Triplet-triplet annihilation (TTA) upconversion is a process in which lower energy light can be converted into higher energy light. The primary use of this emerging technology is to increase the efficiency of solar cells via increased light harvesting which may be otherwise impossible by any other means. TTA upconversion typically uses two distinct molecules to achieve this: a "sensitizer" (for absorbing the lower energy light), and an "emitter" (to produce the higher energy light). Until recently, only small molecule were used as emitters. In this work, the first true measurements of TTA upconversion were performed with conjugated polymer emitters. In doing so, 16 new conjugated polymers were developed to study the role of steric hindrance and the electronic environment on the TTA upconversion efficiency. This study then provides insight into the key design criteria required for efficient TTA upconversion using conjugated polymer emitters.

Electrically conductive, magnetically ordered, and electrochemically active materials are important components for data processing technologies, energy conversion and storage devices, and sensors and optoelectronics. The synthesis of compounds with these properties is therefore an important scientific endeavour to meet the progressively more demanding sustainability and performance targets. Crystalline coordination polymers have recently been proposed as candidate materials to achieve these aims. Coordination polymers can exhibit synergy between electrical conductivity, magnetic ordering and electroactivity, coupled with porosity, flexibility, and tuneable architecture and functionality, not achievable using traditional inorganic materials. This thesis describes studies into anionic tetraoxolene coordination polymers constructed using ligands derived from 3,6-disubtitued-2,5-dihydroxy-1,4-benzoquinones (H2Xan, X = F, Cl, Br; anilic acids), and redox-active viologen countercations. Despite the desirable properties of tetraoxolene coordination polymers previously described in literature, the impact that viologen countercations have upon the structure and properties of tetraoxolene coordination polymers has never been explored. Chapter 2 first presents structural studies on a range of Mn(II) and Cd(II) coordination polymers synthesised using diamagnetic fluoranilate (Fan2-) and chloranilate (Clan2-) ligands and redox-active N,N'-dimethyl-4,4'-bipyridinium (MeV2+) countercations. The structural disparity observed between Fan2- and Clan2- compounds demonstrates the inherent sensitivity of reactions to supramolecular interactions between cations, metals, ligands, and solvents. It also highlights the structural unpredictability associated with the use of viologen cations, compared to redox-inactive alkylammonium countercations. Structural studies on mixed-valence Fe(III)-tetraoxolene coordination polymers containing viologen countercations are subsequently presented, showing resultant anionic tetraoxolene network topology remains difficult to predict. However localisation of the tetraoxolene radical trianion (Xan3-) state is consistently observed, caused by charge-transfer (CT) and Coulombic interactions between the pi-electron deficient viologen cations, and the pi-electron rich anionic networks. This reveals the potential for viologens to modulate the charge-state distribution in mixed-valence tetraoxolene coordination polymers. In Chapter 3, 5,6-dihydropyrazino[1,2,3,4-lmn][1,10]-phenanthrolinediium (PhenQ2+) countercations are incorporated into an isostructural family of mixed-valence 2D Fe(III)-tetraoxolene frameworks (PhenQ)[Fe2(Xan)3] (X = F, Cl, Br). As for the mixed-valence networks obtained in Chapter 2, CT interactions between PhenQ2+ cations and the anionic [Fe2(Xan)3]2- networks cause localisation of the Xan3- state and partial ligand charge-ordering. Spectroscopic studies on (PhenQ)[Fe2(Xan)3].yDMF showed the network-cation interactions impact upon the electronic structure of the material. The inclusion of PhenQ2+ gives rise to additional framework redox states and modifies the conductive and magnetic properties of the material, compared to tetraoxolene frameworks with only redox-inactive countercations. Chapter 4 investigates a family of mixed-valence Fe-fluoranilate frameworks containing MeV2+ countercations, (MeV)[Fe2(Fan)3].solvent (solvent = MeCN, DMF). X-ray diffraction studies reveal the compounds undergo a range of slight structural distortions upon changing the guest solvent. Remarkably, these guest-induced structure distortions cause partial switching of the Fe valence state, never before observed in Fe-tetraoxolene coordination polymers. The guest-induced Fe valence fluctuation in turn modifies the electronic spectra and structure of the frameworks, with resultant switching of the transport properties. In Chapter 5, the mixed-valence Fe-tetraoxolene framework (MeV)[Fe2(Clan)3] undergoes a surprising structural transformation upon lattice solvent loss, causing the isolated compound to exhibit a previously unobserved cation-network packing arrangement. This dramatic structure transformation results in changes to the electronic spectrum of the compound, as well as the electrochemical response and transport properties of the material, compared to topologically similar Fe-tetraoxolene frameworks containing redox-inactive cations. These results demonstrate the impact of structure packing and supramolecular interactions on the network electronic structure. This provides encouragement that the physicochemical properties of the compounds may be tailored by controlling these supramolecular interactions. Finally, Chapter 6 presents a summary of the results obtained in this thesis, highlights the overarching themes of this research, and puts forth possible future research directions for the field.

Process improvement and product improvement in the dairy processing industry is an ongoing dynamic process. Ultrasound processing technology for food processing is in its developmental stages, and dairy sector is a key area for potential applications. The use of low frequency and high frequency ultrasound to modify functional properties of dairy streams is being widely studied by seeking to modify the protein and lipid components of milk. The effects of ultrasound on size of lipid globules and lipid oxidation volatiles have been studied. The effects on functional properties of milk proteins such as viscosity, gelation, heat stability etc. have been documented. However, the present literature lacks information on the effects that ultrasound processing may have on the fundamental properties of dairy proteins. Therefore, it is of importance to document the effects of ultrasound processing on the molecular, structural and nutritional aspects of dairy proteins. As such, the effects of ultrasound processing on dairy proteins have been studied in the context of the amino acid composition, amyloid modifications, and bioactive peptides released. This work aims to bridge the gap in existing literature attempting to illuminate upon these fundamental aspects. Chapter 1 in this thesis introduces the premise of this research by discussing the fundamental properties ultrasound technology and presents dairy proteins as the central theme of this research. A systematic review of literature in Chapter 2 attempts to build familiarity with the effects of processing on milk proteins; and discusses the potential applications of ultrasound in the dairy industry – noting the studies done on whey are caseins. This chapter also discusses the research areas which could be addressed to answer questions related to the objectives of current PhD work. To encourage the application of ultrasound for dairy processing, it would be of significance to understand the extent of operating parameters that ensure nutritional integrity and food safety. The amino acid integrity of skim milk proteins after sonication along with the potential of ultrasound to modify secondary structural conformations of milk proteins has been demonstrated in Chapter 4. Chapter 5 expands the objectives of Chapter 4 into whole milk systems, taking into account milk lipids and the potential for oxidation of lipids on sonication. In Chapter 5 an effort has been made to better understand the underlying cause of lipid oxidation observed due to ultrasound processing of milk lipids. The observations from this study suggest that the enhanced mass transfer of oxygen due to ultrasonic shear forces makes oxygen non-limiting in lipid phase and increases auto-oxidation reactions. An assessment of amino acid integrity of full cream milk after ultrasound treatment confirmed oxidative stability of milk proteins. These findings complement the data in Chapter 4. Along with amino acid integrity, Chapter 4 also demonstrates that the secondary structural conformations of milk proteins can be modified by ultrasound. The work in Chapter 6 builds up greater understanding on such changes by studying the effects of low frequency ultrasound on isolated beta-lactoglobulin (b-lg). b-lg is a b-sheet rich protein with amyloidogenic potential. The effects of high shear and high temperature microenvironments produced by ultrasonic waves were studied on b-lg aggregation. Ultrasound induced formation of amyloid crystals in dilute b-lg solutions at neutral pH and ambient bulk temperatures. The theoretical reasoning for the aggregation phenomenon substantially adds to the understanding of protein energy landscape. Chapter 7 focusses on nutritional properties of milk proteins. It examines the effect of ultrasound pre-treatment on the release of BCM-7 bioactive peptide from milk by simulated gastro-intestinal digestion (SGID), and the effect on overall protein digestibility. It demonstrates that ultrasound processing could be used to downregulate the release of undesirable BCM-7 bioactive peptide in milk, by affecting the rate of enzymatic hydrolysis of certain intermediate peptide fragments. The findings from this body of work add to the existing knowledge for improved use of ultrasound to ensure nutritional integrity of dairy proteins and lipids, minimising oxidative damage. It also builds on current understanding of ultrasound induced protein restructuring and its potential for modification of peptide release from dairy proteins.

The study of molecular nanomagnets is important not only for fundamental scientific reasons, but also for applications in the miniaturisation of technology - the prospect of storing data on individual nanomagnets is particularly exciting. By removing unwanted interactions between dipole moments on neighbouring nanomagnets, non-dipolar toroidal moments may allow for even denser data storage. Motivated by this potential application (and by scientific curiosity for as-yet unknown benefits of toroidal moments), my thesis covers a range of topics related to the modelling of nanomagnets capable of producing toroidal magnetic states. Firstly, I provide the context for my research by introducing the fields of single-molecule magnetism, toroidal moments and molecular spintronics. Secondly, I analyse the toroidal states arising from spin-frustration in a triangular nanomagnet of three spin-1/2 centres with C3 symmetry. One breakthrough of this study, is that by including antisymmetric exchange interactions arising from weak spin-orbit coupling, non-dipolar toroidal states can be prepared in a ground-energy doublet, separated from an excited doublet of non-toroidal dipolar states. I then discuss a hypothetical experiment where the nanomagnet is placed in a tunnelling spintronics device to split the steady-state, non-equilibrium populations of toroidal states. I describe the optimal energetic regimes and device geometries to achieve the best population splitting, and show how the splitting could be monitored by measuring the extent to which a spin current's polarisation is reversed by the toroidal states. Thirdly, I extend the investigation to a spin-frustrated triangular nanomagnet with C2v symmetry, such that two sites have general spin S and the third site has spin S3 = 1/2. The resulting toroidal states are intriguing for their complete lack of reliance on spin-orbit coupling, which is typically required to produce toroidal moments in isolated molecules. Again, I characterise the nanomagnet’s spin textures and performance in a tunnelling spintronics device, describing the optimal energetic regimes. Additionally, I explore the effects of changing S and delve deeper into the mechanism by which the toroidal states’ populations are split. Fourthly, I build on a previous study by Soncini, Langley, Murray, Rajaraman and co-workers (Nat. Commun. 2017) to analyse a family of double-triangle complexes of the type {Dy3M(III)Dy3}X, where M = Cr, Mn, Fe, Co, Al and X = NO3, Cl. Based on crystallographic data and ab initio calculations, I use parameter-free models to calculate the complexes' energy spectra, powder magnetisations and direct-current magnetic susceptibilities. Confirming predicted trends and discovering new trends in the complexes' ferrotoroidic/antiferrotoroidic coupling, I describe the first toroido-structural correlations ever to be reported. I then simulate the dynamical magnetisation of these complexes, and by analysing their Zeeman spectra and various relaxation mechanisms, I suggest how to improve their magnetic hysteresis. Much work still needs to be done to explore the fundamental properties of nanomagnets with toroidal ground states, particularly after these discoveries of toroido-structural correlations, and non-dipolar toroidal moments in ground-energy manifolds of triangles with zero/weak spin-orbit coupling. Thus, I outline the next steps towards implementing toroidal moments in nanotechnology, and end this thesis with a summary of the progress made.

The three-dimensional structure of proteins and receptor binding sites requires small molecule drug candidates with complex molecular shapes, to enable greater receptor specificity and potency. A logical strategy to increase conformational complexity in small molecule drug candidates is to incorporate sp3 hybridised centres into the carbon structural framework. However, the reliance on sp2-sp2 cross coupling methodologies in medicinal and high throughput combinatorial chemistry has resulted in chemical libraries that are dominated by planar molecules. Consequently, the development of new methods to forge new C(sp3)-C bonds and rapidly access conformationally complex molecules is vital to accelerating contemporary drug discovery. This thesis aims to address this challenge in the chemical and medical sciences, by focussing on the development of novel methodologies to access C(sp3)-C bonds. To achieve this, attention is placed on two possible approaches to synthesise saturated carbon skeletons; namely, transition metal catalysed cross coupling and alkene hydrofunctionalisation (including hydrogenation) reactions enabled by visible light mediated catalysis. In chapter one, transition metal catalysed cross coupling of sp3 fragments and alkene hydrofunctionalisation is introduced and their key limitations identified. Next, strategies that have been employed to overcome these limitations are discussed. Specifically, the use of visible light photoredox catalysis has shown to be effective in affording distinct reactivity and selectivity in these reactions, compared to thermal approaches. Finally, the research focus and aims of this thesis are elaborated. Chapter 2 builds on a recent discovery by the Polyzos laboratory, which established that cyclopalladated complex consisting of 8-aminoquinoline auxiliary exhibits a long-lived excited state capable of undergoing light induced single electron transfer with alkyl halides and providing access to Pd(II)/Pd(III)/Pd(IV) redox couples. The use of this complex to achieve light induced C(sp3)-H cross coupling is investigated. Furthermore, an investigation is conducted to establish whether other cyclopalladated complexes similarly display long-lived excited states that can be harnessed for C-C cross coupling. During reaction optimisation, it was found that extensive decomposition of cyclopalladated complex occurs, following single electron transfer to aryl halides, likely due to the formation of hybrid aryl palladium(III) radical pairs. Chapter 3 describes the development of a novel C(sp3)-C cross coupling methodology using energy transfer catalysis. Specifically, the energy of excited state cyclopalladated complex consisting of 8-aminoquinoline auxiliary is transferred to polyaromatic hydrocarbons, to enable the reduction of energy demanding aryl bromides and prevent the decomposition pathways observed in chapter 2. The resulting aryl radical is trapped by ground state cyclopalladated complex with subsequent reductive elimination affording a C(sp3)-arylated product in excellent yield. In chapter 4, a novel mode of alkene activation is developed via photoredox catalysed single electron reduction. This is achieved using the multiphoton, tandem catalytic mechanism of heteroleptic iridium photocatalyst, [Ir(ppy)2dtbbpy]PF6, discovered in the Polyzos group. The reactivity of the resulting olefinic radical anion is effectively controlled to achieve a formal hydrogenation of 1,1-diarylethylenes and substituted styrenes. Mechanistic studies including luminescence quenching, deuterium labelling and radical clock experiments indicate a Birch-type reduction as the major reaction pathway. In chapter 5, an unexpected aminomethylated by-product observed in chapter 4 is optimised to establish the first photoredox catalysed aminomethylation of electron rich alkenes (1,1-diarylethylenes). During this, the ability of other heteroleptic iridium photocatalysts to engage in the tandem catalytic paradigm is investigated, to expand the reaction scope to include unprotected secondary amines. Mechanistic studies indicate that the single electron activation of both alkene and amine coupling partners, via the multiphoton tandem catalytic system, is vital for aminomethylation to occur. Chapter 6 details the experimental procedures used throughout this thesis, including spectroscopic data of all isolated compounds.

Regular monitoring of heavy metal ions concentrations in aquatic systems is essential to determine their availability to the environment and evaluate their potential risk due to their toxicity to aquatic organisms. The passive sampling based on the use of a polymer inclusion membrane (PIM) as the semipermeable membrane barrier between the sampled medium and a liquid receiving phase has been recently introduced as a promising analytical tool, not only due to the superior stability of PIMs compared to supported liquid membranes, but also because it contains a liquid receiving phase which can be analysed directly, thus simplifying its processing prior to analysis. However, passive sampling based on PIMs is relatively new and limited research has been directed towards overcoming the issues associated with the effect of environmental variables on the performance of such passive samplers. Hence, the research described in this thesis aims at further developing PIM-based passive sampling devices for Zn2+ as the model analyte. This research includes the development of a 3D-printed flow-through passive sampling device (PSD), and the study of the influence of several environmental factors (i.e., flow pattern, water matrix, and temperature) on the accumulation of Zn2+ ions, and the assessment of strategies to either minimize or eliminate their effects on the estimated time-weighted average (TWA) Zn2+ concentration.

This work focuses on the measurement and analysis of gas-phase electronic spectra of C4H2+, C4H4+, C4H5+, and C6H4+ cations. The spectra are recorded by photodissociating the cations, or their messenger tagged complexes, in a tandem mass spectrometer and monitoring the photofragment signal as a function of laser wavelength. Ultimately, structural and energetic information extracted from these spectra, complemented by quantum chemical calculations, may provide insights into the roles of cations in the chemistry of flames, plasmas, and extraterrestrial environments. Understanding the vibronic structures of the cations is also fundamental for facilitating their possible detection in remote environments. Electronic spectra of C4H2+-Ar_n (n = 1-3) and C4H2+-(N2)_n (n = 1-2) complexes are recorded over the 290-530 nm range by monitoring C4H2+ photofragments. Intense narrow bands in the visible region arise from the A2(Pi)u<--X2(Pi)g electronic transition of the diacetylene cation, HC4H+. Vibronic transitions are compared with previous results and theoretical predictions for the A2(Pi)u<--X2(Pi)g band system based on calculations at the CCSD/cc-pCVTZ and EOM-CCSD/cc-pCVTZ levels of theory. Hole burning experiments confirm that the weak, broad bands in the ultraviolet region also correspond to excitations of HC4H+. These bands are assigned to the 22(Pi)u<--X2(Pi)g electronic transition based on calculated energies and oscillator strengths, previous experiments, and spectra of isoelectronic molecules. The origin transition is observed at 29723 cm-1 (336.44 nm) for HC4H+-Ar, followed by a progression in the symmetric C-C stretch vibration, spaced by 906 cm-1. Spectral congestion observed toward shorter wavelengths is possibly due to the presence of close-lying electronic states, vibronic coupling effects, and HC4H+ being bent in the 22(Pi)u electronic state. Electronic spectra of Ar- and N2-tagged C4H4+ cations, generated from acetylene ion-molecule reactions, are recorded over the 296-550 nm range by monitoring C4H4+ and C4H3+/C4H2+ photofragments. The spectra exhibit a clearly resolved band system commencing at 511 nm, a set of weak bands around 410 nm, and an intense broad band in the UV. Band assignments are based on previous spectroscopic studies and calculations for the four lowest energy C4H4+ isomers. The visible region of the spectrum is dominated by the B2A’’<--X2A’’ electronic transition of the vinylacetylene cation (VA+) whose origin transition occurs 19558 cm-1 (511.30 nm) for VA+-Ar and at 19551 cm-1 (511.48 nm) for VA+-N2. The spectrum features a strong progression in the central C-C stretching vibration spaced by approximately 806 cm-1 and well defined vibronic transitions associated with two bending vibrational modes. The weaker 410 nm system is assigned to the D2B3<--X2B2 electronic transition of the butatriene cation (BT+). Two broad bands, following the origin transition at 24399 cm-1 (409.85 nm) in the C4H4+-Ar spectrum, arise from excitation of a symmetric C=C stretching vibration and possibly the CH2 twisting vibration. The observation of C4H4+ and C4H3+ /C4H2+ photofragments following excitation of BT+-Ar complexes over the 380-410 nm range accords with calculated dissociation pathways on the ground state C4H4+ potential energy surface. The broad band appearing at wavelengths below 320 nm is predicted to be due to electronic transitions of all four of the lowest energy C4H4 + isomers, including the VA+ and BT+ cations. The B2A’<--X2A’ electronic spectrum of the 1-butyn-3-yl cation (H3CCHCCH+) is recorded over the 245-285 nm range by photodissociating the bare cation and its Ne and Ar-tagged complexes. Origin transitions for H3CCHCCH+ and H3CCHCCH+-Ne are observed at 35936 cm-1 (278.27 nm) and 35930 cm-1 (278.32 nm), respectively. Additional bands in the spectra are assigned to vibronic transitions of H3CCHCCH+ through quantum chemical calculations and comparison of the spectra with those of similar molecules, the propargyl (C3H3+) and methyl propargyl (H3C4H2+) cations. Excitation of H3CCHCCH+ produces C2H3+ +C2H2 (protonated acetylene + acetylene) and C4H3+ +H2 (protonated diacetylene + hydrogen molecule) photofragments. The preferred formation of C2H3+ +C2H2 photofragments is correctly predicted by master equation simulations, generated from calculated dissociation pathways on the ground state C4H5+ potential energy surface. Electronic spectra of Ar- and N2-tagged C6H4+ cations, generated from acetylene ion-molecule reactions, are recorded over the 265-700 nm range by monitoring C6H4+ and C4H2+ photofragments. Bands are assigned to transitions of five isomers based on previous spectroscopic studies, calculated stationary points on the ground state C6H4+ potential energy surface, hole burning experiments, and spectral simulations generated from TD-DFT calculations. In the C6H4+-Ar spectrum, bands over the 526-700 nm range arise from the B2A’’<-- X2A’’ electronic transition of the 1-hexene-1,3-diyne cation (CH2CHCCCCH+) and the C2Bg <-- X2Au electronic transition of the trans-3-hexene-1,5-diyne cation (HCCCHCHCCH+), with origin transitions occurring at 604 and 581 nm, respectively. Over the 375-460 nm range, broad bands at 440, 425, and 423 nm are assigned to vibronic transitions within the C2A’’<-- X2A’’ band system of the 1-ethynyl-3-methylene-cyclopropa-1,2-diene cation (H2C[c –C3H]CCH+). Sharper bands at 416, 407, and 400 nm are ascribed to the B2A’’<-- X2A’’ electronic transition of the propargyl cyclopropene cation ([c –C3H2]CHCCH+). Between 265 and 375 nm, several bands appear, superimposed on a broad band that extends for several thousand wavenumbers. The 371 nm band is assigned to the B2A’’<-- X2A’’ origin transition of the 1-hexene-1,3-diyne cation (CH2CHCCCCH+), agreeing with previous assignments. In light of the TD-DFT calculations, the bands at 365 and 357 nm are tentatively reassigned to the C2B<--X2B electronic transition of the propadienylidene cyclopropene ([c –C3H2]CCCH2+) isomer. The underlying band possibly arises from the C2Bg <-- X2Au electronic transition of the trans-3-hexene-1,5-diyne (HCCCHCHCCH+) cation, which undergoes a reduction in symmetry upon photoexcitation. Formation of C4H2+ photofragments at wavelengths below 426 nm (2.91 eV) agrees with calculated C6H4+ dissociation pathways on the ground state C6H4+ potential energy surface.

The ubiquity of amines in pharmaceutical, agrochemical and advanced materials has incentivised modern synthetic chemists to develop novel and innovative methods for their synthesis and functionalisation. Specifically, the direct alpha-C-H functionalisation of aliphatic amines represents one such transformation which demands further development and improvement of current methodology. Visible-light mediated catalysis has presented a powerful platform to facilitate this transformation, with several pathways established to achieve the alpha-functionalisation of amines. This thesis is an exploration of the visible-light mediated functionalisation of aliphatic amines. Specifically, it explores the formal alpha-functionalisation of amines via the generation of alpha-amino radicals as key intermediates and investigates subsequent pathways of reactivity. The methodologies developed have been applied to the synthesis of biologically relevant amine scaffolds. Upon optimisation, continuous flow protocols were established to enhance the photochemical reaction conditions. Chapter 1 summarises the protocols for the alpha-functionalisation of amines. A brief history of this transformation is explored, highlighting several methodologies and is accompanied by a critical evaluation of their benefits and limitations. The concept and principles of photoredox catalysis are introduced and notable examples examined within the context of photocatalytic protocols for amine alpha-functionalisation. Finally, flow chemistry is presented detailing its advantages with emphasis towards photoredox catalysis. Chapter 2 establishes a visible-light mediated transfer hydrogenation of diarylmethimines. This process makes use of the single electron reduction of imines to engender alpha-amino radicals with triethylamine functioning as both a sacrificial reductant and hydrogen source. The developed conditions enabled the synthesis of a series of diarylmethamines to be synthesised with excellent chemoselectivity. A plausible mechanism was established, highlighting the dual role of triethylamine. Flow engineering enabled this procedure to be efficiently scaled to synthetically useful quantities with retention of the chemoselectivity established in batch. Chapter 3 details the development of the decarboxylative alpha-alkylation of fused heterocyclic amines. This process engages fused heterocyclic amines and N-hydroxy phthalimide esters as radical surrogates to simultaneously establish both alpha-amino and alkyl radicals. Upon in situ generation of alpha-amino and alkyl radicals, radical-radical coupling produces the desired alpha-alkylated amine. The addition of co-reductant, diphenylamine is believed to facilitate a second mechanistic pathway that proceeds concurrently and improves the efficiency of this transformation. A flow protocol established more favourable reaction conditions, enabling conjugation of a variety of biologically active derivatives in typically good yields. Chapter 4 introduces the concept of the tandem photocatalytic cycle revealing that in situ generation of a highly reducing iridium species establishes an effective pathway for single electron reduction of energy demanding substrates. This chapter further extends the knowledge of the tandem photoredox cycle, applying this mechanism towards the radical-radical coupling of alpha-amino and alkyl radicals. Accessing a highly reducing species enabled the single electron reduction of energy demanding alkyl halides; substrates previously difficult to access. This chapter further investigates the tandem photocatalytic cycle and establishes an alternative protocol for alpha-amino sp3 C-C bond formation.

Antibiotic resistance is a global threat to public health due to a combination of limited new antibiotic candidates and the dramatic rise in multidrug-resistant bacteria. Antimicrobial peptides (AMPs) are part of the host innate immune system and are potential alternatives to treat infections is increasing. AMPs have multiple modes of action to kill bacteria, mostly involving non-stereo specific interactions which drastically diminishe acquired-resistance pressure. For instance, one of the typical mechanisms is to target the bacterial cell membrane via electrostatic interactions and disrupt the lipid bilayer integrity. Maculatin 1.1 (Mac1, GLFGVLAKVAAHVVPAIAEHF-NH2) is a cationic membrane-active AMP, isolated from the skin of Australian tree frogs and well-known for its antibacterial ability. The molecular mechanism of Mac1 interaction with bacterial membranes has been mainly studied in vitro using model membrane systems. Although providing critical insights into the lipid-peptide interactions, it is unclear if the peptide retains a similar behaviour against bacterial membrane. Indeed, while the details of how Mac1 assembles into a lipid bilayer, and the lipid composition of model membranes have been shown to play a critical role in the peptide activity. Thus, investigating Mac1 structural arrangement in intact bacteria is an important step towards deciphering how AMPs may interact in situ. Solid-state NMR (ssNMR) is able to reveal structural behaviour of AMP in vitro, but its application is limited in vivo, especially due to the short life span of bacteria. Recent developments in dynamic nuclear polarization (DNP) ssNMR has led to the feasibility to conduct in-cell experiments due to higher sensitivity and longer cell survival rates. Spin probes together with isotope enriched peptides are required for DNP ssNMR experiment. In this thesis, the methodology to determine the structural arrangement of Mac1 in live bacteria by DNP-ssNMR is developed and the initial steps in understanding how AMPs self-assemble will be described.

Copper is a vital but potentially toxic element for all living organisms. Therefore, it is necessary to maintain a balance between a deficiency and an excess level of copper. Cu-ATPase proteins are selective for Cu(I) and are crucial for removal of excess copper from cellular cytosols and for supply of essential copper to the required enzymes. Using the energy derived from ATP hydrolysis, the ATPase ATP7A (Menkes' protein, MNK) plays a key role in maturation of copper enzymes by inserting the essential metal cofactor into the nascent apo-forms. It also maintains copper homeostasis by controlling copper levels in cells. Mutations in the ATP7A gene appear to lead to neurodegenerative diseases such as Menkes' disease (MD), Occipital Horn Syndrome (OHS), X-linked Distal Hereditary Motor Neuropathy (dHMNx), and Brachial Amyotrophic Diplegia (BAD). In the past decade, in vivo studies of the human copper pumps ATP7A/ATP7B have improved the understanding of their cellular functions. However, the investigation of the Cu-ATPase pump at the molecular level has fallen behind due to a number of challenges. In general, molecular characterization of transmembrane proteins requires large amounts of highly purified samples plus the challenge of producing a Cu pump in unmodified native form. It has also proven difficult to express and isolate the Cu pumps. This study details methods to address those challenges. This work also aims to undertake molecular characterisation of ATP7A and selected mutants using a 1H-NMR approach as a sensitive probe of ATPase activity. Asp1044 is the primary phosphorylation site that is essential for ATP7A function and the variant D1044E served as a negative control for the functional assay. The two variants P1386S and M1311V are two mutations identified in patients with dHMNx and BAD diseases, respectively. A baculovirus expression system was used to express His-tagged wild-type protein ATP7Awt and the variants in fully functional form. When dissolved in the detergent n-dodecyl-Beta-D-maltopyranoside (DDM) or embedded in Sf21 microsomes, the expressed proteins were each active in acyl-phosphorylation using the BODIPY FL ATP-Gamma-S assay system. Rates varied with Cu(I) availability, ATP concentration, enzyme concentration and temperature, and other conditions were optimized. The effects of competition for Cu(I) by glutathione (GSH), bathocuproine disulfonate anion (BCS), the metal binding site 1 from the E. coli analogue EcCopA (MBS1), metal binding site 6 of human Wilson disease protein (WLN6) and antioxidant protein 1 (ATOX1) were investigated. The ATPase activity assays evaluated by 1H-NMR demonstrated that: ATPase activity is dependent upon Cu(I) availability to the enzyme; the ATP7Awt protein is most active in the presence of its native metallo-chaperone ATOX1. The M1113V mutation does not affect ATPase activity significantly. Consequently, the problem of this mutation in BAD is likely related to the trafficking of Cu(I) rather than to its enzyme activity. The P1386S mutation associated with dHMNx, however, exhibited a reduced ATPase activity.

Innate immunity is provided by a complex network of cells, soluble factors, and organs that respond immediately or within hours of the appearance of a stimulus in the body. Innate immune processes can involve recognition of metabolites, including those of self or microbial pathogens, by endogenously-expressed pattern recognition receptors. In this thesis, I explored the structure of different antigens that can be recognized by the innate immunity macrophage inducible C-type lectin receptor (Mincle), innate-like natural killer T (NKT) cell, and mucosal-associated invariant T (MAIT) cells. Chapter 2 describes the synthesis of acyl variants of cholesteryl and ergosteryl alpha-mannoside (CAMs and EAMs), proposed structures for glycolipids from Candida albicans. These glycolipids were synthesized by mannosylation of cholesterol or ergosterol, followed by the introduction of the acyl groups by esterification of the sugar primary alcohol. The synthetic glycolipids were assessed for their ability to agonize signaling by mouse and human Mincle. We showed that both CAMs and EAMs elicited strong signaling through both mouse and human Mincle. Chapter 3 discloses the total synthesis of an alpha-galactosylceramide originally reported from Bacteroides fragilis: GalCerBf-716, as well as analogs bearing modified lipid side chains to allow exploration of structure-activity relationships for activation of CD1d-restricted iNKT cells. GalCerBf-716 was synthesized by galactosylation of a sphinganine acceptor, followed by an amide coupling with different acid side chains. All synthesized GalCerBf-716 analogs stimulated mouse and human iNKT cells. In Chapter 4 we proposed a structure for an undefined antigen (5-F-7-RdX) arising from the reaction of 5-A-RU with a dicarbonyl compound. We synthesized a simpler analog, 7-RdX. 7-RdX was shown to act as a weak and selective agonist for MAIT TCR-Tyr94 cell lines, over Tyr95 cell lines. The electron density of 7-RdX from an X-ray structure in complex with the antigen-presenting molecule MR1 is a close match to that for unknown antigen.

Ammonia is commonly used as an indicator of water quality, to assess the impacts of anthropogenic activity on ecosystem function and health. Water quality assessment often relies on the use of expensive equipment requiring a high degree of operator skill, or periodic, discrete, manual sampling and laboratory-based analysis, which is laborious, costly and without the guarantee that episodic pollution events will be detected. Low-cost, portable and/or field-deployable analytical tools are required to overcome this challenge. Hence, research conducted in the context of this thesis involves the development of novel analytical tools for the monitoring of ammonia in marine waters, covering both active and passive sampling. A flow-based analytical method was designed and developed for the determination of total ammonia over a wide concentration range in marine waters using the gas-diffusion spectrophotometric method. Limits of detection similar to that of highly sensitive fluorometric methods was achieved. A novel flow approach was adopted whereby a continuous stream of sample was merged with the sodium hydroxide reagent stream and delivered to a gas-diffusion ammonia separation unit, allowing large sample volumes to be used, rather than being limited by the use of discrete samples. The working range and sensitivity of the method could be tailored by simple modification of the sample volumes used, and by minor adjustments to the program used to control the instrument, without the need to make changes to the manifold. Three working ranges were obtained, and the analytical figures of merit are described. This project was an enabling step in the development of an ammonia gas-diffusion passive sampling device, as it allowed the measurement of low concentrations often found in field samples, as well as high concentrations accumulated in the passive sampler’s receiving solution, using the same instrumentation and reagents. A passive sampling device based on gas-diffusion across a hydrophobic membrane was developed and successfully applied for the determination of the time-weighted average concentration (Ctwa) of ammonia in marine waters for a period of 3 to 7 days. Molecular ammonia (NH3) present in the sampled source solution (SS) diffuses through a hydrophobic membrane into an acidic receiving solution where it is ionised and accumulated as NH4+ which is directly proportional to the NH3 concentration in the SS. Biofouling limited the application of the first gas-diffusion-based passive sampler (GD-PS) prototype to 3 days, and a number of antifouling strategies were therefore assessed, with a copper mesh enabling the sampling period to be extended to 7 days. The effects of environmental variables (temperature, pH and salinity) on NH3 accumulation were also investigated, and the Group Method of Data Handling (GMDH) Algorithm was used to develop a single calibration model for a range of environmental conditions (10 to 30 degrees C, pH 7.8 to 8.2, salinity 20 to 35). PSDs were deployed at four estuarine and marine sites in Nerm (Port Phillip Bay), south eastern Australia, achieving good agreement between passive and automated discrete sampling methods (maximum relative error between -12 % to -19 %). The GD-PS covers the revised water quality trigger value (160 ug L-1 NH3-N) and allows for episodic pollution events to be successfully detected, highlighting this as an exciting new tool for water quality assessment.