A number of privileged starting materials based on aryl halide frameworks have emerged that allow access to a variety of different heterocyclic scaffolds through judicious choice of reaction conditions. This work describes efforts to develop and extend the utility of two of these general heterocycle precursors - ortho-(haloalkenyl)aryl halides A and α-(ortho-haloaryl) ketones B - in conjunction with cascade reactions involving the construction of key carbon-heteroatom bonds via palladium or copper catalysis. Chapter 1 entails an overview of the development of palladium- and copper-catalysed carbon-heteroatom bond forming processes. The application of these processes in heterocycle synthesis using ortho-(haloalkenyl)aryl halide and ortho-haloacetanilides/ α-(ortho-haloaryl) ketone precursors is also described. Chapter 2 focuses on the development of a two-step synthesis of cinnolines using ortho-(haloalkenyl)aryl halides via intermediate protected dihydrocinnoline derivatives C. Chapter 3 demonstrates how the inherent reactivity of protected dihydrocinnoline derivatives C can be harnessed to provide access to functionalised products. A brief target synthesis of a pharmaceutically-relevent cinnoline is also described. Chapter 4 details attempts to develop a novel synthesis of benzothiophenes D from both ortho-(haloalkenyl)aryl halide and α-(ortho-haloaryl) ketone precursors.

The aim of this project was to develop new catalytic methods to control asymmetry in electrocyclic reactions, and to apply these methods to generate complex molecules. Initial efforts were directed towards the catalysis of anionic 8π electrocyclizations (Chapter 2 and Figure i). 8π electrocyclization was not achieved due to issues with alkene geometry and anion stability. Our efforts were then directed towards using phase-transfer catalysis to generate complex polycyclic compounds via a cascade electrocyclization-1,4-addition (Chapter 3 and Figure ii). Pyrrolidines and indolizidines were generated in excellent yield from simple starting-materials with high levels of stereocontrol. Finally, we investigated the catalysis of a 6π [1,6] electrocyclization to generate dihydroquinolones (Chapter 4 and Figure iii). A novel BINOL-derived copper(II) catalyst was developed, and afforded dihydroquinolones directly from their amine and aldehyde precursors with good yields and enantioselectivities.

Chapter 1 is a brief literature review of the most recent progress in the area of C-H functionalization via palladium catalysis. This covers the functionalization of electron deficient arenes and heterocycles with alkenyl and alkyl halides both using inter- and intra-molecular reactions. The chapter also contains an overview of recent work from the Willis group. Chapter 2 presents the functionalization of electron deficient arenes and alkenyl bromides using palladium catalysis, as well as the use of statistical analysis software for optimizing the cross-coupling reaction. Chapter 3 describes the cross-coupling of substituted benzoxazoles, benzothiazole and benzimidazole with a range of alkenyl iodides using palladium catalysis. The reaction can tolerate both (E) and (Z) disubstituted alkenes and tri-substituted alkenyl iodides, with retention of the double bond geometry. Chapter 4 details the synthesis of sultams via an intramolecular C-H functionalization using palladium catalysis. The chapter covers the optimization of the starting material synthesis as well as the cross-coupling reaction. We can access the sulfonamides from cyclohexenone and were able to incorporate a large range of substitution patterns (Scheme 3). Finally, Chapter 5 contains all the experimental details, general considerations and compound data. All the NMR spectra of novel compounds can be found in the appendix.

This work describes the extension of rhodium-catalysed intermolecular hydroacylation to encompass some tandem catalytic processes, wherein a further catalytic process is enacted on the product of an intermolecular hydroacylation reaction in “one pot”. Chapter 1 entails an overview of the development of hydroacylation chemistry, with a focus on the different types of catalytic systems which have been used to facilitate this transformation. A brief description of some precedented examples of tandem catalytic processes which include a hydroacylation reaction is also included. Chapter 2 describes the intermolecular hydroacylation of chelating aldehydes and propargylic alkynes to form γ-hydroxy-α,β-enones, and their subsequent acid-catalysed cyclisation to form substituted furans in a "one-pot" procedure. Additionally, a tandem intermolecular hydroacylation/double-bond isomerisation protocol for the synthesis of 1,4-dicarbonyl compounds is detailed, and the subsequent transformation of this class of compounds to heterocycles is included. Chapter 3 focuses on the development of tandem catalytic hydroacylation/reductive processes, wherein a hydroacylation product undergoes a reduction which is catalysed by the hydroacylation catalyst. Chapter 4 describes an attempt to utilise the rhodium-catalysed conjugate addition of arylmetal species to enomes to create a tandem alkyne hydroacylation/conjugate addition process. Chapter 5 encompasses the use of a small range of different solvents in rhodium-catalysed hydroacylation, in an attempt to find higher-boiling alternatives to acetone and a "green" alternative to the commonly used DCE.

<strong>Chapter 1. Introduction</strong> Scientific background on the development of homogeneous palladium-catalysed cross coupling reactions, focusing on the &alpha;-arylation reaction of enolates and its application to the synthesis of heteroaromatic compounds. The classical syntheses of isoquinolines are discussed, followed by an account of modern methods for their synthesis, including the recent &alpha;-arylation-based methodology developed by the Donohoe group. <strong>Chapter 2. Results and Discussion</strong> 2.1 Studies towards the development of a palladium-catalysed, C–H activation-based &alpha; arylation reaction of ketones, resulting in a C–H bromination/&alpha;-arylation sequence for the synthesis of isoquinolines and isoquinoline N-oxides. 2.2 The one-pot, four component coupling of a ketone, an acetal protected ortho-bromobenzaldehyde or ketone, an electrophile, and an ammonia source is described. This protocol, which ultimately provides C4 functionalised isoquinolines, is later extended to a novel &alpha;,&alpha; heterodiarylation protocol to furnish C4-aryl isoquinolines. 2.3 It is shown that the synthesis of 3 aminoisoquinolines can be achieved via the &alpha; arylation of nitriles. tert-Butyl cyanoacetate can act as a substitute for primary alkyl nitriles, with sequential &alpha;-arylation, in situ functionalisation, decarboxylation and cyclisation reactions provide C4 functionalised 3 aminoisoquinolines. 2.4 The synthetic utility of the &alpha; arylation based methodology for isoquinoline synthesis is exemplified by the total synthesis of the alkaloid berberine in 68% yield over five steps. This is followed by syntheses of pseudocoptisine, palmatine, dehydrocorydaline, and an unnatural fluorine containing analogue, in yields of 46%, 73%, 60% and 37%, respectively. 2.5 Finally, preliminary investigations demonstrate the utility of palladium-catalysed enolate arylation in the synthesis of &beta;-carbolines.

This thesis presents a combined experimental and computational evaluation of the physical-organic properties of butadiyne-linked porphyrin oligomers. The principal result from the thesis is the synthesis and characterisation of the largest aromatic and antiaromatic systems to date, in the form of an oxidised [6]-porphyrin nanoring, with diameter 2.4 nm. This large electronically coherent system provides insight into the connection between aromatic ring currents and persistent currents in metal and semiconductor mesoscopic rings. Chapter 1 briefly reviews the concepts used in the remainder of the thesis, with a particular focus on aromaticity. In Chapter 2, the barrier to inter-porphyrin torsional rotation in a butadiyne-linked porphyrin dimer is determined computationally and experimentally to be 3 kJ mol^-1. The barrier height is closely related to the resonance delocalisation energy between the porphyrin subunits. In Chapter 3 we show that by oxidising a butadiyne-linked [6]-porphyrin nanoring to its 4+ and 6+ oxidation states, the nanoring becomes antiaromatic and aromatic respectively. In contrast, the neutral oxidation state exhibits only local aromaticity for the six porphyrin units. The 12+ cation can also be generated, and exhibits local antiaromaticity for each porphyrin unit. The characterisation of (anti)aromaticity employs NMR and computational techniques. In Chapter 4, the properties of cation radicals of linear and cyclic porphyrin oligomers are explored. Cations generated by spectroelectrochemistry are measured by optical spectroscopies, and chemically generated radical monocations are examined by cw/pulsed EPR spectroscopies. EPR and optical spectroscopies agree that the dimer monocation radical is fully delocalised, in Robin-Day Class III, whereas the monocations of longer oligomers are localised over 2-3 porphyrin units (Class II). In Chapter 5, photophysical and computational investigations into excited state aromaticity in porphyrin nanorings are presented. The computational results suggest the presence of aromaticity in the triplet excited states, but experiment fails to convincingly demonstrate the effect. Computational results in Chapter 6 show that a butadiyne linked [6]-porphyrin nanoring in which one butadiyne (C≡C-C≡C) is truncated to an alkyne (C≡C) exhibits a reversal of aromaticity and antiaromaticity in its oxidised states, compared to the all-butadiyne linked nanoring, consistent with Hückel's law.

JMJD6 or PSR (phosphatidyl serine receptor) was initially proposed to be a membrane receptor involved in apoptotic cell clearance by recognition of apoptotic cells. However, sequence analyses implied the presence of a jelly roll or double stranded beta helix (DSBH) structural domain in PSR/JMJD6 and similarity with JmjC family of enzymes which are involved in chromatin regulation. Subsequently, PSR was renamed as JMJD6 and was reported to be a histone arginine demethylase. Previous work from our group has shown that JMJD6 is a lysine hydroxylase that interacts with nuclear proteins including CROP and U2AF65 which are involved in mRNA splicing. Peptide screening and cell based assays led to the conclusion that JMJD6 catalyses lysine hydroxylation of splicing regulatory proteins containing arginine serine rich domains (SR proteins) including U2AF65 and Luc7like-2. Studies were carried out to investigate the putative arginine demethylation activity of JMJD6 using MS analysis of histone peptides and luminescence-based assays. New substrates from SR proteins were identified by immunoprecipitation of JMJD6 expressed in human cell lines followed by LC-MS/MS analysis and MALDI-MS based assays of synthesised peptide substrates. Work then focussed on studying the mechanism of lysyl-hydroxylation from substrate and enzyme perspective. A crystal structure of seleno-methionine labelled JMJD6 was obtained and it provided insights into the JMJD6 active site and its substrate interactions. Based on this data, single point variants of JMJD6 were prepared and their substrate binding properties were studied by MALDI-MS and 2OG turnover assays. Collagen lysyl-hydroxylases are also 2OG dependent oxygenases. Efforts to investigate the stereochemistry of JMJD6 catalysed hydroxylation, employing NMR and amino acid analyses were carried out. These studies led to the interesting finding that the C-5 stereochemistry of hydroxylysine in LUC7L2 peptide is opposite (2S,5S-hydroxylysine) to that present in collagen (2S,5R-hydroxylysine). It was found that JMJD6 undergoes autocatalytic self-hydroxylation. Lysine residues from both recombinant JMJD6 and that from HeLa cells at endogenous level were identified to be hydroxylated by amino acid and LC-MS/MS analyses. JMJD6 has a strong tendency to form aggregates and gel electrophoresis always reveals multimeric bands of various JMJD6 constructs. Characterisation and identification of oligomeric states of JMJD6 was carried out using Electron Microscopy. Studies were initiated to identify possible inhibitors by screening a set of 2OG analogues. The results from this preliminary inhibition studies have identified the tricarboxylic acid (TCA) cycle intermediates, succinate and fumarate to be JMJD6 inhibitors and form a basis of further studies aimed at identifying selective inhibitors.

An ionic liquid (IL) is a salt, which usually is in the liquid state at normal temperature and pressure. The properties of ILs can be adjusted for various processes and applications by choosing different combinations of ions. Similar to other salts, ILs contain only ions with positive (cations) and negative (anions) charges in equal proportions. However, to prevent solidification, ions in ionic liquids usually contain bulky organic chemical groups, which, apart from electrostatic interactions, promote other types of interactions between ions, such as: (i) van-der-Waals interactions; (ii) hydrogen bonding; (iii) - stacking, etc., depending on the particular chemical structure of the ions. All these interactions, in combination, may lead to formation of specific microstructures in ILs, which may vary with temperature caused by changing thermal rotational and translational energies of the ions. Ions in these microstructures may have preferential orientations relative to each other, maintain anisotropic properties similar to those in liquid crystals or, in some specific cases, may even separate into microscopically organised liquid phases. Therefore, the dynamics of ILs may also be dependent on their microstructure. In many practical applications ionic liquids are placed on surfaces or in confinements. Solid surfaces introduce extra forces, which may be specific to the charge of the ions or/and to functional groups in the ILs. The geometry and interactions of ions in confinements or/and pores of materials may also disrupt specific bulk microstructures of ILs. Both confinement effects and interactions of ions with surfaces are manifested in the translational dynamics of the ions. One of the most direct and informative methods to study translational dynamics of ILs is pulse-field-gradient nuclear magnetic resonance (PFG-NMR).In this thesis the results of PFG-NMR studies on a few classes of ILs are reported: (i) the historically “standard” (since Walden’s discovery in 1914) ionic liquid, the ethylammonium nitrate (EAN) and (ii) halogen-free orthoborate-based phosphonium, imidazolium and pyrrolidinium ILs with varied structure and lengths of alkyl chains in cations, and varied structures of orthoborate anions. These ILs were studied in bulk at different temperatures, and also in confinements, such as between parallel glass and Teflon plates and in mesoporous Vycor glass. It was found that diffusion coefficients of cations and anions in EAN, phosphonium and pyrrolidinium orthoborate ILs in bulk are different, but according to the standard Stocks-Einstein model, they correspond to diffusion of ions in homogeneous liquids. A change in the chemical structure of one of the ions results in a change in both the diffusion coefficient of the oppositely charged ion and the activation energy of diffusion for both ions in an IL. Similar effects were observed from the chemical shifts and diffusion coefficients measured by NMR for imidazolium orthoborate ILs dissolved in polyethylene glycol solutions, in which imidazolium cations strongly interact with PEG molecules, further affecting the diffusion of orthoborate anions via electrostatic interactions. A liquid-liquid phase separation was suggested for a few phosphonium and pyrrolidinium bis(mandelato)borate ILs, in which a divergence of diffusion coefficients and activation energies of diffusion for cations and anions was detected at temperatures below ca 50 °C. In addition, a free-volume theory was invoked to explain the dependences of density of ILs on the alkyl chain length in cations.It was also found that for a phosphonium bis(salicylato)borate IL confined in 4 nm mesoporous Vycor glass the diffusion coefficients of ions increase by a factor of 35! This phenomenon was explained by the dynamic heterogeneity of this IL in micropores and empty voids of the Vycor glass. For EAN IL in confinements between glass and Teflon plates, the diffusion of ethylammonium cations and nitrate anions is significantly anisotropic, i.e. slower in the direction of the normal to the plates and faster along the plates compared to diffusion of the ions in bulk. A plausible explanation of this PFG NMR data is that EAN forms layers near polar and non-polar solid surfaces. A similar phenomenon, to a lesser extent, was also observed for phosphonium cations of bis(mandelato)borate, bis(salicylato)borate and bis(oxalato)borate confined between glass plates. The results of these studies may have implications in modeling tribological performance, i.e., friction and wear reduction for contact pairs of different materials lubricated by various classes of ionic liquids. / För godkännande; 2016; 20160420 (andfil)

Neutral cyclometalated platinum(II) N-heterocyclic carbene complexes [Pt(C^C*)(O^O)] with C^C* ligands based on 1-phenyl-1,2,4-triazol-5-ylidene and 4-phenyl-1,2,4-triazol-5-ylidene, as well as acetylacetonato (O^O = acac) and 1,3-bis(2,4,6-trimethylphenyl)propan-1,3-dionato (O^O = mesacac) ancillary ligands were synthesized and characterized. All complexes are emissive at room temperature in a poly(methyl methacrylate) (PMMA) matrix with emission maxima in the blue region of the spectrum. High quantum efficiencies and short decay times were observed for all complexes with mesacac ancillary ligands. The sterically demanding mesityl groups of the mesacac ligand effectively prevent molecular stacking. The emission behavior of these emitters is in general independent of the position of the nitrogen in the backbone of the N-heterocyclic carbene (NHC) unit and a variety of substituents in 4-position of the phenyl unit, meta to the cyclometalating bond.

This thesis presents the development and redesign of a commercial electrochemical quartz crystal microbalance with dissipation (E–QCM–D). This was used to study factors affecting the efficiency of the four electron reduction catalysed by the fuel cell enzyme bilirubin oxidase from Myrothecium verrucaria immobilised on thiol modified gold surfaces. Within this thesis, the E–QCM–D was used to show that application of a constant potential to bilirubin oxidase adsorbed to thiol-modified gold surfaces causes activity loss that can be attributed to a change in structural arrangement. Varying the load by potential cycling distorts the enzyme by inducing rapid mass loss and denaturation. Attaching the enzyme covalently reduces the mass loss caused by potential cycling but does not mitigate activity loss. Covalent attachment also changes the orientation of the surface bound enzyme as verified by the position of the catalytic wave (related to the overpotential for catalysis) and reactive labelling followed by mass spectrometry analysis. The E–QCM–D was used to show how electrostatic interactions affect enzyme conformation where high pH causes a reduction in both mass loading at the electrode and a reduction in activity. At pH lower than the enzyme isoelectric point, there is a build up of multilayers in a clustered adsorption. When enzyme adsorbs to hydrophobic surfaces there is a rapid denaturation which completely inactivates the enzyme. Changing the surface chemistry from carboxyl groups to hydroxyl and acetamido groups shows that catalysis is shifted to more negative potentials as a result of an enzyme misorientation. Further to this, increasing the chain length of the thiol modifier indicates that an increased distance between surface and enzyme reduces activity, enzyme loading and results in a conformational rearrangement that permits electron transfer over longer distances.