The aim of this thesis was to develop a series of gadolinium(III) contrast agents based on the DOTA and AAZTA molecules used widely in the literature that will locate preferentially in hypoxic tumour cells. Three contrast agents were synthesised with alkyne tags, by adapting compounds already produced in the literature. Whilst contrast agents in the clinic locate preferentially in cancer cells over normal tissues, they do not have the ability to inform a clinician about the type, or the environment of the cancer. One cancer environment that often leads to poor patient prognosis is hypoxia, as hypoxic tumours are both chemotherapy and radiotherapy resistant, whilst also promoting metastasis at a cellular level. Under hypoxic conditions nitro-aromatic compounds can be enzymatically reduced to either the hydroxylamine or amine compounds. Once this has occurred either a leaving group can be lost, or partial ring breakdown occurs, which can then be attacked by molecules within the cell such as glutathione to form a covalent bond. This tethers the hypoxic marker within the hypoxic cell. Currently this technology is only used with nuclear medicine techniques, whilst this thesis outlines how this principle is to be used in conjunction with MRI technology. The hypoxia markers were synthesised with azide functionalities to allow the two halves of these molecules to be conjugated using the copper (I)-catalyzed azide-alkyne cycloaddition. The conjugation occurred as the last step to produce a series of final compounds. Once synthesised these contrast agents were characterised using NMR relaxivity calculations, to prove their effectiveness as contrast agents. They were also to undergo enzymatic tests using xanthine oxidase and glutathione to see if the nitro-aromatics can be reduced under hypoxic conditions, and thus their ability to locate within the hypoxic region of a tumour. Unfortunately this last step wasn’t completed due to time constraints.

The cyclin dependent kinase inhibitor p27 is one of the most frequently dysregulated tumour suppressor protein in human cancers. A reduction in the level of cellular p27 is frequently due to increased proteasome-dependent degradation. Recently, studies show that the macrocyclic octapeptide argyrin A induced an increase in cellular p27 levels by preventing the turnover of the protein via inhibition of proteasome function. In order to investigate this interesting biological property, this project embarked on the total synthesis of argyrin A, a naturally occurring macrocyclic peptide originally isolated from myxobacteria Archangium gephyra. Argyrin A is a non-ribosomal octapeptide containing four standard amino acids and three unusual amino acid-based subunits. The synthesis of these three unusual amino acid components was established. In particular, a novel generic synthetic route to access the optically pure N-Fmoc-4-methoxy-tryptophan and analogues thereof was developed. Key features of the synthetic route include the use of chiral Strecker amino acid synthesis and mild conditions to hydrolyse α-amino nitrile to α-amino acid. Furthermore, the total synthesis of argyrin A and analogues was accomplished by the application of modern solid-phase chemistry and macrocyclisation strategies. This platform technology will enable the robust total chemical synthesis of a focused library of argyrin analogues, which will facilitate a comprehensive SAR study. Additionally, the synthesised argyrin A and analogues thereof comprising unique tryptophan analogues were tested in a cytotoxicity assay against HCT-117 human colon cell line. The results showed that all synthetic argyrin derivatives display growth inhibitory effects at nanomolar concentrations. The best result was obtained for the argyrin A and (5-methoxy-Trp4)argyrin with GI50 value at 1.8 and 3.8 nM, respectively. In summary, it became apparent that the methoxy group at 4- or 5-position of tryptophan-5 residue is essential for the biological activity of argyrin.

In this thesis we investigate and develop analytic models for polymer nucleation and other barrier crossing problems. Our most broadly appealing method for certain multi dimensional barrier crossing problems is a one-dimensional projection which includes a novel technique to extract rate kinetics from simulations [M J Hamer et al., Soft Matter, 2012, 8, 11396-11408]. The scenarios we expect our method to be potentially useful are situations where barrier crossings are rare, and the dominant mechanism is through a series of unlikely incremental steps. The rate kinetics extraction technique is also reliant on the equilibrium energy barrier being relevant to non-equilibrium system, but is not appropriate when strong kinetic contributions dominate the process, and enable crossings over highly unfavourable energetic pathways. We explore and significantly enhance the Graham-Olmsted (GO) polymer nucleation simulation [R S Graham and P D Olmsted, Phys. Rev. Lett., 2009, 103, 115702], producing a combinatorial calculation to obtain exact energy landscapes from it’s basic stochastic rules of monomer attachment [M J Hamer et al., J. Non-Newton. Fluid., 2010, 165, 1294-1301]. We apply our rate kinetics extraction technique to the GO model and find that for most flow rates in purely long chain melts, nuclei tend to grow along similar paths over energy landscapes. The technique reveals a clear signature when this pattern is disobeyed, as in the case of blends of long and short chain polymer melts, some of which display highly anisotropic growth. In addition, we design several one-dimensional barrier crossing models with distinct characteristics, predicting the average and the distribution of crossing times with great accuracy. That finally enables us to completely describe the GO simulation’s nucleation rates with analytic theory, by presenting a model of polymer nucleation featuring crystal rotation, which vastly impacts nucleation rates when polymer melts are subject to flow.

Leptin is an important hormone well known for its role in regulating energy intake and expenditure. DNA methylation levels at the leptin promoter in adult tissues appear to correlate with environmental stresses experienced during early life. This suggests that, once established in early life, DNA methylation is stably transmitted over successive cell generations. The aim of the work presented in this thesis was to determine factors that contribute to the establishment and maintenance of this epigenetic mark at the leptin promoter and to investigate the individual roles of cytosine methylation and cytosine hydroxymethylation at this genomic locus. No effect of a high fat prenatal diet was observed on leptin promoter DNA methylation levels in the adipose tissue of pigs. However, this genomic region exhibited intermediate levels of DNA methylation, which is usually associated with gene silencing, even though adipose tissue is the primary site of leptin expression. Double stranded methylation data obtained from DNA methyltransferase (DNMT) mutant mouse embryonic stem cells (mESCs) was used to investigate the contributions of the three catalytically active DNMT enzymes to leptin promoter DNA methylation patterns. Depletion of DNMT3b resulted in increased methylation levels at the leptin promoter, consistent with preliminary data from mutant DNMT3b mouse tissues where similar increases in methylation levels were observed at specific CpG dinucleotides. Two mESC lines, either hypomethylated or hypermethylated at the leptin promoter, were tested for leptin mRNA expression and neither cell line expressed leptin mRNA, suggesting that some form of methylation may be required for leptin expression. To further investigate the relationship between DNA methylation and leptin expression, in vitro differentiated adipocytes were analysed. 3T3-L1 preadipocytes, which do not express leptin, exhibit high levels of DNA methylation and these high methylation levels are maintained after the cells differentiate into leptin-expressing adipocytes. Induction of cytosine hydroxymethylation at the leptin promoter was detected in differentiating and mature adipocytes and evidence is presented to suggest that cytosine hydroxymethylation at the leptin promoter correlates with leptin expression.

Controlling the interaction of cells with a material surface is of major interest in the field of biomedical material science. Plasma polymers are an attractive way to modify the surface chemistry of a material because this technique is versatile and can be applied to a wide range of different surfaces. The aim of the present work is to prepare a new chemical gradient tool using plasma polymerisation and assess its ability to provoke position dependent cell-surface interactions. A novel diffusion based approach is used to develop gradients from hydrophobic hexane (ppHex) to more hydrophilic allylamine (ppAAm) plasma polymers. The surface of the gradient and that of uniform control samples is characterised using WCA, XPS, ToF-SIMS and AFM. This data shows that the most distinct gradient was found in the wettability profile which can be controlled by changing the size of the opening through which diffusion of depositing species from the plasma occurs. The mechanism of the gradient formation is studied with channels of well defined cross sections. The deposition rate obtained on these samples shows a sharp drop off in the amount of ppHex deposited from the plasma starting 2 mm in advance of the opening. An estimation of the sheath dimensions indicates that this corresponds to the sheath thickness. It is suggested that plasma deposition through small openings such as pores depends on the relative dimensions of the sheath and the pore cross section. Inside the channels, oligomer formation is observed in the gas phase, presumably following a nucleophilic addition reaction mechanism. To study the stability of these plasma polymer surfaces in physiological conditions, surface analysis is also carried out on samples exposed to aqueous solutions. Some changes in the topography of the plasma polymer films are found. Most notably, uniform samples of ppHex deposited on top of ppAAm show the formation of blisters that are not observed on other samples. It is argued that these blisters are the result of water penetrating through the top ppHex layer and interacting with the more hydrophilic ppAAm or glass substrate. 3T3 fibroblasts cultured on the gradients show a gradual increase in cell density. This cell density gradient can be related linearly to the wettability gradient on the surface with non-linear relationships being observed with other surface parameters such as the ppHex thickness. The cell number on uniform ppAAm is much greater than on the ppAAm side of the gradient. Data from experiments with non-proliferating 3T3 fibroblasts indicates that the differences between the gradient and uniform ppAAm as well as the cell density increase along the gradient have their origin in a different number of cells adhered to the surface within the first 24 hours of cell culture. The adsorption of albumin and fibronectin on the plasma polymers demonstrate that displacement of the former by the latter takes place on the surface when adsorbed competitively. However, this displacement does not occur in different extents along the gradient surface, suggesting that protein displacement can not explain the increase in cell density towards the ppAAm end of the gradient.

The interactions of metal-containing molecules and nanoparticles (NPs) with the interior of hollow graphitic carbon nanostructures (CNs) were investigated and their chemical transformations in the nanoscale channels of CNs appraised. The gas phase insertion of Group VI metal hexacarbonyl complexes (M(CO)6, M=Cr, Mo, W) into CNs was successfully developed and optimised to provide good filling rates as confirmed by transition electron microscopy (TEM). Infrared (IR) and Raman spectroscopy demonstrated that Group VI M(CO)6 complexes with greater polarisability exhibit stronger van der Waals interactions with the interior of single walled carbon nanotubes (SWNTs). The synthesis of metal based NPs inside graphitised carbon nanofibers (GNFs) by the in situ transformation of the encapsulated M(CO)6 precursor molecules was successfully achieved and it was demonstrated that GNFs can act as a source of oxygen in these reactions. The nanotube filling methodology was applied for the multi-step synthesis of new inorganic materials inside CNs by the controlled reactions of M(CO)6, I2 and H2S. This approach yielded unusual van der Waals hybrid materials such as “tube inside a tube” and other hybrid structures of MoS2 and GNFs. In SWNTs, with significantly narrower diameters than GNFs or multi-walled carbon nanotubes (MWNTs), metal complexes form unique 1D arrays of octahedral [M6I14]2- clusters with the nanotube acting as a nanocontainer and a poly-cation balancing the charge of the guest-clusters. The iodides of Mo and W were effectively converted into extremely thin MS2 nanoribbons (NRs) within SWNTs, providing a new more efficient route to the hybrid inorganic nanostructures. In MWNTs, the [Mo6Ii8Ia2Ia a4/2] clusters are packed in a hexagonal pattern to optimise filling of the void, and when reacted with H2S they provide a range of multi-layered MS2NRs with their widths controlled by the internal diameter of the host nanotube.

Chapter 1: An introduction is given to high-pressure crystallography with the experimental design and equipment required outlined. The basic theory that underpins X-ray diffraction and structure solution is covered with emphasis given to points that raise considerations for high-pressure crystallographic studies; key software and their uses are briefly introduced. A literature survey of molecular coordination complexes under pressure is given that provides a detailed view of the typical phenomena observed and interrogated in such work. Chapter 2: Recrystallisation of [PdCl2([9]aneS2O)] ([9]aneS2O = 1-oxa-4,7-dithiacyclononane), 1, and [PtCl2([9]aneS2O)], 2, by diffusion of Et2O vapour into solutions of these complexes in CH3NO2 has yielded three phases of 1 and two phases of 2. The phase of 1, herein designated α-1, was obtained under ambient conditions. A second phase, designated β-1, was initially also obtained by this method; following the advent of a third phase, γ-1, all subsequent efforts over a period of a year to crystallise β-1 yielded either γ-1, which was typically obtained by carrying out the recrystallisation at elevated temperature, or α-1, commonly found throughout the study. This persistent absence of a phase which could initially be crystallised with ease led to the conclusion that β-1 was an example of a ‘disappearing polymorph’. The first phase obtained of 2, designated α-2, was obtained by recrystallisation under ambient conditions and is isomorphous and isostructural with α-1. The second phase, β-2, was obtained by slight elevation of the recrystallisation temperature and was found to be isomorphous and isostructural with β-1. Subsequently, β-2 was used to seed the growth of the disappearing polymorph β-1. No third phase of 2 ("γ-2") has been isolated. Density functional theory calculations were employed to aid in rationalising this behaviour. Chapter 3: The three reported phases of the mononuclear macrocyclic Pd(II) complex [PdCl2([9]aneS2O)] (1) were each studied up to pressures exceeding 90 kbar using high pressure single crystal X-ray diffraction. The α and γ phases both exhibited smooth compression of the unit cell parameters with third-order Birch-Murnaghan bulk moduli of 14.4(8) and 7.6(6) GPa, respectively. Between 68.1 and 68.7 kbar β-1 was found to undergo a reversible transformation to a phase denoted β’ and characterised by a tripling of the unit cell volume. Across the phase transition, rearrangement of the conformation of the bound macrocycle at two of the resulting three unique sites gave rise to an extensively disordered structure. This phenomenon was largely owed to a close and approximately linear C−H···H−C approach between macrocycles. Density functional theory calculations were employed to further understand the high-pressure behaviour of the phases. Cooling from 290 to 90 K in complementary variable temperature crystallographic studies revealed similar effects as ca. 5 kbar pressure. Chapter 4: The two reported phases of the mononuclear macrocyclic Pt(II) complex [PtCl2([9]aneS2O)] (2) were each studied up to pressures exceeding 90 kbar using high pressure single crystal X-ray diffraction. The α phase exhibited smooth compression of the unit cell parameters with third-order Birch-Murnaghan bulk modulus of 11.8(5) GPa. Between 65.2 and 69.9 kbar β-2 was found to undergo an incomplete rearrangement of the macrocycle that was not characterised by a phase transition as seen for the corresponding Pd(II) phase. The β phase was also indicated to be more resistant to compression than the α phase with a third-order Birch-Murnaghan bulk modulus of 13.5(5) GPa. The conformational rearrangement was again rationalised by a close and approximately linear C−H···H−C approach between macrocycles. Density functional theory calculations were employed to further understand the high-pressure behaviour of these two phases and why β-1 and β-2 might differ. Cooling from 290 to 90 K in complementary variable temperature crystallographic studies again revealed similar effects as ca. 5 kbar pressure. Chapter 5: The previously unreported solvate [Pd([9]aneS3)2](PF6)2·2CH3NO2 is studied using high-pressure crystallography, high-pressure solid-state UV/vis spectroscopy and density function theory calculations to interrogate the piezochromism previously observed by this group. Up to 49.3 kbar, gradual sky blue to dull green piezochromism was observed with considerable compression of the elongated axial Pd···S interactions. A reversible P21/c → P-1 phase transition with doubling of the unit cell volume was observed between 49.3 and 51.0 kbar. This was accompanied by a dull green to orange stepwise piezochromism and characterised by an organised reorientation of the coordination axes in 50 % of the cations. The phase transition had a range of effects on the axial interactions which remained compressible in the high-pressure phase. No further piezochromism was clearly observed. Density functional theory calculations showed a fair match with experimentally obtained spectra and strongly indicated that the piezochromism is primarily owed to compression of the axial interaction. These calculations also indicated that outer-sphere effects further modulate the piezochromism, but gave no evidence for a cause of the phase transition. The phase transition was thus rationalised as a response to the large value of the PV term of the Gibb’s free energy associated with the transition. The ambient pressure structures of two other previously unreported solvates are also reported. Chapter 6: The templated polyiodide framework [Ag([18]aneS6)]I7 were studied to ca. 45 kbar. Each of the two crystals employed in this study underwent two phase transitions: at ca. 11 kbar an R-3m → R3m transition was observed in both crystals. This appeared to be ferroelectric in nature and was associated with a change in bonding of the polyiodide network from 3∞[I−·(I2)6/2] to 3∞[I7−]. Analysis of the calculated Mayer bond orders for the catenating I−···I2 interactions supported this description of the bonding. Compression of the first phase appears essentially the same for both crystals; compression through the second phase differed between crystals and the second phase transition, at ca. 40 kbar in both cases, resulted in differing monoclinic phases. The second transition was associated with the ordering of the conformation of the macrocycle: one phase appeared ordered from the perspective of the refinement and the macrocycle adopted the previously unseen [84114] conformation by Dale analysis. The other phase appears disordered from the perspective of the refinement but would appear to comprise alternating enantiomers of the [333333] conformer. The differing conformation of the macrocycle in the third phase was taken as indicative of differing major components in the disordered lower phases. This point of difference in turn rationalised the different response to pressure in the second phase: compression of the second phase is limited by interactions between cations while the first phase is dependent on the catenating I−···I2 interactions which are identical between crystals. Chapter 7: A summary of the key findings of this body of work is given along with suggested avenues for future studies. This thesis closes with the wider reaching considerations that are highlighted by this body of work.

This Thesis describes the application of niobium oxide and niobium phosphate as solid acids for conducting continuous flow reactions, such as the Friedel-Crafts Reaction and the Skraup Reaction, and also as supports for photosensitiser immobilisation. Chapter 1 introduces the concepts of green and sustainable chemistry, and give a review of niobium and niobium compounds, especially niobium oxide and niobium phosphate as well as their applications. A summary of flow chemistry is also presented. The continuous flow systems used to conduct the work of this Thesis are described in Chapter 2. Chapter 3 introduces continuous alkylation of aniline with dimethyl carbonate or methanol over niobium solid acids. The synthesis process is automated by a self-optimisation system to search the best conditions for different products, including the NH2 group methylation product monomethyl aniline and dimethyl aniline, and the Friedel-Crafts alkylation product N,N-dimethyl-p-toluidine. Chapter 4 describes the first exploration of the continuous Skraup synthesis of quinolones with heterogeneous catalyst niobium phosphate. A dissymmetrics substituted quinoline compound, 4-(quinolin-6-yl methyl)aniline, was synthesized, and its crystal was grown and the structure was determined by crystallographic analysis for the first time. Chapter 5 discussed the immobilisation of a photosensitiser meso-tetraphenylporphyrin on niobium solid acids, and the activity of these supported photocatalysts in continuous photo-oxidation, including the photo-oxidation of α-terpinene to ascaridole and the semi-synthesis of an antimalarial drug, artemisinin ART. Finally, Chapter 6 summarises the work described in this Thesis and examines the success of the techniques and approaches discussed. A summary of potential routes for further study is also presented.

Metal ions such as silver (Ag+), mercury (Hg2+), zinc (Zn2+) and copper (Cu+/Cu2+) have a long history of antimicrobial usage and some, such as Cu+/Cu2+, Ag+ and Zn2+ compounds are still used as antimicrobials. Prior to the introduction of antibiotics, Ag+ was arguably the most important antimicrobial and with the rapid emergence of antibiotic resistance, interest in Ag+ and its compounds as alternative antimicrobials have recently been revived. However, resistance to Ag+-based compounds has been emerging, with initial reports of carriage of silver resistance on a Salmonella enetrica serovar Typhimurium multi-resistance plasmid pMG101 isolated from burns patients in 1975. The proposed model for the mechanism of Ag+ resistance encoded by the sil genes from pMG101 involves export of Ag+ ions via an ATPase (SilP), an RND family effluxer (SilCFBA) and a periplasmic chaperone of Ag+ (SilE). SilE is a periplasmic protein predicted to be intrinsically disordered until it binds Ag+ ions. This hypothesis was tested using structural and biophysical studies which showed that SilE is an intrinsically disordered and unstructured protein in its free apo-form, but folds to a compact, defined structure upon optimal binding of six Ag+ ions in its holo-form. Sequence analyses and site-directed mutagenesis established the importance of histidine and methionine containing motifs for Ag+-binding, and identified a nucleation core that initiates Ag+-mediated folding of SilE. The data show that SilE is a molecular metal sponge absorbing up to a maximum of eight Ag+ ions.

It has been demonstrated that bakers' yeast reduction of 1-tert-butyl-2-methyl 3-oxo-piperidine-1,2-dicarboxylate gives (2R, 3S), 1-tert-butyl-2-methyl 3-hydroxy-piperidine-1,2-dicarboxylate in 80% chemical yield with >99% d.e. and >97% e.e. Also bakers' yeast reduction of 1-tert-butyl-3-ethyl 4-oxo-piperidine-1,3-dicarboxylate gives (3R, 4S), 1-tert-butyl-3-ethyl4-hydroxy-piperidine-1,3-dicarboxylate in 74% chemical yield with >99% d.e. and >93% e.e. The optical purity and absolute configurations of the hydroxy-ester derivatives were determined by conversion into the corresponding chiral bis-tosylate derivatives of 2- and 3-piperidinemethanol respectively. It has also been shown that bakers' yeast reduction of 1-tert-butyl-4-methyl 3-oxo-piperidine-1,4-dicarboxylate gives (3R, 4R)-1-tert-butyl-4-methyl 3-hydroxypiperidine-dicarboxylate in 81% chemical yield with >99% d.e. and 87% e.e. The optical purity and absolute configuration of the hydroxy-ester derivative were determined by utilisation of the compound in the total synthesis of (R)-3-quinuclidinol via chain elongation at C-4 of the piperidine followed by cyclisation to produce the bicyclic structure. Further work is reported on the diastereoselective synthesis of polyhydroxylated indolizidine alkaloids. 1-Acetoxy-2-hydroxy-3-(hydroxymethyl)-indolizidine has been synthesised as a single diastereomer from 2-piperidinemethanol via attack of an amine onto an epoxide functionality thus producing the bicyclic system.