molecule, TBA, to the counter-ion. Their crystallisation is shown to be transferable from evaporative to slurrying and cooling crystallisation techniques in batch. Chapter 6 also demonstrates the successful transfer of the crystallisation of these two salt systems from batch to continuous platforms, using both the COBC and KRAIC.

This thesis details the development of iron-based catalysts for the hydrophosphination of unsaturated compounds. Conditions were optimised for each process and the substrate scope was established. Experimental and spectroscopic studies were used to investigate the mechanism of the hydrophosphination of styrene. Chapter 1 gives an overview of hydrophosphination, both stoichiometric and catalytic, focusing on the reactions of iron. The value of these hydrophosphination products is discussed. Chapter 2 details the catalytic hydrophosphination to form unusual terminally substituted phosphines using both Fe(HMDS)2THF and KHMDS respectively. Chapter 3 Shows that by introduction of a simple salen ligand to an iron catalysed system gave room temperature reactivity at very low catalyst loadings. Only 0.5 mol% pre-catalyst was required for the room temperature synthesis of a variety of phosphines through hydrophosphination. Further, this work explored the use of an iron-porphyrin μ-oxo catalyst for a range of similar products. Hyrophosphination with phenylphosphine is outlined, wherein a single addition is seen to take place thermally. Chapter 4 outlines kinetic and mechanistic aspects of catalytic hydrophosphination with iron(salen)-μ-oxo. A Hammett study was conducted for a variety of functional groups on the alkene substrate concluding that there was a change in the rate determining step moving from electron withdrawing to electron donating groups. This work culminated in the publication of two papers in impactful peer reviewed journals.

Membrane proteins are proteins which are embedded in (integral membrane proteins) or interact with (peripheral membrane proteins) the plasma membrane. Membrane proteins are responsible for a wide-range of processes, including transport, signalling and enzymatic reactions. Ion channels are an important class of membrane protein which enable the passive diffusion of ions across the membrane. G-protein coupled receptors are another class of membrane protein which propagate chemical signals between the cell interior and exterior. There is substantial interest in understanding the molecular behaviour of such membrane proteins in a physiological and pharmaceutical context, in order to discern how they function and how they can be regulated when they function incorrectly. Simulation methods, such as classical molecular dynamics, are can be employed for this purpose. This thesis details the use of molecular dynamics simulations, and related simulation methods, to analyse phenomena related to membrane transport by ion channels and G-protein coupled receptors. Principally, research presented in this thesis has unveiled several novel aspects concerning the molecular behaviour of K+-channels. The size and dynamics of openings in the surface of ion channels, known as fenestrations, has been assessed in several K+-channels to delineate their potential as drug access pathways. By analyses of the archetypal K+-channel KcsA, a bacterial K+-channel, and an atypical K+ -channel, TWIK-1, from the two-pore domain K+-channel family, specific residues in the domain of the selectivity filter have been shown to be important in maintaining the structural stability of the selectivity filter and/or facilitating quintessential conduction processes. Moreover, the molecular mechanism pairing the dynamics of the KcsA selectivity filter and phospholipid molecules bound on the channel surface has been outlined. Simulation methods have also been applied to structures of other membrane proteins, which have been recently resolved at high-resolution, by either cryo-electron microscopy or X-ray crystallography. The interfacial regions between the transient receptor potential vanilloid channel 1 (TRPV1) and several protein assemblies have been predicted. Furthermore, cholesterol-phospholipid and cholesterol-protein complexes have been characterized, in order to assess the functional effect of membrane cholesterol on the activation state on the 5-HT1B and 5-HT2B G-protein coupled receptors.

The rapid increase in computational processing power and advancement of materials simulation techniques has enabled materials simulations to contribute towards the discovery and optimisation of materials for various applications. The application forming the motivation for this study is thin-film solar cells. There are two main contributions that simulations could make towards the advancement of such technologies. Firstly, to improve fundamental knowledge and understanding of materials to aid in the identification of factors limiting device performance. Such knowledge can be used to assist in the development of optimised synthesis procedures for the materials and devices. Secondly, simulations can allow for the discovery of new materials altogether that are not currently utilised for a given application, but may have relevant properties that are superior to the materials used in existing technologies. The first results chapter in this work focuses on investigating a possible origin of the underperformance of solar cells based on the earth-abundant and non-toxic candidate solar absorber material kesterite-structured {\CZTS} (CZTS). Specifically, this chapter focuses on the possible role of Cu/Zn disorder in limiting the performance of CZTS solar cells. The second results chapter identifies candidate photoactive ferroelectric ('photoferroic') solar absorbers, motivated by the possibility of enhanced photovoltaic performance from photovoltaic phenomena observed in ferroelectric materials. The final chapter seeks to provide insights for the optimisation of new solar cell technologies based on the absorber materials identified in the previous chapter and to further assess their likely performance in a solar cell. This chapter draws on insights gained from previous studies on more mature solar cell technologies. A major theme throughout this work is the role that the defect physics of the absorber material has on determining the performance of a solar cell composed of that material.

The work in this thesis considers the development and optimisation of methods with regards to the synthesis and formation of polymeric nanomaterials. A particular focus is placed on synthesising polymers based on N-2-hydroxypropyl methacrylamide (HPMA) and ε-caprolactone (PCL) with regards to drug delivery applications. Polyethylene glycol (PEG) and PEG-based materials were intentionally avoided due to the growing body of research surrounding the accelerated blood clearance phenomenon. Reversible addition-fragmentation chain transfer (RAFT) polymerisation was employed in the synthesis of linear, block and branched forms of poly(N-(2-hydroxypropyl)methacrylamide) (PHPMA). Linear PHPMA was synthesised according to established synthetic methods and found to yield well defined materials (12 - 17 kg mol-1; Ð 1.02 - 1.08). Homotelechelic PCL with terminal RAFT functionalities was employed as a macro-CTA in the synthesis of PHPMA-b-PCL-b-PHPMA triblock copolymers. After optimisation of the reaction conditions a reasonably well-defined amphiphilic polymer was obtained (Mn 29 kg mol-1; Ð 1.41) which was observed to undergo spontaneous self-assembly in water (average particle diameter 44 nm). Alternative synthetic routes utilising click methodologies (thiol-ene, hetero-Diels-Alder and copper azide-alkyne cycloaddition) were investigated but ultimately did not yield any improvements when compared to the macro-CTA grafting-from approach. Hyperbranched PHPMA was synthesised by a free-radical crosslinking copolymerisation method which utilised ethylene glycol dimethacrylate (EGDMA) as a divinyl crosslinking agent. Extensive characterisation of branching parameters was performed using a combination of triple detection size-exclusion chromatography (SEC) and 1H NMR. After optimising the reaction conditions, three hyperbranched copolymers of HPMA and acetylated-HPMA (APMA) were synthesised; surface RAFT moieties underwent additional polymerisation with HPMA to ultimately yield novel PHPMA-star-(hb-PHPMA-co¬-PAPMA) core-crosslinked amphiphilic star copolymers (Mn 139 - 243 kg mol-1, Ð 1.07 - 1.27). Additionally, charge controlled nanoprecipitation of homotelechelic carboxyl terminated PCLs in a range of alkaline pH buffered solutions was performed according to a literature procedure. The lowest diameter particles were observed to form when precipitation was performed in a pH 9 aqueous phase (14 ± 1 nm), as determined by dynamic light scattering (DLS). Overall, synthesis of PHPMA-b-PCL-b-PHPMA block copolymer at higher molecular weight and lower dispersity than previously reported materials from a homotelechelic dithiobenzoate macro-CTA was achieved. Furthermore, three novel PHPMA-star-(hb-(PHPMA-co-PAPMA)) copolymers were synthesised and the branching parameters of the hydrophobic core characterised by 1H NMR spectroscopy. Preliminary work into developing a scalable synthetic procedure for producing PCL nanoparticles was undertaken. Under optimal conditions PCL-oTHPA nanoparticles were produced with a number-average particle diameter of 14 ± 1 nm (error is ± 1 S.D.).

Skin diseases are common in the UK, especially in children where 34% suffer from such diseases at some point. Wound care and management is also a significant burden to the UK healthcare system, estimated at an annual cost of £5.3 billion. Epidermal pH gives an indication of the physiological condition of the skin and the healing progress of wounds. An effective pH-sensing dermal patch would provide non-invasive skin and wound monitoring, aiding treatment. The aim of this work was to develop a fibre-based flexible electrode to measure skin/wound pH. This will facilitate point-of-care analysis and allow appropriate care to be administrated by medical professionals. Highly conductive wet-spun poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS) fibres, a prior concept developed by Reid et al., were adopted for pH analysis. With an optimised polyaniline (PANi) coating, these fibres displayed Nernstian responses (in a solid-state sensor containing a fabricated quasi-reference electrode) across a pH range of 3.0 to 9.0 when in contact with both pH-adjusted artificial sweat matrix and human plasma; the fibres had additional desirable antibacterial and biocompatible properties. To date, wet-spun PEDOT:PSS fibres have not been adopted in a chemical sensing capacity. This invention provides opportunities for future wearable, fibre-based sensors capable of real-time, on-body pH sensing (to monitor wound healing and skin disease). However, a primary limitation was poor tensile strength (32 ± 11 MPa), which could lead to fibre breakages in real-life wearable applications. To overcome this limitation, another substrate, modified electrically conductive cotton, was explored. A simple and effective "dipping and drying" approach involving cotton yarns in a dispersion of PEDOT:PSS and multi-walled carbon nanotubes (MWCNT) resulted in the development of a flexible, highly conductive cotton fibre. Subsequent PANi deposition yielded electrodes with significant biocompatible and antibacterial properties that could be fabricated (alongside quasi-reference electrodes) into a solid-state wearable pH sensor, which achieved rapid, selective, and Nernstian responses (-61 ± 2 mV pH-1) over a wide pH range (2.0 - 12.0), even in pH-adjusted artificial sweat matrix and human plasma. To date, there is no prior published research that reports on this combination of conductive materials and cotton in such a sensing capacity. Furthermore, few previous reports have described conducting cotton threads with low enough electrical resistances to allow the electrodeposition of functional polymers, like PANi, whilst retaining the necessary flexibility for wearable applications. Thus, this development represents an important progression towards the realisation of real-time, on-body, wearable sensors.

This thesis details the development and application of mass spectrometry (MS) labelling strategies for use in structural biology, and, specifically, how they offer insight into the quaternary structure and dynamics of protein complexes. Chapter 3 first demonstrates the utility of isotopic H/D exchange (HDX) strategies for probing the in solution dynamics and assembly of two protein systems. Firstly, I use solution HDX to probe the light-induced structural change of the FAD-binding protein cryptochrome. Through quantitative analysis, I discover a region at the C-terminus undergoes a long-lived conformational change with high specificity to blue light, suggesting a potential role in the signalling cascade of circadian processes. Secondly, I use HDX-MS to probe the interface of a homo-dimeric ancestor of extant haemoglobin. Differential HDX-MS revealed protected peptide regions consistent with the alpha/beta packing interface in the modernday hetero-tetramer. Studying proteins in the gas-phase by using native MS has the distinct advantage of high resolution separations, manipulations and accurate mass determination, afforded by the exquisite control possible in vacuum. Chapters 4, 5 and 6 describe the implementation of performing gas-phase HDX (gpHDX) inside the spectrometer and how the technique may be used to interrogate protein ion structure with high specificity. I first demonstrate how gpHDX can be used to probe native proteins and show high sensitivity to the surface chemistry of exposed residues. Secondly, I use gpHDX to aid our understanding of how protein complexes asymmetrically dissociate through collisional activation and charge precipitated unfolding. Importantly, I show that the deuterium uptake of a dissociated subunit can be used as a proxy for the intact precursor. Finally I use gpHDX coupled to ion mobility (IM) to reveal how the conformational landscape of an activated protein changes at a global and local level.

Photoacoustic spectroscopy (PAS) and Cavity-Enhanced Raman Spectroscopy (CERS) can detect headspace gases above a microbiological culture in a closed system. PAS and CERS have a detection limit of few ppm per volume. These techniques were used to investigate the aerobic respiration of Escherichia coli (E. coli). Both techniques are able to monitor O2 and CO2 and its isotopomers with excellent sensitivity and time resolution to characterise bacterial growth and metabolism. CO2 can be detected using CERS and a differential Helmholtz Resonator (DHR) because it has Raman and IR active vibrations. However, homonuclear diatomic molecules, such as O2, have only symmetric stretching vibrations that are Raman active but not IR active. In PAS, O2 can be detected by exciting a formally forbidden electronic absorption band in the red, the b 1Σg+ (ν = 0) ← X 3Σg- (ν = 0) band (the "A band") near 760 nm. Identification of different growth phases and changes in the aerobic metabolic activity of E. coli was possible by taking simultaneous measurements of O2 consumption and CO2 production using CERS and DHR in PAS, including optical density (OD) measurements. We demonstrate how 13C isotopic labelling of sugars combined with spectroscopic detection allows the study of bacterial mixed sugar metabolism, to establish whether sugars are sequentially or simultaneously metabolised. For E. coli, we have characterised the shift from glucose to lactose metabolism without a classic diauxic lag phase. DHR and CERS are shown to be cost-effective and highly selective analytical tools in the biosciences and in biotechnology, complementing and superseding existing, conventional techniques. They also provide new capabilities for mechanistic investigations in biochemistry and show a great deal of promise for use in stable isotope bioassays. Finally, PAS in a differential Helmholtz resonator has been employed with near-IR detection of CO2 and H2S in natural gas, in static and flow cell measurements. The set-up has also been used for simultaneous in situ monitoring of O2, CO2 and H2S in the cysteine metabolism of microbes (E.coli), and for the analysis of CO2 and H2S impurities in natural gas.

Antimicrobial resistance represents an ever-increasing threat to world health. A drive for novel, narrower-range antimicrobials is necessary and new bacterial structural targets are being considered. Bacterial flagella are extracellular protein structures commonly found in liquid-borne bacteria. They are used for motility, aid colonisation, and play an essential role in bacterial pathogenesis. It has been found that some bacteria glycosylate their flagella as an important mechanism in flagella assembly. Pseudaminic acid (Pse) is a sialic-acid family nonulosonic sugar, unique to microbes, which decorates the flagella of pathogenic bacteria such as Campylobacter jejuni, Helicobacter pylori and Aeromonas caviae (the focus of this work). The 6-step bacterial biosynthetic pathway for Pse has previously been elucidated with the pseudaminic acid synthase enzyme (PseI) playing a key role. It is hypothesised that inhibiting PseI will disrupt bacterial flagella glycosylation and affect bacterial motility and colonisation without affecting the host and therefore provide a potential new method of antimicrobial therapy. In this project, two potential PseI inhibitors have been designed based on the literature precedent for the inhibition of analogous ulosonic acid synthase enzymes. After the assessment of parallel chemical models, an efficient method of accessing one of the proposed inhibitors was determined and demonstrated on a model phenylpropanal-derived compound. Furthermore, the synthetic route uses a key step aldol reaction, the product of which is a common intermediate that can be used to furnish both inhibitors via a proposed divergent synthesis. Expression and purification of the enzymes used in the A. caviae pseudaminic acid biosynthesis was carried out in order to test inhibition. LCMS reactions confirmed the activity of the expressed enzymes and provided a simple inhibition assay. This was used to test a set of compounds derived from a different potential PseI inhibitor from the literature. Work is ongoing towards the first acquisition of a crystal structure of the PseI enzyme to better characterise its active site.

Recently, bioengineered scaffold molecules have become an area of intense interest. The use of small, robust, monomeric proteins has become a viable alternative to much more complex and expensive antibodies. The protein scaffolds used by the Staniland group, and developed throughout this body of work, include: the coiled coil and a magnetite interacting Adhiron scaffold. Active loop sequences have been displayed on these protein scaffolds and the constructs have been shown to control the nucleation and growth of magnetic nanoparticle crystallization. The range of proteins introduced within this thesis produced a 'toolbox' to promote the synthesis of nanoparticles with favourable crystal morphologies. The structural limit to conformational changes keep the displayed region in the most active conformation. This thesis shows for the first time, how the protein scaffolds are utilised as attachment devices (for the attachment of dyes, antibodies and drug molecules) - making these proteins possible alternatives to antibody-drug conjugate systems and providing the basis for new diagnostic and therapeutic strategies. Magnetotactic bacteria have become a model organism for iron biomineralisation since their discovery in the 1970's. A host of specialised proteins are involved in the production and regulation of the magnetosomes, and are responsible for synthesising high quality, uniform, magnetic nanoparticles under ambient conditions. Several key proteins have been identified from these bacteria and here have been shown to display activity in synthetic magnetite precipitation reactions, improving both the homogeneity and morphology of the crystals. However, these proteins are membrane spanning proteins meaning they have been difficult to produce and characterise. This research has identified regions and residues of importance for biomineralisation, by studying the hydrophilic loops that link the transmembrane helices. The use of both free peptides and constrained stem loop coiled coil scaffolds have been investigated. The active regions have been subjected to mutagenesis studies, for the purpose of identifying essential regions to maintain activity. This approach has generated novel biomimetic reagents for precision nanoparticle synthesis, as well as improving the inherent solubility issues of the full membrane protein. These artificial biomineralisation proteins exist as soluble, monomeric, antiparallel, coiled coil proteins, displaying active peptide regions as a hairpin loop. The coiled coil scaffold overcomes inherent solubility issues associated with membrane-spanning proteins, whilst retaining the activity of the wild-type species. Therefore, this study has developed an artificial membrane protein that expresses well, is versatile and retains activity regarding in vitro biomineralisation reactions.

Pyrrolidinone moieties with a tertiary stereogenic centre at the C-5 position are prevalent in a number of natural products and pharmaceuticals. A method to access these compounds in good enantioselectivity from N-benzyl maleimide has been established. By adapting literature methodology, the Diels-Alder reaction between N-benzyl maleimide and anthrone could be catalysed by quinidine, giving the desired cycloadduct in good yield and selectivity (85% and 85% ee, respectively). Base stability tests proved the cycloadduct to be stable under mildly basic conditions, allowing synthesis to progress without the need to protect the bridgehead hydroxyl group. Grignard addition to the cycloadduct furnished four hydroxy lactam derivatives in moderate yields (24-35%) with complete regioselectivity, confirmed by nOe studies. The Grignard reagent added selectively to the carbonyl distal to the bridgehead hydroxyl group. This is thought to be preferred due to hydrogen bonding between the proximal carbonyl oxygen and the proton on the bridgehead hydroxyl group. Surprisingly, all four derivatives were synthesised as a mixture of diastereoisomers, determined by 1H NMR spectroscopic analysis of the crude products. The hydroxy lactam derivatives were then reduced to the corresponding lactams using BF3.OEt2 and Et3SiH, in varying yields (29-91%). All four lactam derivatives were furnished as a single diastereoisomer, the identity of which was confirmed by analysis of the relevant coupling constants. The benefit of using anthrone was its potential to promote a room temperature oxide-anion accelerated retro-Diels-Alder. Using potassium hydride to catalyse the cycloreversion did not furnish the desired product and attempts to optimise the base catalysed reaction failed. Equally a thermal retro-Diels-Alder reaction of the functionalised cycloadduct was unsuccessful.

This thesis describes the activity of a range of oxime-Zn2+ complexes as catalysts in solution and in bilayer membranes to develop greater insights into the parameters that will allow the development of more effective transducers in artificial signal transduction systems. This is followed by studies where a membrane-embedded thiol is used to try and activate an inhibited enzyme to exploit the greater efficiency of biological catalysts. Chapter one describes key terms in the bilayer membrane field and describes the research that have been achieved in making supramolecular systems that can transfer information across a bilayer membrane. Chapter two presents the design and the investigation of Zn2+ complexes of small ligands containing oxime moieties. The ability of the complexes to catalyse the hydrolysis of two different ester substrates in solution under physiological conditions has been studied using UV-Visible spectroscopy. The stability of the complexes, the dependence of the activity on both ligand and Zn2+ ion concentration was determined. The findings showed the underlying characteristics of these complexes to allow comparison with the activity of analogues that can be used as part of a membrane signalling. Chapter three focuses on using the ligands which were designed and studied in chapter two as headgroups that were attached to cholesterol and lithocholic acid as a lipophilic moiety. These compounds allowed the investigation of the effect of varying the linker between the hydrophilic and lipophilic moieties, and of the effect of the membrane interface, on the characteristics of the complexes. Moreover, the system used in this chapter is compared to the previously reported membrane transducers. In this chapter, we sought to control the reactivity of this metallovesicullar system and enhance the catalytic efficiency of the reaction. Chapter four aims to see if a molecule containing a thiol group that is anchored in a lipid bilayer membrane (in the form of a vesicle) could be utilised to activate an inhibited enzyme in the aqueous phase and whether the enzyme was capable of amplifying a signal once activated. The second aim was to study whether this would provide a system with the ability to be completely inactive in an 'off' state so that it could be used in a membrane translocation system for signal transduction. The final aim was to see if a transducer molecule with a polar headgroup could be made, which could hold the enzyme-activating moiety held inside the vesicle membrane until a primary signal was inputted. Chapter five presents the experimental procedures which used to obtain the synthetic compounds with the yield and characterisation data (NMR, Mass Spectra, IR and HPLC traces).

Cancer is a major disease, affecting people globally. Breast cancer specifically, is one of the primary types of cancer affecting women between the ages of 50 and 70. Many treatments have been developed for this disease, but for certain types of tumour, current treatments are failing. Therefore, there is an urgent need for new treatments. An example of a new type of treatment is the use of magnetic nanoparticles. These particles are nanoscale crystals of iron oxide such as magnetite. They can be magnetically driven to specific targets in vivo using a magnetic field external to the body. Drug molecules can be attached to them for magnetic drug delivery at lower doses. The particles can generate heat when an alternating magnetic field is present. This is known as magnetic hyperthermia, and it is capable of killing tumour cells. The particles can also be used in MRIs for cancer diagnosis. For these applications, the particles must have a narrow size distribution, high purity, be biocompatible and stable, and have specific magnetic properties. Achieving all of these requirements is difficult using synthetic methods. However, magnetotactic bacteria use biomineralisation to produce precise size and shape particles of magnetite, which are known as magnetosomes. This study aimed to test and enhance the leading magnetosomes for cancer treatment. Magnetosomes were synthesized with varying concentrations of Mn2+, Co2+ and Cu2+ in order to optimise their magnetic properties for magnetic hyperthermia in cancer cell lines, where Co-doped magnetosomes displayed the highest coercivity (420 Oe) compared to native magnetosomes (125 Oe). This cobalt doping produced the highest apoptotic cell death in vitro (26.4%) and following the in vivo, testing confirmed that the presence of special magnetosomes with Co-doped magnetosomes within a tumour caused cell death around the sites of magnetosome localisation, compared to areas where there are no magnetosomes. In addition, for their MRI response, Mn doping enhances the T2 relaxation with increasing concentration of manganese, whereas in native magnetosomes, the Mn doping showed the highest saturation magnetisation of Ms 112 emug-1 and the highest value of relaxivity 434 mM-1S-1, which indicates the high degree of sensitivity in MRI. Furthermore functionalising the magnetosome surface with streptavidin has confirmed cell uptake by fluorescence microscopy and flow cytometry for some future applications with bioactive substances. The cell uptake was highest at 0.18 mg/ml concentration with low toxicity, as evidenced by the flow cytometry, MTT, and Endotoxin assays. The outcome of this work is optimised concentrations of magnetosomes for cell uptake and cytotoxicity. The magnetic properties of magnetosomes have been enhanced through Co2+ and Mn2+ doping, and cell uptake has been investigated using TEM and fluorescence microscopy of functionalised magnetosomes. The more promising magnetosomes for magnetic hyperthermia have been tested in tumours in mice.

The lack of reversibility in traditional adhesives has led to the development of a range of switchable adhesives. However, most switchable adhesives cannot be applied to a substrate, and must be created on the surface using stringent laboratory conditions. In this thesis, a new type of pH switchable adhesive which could be applied directly to a surface was developed and tested for adhesive strength. This material was compared to the 'grafted-from' pH switchable adhesives in the literature, and found to have a similar adhesive strength. A series of synthetic transformations were used to mono-functionalise a calix[4]resorcinarene, which can modify surfaces, with either poly(2-(dimethylamino)ethyl methacrylate) or poly(methacrylic acid) using atom transfer radical polymerisation. This new material was then deposited onto hydrophobic silicon wafers using Langmuir-Schaefer deposition to give densely grafted monolayers of adhesive. Adhesion studies using hydrogels of oppositely charged polyelectrolytes showed that the measured adhesion was due to adhesive failure at the gel-monolayer interface, rather than the monolayer-wafer interface. This deposited material was shown to have a similar adhesive strength to material grafted from the surface, demonstrating that the calixarenes are sufficiently anchoring the polyelectrolytes to the substrate. When the calixarene brush layer was replaced with a polyelectrolyte multilayer deposited by layer-by-layer deposition for comparison, it could be concluded that the strength of the calix[4]resorcinarene binding compensates for any reduction in surface coverage in this system. Variation of the load applied showed that there is a dependency on the observed adhesion due to the onset of plastic deformation of the hydrogel. Overall, these experiments provide a first step towards creating a reversible adhesive that would be practicable in commercial applications. Although further work needs to be done to improve the quality of this adhesion, this thesis demonstrates that a one-pot route to reversible and repeatable adhesion is viable.

This work aims to understand the formation routes of a variety of interstellar molecules. The formation of molecules in the interstellar medium (ISM) is a key process to understanding the chemical diversity of the universe as well as the origins of biological life on Earth. Some of the molecules (methyl formate and glycolaldehyde) under study have been identified in the ISM via telescopic detec- tion. Other molecules investigated have been proposed to be present in the ISM as a result of terrestrial laboratory studies on simulated ISM ices (urea, ribose and benzoic diacids). Quantum chemical calculations were used to follow the re- action pathways of these molecules and test their feasibility under astrochemical conditions. It was found that the presence of hydrogen bonding ices around the reaction species greatly affects the energetics of the reactions and increases their likelihood to occur in the ISM. Additionally, water ice was found to have a large im- pact on the dissociation of methanol into radical species allowing for much more facile subsequent reactions than previously thought. Water ice was also found to affect the ease of ionisation of polycyclic aromatic hydrocarbon (PAH) species which have been proposed as a constituent of ISM dust grains.

Pseudaminic acid is a carbohydrate glycoside which is found on post-translationally glycosylated bacterial flagella. Disturbance of the biosynthetic pathway for this sugar nullifies the pathogenicity of the bacteria A. caviae, H. pylori & C. jejuni. In order to explore this possibility, attempts were made to develop a novel synthetic route. Parallel to efforts to synthesis the side chain of pseudaminic acid, L-allo-threonine, N-chiral imines derived from cheap and readily available (2S)-ethyl lactate were prepared and subjected to Lewis acid-mediated trimethylsilylcyanide additions as part of new methodology for robust and facile asymmetric Strecker reactions. 2,3-anti¬-β-Hydroxy-α-aminonitriles were prepared in excellent yield (77%, 4 steps) and good diastereoselectivity (90 : 10). L-allo-threonine was accessed and further functionalised to Garner-like cyclic aldehydes which were used as substrates for a doubly diastereoselective nitroaldol reaction to construct the carbon chain of pseudaminic acid. These reactions proceeded with mild selectivity and conversion. Models for the addition to both Garner aldehydes and N-chiral imines were discussed in detail.

In this work, I develop theories, and their implementations, for the high-accuracy study of large molecular systems. Intermolecular inter- actions are fundamental in nature, in particular in materials chemistry and biological systems. They are difficult to study theoretically due to the small energy differences and vast numbers of molecules involved. Present high-accuracy methods can typically only deal with at most a few molecules in a single calculation, limiting applications to the gas phase. Using absolutely localised molecular orbitals (ALMOs), I develop a new correlated method for intermolecular interactions that is linear scaling in the number of molecules, with accuracy sim- ilar to coupled-cluster with single and double excitations (CCSD). I give details of an implementation that minimises the memory imprint and processor time, as well as allowing for extensive parallelisation. Results over benchmark databases of non-covalent interactions show consistent agreement within 0.5 kcal/mol of the CCSD result, with timings two orders of magnitude smaller. Subsequently, I derive an- alytical derivatives for the total energy, allowing for rapid geometry optimisations on large scale systems. Again, geometrical parameters and vibrational frequencies are shown to agree well with CCSD results. Finally, I extend the ALMO approach to multi-configurational systems, and in particular excited states, demonstrating how it can then be used as an embedding-type method, where different subsys- tems are treated to different levels of accuracy. This culminates in the reproduction and elucidation of experimentally observed shifts in the photoelectron spectrum of phenol when in water, compared to the gas phase. The methods developed herein thus allow for the high- accuracy treatment of much larger condensed-matter systems than has previously been possible.

Strong demand for clean, renewable sources of energy has led researchers to examine every area for alternative renewable resources. Solar energy is the only renewable source that has the potential to satisfy the world's large and increasing energy demand. The Earth receives enough solar irradiation in one hour to fulfil the world's energy needs for one year. Commercially available solar cells based on inorganic materials dominate photovoltaic (PV) technologies. However, these have drawbacks such as high production costs and environmental concerns. Therefore, organic photovoltaic cells (OPVs) have shown promising potential as they show advantages over their inorganic counterparts. These include: high absorption coefficients; better operation at lower light-intensity levels; flexible substrates; and low-cost production. Bulk heterojunction (BHJ) architecture has been frequently applied to fabricate the active layer in polymer-based solar devices. Previous studies have shown that BHJ solar cells fabricated from polymers that consist of an electron-rich donor unit and an electron-deficient acceptor monomer in an alternate donor-acceptor (D-A) arrangement result in a higher power conversion efficiency (PCE). Therefore, designing conjugated polymers that consist of alternating donor-acceptor units is a promising strategy to produce high-efficiency BHJ solar cells.

Microporous organic polymers are typically insoluble materials possessing high surface areas alongside a chemically and thermally stable low density framework. As such they have been intensively studies over the past two decades towards applications in removal of pollutants from water, gas capture and storage, catalysis and more. Part B demonstrates the design and application of functionalised microporous materials applied towards sustainable applications. A sulfonated microporous polymer, synthesised using metal-free synthesis conditions is reported and applied towards the removal of heavy metals from aqueous solution. The material, SHCP-1, has a BET surface area in excess of 800 m2/g and is capable of removing over 95 mg/g of Sr and 273 mg/g of Cs in the presence of large amounts of other competing ions. In other work, a series of monomers are hypercrosslinked to yield microporous materials containing different chemical moieties and applied towards the capture of CO2 using a pressure-swing methodology. Initially the CO2 uptake of each network was measured at high pressure (20 bar) before a pressure-swing approach was applied to separate industrially relevant mixes of CO2 and N2. Networks based on carbazole, triphenylmethanol and triphenylamine were capable of converting a dilute CO2 stream (> 20 %) into a concentrated stream (> 85 %) after only two pressure swing cycles from 20 bar (adsorption) to 1 bar (desorption). Though microporous materials can be applied towards a diverse range of applications they are not without their drawbacks. The main disadvantage of most microporous polymers is their insolubility in all common organic solvents which limits their processability and scalability. Part A of this thesis discusses work carried out on the design, synthesis and characterisation of a new class of microporous and solution-processable polymer. These materials are synthesised through the controlled radical polymerisation of a bifunctional crosslinking monomer alongside a second co-monomer. A Reversible Addition Fragmentation Transfer Polymerisation Induced Self-Assembly (RAFT-PISA) approach was applied to yield polymer nanoparticles comprised of a porous insoluble core dispersed in solution by long hydrophilic polymer chains (Figure A1.1). This allows for the design of porous colloidal suspensions that can be applied towards applications in solution. This synthesis is reported for the first time using the monomers divinylbenzene and fumaronitrile. Fine-tuning of the reaction resulted in the synthesis of microporous materials with surface areas ranging from 270 - 409 m2/g that were capable of forming stable dispersions in various solvents. As a result of their fluorescent properties they are able to act as selective chemosensors towards nitroaromatic compounds in solution. A fluorescent quenching effect is observed when the electron-rich porous core interacts with the electron-deficient nitroaromatic compounds with a limit of detection of 170 ppb being observed. The versatile nature of this synthetic approach is demonstrated by swapping the fumaronitrile monomer for acrylic acid which still results in the formation of a porous material. The resulting material can be post-synthetically modified through exploiting the carboxylic acid moieties within the core to yield anthracene-incorporated porous materials. These porous polymers demonstrate blue fluorescence emission under UV irradiation in the visible region of light. This fluorescence alongside the porosity of the material can be exploited and used to encapsulate other fluorophores which when irradiated by UV-light give rise to a white-light emitting solution.

This Thesis describes the polymerization of methyl methacrylate (MMA) in the presence or absence of 1,1-diphenylethylene (DPE) in surfactant-free emulsion polymerization (SFEP), with subsequent polymerizations of either styrene (St) or benzyl methacrylate (BzMA) in the presence of the latex formed. The effect of varying amphiphilicity of several RAFT agents in reversible addition-fragmentation chain-transfer (RAFT) SFEP was also investigated. Firstly, the precursor polymer is synthesised by SFEP of methyl methacrylate in the presence of varying concentrations of DPE. The molecular weight and (dispersity) Ð of the resulting PMMA can be reduced by increasing the DPE concentration in the polymerization, with varying initiator concentration having little effect. Increasing the DPE content also reduced the rate of polymerization. Mass spectroscopy (MS) indicated the presence of only 1 DPE unit per polymer chain, contrary to other emulsion polymerization studies, with diffusion-ordered nuclear magnetic resonance (DOSY NMR) spectroscopy showing the presence of free DPE and DPE bound to the polymer chains. Utilizing DPE in SFEP yielded a bimodal particle distribution as judged by transmission electron microscopy (TEM), with a secondary particle distribution forming over the first hour of the polymerization. Secondly, St and BzMA are polymerized in the presence of PMMA latex synthesised in the presence or absence of DPE. The rate of polymerization of each of these two monomers is increased by the presence of DPE in the precursor, indicating that the precursor is a source of radicals by either thermal cleavage of the polymer chains or the uncapping of the polymer by DPE. Only very low BzMA conversion is achieved when the precursor did not contain DPE. Polymerizations of St contained a considerable amount of precursor after the attempted extension, whereas the polymerization of BzMA contained very little precursor, as judged by SEC. PSDs analysed by TEM show an increase in particle diameter, broadening of the size distribution, and the formation of a secondary particle size distribution during the polymerization of St or BzMA. Finally, the polymerization of methyl methacrylate is conducted in the presence of several RAFT agents. Solution polymerizations confirmed that these RAFT agents enabled good control over the molecular weight and Ð, but their success in SFEP depended on the amphiphilicity of the RAFT agent. For two RAFT agents, this could be altered by changing the pH, with the anionic or cationic derivatives giving considerably better control. Size exclusion chromatography (SEC), incorporating a UV detector at λ = 260 nm, showed the presence of the amphiphilic RAFT agents throughout the MWD and the absence of RAFT end-groups when using hydrophobic RAFT agents. However, control over molecular weight and Ð is achieved at the cost of reduced control over the particle size distribution (PSD) of the latex. Overall, the information given in this Thesis brings us closer to the controlled SFEP synthesis of diblock copolymers. With the DPE method being used to form diblock copolymers of PMMA-b-PBzMA, despite the hydrophobicity of DPE. While the success of the use of RAFT agents to form precursor polymers for later extension is dependent on the amphiphilicity of the RAFT agent. These methods can be used in the SFEP synthesis of diblock copolymers for coatings where the use of diblock copolymers helps to prevent polymer phase separation and the presence of a surfactant can have negative effects on the quality of the final product.

This research described in this thesis examined two main macromolecules as ligands for protein binding, namely dendrimers and graphene oxide. The architecture of these materials was exploited and functionalised with amino acid to moderate protein binding and recognition. The first area studied involved dendrimers that had been functionalised using non-covalent methods. Specifically, the amino acid was added to the end of a hydrophobic linear chain that could bind to the interior of the dendrimer using hydrophobic and hydrogen bonding interactions. A number of different linear chains were synthesised and added to various dendrimers to give a surface functionalised system. The dendrimers included an anionic dendrimer that was functionalised with linear chains in order to provide secondary interactions that could bind to the positively charged surface of α-chymotrypsin (Chy). Neutral dendrimers that could not bind to the positive surface were also studied. In this case, binding could only occur if the dendrimers were functionalised with the linear chains. The results showed that the highest affinity occurred for the G3.5COOH-Tyr, with the inhibition constant (Ki) of 0.17 µM, which compares to the Ki for non-functionalised dendrimer of 0.31 µM . When the non-binding dendrimer (G3.5-OH) was functionalised with different amino acids (tyrosine, phenylalanine and valine), the G3.5-OH-Tyr was found to bind the most strongly via polyvalent interactions between the amino acids and the surface of the Chy. All the inhibitors studied were found to be competitive inhibitors, with the exception of the valine functionalised dendrimer, which did not bind. Circular Dichroism (CD) spectroscopy confirmed that denaturation of the protein did not occur during dendrimer binding. The next area of study focused on cytochrome- c. The same non-covalent methodology used for α-chymotrypsin binding was utilised for this area. Binding could be measured directly using encapsulated Tetrahydroxyphenyl Porphyrin (THPP) as an internal quench. To coordinate THPP to the dendrimer, this was strengthened by inserting zinc, which could coordinate the dendrimer's internal amines. The results showed that the G3.5COOH-Tyr was bound with a dissociation constant (Kd) of 5.55 nm. CD spectroscopy showed that the dendrimer-porphyrin-chains did not cause denaturation of the protein during binding. The final area focused on the use of functionalised graphene oxide (GO). This material was synthesised with amino acids to form a monomeric and an oligomeric functionalised surface of GO. The effects of functionalisation on the binding of GO to Chy was also studied. The binding of the functionalised GO was compared with the binding of the unfunctionalised GO and the results showed an inhibition constant (Ki) of 0.14 µg/mL for the monotyrosine, which was higher than either the oligomeric system or GO alone. In all cases, competitive inhibition was observed. CD spectroscopy confirmed that GO does not induce structural changes within the protein when bound and the spectroscopy also demonstrated that the GO inhibitors had no effect on the thermal stability of the enzyme.

In recent years, the use of polymers in modern society has become ubiquitous. With ever increasing applications, polymer science has had to adapt and evolve to meet a wide range of complex requirements. It was less than 100 years ago when Staudinger first proposed that polymers were long-chain molecules made up of covalently-bound building blocks or repeat units called monomers. When this revolutionary and controversial concept was finally established in 1929, Carothers proposed that there were two categories of synthetic polymers: 'addition' polymers and 'condensation' polymers. While the repeat unit of an 'addition' polymer is identical to that of the monomer being polymerised, 'condensation' polymers are typically formed via elimination of a small molecule such as water, with one such side-product being eliminated for every repeat unit linkage. This initial classification system worked well for the majority of polymers but over time it became apparent that there were some obvious exceptions, such as polyurethanes. In 1953, this system was updated by Flory, who proposed that polymers should be classified as either 'step' or 'chain' depending on their reaction mechanisms. Step-growth polymers involve the gradual build-up of long-chain polymers via dimers, trimers, oligomers etc., whereas the formation of chain-growth polymers proceeds by sequential addition of a single (monomer) unit. The latter mechanism is used for the polymerisation of vinyl monomers, as discussed in this thesis.

In this thesis, the effect of copolymer composition, molecular weight, and monomer hydrophobicity on the self-assembly of anionic amphiphilic statistical copolymers in aqueous solutions was investigated using structural characterisation techniques such as small angle X-ray scattering (SAXS) and transmission electron microscopy (TEM). It was found that they preferably form spherical particles. The size of the particles formed by the aggregation of amphiphilic statistical copolymers is heavily dependent on the copolymer composition but is largely independent of molecular weight, where particles with larger ratios of the hydrophilic monomer produced smaller particles. Particle size was only found to be dependent of molecular weight when unimolecular micelles (single chain nanoparticles) were formed. Additionally, the hydrophobicity (logP) of the hydrophobic comonomer has a great influence on particle size, where increasing the hydrophobicity increases the copolymer particle size. The relationship between copolymer composition and particle size was rationalised in terms of particle surface charge density, where the copolymers aggregate together to induce a critical surface charge density that allows colloidal stability to be achieved. The critical surface charge density was quantified as the fraction of the particle surface covered by the charged monomer (SAfrac.MAA), leading to the development of the particle surface charge density (PSC) model. It was found that the PSC model fit well to the experimental data collected for all the copolymer series and a SAfrac.MAA was calculated for each series where the hydrophobic monomer was varied. Furthermore, a linear relationship between the logP of the hydrophobic component and the SAfrac.MAA required to induce stabilisation of the particle dispersion was observed. Additionally, the effect of hydrophile-hydrophobe distribution along polymer backbones has been examined. It was found that there was a clear correlation between the monomer distribution and the particle size, where blockier structures, in comparison with evenly distributed monomers, produce larger copolymer particles. This result was rationalised as a reduction in the efficiency by which the charged hydrophile, when in a blocky arrangement, can stabilise the hydrophobic component leading to an increase in particle size. Finally, a range of amphiphilic triblock copolymers were synthesised, where the DPs of the individual hard and soft blocks were varied. The amphiphilic triblocks were found to assemble into spherical particles in water but remained dissolved in methyl ethyl ketone (MEK). Films were cast of the triblock copolymers from both solvent environments, and the structural phase separation in the films was studied using a combination of SAXS and AFM. It was found that the copolymer films cast from MEK were able to phase separate into well-defined structures, where the size and morphology of the phase separation was dependent on the block length and hard-to-soft block ratio, respectively. These morphologies were consistent with the predicted self-assembly of diblock copolymers in the bulk. Conversely, the water-cast films partially retained the particulate structure present in solution, produced kinetically trapped phase separated structures. However, by annealing the water-cast film at 150 °C the lower energy phase-separated structure observed in the MEK films can be achieved.

Nicolò Ferri: Interference effects in molecular nanojunctions From the earliest theoretical investigation of the possibility of single molecule conductance, to today where single molecule conductance techniques are becoming routine operations, the field of molecular electronics has grown exponentially, becoming an important research topic with possible future applications. Understanding electron transport in nanojunctions has lately been a hot topic and represents a fundamental step for the advancement of molecular electronics. This thesis aims at unravelling some of the mysteries and mechanisms that revolve around the behaviour of some molecular wires. This thesis focusses its attention towards interference effects in organic molecular wires: in this thesis two main types of interferences are studied: one located on the contacts of a series of molecular wires and one regarding the structure-property relationships within molecular wires. The novelty of this work lies in the synthesis of new molecular wires and their conductance studies with STM-based techniques. The first project demonstrated the existence of strong interactions between thiol contacts and gold electrodes (so-called 'gateway states') that were interfering with the conductance decay of a series of double barrier tunnelling molecular wires of increasing length by suppressing the attenuation of their conductance over their length. A simple experiment supported by theoretical calculations featuring the synthesis of molecular wires with thiols replaced by thioether contacts demonstrated the existence of these interactions by cancelling their effects. The second project was focussed on the study of interference effects in thiophene-based molecular wires. Several series of molecular wires were synthesized in multiple subprojects to gain a better understanding of these effects by finely tuning the molecular wires structures such as the introduction of heteroatom bridges and the insertion of carbonyl moieties as cross conjugation points within the backbone of a molecular wire. On this project some unusual switching properties of some of the wires were discovered and investigated. Finally, this study managed to shed some light on the behaviour of all the bithiophene-based molecular wires analysed and the information discovered will be useful in the tool-box for finely tuning properties of molecular wires.

Photodynamic medicine has been known for more than 5000 years when Egyptians, Chinese and Indians used sunlight in combination with some "magic" plants to treat various disorders. Contemporary photodynamic therapy began in the 1900s, received its revival in 1970 due to hematoporphyrin derivative (HpD), and it is now an FDA approved therapeutic option for skin, early lung, and advanced oesophagal cancer in several countries. Although a few photosensitisers have been approved for clinical use, they suffer from several drawbacks such as biological and light instability and lack specificity toward specific types of cells. In this thesis work, we propose plasmonic gold nanoparticles as photosensitisers to overcome the drawbacks of first- and second-generation photosensitiser and investigate their 1O2 photogeneration efficiency upon CW-laser irradiation at their surface plasmon resonance. First, the singlet oxygen sensitivity of two molecular probes (ABDA and DPBF) in different solvent systems was determined, using Rose Bengal as a photosensitiser. Second, we showed conclusively, for the first time, that gold nanoparticles photogenerate 1O2, and that the quantum yield is extremely small. Lastly, gold nanoparticles were functionalized with bovine serum albumin, and their singlet oxygen quantum yield re-evaluated. Our irradiation results showed that the protein corona, i.e. bovine serum albumin, did not affect the 1O2 production.

The Chemicals Weapons Convention, effective since 1997, has helped to reduce the proliferation of chemical warfare agents (CWAs). However, despite 193 states being bound by this agreement, there are countries who continue to produce, stockpile and use CWAs. Incidents involving CWAs, whether in conflict, terrorism or assassination such as the attempted assassination which occurred in Salisbury, UK, in 2018 highlight the continuing need to control the production, stockpiling and use of CWAs. Decontamination of CWA stockpiles is therefore of significant interest. One potential way to achieve this is by using porous materials as sorbents in order to allow for the bulk uptake and deactivation of CWA stockpiles. In this work, the use of hypercrosslinked polymers (HCPs), which represent a class of such sorbents, that are produced using a facile and tuneable 'knitting' procedure are explored for this application. The performance of the HCPs for the uptake of CWAs are investigated using simulants due to the lethal toxicity of the CWAs, prior to testing of the best performing polymers against CWAs including sarin (GB) and sulfur mustard (HD) (Figure 1). Routes to allow for the chemical decontamination of CWAs are then investigated by screening a range of nitrogen containing bases against a nerve agent simulant, methyl paraoxon (MP) and CWAs, GB and VX. This led to the development of hydroxide containing polymers derived from a range of porous organic polymers (POPs), including hypercrosslinked polymers (HCPs), conjugated microporous polymers (CMPs), and porous aromatic frameworks (PAFs), and conventional hydroxide resins. Finally, methods to combine physical and chemical decontamination of CWAs are explored using HCPs and hydroxide containing polymers, respectively, to create effective absorbents to immobilise and breakdown CWA stockpiles, under practically relevant conditions.

Chronic conditions are on the rise due to an ageing and increasing global population. Medication adherence to treat chronic conditions is low, with good adherence on average ≤ 50% across a wide range of chronic conditions. Poor adherence is estimated to cost between $100 and $300 billion of avoidable health care costs annually in the US alone. One was to tackle this issue is the use of implants, which provide sustained release of drug over a long time period, removing the reliance on daily oral medication. In situ forming implants are particularly of interest as they can be injected through a standard gauge needle, reducing pain and discomfort for the patient. They are injected as a liquid and then solidify at the injection site. Three different solidification methods were explored to allow a dispersion of poly(N isopropylacrylamide) nanogels to act as an in situ forming implant for drug delivery. Two of these solidification methods were based on the modification of existing methods and utilised the modification of the nanogel behaviour with the incorporation of comonomers of acrylic acid and allylamine. The stabiliser polyvinylpyrrolidone (PVP) was included in the synthesis of these nanogels to attempt to aid nanogel dispersion and formulation with a drug payload. A third novel method of solidification was found to work successfully and so was developed and investigated further. This was based on the aggregation of poly(N-isopropylacrylamide) nanogels to rapidly form a drug depot at an injection site in response to both physiological temperature and ionic strength, giving a new in situ forming implant. Nanogels without surfactant, with sodium dodecyl sulphate (SDS), and with PVP were synthesised to determine if this would effect the suitability of the nanogels to undergo triggered aggregation under the correct conditions. The system was found to be easy to inject, and could be used to deliver hydrophobic drug or hydrophobic drug formulated into solid drug nanoparticles. Unlike the majority of in situ forming implants, a low burst release of drug payload was achievable, < 3.4 wt%, and sustained release was possible for over 120 days. The rate of release could also be tuned by altering the ratio of two different nanogels used to create the depot formulation which has not previously been demonstrated. One of these nanogels contained the comonomer allylamine alongside the monomer N-isopropylacrylamide. This gave a depot with a higher water content and more porosity. Release was also shown to occur through Fickian diffusion. The nanogels were also found not to exhibit any cytotoxicity. Nanogels of different sizes were also synthesised, and it was found that these exhibited different phase behaviour and rheological properties. The rate of drug release from the depot could also be tuned by the size of the nanogel used, which has not previously been demonstrated. Finally nanogels were synthesised with the degradable cross-linking agent N,N'-bis(acryloyl)cystamine (BAC). This allows a depot to degrade into polymeric fragments once it has served its purpose. Alongside BAC, the comonomer N-isopropylmethacrylamide (NIPMAM) was utilised to reduce non-degradable cross linking formation. The NIPAM and NIPMAM monomers were used to create core-shell nanogels. The ratio of each monomer used gave nanogels with a tuneable aggregation temperature. The nanogels were shown to be fully degradable into polymeric fragments beyond the lower detection limit of dynamic light scattering when the count rate of the nanogel dispersion was monitored using DLS. The degradation rate was also very sensitive to temperature, with degradation shown to take place at a much slower rate as temperature increased from 25 °C up to 40 °C, where the nanogels are deswollen and more hydrophobic in nature. This could potentially allow a depot to degrade slowly over a period of months, allowing it to provide a sustained release of drug over this time period, whilst also being fully degradable into polymeric fragments when subjected to an average body temperature of 37 °C.

Molecular electronics holds great promise to realize the ultimate miniaturization of electronic devices and the investigation of charge transport properties through molecules tethered between pairs of electrode contacts is one of the most active areas of contemporary molecular electronics. To date, metallic materials have been widely used as the electrodes to construct molecular junctions, where desired characteristics are outstanding stability, conductivity, and fabricability. However, there is an increasing realization that new single molecule electrical junction functionality can be achieved through the use of non-metallic electrodes. Fundamental studies suggest that carbon based materials have the potential to be valuable alternative electrode materials for molecular electronics in the next generation of nanostructured devices. In light of the discussion above, we symmetrically investigate the possibility of constructing non-metallic molecular junctions and the corresponding charge transport properties through such junctions by replacing the common gold electrodes with graphene electrodes. We have measured the electrical conductance of a molecular junction based on alkanedithiol/alkanediamine chains sandwiched between a gold and a graphene electrode and compared the effects of anchoring groups in graphene based junctions. We also studied the technical effects of molecule-electrode contacts by comparing methods for capturing and measuring the electrical properties of single molecules in gold−graphene contact gaps. The decay obtained by STM based I(s) and CP-AFM BJ techniques, which is much lower than the one obtained for symmetric gold junctions, is related to the weak coupling at the molecule−graphene interface and the electronic structure of graphene. This asymmetric coupling induces higher conductance for alkanediamine chains than that in the same hybrid metal−graphene molecular junction using thiol anchoring groups. Moreover, we introduce an efficient data sorting algorithm and demonstrate its capacity on real experimental data sets. As a consequence, we suggest that novel 2D materials could sever as promising electrodes to construct nonsymmetric junctions and the use of appropriate anchoring groups/techniques may lead to a much lower decay constant and more conductive molecular junctions at longer lengths.