The majority of research in this thesis uses X-ray crystallography to investigate the structural features of peri-substituted naphthalene compounds. X-ray crystallography is introduced in chapter one, followed by a discussion on modes of distortion peri-substituted naphthalene derivatives can undergo, in chapter two. In chapter three, compounds having non-bonded -SPh and -EPh (E = S, Se, or Te) peri-substituents are compared. These similar compounds react differently when oxidized with bromine. The oxidation products are used to discuss a recently proposed mechanism and a more specific mechanism is suggested. In chapter four, a one-pot synthesis for naphtho[1,8-c,d]-1,2-diselenole (Se₂naph) is reported. Substituents were added to Se₂naph to form two new naphthalene compounds. The substituents are found to distort the Se-Se bond and influence packing. In chapter five, several diselenium-containing compounds are used as ligands in platinum(II)-bisdiphosphine complexes. The preference for platinum(II) to stay square planar dictates the geometry around the metal center, not the rigidity of the naphthalene backbone. Chapter six introduces (8-phenylsulfanylnaphth-1-yl)diphenylphosphine, a peri-substituted naphthalene containing -SPh and -PPh₂ substituents, and several derivatives. This ligand is used in a variety of complexes containing platinum(II), ruthenium(II), and copper(I) metal halides, whose coordination geometries are discussed in chapter 7. The naphthalene-based ligands in Cu(I) and Ru(II) seem to determine the geometry around the metal, whereas the metal center d-orbitals dominate in the Pt(II) examples. Chapters eight and nine deviate from the naphthalene theme. In chapter eight, X-ray analysis of sulfoxide compounds is used to discuss the structural environment around the sulfur. Various intra- and inter-molecular interactions were discovered in crystal packing. Finally, chapter 9 uses STANDARD (St ANDrews Automated Robotic Diffractometer) to statistically analyze numerous E₂Ph₂ (E = S, Se, or Te) crystals to determine chirality. It is intriguing that Te₂Ph₂ shows a preference for one enantiomer over the other.

Determination of the three-dimensional structure of enzymes at atomic resolution is a key prerequisite for elucidation of molecular mechanisms of catalysis and catalysis mechanism prediction. X-ray protein crystallography is the most widely used method today for determining protein structures. In this thesis we describe the expression, purification, crystallization and structure solution of two new enzymes: PyrH and PrnB. PyrH is a member of the new emerging family of FADH dependent tryptophan halogenases. It catalyzes the regioselective halogenation of tryptophan at the C-5 position of the indole ring. Elucidation of its structure (Chapter 2) and comparison with PrnA, aregioselective 7th tryptophan halogenase whose structure has already been solved confirmed the proposed mechanism of action for this class of enzymes. PrnB is the only enzyme known to perform exquisite and peculiar ring rearrangement chemistry: it converts 7-Cl-tryptophan and tryptophan into respectively monodechloroaminopyrrolnitrin and aminophenylpyrrole. We developed a method for expression and purification of milligrams of pure and homogeneous recombinant PrnB (Chapter 3). We identified suitable crystallization conditions and determined PrnB structure (Chapter 4). Analysis of the PrnB structure helped us to propose a reaction mechanism for this unique enzyme.

This study investigates the self-assembly of ligands consisting of sterically hindered backbones. Ligands synthesised in this study took advantage of the twisted nature of benzil-2,3-dihydrazone brought about by the steric repulsion between two neighbouring phenyl groups. Synthesis of all ligands used a simple imine condensation reaction, where benzil-2,3-dihydrazone was combined with a chosen aromatic aldehyde. Coordination studies were conducted using first row transition metals and described in text are the solid state structures of twelve new discrete supramolecular complexes, characterised by single crystal X-ray crystallography. Chapter 1 outlines an introduction to the topics discussed in this text, while providing examples drawn from literature and nature. Chapter 2 details the modified synthesis of bis-2-pyridyliminohydrazono-1,2-diphenylethane, L1, and the in-depth background of previous studies with the ligand. The complexes of L1 with Mn(II), Fe(II), Co(II), Cu(I) and Zn(II) determined by single X-ray crystallography are presented, noting the structural effects different metal ion sources have upon L1. In chapter 3 the modified synthesis and characterisation of bis-2-imidazolyliminohydrazono-1,2-diphenylethane, L2, is presented. Crystallographically characterised complexes from the combination of L2 with Mn(II), Ni(II), Co(II) and Zn(II) show the formation of interesting topologies which are compared to structures previously determined. Chapter 4 begins with a brief introduction to clusters, followed by the synthesis and characterisation of a recently synthesised ligand, bis-2-salicyliminohydrazono-1,2-diphenylethane, L3,. The formation of a Ni(II) cluster with L3 is further discussed in detail, and outlines the future scope for the work with these ligands. The synthesis and characterisation of L4, and the discussion of mononuclear complex formed between L4 and Cu(II) is also introduced. The chapter concludes with a discussion with the potential future direction of this work with these ligands and their related compounds. Chapter 5 concludes the results and discussion with a brief summary of these results. Chapter 6 outlines the synthesis and characterisation of all ligands and complexes used in this study as well as potential ligands for future studies.

Neuropeptidases are responsible for degradation of signaling peptides in the central nervous system and periphery. Some neuropeptidases have also been shown to play a role as part of the cell’s hydrolytic machinery responsible for breaking down proteins and peptides into amino acids, and these enzymes therefore influence small peptide availability for antigen presentation. A better understanding of how neuropeptidases recognize their substrates could lead to therapeutics that modulate the activity of these important enzymes. Alternatively, re-engineering these enzymes to selectively hydrolyze undesirable peptides could make them attractive as therapeutics themselves. A key question in understanding the activity of these enzymes is how they are able to recognize a variety of seemingly unrelated amino acid sequences as cleavage sites. We are investigating the basis for this general substrate recognition in neuropeptidases using thimet oligopeptidase (TOP) as a model. Crystal structures of TOP in complex with a variety of substrates and inhibitors shed light on the mechanisms underlying substrate recognition and pave the way for re-targeting substrate recognition in these enzymes. Nano test tube particles have been proposed as a means of delivering therapeutics such as enzymes. However, the template synthesis method for nano test tube production does not produce therapeutic quantities. In order to take full advantage of re-engineered neuropeptidases a new method for nano test tube synthesis has been developed. We show that a non-destructive template synthesis methodology can be applied to produce nano test tube particles in quantities useful for therapeutic enzyme immobilization.

The synthesis and coordination chemistry of eleven bridging ligands, eight of which are new compounds, are described. These ligands are all based on the tridentate terpyridyl system. The other metal ion binding sites of these ligands contain pyridine/bipyridine/pyrazole rings or amine/azamacrocycles domains. In these ligands, the two metal ion binding sites are differentiated by the number of atoms in each site, the configuration of the binding site or the types of donor atom that are present. This binding site differentiation allows to use the different coordination properties of the binding sites to control the regiochemistry of the complexation, ensuring that the correct metal ion is incorporated at the correct binding site in the ligand. Many of the complexes synthesised are mono-ruthenium(II) complexes where Ru(II) ions are situated in the terpyridyl sites of the ligands. These include heteroleptic Ru(II) complexes of the type [Ru(ttp)(L)]2+, where ttp is 4'-(p-tolyl)-2,2':6',2ʺ- terpyridine, and L is the bridging ligand. Reactions of the Ru(II) complexes with a range of metal ions including Co(III) ion have been investigated. The Ru(II) complexes can be classified into three main categories depending on the type of ligands that have been employed: (1) Ru(II) complexes which can react with Co(III) ions to form heterodinuclear Ru(II)-Co(III) complexes; (2) Ru(II) complexes which react only with Ag(I) ions and no other common metal ions that we have tried; (3) Ru(II) complexes with no detectable ability to coordinate other common metal ions. Following standard cobalt chemistry, some heterodinuclear Ru(II)-Co(III) complexes of the type [(ttp)Ru(cymt)Co(X)2]3+, where X = NO2 -, Cl-, and OH-, have been successfully prepared from the corresponding Ru(II) complexes. In these heterodinuclear complexes, anions such as NO2 -, Cl-, or OH- can be readily attached to the Co(III) ions. However, attachment of a neutral species such as en ligands to the Co(III) ions in the complexes proved to be more difficult. Reactions of heterodinuclear Ru(II)-Co(III) complexes with en ligands result in removal of the cobalt ions from the complexes. This is may be a result of a significant difference in the overall charges between the complexes with anionic and the complexes with neutral ligands (3+ vs 5+). Higher overall charge of the complexes when protonable ligands such as monodentate en are present, may destabilize the complexes even more. A combination of NMR spectroscopy, ESI-MS, UV-vis spectroscopy, elemental analysis, and X-ray crystallography has been used to characterise the ligands and their complexes. The crystal structures of one new ligand and sixteen complexes are described.

This thesis describes the preparation and characterisation of a number of homochiral coordination and metallosupramolecular assemblies. These species were formed from the reaction of chiral pyridine and quinoline containing ligands and metal ions. The combination of traditional coordination chemistry and supramolecular interactions led to a range of polymeric and network structures being formed. The ligands used in this thesis can be divided into two broad categories: alkaloids and ligands derived from them, and amino acid-based ligands. In the first category three new ligands were synthesized, and a variety of routes towards alkaloid-based homochiral ligands were investigated. The second category focused on three ligand motifs, and resulted in the preparation of 16 ligands. These two categories of ligands were reacted with a range of metal salts to investigate their coordination and supramolecular chemistry. The structure of twenty complexes was determined by single crystal X-ray crystallography. The complexes had a range of structures, with discrete and polymeric species being formed. Hydrogen bonding was an important feature in the supramolecular chemistry of the complexes, playing a different role in different series of complexes. Two chiral coordination polymers and one chiral coordination network were synthesized. All three of these structures possessed directionality to some degree: in the coordination network and one of the polymers the directionality is counterbalanced by the opposite directionality being present in the crystal, while the second coordination polymer is generated by the screw axis present and has a high degree of overall directionality.

The potential energy surface of naphtho (1,8-b,c) -1,5-dithiocin and its mono-, di-, tri-, and tetraoxides was analyzed by dynamic ¹H NMR spectroscopy, AM1 semiempirical calculations, and x-ray crystallography. The lowest energy conformers of these compounds in the solid state, the gas state, and in solution, as well as the energy barriers for the interconversion between their conformers are reported. The electronic structure of naphtho (1,8-b,c) -1,5-dithiocin was analyzed by the AM1 semiempirical method. An experimental method was developed to verify these calculations. Comparison of the relative intensities of the bands observed in the He I and He II photoelectron spectra of aromatic thioethers provides an effective means for assigning bands to ionizations from specific molecular orbitals. Such methodology confirmed the calculations which showed that naphtho (1,8-b,c) -1,5-dithiocin has a large sulfur-sulfur lone pair splitting of 1.6-2.0 eV. Dissolution of naphtho (1,8-b,c) -1,5-dithiocin-1-oxide in concentrated sulfuric acid produced the corresponding disulfide dication, which upon hydrolysis regenerated the sulfoxide. The mechanism of this reaction sequence was investigated using 2-monodeuterated naphtho (1,8-b,c) -1,5-dithiocin-1-oxide. This stereochemical probe showed that both the formation of the disulfide dication and its hydrolysis occurred with retention of stereochemistry at the sulfoxide sulfur. The molecular structure of naphtho (1,8-b,c) -1,5-dithiocin-1-oxide, determined by x-ray crystallographic methods, showed evidence of transannular interaction between the sulfur atoms. Vibronic analysis on naphtho (1,8-b,c) -1,5-dithiocin and naphtho (1,8-b,c) -1,5-dithiocin-1-oxide using the Hartree-Fock method with the STO-3G basis set showed no evidence of bond formation in naphtho (1,8-b,c) -1,5-dithiocin-1-oxide compared with naphtho (1,8-b,c) -1,5-dithiocin. Thus this transannular interaction in the sulfoxide must be due to electrostatic interaction and not incipent sulfurane formation. The mechanism of the photodecompositions of perester and aldehyde compounds with β substituted sulfur moieties was investigated. The photodecomposition of these compounds produced their corresponding alkenes without stereocontrol. These results suggest that the decompositions occur via a stepwise non-stereoselective mechanism. Flash photolysis of peresters β substituted with sulfonium salt groups was shown to produce thioether cation radicals, e.g., the 1,5-dithiocane cation radical. This demonstrated that the photodecomposition of β sulfonium salt peresters is potentially a powerful and novel method for making cation radicals.

The ubiquitin proteasome system targets proteins to the proteasome where they are degraded. Substrate recognition and processing prior to degradation take place at the 19S regulatory particle of the proteasome. A polyubiquitin chain, linked through isopeptide bonds formed between the C-terminal G76 and K48, is the signal responsible for delivery to the proteasome. Because chains linked via any of the seven lysine residues of ubiquitin exist in vivo and encode signals unrelated to protein degradation it is crucial for cells to avoid crosstalk between these different pathways. Several ubiquitin receptors related to proteasomal degradation have been identified but the selectivity between the different ubiquitin chains has not been assessed quantitatively while avoiding artefacts attributed to GST-dimerisation. By employing isothermal titration calorimetry, analytical ultracentrifugation and nuclear magnetic resonance, discrimination between K48- and K63-linked diubiquitin was established for the S. pombe proteasomal receptor Rpn10 and the shuttle protein Rhp23. The same methods allowed us to propose a discriminatory model for Rpn10. The crystal structures of the 19S regulatory particle subunits Rpn101-193 and Rpn121-224 have been determined and possible protein-protein interaction sites were identified by surface conservation and electrostatics analysis. Rpn12 surface residues were identified that had a negative effect on Rpn10-binding. This interaction was studied by surface plasmon resonance, fluorescence anisotropy and nuclear magnetic resonance. These experiments revealed a binding site on Rpn10 that is exclusively occupied by either ubiquitin or Rpn12 and for the first time demonstrated the interaction of a ubiquitin interacting motif with a protein other than ubiquitin.

A series of Pt(S₂N₂)(P(OR)[subscript n]R′[subscript(3-n)])₂ complexes were prepared and analysed using ³¹P NMR and IR spectroscopy, elemental analysis and X-ray crystallography. Similarly, a series of Pt(SeSN₂)(P(OR)[subscript n]R′[subscript(3-n)])₂ complexes were also prepared and analysed. The ¹J[subscript(Pt-P)] coupling constants and Pt-P bond lengths for these complexes are influenced by the oxygen content of their phosphorus ligands. The ³¹P NMR spectra for a series of [Pt(S3N)(P(OR)[subscript n]R′[subscript(3-n)])₂][BF₄] complexes are also reported. Planar [S₂N₂H]⁻ complexes were prepared and the X-ray crystal structure of [Pd(S₂N₂H)(bipy)][Cl] is reported. The X-ray structures of MX₂(P(OR)[subscript n]R′[subscript(3-n)])₂ are reported and compared with the previously reported analogues. The magnitude of the ¹J[subscript(Pt-P)] varies linearly with the Pt-P bond length (l[subscript(Pt-P)] = 2.421 – J/24255) for the 12 platinum-containing complexes. This correlation is compared to that of a larger series of complexes. A series of M(ndsdsd₂ (ndsdsd = bis[(nitrilo(diphenyl)-λ⁶-sulfanyl)](diphenyl)-λ⁶-sulfanediimide (Ph₂S(=N-(Ph₂)S≡N)₂)) complexes were prepared and characterised using elemental analysis and multinuclear NMR and IR spectroscopy where appropriate. The X-ray crystal structures of five examples are reported.

The influenza virus causes a disease that kills approximately 500,000 people worldwide each year. Influenza is a negative-sense RNA virus that encodes its own RNA-dependent RNA polymerase. This protein (FluPol) carries out both genome replication and viral transcription. Therefore, like the L-proteins of non-segmented negative-sense RNA (nsRNA) viruses, FluPol also contains mRNA capping and polyadenylation functionality. In FluPol, capping is achieved by snatching cap structures from cellular mRNAs, so requiring cap-binding and endonuclease activities. This makes FluPol a substantial machine. It is a heterotrimeric complex, composed of PB1, PB2 and PA/P3 subunits, with a total molecular weight of 255 kDa. PB1 houses the polymerase active site, whereas PB2 and PA contain, respectively, cap-binding and endonuclease domains. Currently, we only have high resolution structural information for isolated fragments of FluPol. This severely hampers our understanding of influenza replication and consequently inhibits the development of therapies against the virus. In this DPhil project, I have determined a preliminary structure for the heterotrimeric FluPol of influenza C/Johannesburg/1/66, solved by x-ray crystallography to 3.6 Å. Overall, FluPol has an elongated structure with a conspicuous deep groove. PB1 displays the canonical right-hand-like polymerase fold. It sits at the centre of the particle, sandwiched between the two domains of P3, and with PB2 stacked against one side of this dimer. In the structure, the polymerase and endonuclease catalytic sites are both ~40 Å away from the cap-binding pocket. This pocket also faces a tunnel leading to the polymerase core. This suggests a mechanism for how capped cellular mRNAs are cleaved and then fed into the polymerase active site to prime transcription. The structure also hints at a unique trajectory for template RNA, in which the RNA exits at an angle ~180° from which it came in. This provides an explanation for how the polymerases of influenza, and other nsRNA viruses, can copy templates that are packaged into ribonucleoprotein complexes. My work reveals the first molecular structure of any polymerase from an nsRNA virus. It uncovers the arrangement of functional domains within FluPol, illuminating the mechanisms of this and related viral polymerases. This work will help focus future experiments into FluPol biology, and should hopefully spur the development of novel antiviral drugs.