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Janus face fluorocycloalkanes (JFC) represent a novel subject of study. The fluorinated electronegative face and the hydrogenated electropositive face of the rings create an extraordinarily high dipole moment which induces facial polarity. This thesis carries out various studies on this new class of compound. In Chapter 1, a discussion of the background and general interest in fluorine chemistry is given. The role of fluorine in pharmaceutical chemistry is demonstrated. The most recent studies on the JFC are summarised and discussed, including their preparation and applications in ionic binding, supramolecular chemistry, and biological chemistry. In Chapter 2, a recently reported stereoselective Rh-catalysed hydrogenation was further explored, and its substrate scope was extended to aryl-CF₃ to deliver facially polarised CF₃-cyclohexane motifs in high diastereoselectivity. The direct preparation of CF₃-containing cyclohexanes form a library of stereoselective motifs for further studies. In Chapter 3, the study of facially polar CF₃-cyclohexane was extended to the preparation, properties and physiochemistry of all-cis-multi-CF₃ cyclohexanes with between 3 and 6 substituent CF₃ groups. The prepared all-cis-hexakis-CF₃-cyclohexane has a high barrier to ring inversion (27 kcal mol⁻¹), more than twice that of cyclohexane. This ring also coordinates chloride (Cl-) ion to the hydrogen face with a modest affinity constant (K = 10³ M⁻¹). In Chapter 4, the surface behaviour of the all-cis-hexafluorocyclohexane was studied on HOPG and gold surfaces. The reactivity of JFCs was studied, and a number of functional groups were installed onto the ring. of A novel amino acid of with a JFC side chain was prepared and incorporated into peptide synthesis. In Chapter 5, trifluoro substituted cyclohexanes were prepared. An unexpected triaxial preference was found in all-cis-1,3,5-trifluorocyclohexane and some of its derivatives. The conformational preferences of these derivatives were also investigated. In Chapter 6, the JFC motifs were transformed into multi-dentate supramolecular architectures. The proposed frameworks were synthesized in modular approaches. The crystal structure of a number of the building blocks were demonstrated with voids in their supramolecular architectures.

Considerable progress has been made in the Hunter group towards the development of sequence oligomers equipped with H-bond donor and acceptor recognition units, which are able to assemble into duplexes by H-bonding between sequence-complementary oligomers. This thesis describes a new class of melamine oligomers composed of alternating triazine and piperazine units, which are equipped with phenol and phosphine oxide recognition groups. The order of the recognition groups defines the sequence of the oligomers. Complete sequence library of 1-mers, 2-mers and 3-mers, along with the homo 4-mers were synthesised by sequential temperature-controlled nucleophilic aromatic substitutions between cyanuric chloride and secondary amines. Complementary homo-oligomers undergo cooperative duplex formation, and hetero 3-mers form sequence-selective duplexes. H-bond templated synthesis of a similar melamine oligomer was attempted in toluene, but the template was inefficient at promoting the formation of sequence-complementary oligomers. The central H-bonding recognition unit of the melamine 3-mers was replaced by benzaldehyde or aniline side chains, giving oligomers that could assemble by imine formation as well as H- bonding. The 3-mer bearing two phosphine oxides and a benzaldehyde was converted to an imine with excess aniline, and then subjected to transimination in CDCl3 with the 3-mer bearing two phenols and an aniline. Transimination reached equilibrium at 70% conversion. The product duplex never fully assembled, indicating geometric incompatibility between the chosen H-bonding and dynamic covalent base pairs. Previously, a family of oligotriazoles equipped with phenol and benzoic acid recognition units was developed in the Hunter group, and shown to be capable of sequence information transfer by covalent templated synthesis of new oligomers. However, there are limitations associated with the choice of triazole backbone used in these systems. Here a novel strategy was developed for the rapid discovery of diazide and dialkyne building blocks for the synthesis of alternative backbones. Supramolecular scaffolds were created by mixing bidentate ligands and a metalloporphyrin appended with a dialkyne. The scaffolds were trapped by copper-catalysed azide alkyne cycloaddition with different diazides. The longest bidentate ligands gave the highest yield of linear triazole oligomers with any of the diazides used. No diazide gave the linear triazole oligomer as the major product with the dialkyne studied. A different backbone made by ring opening metathesis polymerisation was also investigated. An attempt was made for the synthesis of new oligomers from norbornenes functionalised with phenol and benzoic acid recognition units. Metathesis polymerisation gave a mixture of stereoisomers, and the monomers did not undergo successful base pair formation and cleavage cycle, making this system unsuitable for further studies.

Chapter 1 introduces the chemistry of 1,3,4-oxadiazoles with a specific focus on currently available strategies, and methodologies for their synthesis. Five distinct synthetic approaches - 1) dehydration of 1,2-diacylhydrazines; 2) oxidative cyclizations of N-acyl hydrazones; 3) C-H functionalization of 2-substituted 1,3,4-oxadiazoles; 4) rearrangements of N-H tetrazoles; 5) reactions using (N-isocyanoimino)triphenylphosphorane (NIITP) as a three atom CNN source - are discussed in detail and their limitations evaluated. Chapter 2 focuses on a novel three-component reaction for the reductive synthesis of α-amino 1,3,4-oxadiazoles (or heterodiazoles), from tertiary amides and lactams, feedstock carboxylic acids (or appropriate C-, S-, N-Brønsted acids), and NIITP. Taking advantage of the mild and chemoselective reductive activation of tertiary amides provided by the combination of Vaska's complex and 1,1,3,3-tetramethyldisiloxane (TMDS) the reaction was applied to the late-stage functionalization of ten drug-like amides and carboxylic acids and culminated in the synthesis of three heterodiazole-fused drug-drug conjugates. Chapter 3 demonstrates that N-carbamoyl imines, with carboxylic acid (or N-acyl sulfonamide) coupling partners and NIITP, can efficiently generate N-carbamoyl α-amino 1,3,4-oxadiazole (or 1,2,4-triazole) structures in a three-component reaction - expanding the existing scope of C=N electrophiles used with NIITP. A successful scale-up of this methodology allowed the gram-scale synthesis of a primary α-amino 1,3,4-oxadiazole, and a subsequent investigation into its derivatization. Chapter 4 presents the merger of two modern approaches for 1,3,4-oxadiazole synthesis - 2-substituted 1,3,4-oxadiazole construction using NIITP and the C-H functionalization of 2-substituted 1,3,4-oxadiazoles - into a one-pot and multicomponent protocol for synthesis of 2,5-disubstituted, or 2-amino-5-substituted, 1,3,4-oxadiazoles. A preliminary investigation into the use of nucleophilic secondary amine coupling partners for synthesis of 2-amino-5-substituted 1,3,4-oxadiazoles is additionally discussed.

This thesis describes the development of novel catalytic enantioselective reactions. Chapter 1 describes the development of transformations mediated by chiral ammonium salts. The historical context of enantioselective phase transfer catalysis is provided and the key fundamental advances are detailed. The development of a cation-mediated kinetic resolution of atropisomeric biaryls is described as well as the synthesis and resolution of a range of substituted BINOLs. The extension of the chiral cation mediated approach to the dearomatization of 2-naphthols by electrophilic amination and of indoles by C3 alkylation is also described. In both cases, good reactivity and moderate enantioselectivity were achieved. Chapter 2 focuses on the development of a Lewis acid mediated approach to the catalytic enantioselective [6π] photocyclization of acrylanilides. The work is contextualized by a discussion of the previous approaches to enantioselective photochemical reactions covering direct irradiation, triplet energy transfer and photoredox strategies. The elucidation of competing triplet energy transfer and photoredox pathways to the same product is described alongside an account of the design and development of a photocatalyst that engages predominantly in the photoredox pathway. The reaction was tested on a range of substrates to determine the scope and limitations of the method.

Recent advances in the incorporation of attractive non-covalent interactions into small molecule catalysts have greatly increased the understanding of how such approaches can be applied to regioselectivity and enantioselectivity challenges in synthetic chemistry. The most widely used interactions, hydrogen bonding and ion-pairing, are employed in this thesis for the accomplishment of two important transformations in an enantioselective manner. The directionality of hydrogen bonding makes it a valuable tool for engendering asymmetry in organic synthesis and the application of this interaction to the Minisci-type addition of prochiral radicals to azines is described in chapter 2. Several strategies for the asymmetric hydroxyalkylation of pyridines and benzopyridines were attempted including generating radicals through the fragmentation of α-hydroxy and β-hydroxy redox-active esters, hydrogen atom transfer using Selectfluor®, and hydrogen atom transfer using organic peroxides. Chapter 4 describes the application of hydrogen bonding and ion-pairing approaches to meta-selective iridium-catalysed C-H borylation. Although there are a several reports of enantioselective ortho-selective borylation of arenes, a reaction that reached more remote positions had not yet been realised. The association of a chiral countercation with an anionic sulfonated ligand gave rise to a complex which could perform the desymmetrisation of benzhydrylamides and phosphinamides with high enantioselectivities. As the sulfonated ligand used in this transformation was originally developed for regioselective borylation of arenes, the application of this chiral countercation approach was demonstrated for benzhydrylamides where there was also a regioselectivity choice. Good regioselectivity was observed with such substrates, albeit with a slight drop in enantioselectivity. Chapter 4.7 then details the attempted extension of this desymmetrisation protocol to kinetic resolutions of unsymmetrical phosphinamides. Unfortunately, poor enantioselectivity was observed with these substrates, despite their structural similarity to the substrates which had previously given excellent enantioselectivity. Chapter 4.8 then details a collaborative project with Dr Kristaps Ermanis on the nature of the transition states for oxidative addition of symmetrical benzhydrylamides and phosphinamides. Density functional theory (DFT) calculations by Dr Ermanis suggested contrasting conformations for the oxidative addition of the two substrate classes and synthetic investigations lent support to the proposed interactions in these transition states.

This thesis is separated into three sections: 1) Slight changes in the chemical structure of haemanthamine greatly influence the effect of the derivatives on rumen fermentation in vitro. Nine compounds (i-ix) were synthetized from the natural alkaloid haemanthamine and tested in vitro for their effects on rumen protozoa and fermentation parameters. Our results showed that acetate, butyrate, pivalate or hexanoate derivatives of haemanthamine or dihydrohaemanthamine (v) gave compounds that had significant differences in their effect on rumen fermentation. 2) Synthesis of zephycandidine A from haemanthamine. Zephycandidine A (x) the first naturally occurring imidazo[1,2–f]phenanthridine alkaloid, isolated from Zephyranthes candida (Amaryllidaceae) was prepared in three steps from the naturally occurring alkaloid haemanthamine. 3) Quorum sensing N-Acyl homoserine lactones are a new class of anti-schistosomal agents. Through evaluating and screening fourteen compounds (initially developed for anti-cancer and anti-viral projects) against Schistosoma mansoni, one of three species responsible for most cases of human schistosomiasis, a racemic N-acyl homoserine derivative demonstrated good efficacy against all intra mammalian lifecycle stages including schistosomula (EC50 = 4.7 µM), juvenile worms (EC50 = 4.3 µM) and adult worms (EC50 = 8.3 µM). To explore structural activity relationships, a further 8 analogues of this initial compound (xi-xx) were generated, including the separate (R)- (xv) and (S)-enantiomers (xvi). Anti-schistosomal screening of these analogues demonstrated that the (R)-enantiomer retained activity, whereas the (S)- was far less activity. Furthermore, modification of the lactone ring to a thiolactone ring improved potency against schistosomula (EC50 = 2.1 µM), juvenile worms (EC50 = 0.5 µM) and adult worms (EC50 = 4.8 µM). As the effective racemic parent compound is structurally similar to quorum sensing signalling peptides used by bacteria, further evaluation of its effect (along with its stereoisomers and the thiolactone analogues) against Gram+ (Staphylococcus aureus) and Gram- (Escherichia coli) species was conducted. While some activity was observed against both Gram+ and Gram- bacteria species for the racemic compound (MIC 125 mg/L), the (R)-stereoisomer had better activity (125 mg/L) than the (S) (>125mg/L). However, the greatest antimicrobial activity (MIC 31.25 mg/L against S. aureus) was observed for the thiolactone containing analogue.

Inspired by enzymes, strategies incorporating attractive non-covalent interactions have emerged as a powerful tool to control selectivity in organic synthesis through small molecule catalysis. The ubiquity of charged intermediates across these transformations has recently highlighted ion pairing as a promising interaction to this end. The formidable challenge of selective C-H bond functionalisation through transition metal catalysis offers an ideal platform to investigate the potential of invoking control through ion pairing interactions. The ion pairing strategies explored in this thesis focus on how cations may be used to influence such reactivity at their closely associated anions. Chapter 2 focusses on the iridium-catalysed borylation of aromatic C(sp2)-H bonds. The lack of regiocontrol for 1,2-disubstituted arenes under standard conditions has previously been addressed by introducing an ion pairing interaction between a cationic substrate and an anionic ligand to favour meta-selective borylation. Building upon this work, Chapter 2.2 explores whether selective borylation may still be achieved when inverting the polarity of the substrate-ligand interaction. Disappointingly, the cationic ligands investigated were unable to promote meta-selective functionalisation of tetrabutylammonium salts of anionic aromatic sulfonates. Concurrent studies by Madalina Mihai revealed that borylation of the same substrates with neutral bipyridine ligands proceeded with an unexpected para-selectivity. Working closely with Madalina, Chapter 2.3 extends this methodology to the tetrabutylammonium salts of sulfonated phenols, benzyl alcohols, anilines, and benzylamines, as well as benzenesulfonates. Mechanistic studies suggest that the bulky tetrabutylammonium counterion sterically inhibits catalyst oxidative addition into the meta-C-H bond, thereby promoting para-selective borylation. Chapter 3 investigates the rhodium-catalysed intermolecular amination of benzylic C(sp3)-H bonds. Though amination at a methylene C-H bond typically introduces a new stereocentre in the product molecule, sparingly few enantioselective variants of this transformation are known. Taking inspiration from previously reported ion pairing strategies and building upon preliminary results obtained by Alex Fanourakis, Chapter 3.2 details how chiral cations may induce enantioselectivity in the intermolecular benzylic amination of phenyl alkyl alcohols and carboxylic acids through ion pairing to a negatively charged dirhodium complex. This thesis highlights the generality of ion pairing strategies towards addressing selectivity challenges in transition metal-catalysed functionalisations of C-H bonds. It is hoped that the results presented herein will stimulate novel ion pairing strategies to further realise their potential in organic synthesis.

Chapter 1 introduces enantioselective organocatalysis with a specific focus on bifunctional catalysts and chiral superbases. Subsequently, the discovery and applications of bifunctional iminophosphorane (BIMP) catalysts will be described. Chapter 2 focuses on the development of a novel enantioselective sulfa-Michael addition employing alkenyl-benzimidazoles as electrophiles. The work in this chapter will showcase a rare example of organocatalysed enantioselective addition to alkenyl heterocycles for the rapid generation of 3-D druglike scaffolds. Chapter 3 introduces approaches to enantioselective P(V) synthesis, highlighting the strengths and shortcomings of current methods to then focus on the development of an unprecedented enantioselective nucleophilic desymmetrisation of phosphonate esters. The unique ability of a novel ureidopeptide BIMP catalyst to promote this reaction enantioselectively will be demonstrated against a wide array of other BIMPs as well as Chinchona alkaloid and phase transfer catalysts. The downstream utility of the desymmetrised product will be demonstrated in the synthesis of numerous attractive nucleoside derived compounds. Chapter 4 will disclose an improved enantioselective nucleophilic desymmetrisation of P(V) containing species. Via a superior BIMP catalyst scaffold and a thiazolidinone leaving group on the P(V) electrophiles, higher enantioselectivities, lower catalyst loadings, and improved nucleophile scope were obtained.

This thesis describes work focused on the application of potently oxidising organophotocatalysts to synthetic methodologies. The main motivation for this work is to enable chemical transformation of otherwise unreactive species. There are many organophotocatalysts described in the literature, and they often exhibit from high reduction potentials. However, most of the work herein is centered around the common reagent 2,3-dichloro-5,6-dicyano- 1,4-benzoquinone (DDQ), 1. An overview of the relative benefits of organophotochemistry and a discussion of DDQ photochemistry is given in Chapter 1. Also included in this chapter is an analysis of the chemistry of aryl radical cations - a key intermediate in the work that follows. Chapter 2 covers our investigations into net oxidative organophotochemistry. Chapter 3 covers the work undertaken on net redox neutral transformations. This later class was more productive on the whole, and led to a new defluorinative organophotochemical SNAr process. The conclusions of this thesis, and an outline for future work, is then provided in Chapter 4. Finally, all pertinent experimental details are provided from Chapter 5 onward.

G-quadruplex ligands, which can intercalate the G-quadruplex structures, have been studied as a strategy for indirect inhibition of telomerase activity, alongside targeting other G-quadruplexes found in other genes, including oncogenes. The scope of G-quadruplex ligands as cancer targeting drugs is particularly high as there more than 350000 DNA sequences within the human genome that can be targeted. In light of this, several small molecules have been introduced, which can induce and stabilise G-quadruplexes, which are classified as new drug agents for cancer therapy. This thesis looks at the synthesis of suitably functionalised polyaromatic compounds to achieve this stabilisation. Deoxyribonucleic acid (DNA) in our cells contains the instructions for all aspects of life, from cell division to immune responses. The discoveries and structural determination of DNA, leading to the human genome project, provides a great resource for genetic understanding. The pairing of nuclear bases is typically represented as Watson-Crick. When DNA is chemically changed, disruption to cell processes occurs. Cancer is one outcome of this damage, where DNA is damaged to a point where cell cycle control is incapacitated. One key aspect of cancer is that cells lose the ability to undergo apoptosis. Telomeres are integral structures present in the DNA of eukaryotic cells. They consist of regions of DNA motifs that are repeated throughout the structure. These conserved motifs contain an abundance of Guanine in sequences of 3-4 repeat units. These Guanine units make up the Guanine tetrad structures that allow the telomere to function as genomic stabiliser and protective agent against DNA damage or cross chromosome fusion such that all telomeres have a single stranded Guanine motif overhang at the 3' end of the chromosome. Telomere length will usually dictate the lifespan of a cell, however in cancer cells we see this mechanism for programmed cell death, hijacked by the expression of telomerase, which extends telomere length and inhibits programmed cell death. The well-established principle behind the development of G quadruplex ligands is that inhibition of telomerase, which isn't expressed in healthy cells, can selectively facilitate apoptosis of cancerous cells. G-quadruplexes are structures that have shown the potential as therapeutic targets through 5 their propensity to associate with themselves and structures that are similar which will intercalate. Because of this, small molecules that intercalate within the structure and stabilise them within DNA have targeted G-quadruplexes. This stabilised DNA G-quadruplex structure will then inhibit the division of the cell through prevention of unwrapping and recognition of regulation regions and telomeric regions, which are normally cleaved off . In this research we aimed to make a number of G-quadruplex ligands to specifically target this inhibition and show activity against the HeLa cancer cell line. Throughout the research we synthesised several G-quadruplex ligands with different synthetic methodologies. Our success with these ligands was mainly achieved with imine couplings and these compounds showed cytotoxicity to HeLa cells. Compounds that showed cytotoxicity were further analysed for drug G-quadruplex interaction by 1D, 1H NMR titration experiments. Five of the compounds that showed cytotoxic effect demonstrated drug G-quadruplex interactions.

Molecular knots and links can be found in natural biomolecules and synthetic polymers. Like their macroscopic counterparts, molecular knots and links are known to affect the properties of the systems that contain them, in some cases giving rise to interesting functionality as a direct consequence of their complex topology. Although the synthesis of molecular knots and links has experienced significant advances over the last few decades, the in-depth study of the functions of these topologies has been limited to several anecdotal examples. These functions are usually found serendipitously as a result of the arrangement of the functional groups on which the templated synthesis of the topology relies, and therefore allow for little design or tunability. This thesis presents a further exploration of the structure and function in molecular topologies. First, a study of the factors that influence the binding ability of a molecular knot aims to provide the knowledge required to employ it as a tunable system. Alternatively, the design and synthesis of a photoactive iridium-containing circular helicate demonstrates the possibility to design topologies with a specific function in mind. Finally, the synthesis of a novel molecular link employing a metal templation strategy contributes to expand the portfolio of available molecular topologies.

Chapter 1 - Introduction. This chapter aims to highlight the importance of enantioselective fluorination in modern organic chemistry. The peculiar and sometimes contradictory properties of fluorine and fluorinated organic molecules are detailed along with examples of their applications in the life sciences. The origin and the chemistry of fluorinating reagents are also discussed, with a particular emphasis on the fluoride anion's uses and challenges in organic synthesis. Lastly, a summary of the current methodologies to access enantiopure fluorinated compounds is presented and discussed. Chapter 2 - Hydrogen Bonding Mediated Asymmetric Nucleophilic Fluorination. The work describes the development of the first protocol for asymmetric nucleophilic fluorination utilising alkali metal fluorides as fluorine source and a newly developed tridentate bis-urea organocatalyst. This novel strategy, named Hydrogen Bonding Phase-Transfer Catalysis (HB PTC), embraces the poor solubility of fluoride salts in organic solvents and their tendency to engage in hydrogen bonding to deliver fluorinated molecules in high enantioselectivity. Chapter 3 - Structure and Conformation of bis-Urea Catalysts for Hydrogen Bonding Phase- Transfer Catalysis: Insights from NMR Spectroscopy. A detailed NMR spectroscopic investigation is presented herein in order to unveil the mechanistic details of HB PTC. The work investigates the conformational preferences of bis-urea catalysts under relevant reaction conditions and their changes upon binding of fluoride. The characterisation of bis- ureas-TBAF and bis-ureas-CsF complexes, in solution and in the solid state, provides information about the hydrogen bonding network around fluoride. The detection of scalar coupling across hydrogen-bonding, 1hJNH...F-, represents a key parameter to study catalyst-fluoride interactions. NMR data are used to investigate how the structural features of the catalysts influence the outcome of HB PTC fluorinations.

In recent years, enzymes, and their uses as biocatalysts for synthetic organic chemistry, have been positively disrupting the pharmaceutical and chemical industries. With the development of the third wave of biocatalysis and directed evolution, enzyme engineering has become easier, cheaper and quicker. However, while random enzyme evolution is possible in the absence of structural data, the development of efficient biocatalysts is accelerated when 3D structures and mechanistic information of the target are available. In this work, two enzymes, each catalysing different chemical transformations will be studied, with the aim of gaining structural and mechanistic data which shall be used to guide future engineering strategies. The first enzyme studied is the pimeloyl-ACP methyl ester esterase, BioH, from E. coli (EcBioH). Previously it was found that EcBioH is able to catalyse the Morita-Baylis-Hillman (MBH) coupling of 4-nitrobenzaldehyde (4-NBA) and methyl vinyl ketone (MVK), with less than 50% conversion. The MBH reaction forms a C-C bond by coupling an aldehyde and an electron-poor alkene, and leads to the formation of a chiral alcohol. However, the mechanism of the enzyme-catalysed biotransformation is unclear. Specifically the identities of the active residues involved in substrate binding and catalysis are not known. Here we describe the characterisation of recombinant EcBioH and study its role in catalysing the MBH reaction. We used site directed mutagenesis to probe the role of a proposed catalytic triad of conserved residues (Ser-Asp-His) in the mechanism. We also investigate the involvement of a cysteine residue by covalent modification and mass spectrometry. Since none of these residues were found to be essential for MBH catalysis, this suggested that the protein hexahistidine (also known as 6His) affinity tag used to purify the enzyme displays inherent MBH activity. This hypothesis was confirmed by screening other hexahistidine tagged proteins available in the laboratory and discovering that they also displayed MBH activity. Furthermore, an engineered EcBioH "double-tagged" at both the N- and C- termini displayed the highest MBH activity. No enzyme displayed enantioselectivity in the MBH product distribution. These results provide strong evidence that this commonly-used tag plays an important role in MBH biocatalysis. These observations suggested that the intrinsic MBH activity of the tag arises from a synergistic acid/base relationship between the histidine residues and oxo-anion intermediates. In a second, independent project, a small family of enzymes, the nitrile synthetases (NS) was investigated. Interestingly, members of this family catalyse the conversion of a carboxylic acid to a nitrile in an ATP-dependent process. The reaction proceeds in two steps; the first involves the formation of an amide intermediate, and the second step results in amide to nitrile conversion. There is still a lack of clarity of the mechanistic role of ATP in the two steps catalysed by NS. Most notably, no attempts at separating/decoupling the two steps catalysed by the NSs have been successful so far. In this work, two members of the NS family, QueC from Bacillus subtilis (BsQueC) and ToyM from Streptomyces rimosus (SrToyM) were purified from E. coli and characterised. Both NSs were assayed for their natural reaction, the transformation of 7-carboxydeazaguanine (CDG) into 7-cyanodeazaguanine (PreQ0), via the corresponding primary amide (ADG). Their substrate scope was assessed and it was found that both enzymes had a very restricted acid substrate selectivity but were able to form a small range of secondary and tertiary amides with primary and secondary amines. Crystal trials resulted in the preparation of diffraction-quality crystals and the determination of the X-ray structure of the BsQueC:ADP complex at a resolution of 2.1 Å. This structure, was combined with the structure of a previously published BsQueC:phosphate complex and a sequence alignment of various members of the NS family. This analysis located well conserved residues and guided rational engineering of BsQueC. Well-conserved hydrophilic residues in close proximity to the phosphate moiety of the ADP molecule identified three residues for mutagenesis. A large decrease of the amide to nitrile conversion activity was observed for two of the single-point mutants generated (BsQueC K163A and BsQueC R204A). Importantly, a double-mutant enzyme which combines both these mutations (BsQueC K163A R204A) was not able to catalyse nitrile formation. However, this rationally-designed biocatalyst displayed bone-fide amide synthetase activity and allowed kinetic parameters for the CDG substrate to be determined for the first time. Finally, the first large scale biocatalysed transformation of CDG to ADG was carried out and the amide product was isolated with >95% purity. These studies provide the necessary insight and strategy required to carry out further directed evolution of the NS family to expand their substrate scope and allow synthesis of commercially-relevant amide- and nitrile-containing compounds.

Epigenetic signalling is regulated by 'writer', 'reader', and 'eraser' proteins, which add, identify and remove histone modifications, respectively. Simultaneous recognition of multiple epigenetic marks by proteins containing tandem reader domains increases the complexity of the information transmitted, making these proteins interesting targets for probing epigenetic regulation. Tripartite motif-containing (TRIM) protein 24 and 33 are transcriptional regulators, each containing a C-terminal tandem PHD-bromodomain motif which recognises methylation states and acetylation of modified histone lysine residues. TRIM33 functions within the PARP-dependent DNA damage response pathway, where it is responsible for the timely removal of chromatin-remodelling enzyme ALC1 from sites of DNA damage through its bromodomain. Loss of TRIM33 causes prolonged association of ALC1, and therefore extended chromatin relaxation, which leaves DNA exposed and increases the susceptibility of cells to further DNA damage. The aim of this study was to develop tool compounds to probe the functions of TRIM33 in epigenetic regulation, and to validate this protein as a therapeutic target in situations where DNA damage is increased. This work describes the two approaches taken; targeting the bromodomain with small molecule ligands, and incorporating these ligands into the design of proteolysis-targeting chimeras (PROTACs) to induce degradation of TRIM33 in cells. Initial work identified a compound as binding to the bromodomains of TRIM33 and TRIM24. Subsequent removal of the sulfonamide moiety and extension of the amine chain gave selective binding of the TRIM33 bromodomain over the KAc binding pocket of TRIM24. The ionic interaction between E981 and the protonated benzylic amine proved essential for both TRIM33 affinity and selectivity. Dose-response AlphaScreen™, WaterLOGSY NMR experiments, and ITC were used to evaluate ligand binding. Two additional acetyl-lysine mimicking head groups were assessed, but the original benzimidazolone core appeared to produce the optimal orientation of the head group relative to N1039, the residue responsible for recognition of acetylated lysine residues. Probing the hydrophobic region above the KAc binding pocket through lipophilic extension of the head group, sulfonamide projection adjacent to the benzylic amine, and projection of small groups from an alternative vector, all reduced affinity for TRIM33β. Focusing on the amine chain, aiming to bias the 'pincer' interaction of the two amines around E981, produced several low micromolar ligands with selectivity over TRIM24. These are the first confirmed ligands for the TRIM33 bromodomain. These ligands, and knowledge gained from the SAR studies, were subsequently used in the design of a series of TRIM33-targeting PROTACs. The initial PROTAC series incorporating the lead ligand had low cell permeability, with only three of the 17 PROTACs synthesised appearing in the cell at low concentrations. Consequently, no degradation of TRIM33 was observed in RKO cells. A second series was designed to increase cLogD values by focusing on alkyl linkers and masking hydrogen bond donors. This aimed to increase the concentration of PROTAC within the cell, thus improving the likelihood of ternary complex formation and degradation. Of the six PROTACs synthesised, three were shown to have high cell permeability. Assessment of these three PROTACs in RKO cells revealed that one PROTAC showed time-dependent reduction in TRIM33 levels, with the lowest levels showing around 70% reduction at 16 h after treatment. Therefore, this work describes the discovery of a range of chemical tools that can be used as a basis for further optimisation. This will ultimately enable us to establish the impact of either degrading or inhibiting the bromodomain of TRIM33 in cancer cells, in situations where DNA damage is increased such as radiotherapy. Additionally, work to determine if TRIM24 can be recruited as an E3 ligase in PROTAC-mediated degradation of BRD4 was also explored, which has the potential to allow context-specific degradation, as TRIM24 is overexpressed in many cancers.

The chemical modification of proteins has provided a toolbox enabling many experiments in chemical biology. However, new strategies are required to be able to specifically target (hetero)aromatic residues. Fluorine atoms installed in proteins can serve as useful tags, but methods for efficient and selective chemical fluorination are limited. This thesis has explored the modification of native residues in proteins with fluoroalkyl radicals to address the shortage in current methodologies. The study began with the investigation of trifluoromethylation, using biocompatible oxidative generation of CF3 radicals from a sulfinate precursor, and resulted in a robust protocol for selective modification of tryptophan residues. Proteins modified with this minimally perturbing tag could be readily studied by protein observed 19F NMR. To evaluate possibility of 18F-trifluoromethylation, the automated radiosynthesis of the radical precursor was achieved, but unfortunately, the protein radiolabelling proceeded with a limited efficiency. On the other hand, the study of protein difluoroethylation, using the same radical generation system, revealed an unexpected N-modification of proteins, for which the mechanism was proposed (oxidative hydrolysis of fluoroalkyl sulfinates). To reduce this side reactivity, an improved fluoroalkylation protocol was developed, based on the photoredox activation of heteroaryl sulfones as radical precursors. The platform was used to study reactivity and selectivity trends of various fluoroalkyl radicals, which resulted in the detailed investigation of difluoromethylation. The preference for the formation of unstable difluoromethyl tryptophan products was used for the development of selective C-formylation of proteins, relying on a key step of the denaturative hydrolysis of the CF2H group. As such, a new method was established for the installation of a masked aldehyde, also serving as a minimal size fluorescent probe. Overall, the studies of radical fluoroalkylation of proteins yielded useful methods for modification of typically solvent inaccessible residues (specifically tryptophan), under-targeted in protein chemistry, with applications in protein observed NMR and bioconjugation.

This thesis reports two projects aimed at addressing challenges within fragment-based drug discovery. The first project describes efforts towards utilising synthetic methodology to address deficiencies within fragment screening collections. This involved the development of a modular, robust and scalable route to access α,α-disubstituted amino ester building blocks, which in turn were derivatised to allow the rapid assembly of five (a total of eight in collaboration) spirocyclic scaffolds. Importantly, this library was structurally diverse, comprising three (a total of six in collaboration) pharmacophore-like heterocycles and carbocycles. Moreover, numerous three-dimensional exit vectors were incorporated within each core spirocycle, and the ability of these handles to effect a diverse set of chemical modifications was exemplified through the generation of 16 (a total of 21 in collaboration) examples. Computational studies highlighted the excellent physicochemical and 3D properties of the library, as well as the broad coverage of underexplored chemical space that was achieved. This library was also screened for antibacterial activity in a phenotypic assay against the clinically relevant bacterial strains, Pseudomonas aeruginosa and Staphylococcus aureus. The second project examined the inhibition of propionate detoxification mechanisms in bacteria as an attractive strategy for the development of antibacterial agents. A fragment screening campaign against 2-methylcitrate synthase (PrpC) from Pseudomonas aeruginosa identified several hit compounds based on an indole unit. Synthetic efforts were undertaken to elaborate these fragment hits to increase potency. The adopted strategy focused on growing the indole fragment towards the nearby oxaloacetate binding pocket and occupying it with a fragment mimicking its natural substrate. This approach yielded a compound with an in vitro half maximal inhibitory concentration of 130 μM against the enzymatic activity of PrpC.

Cytochrome P450 enzymes are known for their characteristic activity of C–H bond oxy-functionalisation whereby one oxygen atom of atmospheric dioxygen is inserted in an available carbon-hydrogen bond of their substrates, such as drugs and natural products, to form the alcohol derivative. Cytochrome P450BM3 from Bacillus megaterium has been extensively engineered to develop biocatalytic pathways to bioactive compounds due to its self-sufficiency, high expression level and promiscuity in substrate recognition. In this thesis, a high proportion of available carbon-hydrogen bonds in cyclic amines and lactams have been shown to be oxidised by engineered P450BM3 variants with high turnover and reasonable regioselectivity (Figure 1). A combination of substrate engineering via introducing substituents (methoxy and methyl), N-protecting groups (phenyl, benzyl, acyl, Boc, mesyl, tosyl, and isopropylsulfonyl) and auxiliary carbocycles (cyclopentane and cycloheptane), and protein engineering by site-directed and site-saturation mutagenesis at active site residues identified by screening with a 48 P450BM3 variant library of diverse substrate pocket topology and polarity, have enabled the oxidative diversification of these core motifs in numerous FDA-approved drugs. Unusual activities of P450BM3 – the Povarov reaction with N-phenyl cyclic amines and N1-C8' coupling (amination) of 6-methoxy-1,2,3,4-tetrahydroquinoline – were also discovered. Biotransformation in vivo and in vitro of these substrates reached 1 g/L/day with 20 mM substrate conversion at turnover numbers of up to 15,000. The research has provided the basis for developing alternative routes to hydroxy and multi-functionalised cyclic amines and lactams, introducing synthetic handles for functional group elaborations of such compounds which are frequently used in fragment-based drug discovery.

Chapter 1 introduces tertiary amines, and the main strategies available for their synthesis. Vaska’s complex is introduced, and its recent use for the reduction of tertiary amides and lactams is exhaustively described. Chapter 2 details the development of a spirocyclisation methodology from indole-tethered tertiary amides and lactams. The selectivity observed and the broad substrate scope make it a method of choice for the synthesis of spirocyclic indolines. Chapter 3 describes the development of a cycloaddition methodology, based on accessing azomethine ylides from tertiary amides and lactams, and reacting these 1,3-dipoles with a range of dipolarophiles, generating polycyclic amines. It is of value for the synthesis of polysubstituted pyrrolidine ring-containing amines. Chapter 4 details the investigations towards the design and application of a synthetic sequence leading to the total synthesis of a pentacyclic alkaloid, catharanthine. Previous syntheses are described, before model studies establish the feasibility of an IMDA cascade sequence triggered with Vaska’s complex. The natural product synthesis is then described. Chapter 5 details our efforts towards making the previously described methodologies amenable to large scale, and why they should be particularly attractive for industrial applications. Finally, preliminary results for the synthesis of new Vaska-type Iridium complexes for the reduction of non-tertiary amides functional groups are described.

This thesis details the development of a protocol for the catalytic enantioselective Minisci-type addition of prochiral radicals to heteroarenes through the dual techniques of chiral Brønsted acid catalysis and photocatalysis. The first research section details the initial hypothesis, design and implementation of our strategy for the enantioselective -C–H heteroarylation of alcohols by regio- and enantioselective Minisci reaction. The encountered barriers to fully successful realisation of the transformation are discussed. Subsequently, an enantioselective Minisci reaction involving N-acetyl-aminoalkyl radicals, generated by photocatalytic reduction of redox-active esters, is described. The reaction is found to be successful for a range of N-acetyl-aminoalkyl radicals on a range of quinolines and electron-deficient pyridines with high levels of regio- and enantioselectivity. The third research section describes a collaborative effort with Dr Jolene Reid and Prof. Matthew Sigman to establish a quantitative structure-activity relationship (QSAR) between reaction components. The resultant mathematical model allowed the prediction of enantioselectivity for then-undescribed asymmetric Minisci-type reaction of pyrimidines and pyrazines. The final research section addresses the possible degradation pathway observed in our initial hydroxyalkylation strategy by controlling reaction temperature and a crucial switch of photocatalytic system through consideration of the reaction mechanism. Hydrogen atom abstraction is also demonstrated to be effective for radical generation from linear amides, as a synthetically preferable alternative to redox-active esters.

Non-covalent interactions are commonly used in nature to control the selectivity of chemical transformations. Inspired by this, synthetic chemists have begun to use them to control selectivity in small molecule catalysis. Two types of interaction that are frequently exploited are hydrogen bonding and ion-pairing. This thesis details efforts to use these interactions to control both the regio- and enantioselectivity of iridium-catalysed arene borylation, an incredibly synthetically useful transformation that commonly suffers from a lack of regioselectivity, and for which enantioselective variants are very few. The strategy followed involved the design and synthesis of novel bipyridine ligands containing a distal anionic sulfonate group, that when bound to iridium can interact with substrates, either through ion-pairing or hydrogen bonding interactions, controlling the selectivity of the transformation. Building on previous work in which a sulfonated bipyridine ligand was developed to promote the meta-selective borylation of aromatic ammonium salts and amides through ion-pairing and hydrogen bonding respectively, the first part of this thesis explores the design and synthesis of larger bipyridine ligands with a more remote sulfonate functionality, with the aim of promoting para-selective borylation. Through exploring various ligand scaffolds some promising outcomes were obtained, relative to the control, although selectivities were still only moderate. Despite their often-privileged nature, chiral cations have generally found limited use in transition metal catalysis. The second part of this thesis explores a strategy in which a chiral cation, derived from the privileged class of cinchona alkaloids, is associated with an anionic sulfonated bipyridine ligand through ion-pairing. This chiral ligand enables a long-range, desymmetrising arene borylation to occur, forming new carbon or phosphorus stereocentres with high levels of enantiocontrol. The optimisation and scope exploration of this reaction is documented, as well as attempts to expand this methodology to kinetic resolution, although this was met with limited success. Additionally, mechanistic investigations identified both ion-pairing and hydrogen bonding interactions to be key for enantioinduction. Overall, this work aims to demonstrate that non-covalent interactions are an incredibly useful tool for controlling the selectivity of transition metal catalysis, particularly in achieving remote enantioselective functionalisation.

Oxygen- and nitrogen-containing heterocycles are precursors of many valuable synthons in both synthetic and medicinal chemistry, which facilitate the synthesis of a broad array of natural products with biological activities such as antitumor, anthelmintic, antimalarial, antimicrobial, and antiprotozoal. I have found that the polar and protic bonding solvent hexafluoroisopropanol (HFIP) plays an important role in the stereocontolled synthesis of complex oxygen- and nitrogen-containing heterocycles from simple linear precursors. My novel method for the stereoselective functionalisation of homoallyl alcohols/amines uses readily available allylic or benzyl alcohols as alkylating agents. Only one equivalent of the electrophilic partner is required for the cyclization process, and most of the products are obtained selectively as 2,3-trans diastereomers. Mechanistic studies reveal that Ti(OiPr)₄ in HFIP plays a unique role in this reaction, as the in-situ formation of the complex Ti(Oi-Pr)₂(OHFIP)₂, was found to initiate the cyclization, leading to a formal 5-endo-trig cyclization that involves the stereoselective formation of both a C-C and a C-O/C-N bond in a single synthetic step. This method has been proven to be efficient and atom economic especially because only a catalytic amount of Ti(OiPr)₄ is used and water is the only by product. Moreover, a wide range of the homoallyl alcohol or amine and electrophilic initiators show excellent compatibility with the system; finally, further functionalization of the products enables access to the synthetically useful heterocyclic molecules.

This thesis consists of the development of novel methodology to access difluoromethylated compounds both in the context of photoredox catalysis and fluorine-18 radiochemistry for Positron Emission Tomography (PET). First a general introduction to late-stage difluoromethylation will be showcased in Chapter I. In Chapter II, a metal-free visible light catalysed synthesis of difluoromethylarenes via a controlled hydrodefluorination of electron-poor trifluoromethylarenes is described. The reaction works both in batch and in flow and proves to be useful in the context of late-stage functionalisation. In Chapter III, a general introduction to PET is provided. General radiochemistry concepts are also introduced. In Chapter IV, a facile and robust radiochemical methodology for PET describing the synthesis of 18F-difluoromethylarenes from aryl boronic acids, ethyl bromofluoroacetate and cyclotron produced [18F]fluoride is presented. The two key steps involve a copper catalysed cross-coupling reaction using bench-stable aryl boronic acids to yield 2-fluoro-2-arylacetic acids in a two-step one-pot reaction followed by a manganese mediated 18F-fluorodecarboxylation to afford 18F-difluoromethylarenes in a streamlined fashion. Chapter V discusses the synthesis of the first 18F-difluorocarbene reagent and its application to react as a difluoromethylating reagent with phenols, thiophenols, N-heterocycles, and boronic acids. Chapter VI provides experimental data for compounds described within this thesis.

Chapter 1: Introduction This chapter provides the background of the pectenotoxins (PTX), which includes details of their isolation, structure, and biological activity. Subsequently, the total syntheses of PTX-4 by Evans and of PTX-2 by Fujiwara are discussed. Finally, past efforts of the Donohoe group towards the synthesis of PTX-4 are summarised. Chapter 2: Synthesis of the ABC fragment This chapter details the retrosynthesis and forward synthesis of the C1–C16 ABC fragment of PTX-4. Moreover, the chapter features extensive discussions on the optimisation efforts for key steps, including the osmium-catalysed double oxidative cyclisation step and the 1,2-hydride shift spiroketalisation cascade. Other major challenges, such as the unexpectedly difficult removal of an Evans oxazolidinone auxiliary, are also discussed. Chapter 3: Synthesis of the E fragment This chapter describes the retrosynthesis and forward synthesis of the C19–C30 E fragment of PTX-4. Experiments to troubleshoot and develop workarounds for an irreproducible regioselective hydroiodination step to give a vinyl iodide product early in the synthesis are documented. Finally, the synthesis of the C31–C40 F fragment of PTX-4 is briefly covered. Chapter 4: Uniting the ABC and E fragments This chapter discusses the elaboration of the ABC fragment into its vinyl boronic ester analogue for the planned rhodium-catalysed Hayashi–Miyaura 1,4-addition with the E fragment to unite the two major PTX-4 fragments. Optimisation studies for key reactions arealso discussed and include an allylation reaction, the 1,4-addition, and a dihydroxylation–ketalisation cascade to form the D ring. Chapter 5: Experimental This chapter lists all experimental procedures for the reactions described in this thesis, as well as the characterisation data for the compounds synthesised.

Dissolved organic matter (DOM) in the oceans stores as much carbon as the atmosphere for thousands of years. However, our understanding of production, transformation and removal processes of DOM is still incomplete. At the West Antarctic Peninsula (WAP), rapid warming led to increased atmospheric and oceanic temperatures during the second half of the 20th century with reduced sea-ice cover and increased glacial melting. The WAP supports a productive ecosystem with intense primary production during the austral spring and summer when solar radiation is high and sea ice cover is reduced. Research on dissolved organic matter in this region is scarce. Concentrations of DOM here are low compared to lower latitudes but reasons for this remain unclear and the cycling of DOM is not fully understood. Because of the recent climate change in this region, its geographical distance from anthropogenic sources and the distinct seasonality of the ecosystem’s productivity, the WAP represents an ideal location to study processes involved in autochthonous DOM dynamics. This thesis integrates a suite of biogeochemical and physical data to develop an understanding of dissolved organic carbon (DOC) and nitrogen (DON) cycling at the WAP. Samples have been collected for spatial analysis with the U.S. led Palmer Longterm Ecological Research Program (PAL LTER) cruise team in 2017 and samples for temporal analysis are available from the UK’s Rothera Research Station as part of the Rothera Time Series (RaTS) from 2013 to 2016. In combination with other available physical, biogeochemical and biological data, processes driving the distribution and cycling of DOM over a range of spatial and temporal timescales are investigated. The temporal analysis from the RaTS data found DOC production occurring alongside particulate organic carbon production contrasting earlier studies where DOM production was found to occur later with a time lag of a few days to weeks. This thesis shows that DOC is produced and released directly by phytoplankton while DON shows more variable results. This might be due to high rates of DON cycling by both bacteria and phytoplankton. The spatial analysis (PAL LTER) confirmed earlier studies showing low concentrations of dissolved organic carbon and nitrogen. There is more variability and slightly higher concentrations of DOM in coastal waters compared to offshore regions. This is potentially due to higher primary production and bacterial responses but could also be affected by the introduction of glacial meltwater. DON correlates well with bacterial activity while DOC can be related to either bacterial or phytoplankton activity showing the different mechanisms affecting both DOC and DON production and removal. At stations with high bacterial activity in the surface waters, DOC and DON concentrations were found to be high but decrease rapidly with increasing depth. Due to a temporal offset in the retreat of sea ice from the open ocean towards the shore, the sampled stations are found to be at different stages of the phytoplankton bloom which is reflected in the biogeochemical data including DOC and DON concentrations. Particulate and dissolved organic matter cycling is coupled to some extent. DOC appears to be produced during the development of the first phytoplankton bloom of each season but is decoupled from direct production of POC thereafter, possibly due to bacterial removal and production processes. DOC and DON are highly decoupled throughout the investigated seasons and across the WAP shelf. The C and N isotopic compositions of particulate organic matter in both the spatial and the temporal data sets confirm intense upper-ocean recycling of organic matter with little export to greater depths. Further, the N-isotopic composition shows that nitrification plays an important role in the upper ocean at the WAP with nitrified nitrate and potentially ammonium being produced and taken up by phytoplankton at the later stage of phytoplankton activity. Ammonium measurements were only available for the RaTS data sets but show that the seasonal variability is intense. Increased production of ammonium in the upper ocean is related to lowered DON concentrations showing rapid ammonification. The contribution by meltwater from both glaciers and sea ice was analysed. While direct contributions of DOM from these sources are likely, they are suggested to be minor due to intense dilution with seawater. However, indirectly, DOM dynamics are likely affected intensely by the addition of sea-ice algae, bacteria, particulate organic matter and nutrients and effects on the physical structure of the water column, all of which can affect the production, transformation and removal of DOM. This thesis shows that processes driving DOC and DON dynamics are complex in the ocean of the WAP. There are different processes acting on DOM compounds in different regions of the WAP at different timescales. DOM produced at the WAP seems to be of a highly labile nature, supported by low DOC:DON ratios overall. High surface DOM concentrations decreased rapidly with depth which shows high rates of bacterial degradation. These findings suggest that if DOM production increases in this region, as projected by various studies due to a warming climate and increased meltwater addition, upper-ocean cycling of carbon and nitrogen might increase while carbon export decreases. This thesis contributes to our understanding of carbon and nitrogen cycling in high productivity Southern Ocean shelf environments with implications for the functioning of the regional biological carbon pump.

The formation of rings in carbon backbones is essential for the biological activity of many natural products. The polyether tetronate antibiotics tetronasin, tetronomycin, and tetromadurin (SF2487/A80577) are notable for their ring diversity, each possessing a tetronate, cyclohexane, tetrahydropyran, and at least one tetrahydrofuran ring. The antibiotic activity and complexity of these polyether tetronates has led to research on their biosynthesis from actinomycete bacteria. Despite this, the mechanism of stereospecific cyclohexane and tetrahydropyran formation has remained mysterious. Although no formal [4+2] cycloaddition (Diels-Alder reaction) is predicted in the biosynthesis of these compounds, the biosynthetic gene clusters of all three were found to contain a pair of genes that encode homologues of two different [4+2] cyclases previously identified in complex spirotetronate pathways. Specific gene deletions demonstrated that both classes of [4+2] cyclase homologue are essential for polyether tetronate biosynthesis. In the tetronasin producer, Streptomyces longisporoflavus, deletion of the [4+2] cyclase enzyme homologue gene tsn11 resulted in production of a new metabolite that was characterised as an open form of tetronasin lacking both cyclohexane and tetrahydropyran rings. Incubating this metabolite with purified Tsn11 resulted in the production of an unknown intermediate labelled T-22. The structure of T-22 was determined using NMR to contain an unexpected oxadecalin moiety but still lack the tetrahydropyran ring, implicating Tsn11 as catalysing an apparent inverse-electron-demand hetero-Diels-Alder reaction. Remarkably, incubating T-22 with purified Tsn15, the other [4+2] cyclase homologue, formed the tetrahydropyran ring and fragmented the oxadecalin moiety to a cyclohexane ring, producing tetronasin. To gain structural insight into the novel activity of Tsn15 it was successfully crystallised. The structure of Tsn15 was then solved at 1.8 Å using SAD phasing; and Brazilian collaborators solved a Tsn15-ligand structure at 1.7 Å. Tsn15 shares the same eight-stranded β-barrel fold as its [4+2] cyclase homologues. The two main mechanisms considered here for the Tsn15-catalysed conversion of T-22 into tetronasin were a general acid/ base or a pericyclic mechanism. Site-directed mutagenesis of the Tsn15 active site indicated that none of the acid/base amino acid side chains were essential for activity, favouring instead the pericyclic mechanism.

Transition metal catalysed C-H activation is a highly desirable strategy for the functionalization of organic molecules. It allows for a rapid generation of structurally complex products from simple precursors in an atom- and step-economic fashion. Iridium catalysed borylation of arenes is a powerful yet mild C-H activation transformation which yields synthetically useful boronate esters. Interestingly the selectivity of this reaction is largely based upon steric considerations. As a result, the process is highly effective for 1,3-disubstituted arenes but produces a statistical mixture of regioisomers for 1,2-disubstituted arenes. Non-covalent interactions are a very powerful tool, utilized beautifully in enzymatic catalysis to address issues of regio- and enantioselectivity. In sharp contrast however their utilisation in directing the same aspects of selectivity in transition metal catalysed transformations is rather underexplored. This doctoral thesis aims to explore the use of non-covalent interactions in this setting. Chapter 2 of this thesis discloses the evaluation of an anionic sulfonated bipyridine ligand, previously reported within the group, to act as a hydrogen-bond acceptor to interact with aromatic amides. This interaction was shown to be crucial for the development of a meta-selective borylation process with excellent levels of meta-selectivity seen on three distinct substrate classes: benzylamine, phenethylamine and phenylpropylamine derived amides. Chapter 3 explores the further development of the sulfonated bipyridine scaffold with the introduction of a chiral counter-cation. The approach allows for the formation of a chiral environment around the metal centre via a chiral counter-ion directed catalysis and was demonstrated on the example of desymmetrising iridium catalysed borylation of arenes. The design and development of a modified version of the sulfonated bipyridine ligand bearing a cinchona alkaloid derived counter-cation is presented. The novel ligand design has enabled the borylation of meta-substituted benzhydrylamides and phosphinamides giving enantioenriched products in great enantioselectivities and good yields. When utilised for borylation of ortho-substituted benzhydrylamides, the process was demonstrated not only to be enantioselective, but also regioselective for the meta-position. The reaction represented a rare case of utilising a chiral cation to direct enantioselectivity of a transition metal catalysed process, enabling a challenging enantioselective remote C-H activation to yield highly versatile boronate ester products.

The work outlined in this thesis covers the development of visible light-mediated cyclizations of cyclic enones. Chapter one provides an overview of photochemical cyclizations, focusing on visible light-mediated cyclizations using triplet energy transfer from a suitable sensitizer, as well as an overview of the photochemical cyclizations of cyclic enones. Chapter two discusses the development of a visible light-mediated intramolecular arylation of cyclic 2-arylheteroenones to generate a wide range of cis-fused heterocycles. Chapter three details efforts into the photochemical synthesis of spirocyclic compounds via intramolecular hydrogen atom abstraction using a cyclic enone chromophore. Chapter four discusses the development of a visible light-mediated spirocyclization of cyclic 2-amidoenones. After initial optimization, the scope and scalability of the reaction was explored, and derivatization of the products investigated. Subsequent mechanistic experiments provided insight into the high diastereoselectivity of the reaction. Chapter five looks at applications of the previously developed reactions to acyclic chromophore systems, and the challenges present in this modification.

Mupirocin, produced by Pseudomonas fluorescens, displays antibiotic activity against a wide range of Gram positive bacteria including methicillin-resistant Staphylococcus aureus (MRSA). It is a mixture of pseudomonic acids A, B and C as described in chapter one. Biosynthetic studies have provided an insight into the assembly of the polyketide backbone and post assembly modifications. However, some features of the biosynthetic pathway remain unknown including the timing and mechanism of 6-hydroxylation and the mechanism of tetrahydropyran (THP) ring formation. Chapter two describes investigations into the gene responsible for 6-hydroxylation, tentatively assigned as mupA in mupirocin biosynthesis. Thioester 28 was prepared in 11 steps via a key cross metathesis step to install the 10,11-alkene (pseudomonic acid numbering), followed by an aldol reaction to install the stereocentre at C-7. The synthesis of pantetheinic substrate 29 utilised a hydroboration to install the stereocentre at C-8, followed by a Suzuki cross coupling to establish the E alkene. Enzyme assays of these substrates were carried out with MupA, the results of which are discussed herein. Chapter three describes the synthesis of linear substrates 161 and 187, and studies towards the preparation of amine 196, to probe the specificities of MupW and MupZ, the enzymes responsible for the formation of the THP ring. The synthetic route to thioester 29 was adapted to introduce the fatty acid side chain of substrates 161 and 187 via a Mukaiyama aldol reaction. Bioassays of substrates 161 and 187 were carried out to provide insight into both the mechanism of the ring closure and the specificities of MupW and MupZ.

This thesis concerns the development of a stannane-free method for generating reactive free radicals adjacent to a 2,5-disubstituted furan, the development of a furan oxidation method, and the total synthesis of the legonmycins, bacterial pyrrolizidine alkaloids. The synthetic utility of free radicals, and the effectiveness of organotin compounds in generating them, are discussed in Chapter 1, as are the reasons for avoiding organotin contamination of synthetic compounds, established means for doing so, and photoredox catalysis. The synthesis of model substrates for photoredox-mediated hydrogen abstraction from 2,5-disubstituted furans is described in Chapter 2. Visible light-mediated cyclisation did not occur as intended, but the use of a polyoxometalate cluster and ultraviolet light to effect the same transformation is also described. Chapter 3 concerns the synthesis of precursors to tin-mediated generation of free radicals adjacent to furan, the behaviour of those radicals once formed, and the implications for the work described in Chapter 4. A side reaction was observed when carrying out the work described in Chapter 2; Chapter 4 describes the development of this into a method for complete and efficient conversion of furans into 2-ene-1,4-dicarbonyls, complementing existing methods for the same transformation. Chapter 5 describes abortive routes for the total synthesis of legonmycin A, via the methodology described in Chapter 4 and via nitrile activation upon acylation, and a successful route based on an existing synthesis of the jenamidines, incorporating an iodine-catalysed hydroxylation with O2 as the terminal oxidant. This transformation proved problematic in previous syntheses of similar structures.

This thesis centres on the asymmetric syntheses of a family of synthetic products: dihydroconduramines and conduramines. The work aims to use the ammonium-directed epoxidation methodology as a key step in all cases. Chapter 1 introduces a review of literature reports relating to the biological activity and synthetic strategies to access dihydroconduramines and conduramines. Chapter 2 investigates the olefinic oxidation protocol of racemic N-protected anti- and syn-2-aminocyclohex-3-en-1-ols. Concise syntheses of racemic dihydroconduramines (±)-A-2 and (±)-C-2 are also presented. Chapter 3 describes the syntheses of enantiopure N-protected anti- and syn-2-aminocyclohex-3-en-1-ols in order to access enantiopure dihydroconduramines. Investigation of the surrogacy of these substrates to the racemate is also undertaken. Chapter 4 details the asymmetric synthesis of four new enantiopure dihydroconduramines from an appropriate enantiopure anti-2 aminocyclohex-3-en-1-ols. Chapter 5 details the asymmetric synthesis of six enantiopure dihydroconduramines from an appropriate enantiopure syn-2 aminocyclohex-3-en-1-ols. Chapter 6 investigates the olefinic oxidation protocol of primary, secondary and tertiary racemic allylic amino alcohols, derived from ring-opening of benzene oxide with primary, secondary and tertiary amines. Chapter 7 describes concise asymmetric syntheses of six conduramines, including four new, from enantiopure allylic amino alcohols, derived from ring-opening of benzene oxide with (R)-α-methylbenzylamine. Chapter 8 contains full experimental procedures and characterisation for all compounds synthesised in chapter 2-7.

The structural complexity and biological activity of marine natural products have made them attractive targets for synthetic chemists. In cases where their relative and/or absolute configuration is unknown, total synthesis becomes a powerful method to enable their structural elucidation, as highlighted in Part I. This thesis discusses synthetic efforts towards two marine natural products, hemicalide (1) and phormidolide A (2), with the end goal of establishing and/or confirming the compound's full stereochemistry. Hemicalide's low isolation yield from its marine sponge source meant that none of the 21 stereocenters were assigned in the original patent literature. Previous computational and synthetic work by Ardisson and Cossy, as well as the Paterson and Goodman groups, have narrowed down the possibilities for the C1-C15, C16-C25 and C35-C46 fragments to a single diastereomer with reasonable confidence. However, the relative configuration between fragments and the absolute stereochemistry remains unknown. Part II describes the synthesis of the C16-C28 dihydroxylactone fragment, which was used to successfully assemble a diastereomer of the C1-C28 truncate. Comparisons with the alternative configuration synthesised by Han enabled the definitive assignment of the relative configuration between the C1-C15 and the C16-C25 region of hemicalide. These studies also illuminated the nature of the C1 carboxyl group in the natural product. Phormidolide A possesses several fascinating structural motifs. Its terminal bromomethoxydiene (BMD) motif in particular, is unprecedented among natural products. Furthermore, inconclusive stereochemical evidence presented in the literature meant that a synthesis-guided stereochemical evaluation is required. Part III discusses synthetic efforts to the natural product, involving the expedient synthesis of the C18-C23 vinyl iodide and the C25-C33 side chain bearing the unique BMD motif. Towards the end goal of a total synthesis, this chapter also illustrates the evolution of the fragment coupling strategy, which led to the reassignment of seven of the 11 stereocentres present in phormidolide A.

Understanding the contribution of small molecule dynamics to bulk mechanical properties is of increasing importance in progressing the field of smart materials from benchtop curiosity to a design-based approach with myriad application. Hydrogels based on cucurbit[8]uril (CB[8]) supramolecular interactions are ideal candidates to study this relationship due to the variability in guests and binding modes it accommodates. In the first chapter earlier studies on pressure-induced changes in CB[8] hetero-ternary complexes, where the association rate was found to increase with external pressure, are extended to hydrogels harnessing these interactions. It appears that changes observed in the complexes are too small to be translated into viscosity changes of the bulk material, but unlike other systems used commercially, this system is unaffected by pressure. In an attempt to design a stimuli responsive, reversible system, dicationic azobenzene derivatives with various binding modes to CB[8] are studied in the second chapter. The isomerisation rates of the various derivatives are studied as a function of temperature, irradiation, presence of CB[8] and pH. Finally, a polymer bearing one of the azobenzenes is studied via rheometry for it's light-responsiveness. As pressure did not perturb the association event to a large enough extend to allow for studies on bulk mechanical behaviour as a function of association rate, several first guests were synthesised in an effort to amplify these differences. N,N -Dimethyl-4,4-bipyridine, N,N -dimethyl-2,7-diazaphenantrene and N,N -dimethyl-2,7-diazapyrene were synthesised in a systematic study based on increase in surface area of the first guest. Through use of complexation techniques as isothermal titration calorimetry (ITC) and stopped-flow fluorescence, the kinetics of complexation between these auxiliary guests in CB[8] and four second guests were studied. To translate the results of the small molecule techniques to bulk mechanical properties, functional derivatives of these first guests were prepared. Through semi-batch RAFT polymerisation these reactive first guests created branched polymers with CB[8] rotaxanes, which formed gels upon mixing with hydroxyethyl cellulose (HEC) bearing pendant second guests. Lastly, the effect of different binding modes between guest molecules and CB[8] on gel behaviour was studied for systems based on two different polymers, HEV and poly(vinyl alcohol) (PVA). These polymers were chosen to be of similar molecular weight but differ in rigidity. Through looking at the relaxation spectrum of gels composed of one or both of these polymers with either hetero or homo-ternary guests, the contribution of both polymer and host-guest chemistry is further elucidated.

This thesis explores two approaches to fragment-based drug discovery. First, protein target CK2 was chosen due to its importance in the cancer phenotype. A literature fragment, NMR154L, proved to be a promising compound for fragment development, due to its binding at the interface site of the protein rather than the highly conserved ATP pocket. Analogues were synthesised of this fragment leading to a candidate with a better IC50. Additionally, computer modelling of the interface site suggested that a series of spirocyclic compounds would inhibit this protein. These were synthesised and tested in vitro. Results from these tests were analysed and informed the synthesis of new inhibitors with the aid of crystal structures and computer modelling. Secondly, to address the lack of spirocyclic scaffolds in fragment screening libraries a number of diversity-orientated synthetic campaigns were undertaken. The first of these utilised glycine as starting material. Two terminal alkenes were installed. The alkenes were linked and the amino and acidic residues cyclised. This allowed for the formation of a diverse range of spirocyclic scaffolds from this one starting material. Having established chemistry for linking amino and acidic residues a campaign with dehydroalanine was under taken. This would allow for the installation of the second ring by pericyclic chemistry as well as using chemistry previously established. This pericyclic chemistry was also applied to synthesising spirocycles from rings with exocyclic double bonds. These being readily installed from Wittig chemistry, this allowed utilisation of starting materials which contained a cyclic ketone. Of these azetidinone was a good candidate due to the fact it was a commercially available building block and allowed access to spirocycles containing a 4-membered ring; an underrepresented ring size. Finally, computation analysis was carried out on the library to assess it diversity and any potential biological targets which these fragments may inhibit.

The brevianamides are a family of fungal derived prenylated indole alkaloids. Their range of complex structures are accompanied by a diverse array of biological activity. The brevianamides were the first reported examples of the wider bicyclo[2.2.2]diazaoctane class of natural products, which have been of continued interest due to their impressive polycyclic structures and the potential role of Diels-Alderase enzymes in their biogenesis. Despite prolonged synthetic attention, several important brevianamides have yet to succumb to total synthesis and many aspects of their biosynthesis remain unclear. This thesis describes our biomimetic synthetic studies towards these complex natural products, which has resulted in several short and efficient total syntheses. These syntheses have been enabled by a substantially improved synthesis of key intermediates, which are of general utility for the wider family of natural products.

Duchenne muscular dystrophy (DMD) is a muscle wasting disease arising from mutations in the dystrophin gene, affecting about 1 in 5000 boys. Whilst there is currently no available cure for DMD, a number of therapeutic strategies are under development. One such therapy aims to promote expression of utrophin, an autosomal paralogue of dystrophin. Utrophin upregulation rescues the dystrophic phenotype in disease model mice. A novel small molecule utrophin modulator, ezutromid (Summit Therapeutics; formerly SMT C1100), which was identified using a phenotypic screen, progressed to Phase II clinical trials in DMD patients. Interim 24-week data demonstrated reduced muscle fibre damage and increased levels of utrophin, providing the first evidence of ezutromid target engagement and proof of mechanism. However, these effects were not seen after the full 48 weeks of the trial. This work aims to define the mechanism of ezutromid in order to help understand the trial results, and to aid development of new generations of utrophin modulators. Target identification through affinity based protein profiling (AfBPP) has been carried out in this work alongside phenotypic profiling studies. AfBPP requires bioactive analogues suitable for affinity purification. Biotinylated and photoaffinity-labelled analogues of ezutromid designed to be positive and negative control probes have been synthesised and bioactivity confirmed. These probes were used in AfBPP experiments with disease model mouse myoblasts followed by LC-MS/MS. The results from this experiment and phenotype profiling converged on the aryl hydrocarbon receptor (AhR) as a target of ezutromid. Target validation studies demonstrated that ezutromid binds AhR potently, behaving as an AhR antagonist. Moreover, reported AhR antagonists also upregulate utrophin, showing that this pathway could be exploited in future DMD therapies.

Potassium (K+) efflux systems (Kef) are K+/H+ antiporters found in most Gram-negative bacteria. Kef systems play a vital role in the protection of bacteria from toxic electrophiles by regulating cytoplasmic pH and consequently demonstrate potential as an antibiotic target. Kef is inhibited by glutathione (γ-L-Glu-L-Cys-Gly, GSH) and activated by glutathione S conjugates (GSX). The proposed model of Kef activation in both EcKefC, from Escherichia coli (E. coli), and SdKefQCTDH6, a construct of Kef from Shewanella denitrificans (S. denitrificans), is a single amino acid switch at the F441 or F448 capping residue, respectively. The aims of this dissertation were to confirm the proposed mechanism of Kef activation and to investigate novel Kef systems in pathogenic bacteria as an antibiotic target. In work to probe the mechanism of Kef activation, p-trifluoromethyl-L-phenylalanine (ptfmF) was incorporated into SdKefQCTDH6 at position 448 to give SdKefQCTDH6(F448ptfmF). The conformational change of SdKefQCTDH6(F448ptfmF) upon adding inhibitory or activating ligands was analysed using 19F NMR spectroscopy. The data obtained are consistent with the proposed model for Kef activation: activators displace the capping residue, whereas inhibitors, including GSH, do not. This novel 19F NMR based assay is an efficient method to determine whether a compound is a Kef activator or inhibitor, vital in the design of new Kef ligands. To investigate whether the role played by Kef in E. coli is conserved across Gram negative bacteria, Kef systems were identified in two pathogenic bacteria: Yersinia pestis (YpKefB; with ancillary proteins -G and -P) and Burkholderia pseudomallei (BpKef1 and BpKef2). Dipeptides OXFKEF12-14 were synthesised and tested in E. coli expressing YpKefGBP, BpKef1, or 2 using the Kirby Bauer disc diffusion assay (Figures A and B). In E. coli MJF645 (mutant strain lacking GSH) and Frag 1 (GSH containing strain) expressing YpKefGBP, OXFKEF13 and 14 were active only in the MJF645 transformant, as a zone of growth inhibition/death was observed (Figure A). To rationalise these results, the expression level of YpKefBH6 (a His-tagged variant of YpKefB) was determined using western blotting and was found to be similar in both MJF645 and Frag 1. Due to its sequence similarity to YpKefBH6, it can be inferred that the expression level of YpKefB is also comparable in both cell strains, and so the opposing disc assay results must be caused by another factor. GSH may be inhibiting YpKefB, and so the dipeptides may be unable to outcompete it in the ligand binding site. OXFKEF12-14 could also be being degraded by GSH, giving compounds which inhibit YpKefB or are inert. As OXFKEF12-14 may be unstable in the presence of GSH, we wanted to synthesise dipeptides with improved stability with respect to GSH. Novel thioether analogues with aromatic S substituents were synthesised using the thiol-ene reaction: two methyl esters for the disc assay and their carboxylic acid analogues for biophysical assays. Both carboxylic acids were shown to bind to SdKefQCTDH6 using two orthogonal assays. Both methyl esters did not inhibit or kill MJF645 expressing SdKef or YpKefGBP in the disc assay. The inactivity of the compounds may have been caused by several factors, including their poor solubility. The results indicate that aromatic S substituents are tolerated in terms of Kef binding. In conclusion, we have shown that YpKefB is similar to EcKefC, both in terms of protein structure and function. In contrast, BpKef1 and BpKef2 behave differently from EcKefC. In Burkholderia pseudomallei, the endogenous low molecular weight thiol may not be GSH or the role of its Kef systems may be dissimilar from E. coli.

A dearomatisation approach to assemble the 6-5-9 fawcettimine core of Lycopodium alkaloids is examined.

Madeirolide A (1) is a structurally novel polyketide natural product first isolated from the deep-sea sponge Leiodermatium sp. by Wright in 2009. Initial biological investigations of madeirolide A revealed potent inhibition of the fungal pathogen Candida albicans but failed to determine any appreciable cytotoxicity when tested against a limited range of cancer cell lines. The unusual bioactivity of madeirolide A coupled with uncertainty over the true stereostructure of the natural product makes it a compelling target for synthesis. This thesis discloses synthetic efforts towards the total synthesis of madeirolide A with an emphasis on the construction of the all-cis C21 - C27 eastern tetrahydropyran. Chapters 1 and 2 provide an introduction to the importance of natural products in drug discovery and outline the context of this project with details of the isolation and biological activity of madeirolide A. Previous synthetic efforts are also reviewed including those from within the group which formed the basis of the present studies. Chapter 3 describes the synthesis of a fully elaborated C1 - C11 fragment, building upon previously published work in the group. Specifically, it details the successful completion of a modified approach designed to avoid some of the major challenges previously encountered such as undesired migration of protecting groups and challenges in selectively installing an (E)-vinyl iodide. Chapter 4 discusses ongoing efforts towards the challenging C12 - C27 fragment of madeirolide A. The stereocontrolled synthesis of several linear C19 - C27 precursors is outlined, followed by details of screening reactions conducted to affect the desired oxy- Michael cyclisation. Additionally, extensive computational studies have been undertaken in an attempt to rationalise the frustrating lack of reactivity observed with the goal of developing a substrate suitably elaborated to cyclise. Finally, the asymmetric synthesis of the C13 - C17 subfragment is outlined, which will provide eventual access to the eastern tetrahydrofuran. Chapter 5 summarises the synthetic work carried out thus far and explores potential strategies for the future completion of the natural product with a focus on alternative disconnections of the eastern tetrahydropyran.

Carbonyl compounds are of central importance to organic chemistry and their reactions have been described as the ‘backbone of organic synthesis’. Over recent decades, palladium-catalysed C–H carbonylation reactions have emerged as a powerful means of introducing carbonyl motifs to organic molecules. This thesis describes the development of a general C–H carbonylation reaction of secondary aliphatic amines, which provides facile access to synthetically useful β-lactam products. The first part of the thesis explores the scope and limitations of this reaction. Whilst previous C(sp3)–H carbonylation methodologies were restricted to ‘Type F’ secondary aliphatic amines, the reaction described in this thesis was found to be broadly applicable all structural sub-classes of secondary aliphatic amine. Furthermore, the reaction was found to be remarkably tolerant of functional groups, even those that commonly cause issues in palladium-catalysed C–H activation reactions such as heteroaromatics and thioethers. The second part of this thesis investigates the mechanism of this C–H carbonylation reaction. Interestingly, the reaction was found not to proceed via a traditional C–H carbonylation mechanism comprising of C–H activation, 1,1-migratory carbon monoxide insertion and reductive elimination. Instead, a new mechanistic paradigm for palladium-catalysed C–H carbonylation is proposed, which invokes a putative ‘palladium anhydride’ intermediate. A series of DFT calculations and experiments were conducted in order to support this mechanistic proposal. The work described within this PhD thesis was published in Science.

Over billions of years Nature has mastered the use of molecular factories that are not only able to perform chemical transformations with extreme efficiency, but are also controlled in a very detailed and specific way using a myard of molecular signalling systems. This amazing level of control over catalytic reactions has been our inspiration to design artificial catalytic systems that are able to be controlled using an external stimulus. These systems have been employed for anion-binding catalysed reactions and we have achieved a high level of control over the rate of the reactions, paving the way for new exciting processes. Chapter One contains an introduction to the most relevant concepts involved in the development of molecules able to interact with anions and reviews the current state-of-the-art in the emerging field of Anion-Binding Catalysis. Chapter Two details the development of a fully organic Pentafoil Knot, its reversible metalation and demetalation, its use for anion-binding catalysis and the allosteric regulation of catalysis with the in-situ generation of trityl carbocation as a catalyst. Chapter Three describes the use of Fe-metalated Pentafoil Knot in the catalytic Ritter reaction of activated halo-benzyl and -benzhydryl compounds for the generation of corresponding deuterated acetamides. Chapter Four illustrates the use of a [2]rotaxane-based dual switchable catalyst for total control over the rate of various anion-binding catalysed reactions and the development of a tandem process in which the two catalytic sites of the rotaxane system are employed sequentially.

The work presented in this thesis focuses on the total synthesis of (-)-6,7- Dideoxysqualestatin H5. Particular emphasis was the development of a cross- coupling strategy for direct delivery of the side chain towards the end of the synthesis. Various methods investigated to perform the key Csp3-Csp2 coupling initially led to the Fu variant of the Negishi coupling at elevated temperatures and subsequent cross- electrophile coupling at rt. Key features of the asymmetric synthesis of (-)-6,7- dideoxysqualestatin H5, include: (1) highly diastereoselective n-alkylation of a tartrate acetonide enolate and subsequent oxidation-hydrolysis to provide an asymmetric entry to a Î2-hydroxy-α-ketoester motif; (2) facilitation of Rh(II)-catalysed cyclic carbonyl ylide formation-cycloaddition by cogeneration of keto and diazo functionality through ozonolysis of an unsaturated hydrazone; and (3) stereoretentive Ni-catalysed Csp3-Csp2 cross-electrophile coupling between tricarboxylate core and unsaturated side-chain to complete the natural product. Following completion of the natural product, further work was carried out on the ozonolysis of unsaturated tosylhydrazones as a direct approach to diazocarbonyls. The scope and limitations of reacting unsaturated tosylhydrazones with O3 followed by Et3N for the generation of 1,4- and 1,5-diazocarbonyl systems were explored. Tosylhydrazones, from tosylhydrazide condensation with readily available Î ́- and Îμ- unsaturated α-ketoesters, led in the former case to a 2-pyrazoline whereas the latter cases led to α-diazo-Îμ-ketoesters, although a terminal alkene produced a tetrahydropyridazinol. Tosylhydrazones from cyclic enones also allowed access to 1,4- and 1,5-diazocarbonyl systems using the ozonolysis-Et3N strategy.

Introduction - Hydrogen Borrowing Alkylation Reactions Using Alcohols The introduction reviews the origins of hydrogen borrowing catalysis and how it has been applied to utilise alcohols as alkylating agents. The predominant focus is on highlighting the scope for the use of primary alcohols in the α-alkylation of ketones. Other nucleophiles are discussed with respect to the use of secondary alcohols as alkylating agents. Examples of related methodologies are also briefly discussed. Results and Discussion - Formation of α-Branched Products Using Primary Alcohols This chapter explores the alkylation of several ketone substrates and identifies cyclopropyl ketones as key structural motifs that facilitate the formation of α-branched products using primary alcohols. The development of an iridium-catalysed protocol for this reaction is described, including the optimisation of reaction conditions and investigation of the substrate scope with respect to the ketone and alcohol. The derivatisation of the resulting α-branched cyclopropyl ketones is also explored through utilisation of several ring-opening reactions. Results and Discussion - Formation of β-Branched Products Using Secondary Alcohols This chapter focuses on the development of an Ir-catalysed procedure for the alkylation of methyl ketones using secondary alcohols to form β-branched products. In developing this procedure, ortho-disubstituted aryl ketones were identified as key structural motifs that facilitated the reaction due to the unique properties they possessed. An overview of the optimisation of reaction conditions is provided, followed by exploration of the substrate scope with respect to the methyl ketone and the secondary alcohol. Derivatisation of the resulting β-branched products through bromine-initiated release of the aryl group, followed by trapping with several nucleophiles led to the formation of carboxylic acid derivatives. The final part of the chapter introduces preliminary studies towards the development of an asymmetric route to β-branched products. Results and Discussion - Formation of Cyclic Products Using Diols This chapter explores the development of an unprecedented Ir-catalysed procedure for alkylation of a methyl ketone using diols to form five-, six- and seven-membered carbocyclic rings. The optimisation of the reactions conditions is described followed by a systematic investigation into the diastereoselectivity observed in the formation of the carbocyclic rings. With the formation of cyclohexane rings identified as being most effective under the reaction conditions, these were then explored further in a more general substrate scope. The derivatisation of the cyclic products was also explored through a bromine-mediated release of the aryl group followed by trapping with a variety of nucleophiles. Experimental Section Experimental procedures are provided along with full spectroscopic characterisation of the compounds synthesised.

The health benefits of fish oil supplementations have been proven to be effective by several studies which are discussed in this thesis. It was found that these compounds had potent anti-inflammatory properties and since then has prompted much research into the use of these compounds as potential treatments for chronic inflammation based diseases, where the overuse of current anti-inflammatory drugs cause many problems with undesired side-effects. The aim of this research is to study the bioactivity of resolvin E1 and various analogues, and to determine a novel route towards resolvin E1 natural product so that bioactivity tests may be conducted in comparison of synthetically produced resolvin E1 and naturally extracted resolvin E1. The initial aim of this research was to develop a range of analogues of a fragment of Resolvin E1. This was so that a series of compounds could be produced with various R groups to identify any structure-activity relationships for this part of the natural product. There is one stereocentre in this fragment of resolvin E1 and it was decided that a racemic version of these compounds would be tested for bioactivity, and if any of the compounds had significant anti-inflammatory properties then the R and S versions could be separated, allowing for the testing of both enantiomers to determine which gave the most potent anti-inflammatory response. This led to the creation of several novel fragments and their biological testing. The secondary aim of the project was to complete the total synthesis of the resolvin E1 natural product. We devised a novel route towards resolvin E1 which used MIDA boronate protecting group to introduce a fixed trans double bond which was useful in a compound with multiple alkene systems. Resolvin E1 also contains three stereocentres, the synthesis from the fragment work was recycled to begin the synthesis, and made use of 1,2:5,6-di-O-isopropylidene-D-mannitol and Noyori s catalyst to setup the stereocentres. The use of new MIDA-boronate moieties were also explored in order to develop a new, efficient synthesis toward resolvin E1.

The aplyronines are a family of 24-membered macrolides of polyketide origin, isolated from the Japanese sea hare Aplysia kurodai. They exhibit an exceptional biological activity profile, acting through an actin and tubulin dual-targeting mechanism, with subnanomolar growth inhibitory potency against a diverse range of cancer cell lines. These characteristics render the aplyronines ideal payloads for antibody-drug conjugates but their prohibitively low natural abundance calls for an efficient total synthesis to overcome the supply issue. This dissertation describes the efforts towards developing a second-generation Paterson synthesis of the macrocyclic core of the aplyronines, focused on improving the scalability and selectivity of key transformations. Chapter 1 details the isolation, biological background and previous synthetic efforts towards the aplyronines to illustrate their therapeutic potential and the challenges associated with material sourcing by chemical synthesis. Chapter 2 presents the existing body of work on the aplyronine project within the Paterson group, highlighting the lessons learned over the past two decades and shortcomings to be addressed. Chapter 3 discusses a revised protecting group strategy towards the C1-C27 macrocyclic alcohol 159 with fewer manipulation steps. A refined reaction sequence featuring titanium aldol methodology and an enzymatic desymmetrisation process delivered multigram stocks of the C15-C27 aldehyde 161 upon scale- up, testifying to the robustness of the devised route. Synthesis of the C1-C14 northern fragment 253 closely followed the existing boron aldol approach with optimisation of the C11-C12 alkylation step, geared towards enhancing the regioselectivity. Chapter 4 describes the coupling of the two major fragments using an Horner-Wadsworth-Emmons reaction to assemble the C1-C27 backbone of the cyclic aplyronine core and suitably adjusted endgame steps to enable a one-step oxidative unmasking of the macrolactonisation sites. The first-generation intermediate 159 was accessed via site-specific Yamaguchi esterification and orthogonal deprotection of the C27 allyl carbonate. Discussion in Chapter 5 includes the appendage of the C28-C34 side chain 118, prepared by the known sequence, and suggestions for the future direction of the second-generation route with the outlook of linker appendage for the purposes of antibody-drug conjugate development.

This PhD project investigates the use of (Lewis or Brønsted) bases in catalysis. While the first chapter explores the use of main group metal amides in C–H bond activation reactions, the second chapter focusses on metal-free organocatalysis using so-called carbones. In the first chapter, formal allylic C(sp3)–H bond activations of unfuctionalised alkenes for C–C bond formations with imines were investigated. Alkali metal amides were used as catalysts for these transformations, giving homoallylic amine products. The investigations showed the unique reactivity of the Na-amide catalyst compared to other metal base complexes. The reaction scope and robustness was explored and initial insights into the reaction mechanism were obtained. A related K-amide catalyst was then developed for the isomerisation of allyl benzenes, as well as functionalised olefins such as allylic silanes, boronic esters, phosphines, amines, ethers, and thioethers. This part explored the use of ligands to increase the catalyst’s selectivity. Finally, the metal- or functional group-substituted classes of reagents were used in the functionalised allylation of imines, giving highly complex molecules with a diverse range of applications. Here, unprecedented reactivities were observed for the use of allyl–M reagents, as the allylation involved the activation of C–H bonds rather than C–X bonds. Furthermore, new catalytic formations of heteroatom-substituted homoallylic amines were described. The following chapter focussed on the use of carbodiphosphoranes (CDPs) in catalysis. These C(0) bases, or carbones, represent a class of heteroallene compounds that exhibit a high electron density on a P(V)-flanked carbon centre. Their potential as either a Lewis or Brønsted base was examined. Different CDPs were synthesised and reacted stoichiometrically with CO2, boron Lewis acids and metal salts. The generated intermediates were then studied in their reaction behaviour, taking advantage of a potentially available second pair of electrons. The results of these reactions were compared to other carbon bases, such as carbenes or other carbones. Finally, the Brønsted basicity of the CDP was examined in reactions with acidic pro-nucleophiles. The conjugate addition of alkylnitriles to α,β- unsaturated amides was developed using a catalytic amount of CDP. To the best of our knowledge, the first catalytic use of a CDP, as well as the first C–H bond activation of acetonitrile in Michael additions was reported.

This thesis centres on the synthesis of taxol analogues via late-stage hydroxylation with P450 enzymes. To accomplish this, the taxane core, specifically taxa-4(5),11(12)-dien-2-one, was synthesised by classical synthetic methods, and subsequently oxidised using P450BM3 mutants. Chapter 1 introduces enzymatic catalysis, and the advantages and disadvantages of its application to organic synthesis. Additionally, an overview of taxol, including its discovery, mode of action, biosynthesis and large-scale production, and a summary of the previously reported approaches to the taxane core are described. Chapter 2 details the problems encountered and solutions implemented when reproducing Baran's route to taxa-4(5),11(12)-dien-2-one. Furthermore, approaches to some of its intermediates and an alternative route to taxa-4(5),11(12)-dien-2-one, which is based on Baran's, are discussed. Chapter 3 describes the development of a new, practical and short synthetic route to taxa-4(5),11(12)-dien-2-one which, ultimately, led to 1,3-di-epi-taxa-4(5),11(12)-dien-2-one. Additionally, the application of this route to the synthesis of a model compound and attempts to convert this racemic synthesis into an enantioselective route are reported. Finally, the enzymatic oxidation of taxa-4(5),11(12)-dien-2-one and related molecules using P450BM3 mutants is explored in Chapter 4. A preliminary study to determine the substrate enantioselectivity of the mutants is also described, along with the biological assays of the oxidised compounds produced during the study.

Chapter 1: Introduction The isolation, biological activity and importance of the furanocembranoid family of natural products is outlined and a review of synthetic efforts towards their total synthesis provided. Both classical and catalytic methods for the synthesis of polysubstituted furan heterocycles are summarised, with an emphasis on olefin metathesis methods and their impact on the field. Chapter 2: Methodology Development and Model Studies Towards (+)-Lophotoxin The development of a temporary-silicon-tether ring-closing metathesis approach to trisubstituted furans is described. The discovery of Brønsted acid and photochemical cyclisation conditions is discussed and the scope of all procedures evaluated. The results of model studies towards to a total synthesis of (+)-lophotoxin are also reported. Chapter 3: Progress Towards the Total Synthesis of (+)-Lophotoxin The development of the retrosynthetic strategy and current progress towards a total synthesis of (+)-lophotoxin is discussed. Asymmetric routes to two key fragments are described, along with their union, and the application of the photochemical aromatisation procedure to the furan core of (+)-lophotoxin is disclosed. Chapter 4: Site-selective Modification of the Thiopeptide Anticancer Agent Thiostrepton This chapter focusses on a separate project, which aimed to provide synthetic tools to assist in structure-activity investigations of the natural product Thiostrepton. The natural product and its biological activity are introduced along with previous examples of its modification. The development of a general site-selective acylation reaction and the synthesis of a library of analogues is discussed. The results of their biological evaluation is also reported.