The opening chapter of this thesis gives an overview of the existing methods to functionalise palladium(II)-alkyl intermediates resulting from oxy- or carbopalladation of unactivated alkenes, outlining the range of heterocycles which can be formed using this type of methodology. A summary of Pd(IV) species in synthesis and catalysis follows, with a focus on Pd(IV) intermediates arising from oxidative addition of alkyl halides to Pd(II) and those suggested in alkene difunctionalisation reactions. As the subsequent formation of sp3–sp3 C–C bonds from Pd(II)-alkyl intermediates was noted as a limitation of prevailing nucleopalladation methods, the second chapter of this thesis outlines the work towards development of an oxypalladation reaction of hydroxyalkenes, with concomitant formation of an sp3–sp3 C–C bond. Allyl halides proved to be competent electrophiles for this transformation. The oxyallylation reaction was successfully applied to a range of hydroxyalkene substrates, with the methodology developed also applied to a 5-step synthesis of anti-depressant citalopram. The oxyallylation reaction constructs heterocycles substituted in the 2-position, forming two new bonds in a single step. Ensuing work, detailed in Chapter 3, focused on the development of an analogous carboallylation reaction, using aryl boronic acid derivatives. This transformation gives rise to the formation of two new C–C bonds in a single step, including the construction of a fully substituted carbon centre. Experimental procedures and data are summarised in Chapter 4.

Hexacyclinic acid is a polyketide isolated from Streptomyces cellulosae bacteria in 2001. It possesses a complex and challenging hexacyclic ring system with various oxygen functionalities throughout. Hexacyclinic acid has also demonstrated some cytotoxic activity, making it an attractive target for total synthesis. However to date no full synthesis has been reported. Previously within the group significant progress had been made towards the synthesis of hexacyclinic acid, with construction of the ABC 5/6/5 tricyclic core being achieved via a diastereoselective Michael addition and Snider radical cyclisation. The synthesis ran into difficulties however when hydrolysis of the ethyl ester could not be accomplished and removal of the superfluous carboxylic acid moiety could not be realised. The approach within the group for the formation of the ABC tricycle was to continue the current strategy, joining the A and C-rings via the diastereoselective Michael reaction, and the closure of the 6-membered B-ring by Snider radical cyclisation. Progress was made using the tert-butyl and 2,2,2-trimethylsilylethyl ester analogues in an attempt to improve diastereoselectivities Progress was also made on the synthesis of the CDEF tricyclic system, utilising (R)-isopropylcyclopentenone as a C-ring model system. The DEF framework was attached to the model by a Michael addition, with further functionalisation setting up the necessary functionalities for cyclisation. Conditions were attempted to effect a challenging aldol condensation to form the 9-membered ring, however all attempts effect this transformation were fruitless. It was discovered that 2,2,2-trifluoromethylacetophenone can act as a replacement for benzaldehyde in the synthesis of protected syn-1,3-diols from homoallylic alcohols, with comparable yields and easier purification. Finally, an investigation was also made into the use of a bispidine ligand as a replacement for (−)-sparteine in Crimmins asymmetric aldol reactions, with the bispidine shown to give superior yields and diastereoselectivity when compared to TMEDA.

The Translocator Protein (18 kDa) (TSPO) resides mainly in microglia and is upregulated in response to neuronal injury and inflammation, rendering it an interesting target for imaging focal neuroinflammation in a range of diseases. A library of TSPO ligands based on PK11195 with positions suitable for [11C]-, [18F]- and [123I]-labelling was prepared using three synthetic approaches. Implementation of a physicochemical study enabled selection of compounds most likely to be brain penetrant, and biological evaluation identified those with high binding affinities for the TSPO. From this, a lead candidate (compound 170) was identified. Radiofluorination and in vitro autoradiography revealed the ability of this compound to image tumour tissue in a mouse model of glioblastoma. Poly(ADP-ribose) polymerase-1 (PARP-1) is an enzyme involved in the repair of DNA strand breaks, and widely regarded as a therapeutic target for cancer treatment. Many inhibitors of PARP-1 activity exist, e.g. olaparib. A programme of research focussing on the preparation of a potential PET imaging agent for measurement of PARP-1 activity, based on olaparib, was initiated. An expeditious seven step synthetic route was used to prepare a small library of compounds. Preliminary cell-free biological screening of these compounds indicated PARP-1 inhibitory potencies in the low nanomolar range demonstrating potential leads for development of a PET imaging agent, e.g. compound 223. Extracts of Carduus crispus linn., traditionally used in Chinese folk medicine, yield a family of isoquinoline alkaloid natural products (Crispine A–E). Upon commencement of this project no reported synthesis of Crispine C existed in the literature. As such, a facile route utilising a key Pictet-Gams modification of the Bischler-Napieralski reaction for isoquinoline core formation was developed, enabling the first total synthesis of Crispine C to be achieved in seven steps and with an overall product yield of 25%.

With the use of a one-pot process, a diastereoselective synthesis of bicyclononanes and decanes has been developed. Initial treatment of an allylic alcohol with trichloroacetonitrile, in the presence of DBU, afforded the corresponding allylic trichloroacetimidate. The trichloroacetimidate was then subjected to a one-pot process involving a thermal Overman rearrangement, ring-closing-enyne-metathesis and a hydrogen-bond directed Diels-Alder reaction to form polycyclic products in good isolated yields and as single diastereomers. Research was then carried out on how this process could be extended. Through the use of Grubbs second generation catalyst, the process was extended to include a cross-metathesis reaction forming highly functionalised 1,3-dienes. These 1,3-dienes were then used in the hydrogen bond directing Diels-Alder reaction to generate highly functionalised polycycles, again as single diastereomers. This process was then employed towards the first total synthesis of the natural product, netamine A. Further studies showed that carbo- and heterocyclic 1,3-dienes could be used in a one-pot Diels-Alder reaction and aromatisation step for the rapid preparation of partially saturated indane and tetralin motifs, which are present in biologically active molecules.

A series of model compounds and a commercial Pd/C catalyst were used to study the issues relevant to the hydrogenation of aromatic nitrile molecules that are associated with an industrial agrichemicals process, where a primary amine is the target product. Benzonitrile hydrogenation was found to be converted to high value benzylamine before an unexpected hydrogenolysis reaction led to the loss of ammonia to ultimately yield toluene as the final product. Indeed, gas phase infrared studies unambiguously showed the formation of ammonia for the first time. On closer investigation, the reaction was found to be a consecutive process where the order of reaction changed from first order for hydrogenation to zero order for hydrogenolysis. Co-adsorption studies proved that the two reactions occurred independently on two distinct Pd sites. The choice of catalyst and the use of an acid additive were shown to improve selectivity to benzylamine. A dramatic change was noted when the aliphatic chain was extended. For benzyl cyanide hydrogenation, conversion was observed but, by way of a “spillover” process, the amine product was retained by the catalyst. Extending the chain further resulted in a complete loss in reactivity showing that electronic and structural factors had a major effect on activity and product distribution. Mandelonitrile hydrogenation required an acid additive to facilitate conversion since a series of co-adsorption studies showed that under neutral conditions an intermediate hydroxyamine acted as a poison. Recycling of the catalyst showed that a cumulative poisoning effect was evident, but manipulation of Pd particle shape and size resulted in an extended lifetime and superior selectivity. Introducing additional functionality to the aromatic ring meant that stabilised imine species were observed in the liquid phase. The nature of the substituent also affected product distribution and catalyst lifetime. MeO-, Me- and Cl-substituents all showed signs of reduced catalyst performance, but an OH-substituent exhibited greater durability, albeit with reduced selectivity to the primary amine. These systems also indicated the presence of a high energy site on the catalyst, which was responsible for the formation of secondary and tertiary amines.

This thesis records an investigation into the biosynthesis of the aranotins, a group of sulphur-containing dioxopiperazine metabolites produced by the fungi Aspergillus terreus and Amauroascus aureus. A series of analogues of the known aranotin precursor, cyclo( L-phenylalanyl-L-phenylalanyl), fluorinated on one or both aromatic rings, was prepared, both unlabelled and labelled with 14C• These compounds were fed to Aspergillus terreus, as were £-, ~-, and ~-fluorophenylalanines, and their metabolism was followed by 19F n.m.r. spectroscopy of the extracts. A fluorinated bisdethiodi(methylthio)- acetylapoaranotin was isolated from cultures which had been fed DL-~-fluorophenylalanine or cyclo-(L-phenylalanyl-L-~-fluorophenylalanyl) • A new natural metabolite of A. terreus, cis-~,~'-di(methylthio)cyclo-( phenylalanyl-phenylalanyl), of unknown absolute configuration, was isolated and characterised. Several fluorinated analogues of this compound were detected spectroscopically in extracts which had been fed fluorinated precursors. cyclo-(L-Phenylalanyl-L-~-fluorophenylalanyl), stereospecifically monodeuteriated at the methylene group of the E-fluorophenylalanyl residue, was fed to A. terreus, and it was shown that neither the 3Rnor the 3S-deuterium was lost obligatorily during the conversion of this compound into cis-~,~'-di(methylthio)-cyclo-(phenylalanyl-E-fluorophenylalanyl), although there was a partial loss from each position. The natural product, cis-cA,c(' -di (methylthio) -cyclo-(phenylalanylphenylalanyl), was synthesised as a racemate. The compound, labelled with 35S , was fed to A. terreus, and was not significantly incorporated into bisdethiodi(methylthio)acetylaranotin. The racemic epidisulphide, ~,~'-epidithio-cyclo-(phenylalanyl-phenylalanyl), was synthesised. This compound, doubly labelled with 3H and 35S , was fed to A. terreus, and was incorporated into acetylaranotin and bisdethiodi(methylthio)acetylaranotin, with some changes in the isotopic ratios. An "intermediate trapping" experiment confirmed the ability of the fungus to biosynthesise ~,~'-epidithio-cyclo-(phenylalanyl-phenylalanyl), of unknown absolute configuration, from L-phenylalanine.

This study of the measurement and behaviour of nitrogen in soil is split into three main parts: 1) An investigation of the Kjeldahl digestion method for measuring total nitrogen in soil and plant materials. 2) A study of the effect of air drying, temperature and repeated ammonium application on nitrification rates and 3) An investigation of ammonium contamination at a former nylon factory site. The investigation of the Kjeldahl digestion method was made by comparing measured values of total nitrogen using a standard Kjeldahl digestion method and salicylic acid modification digestion method. For each method three different catalyst mixtures were used. Measurements were made of certified reference plant materials (hay and cabbage) and a comparison was made of two soil samples. The standard Kjeldahl digestion method with 1 g of sodium sulphate/copper sulphate mixture (100:10) measured significantly lower nitrogen (P<5%) than the certified reference value for hay but not cabbage. Significantly lower (P<5%) total nitrogen was measured in soil samples than with 2.5 g of sodium sulphate/copper sulphate mixture (110:10) and Kjeltabs (2.5 g potassium sulphate/copper sulphate/selenium, 100:10:1). The reason for the lower recovery of total nitrogen with 1 g of catalyst is the lower digestion temperature which causes incomplete digestion. The 2.5 g of catalyst mixture and Kjeltabs with the standard method gave significantly (P<5%) higher total nitrogen than the certified values for both hay and cabbage. The high values of total nitrogen measured for plant material were probably due to variable recovery of the high levels of nitrate which were present in the plant material at 3.1 mg g -1 (hay) and 3.2 mg g-1 (cabbage).The salicylic acid modification method measured significantly higher total nitrogen than the certified reference values using all catalyst mixtures with both plant materials. This higher recovery of total nitrogen was due to partial recovery of nitrate as the method used for the certified values would not have recovered nitrate.

A series of core and core-shell nanoparticles with superparamagnetic properties were synthesised and surface functionalised using three different amino-silanes by a chemical conjugation method. The functionalised nanoparticles were characterised and further modified by chemical conjugation with two different classes of bio-molecules; (i) enzymes and (ii) single stranded DNA primers. The resultant nanoparticles (nano-bio conjugates) were used for applications in (i) enzyme catalysis and (ii) bio-separation / bio-sensing. Magnetite and amorphous silica-coated core-shell nanoparticles were synthesised on both small (5 g) and large (20 g) scales and were characterised using transmission electron microscopy (TEM), X-ray diffraction (XRD), Brunauer-Emmett-Teller (BET) surface area measurement and vibrating sample magnetometry (VSM). Silica-coated core-shell nanoparticles were functionalised by silanisation with three different aminosilanes [3-aminopropyl tri-ethoxysilane (APTS), 3-aminopropyl di-ethoxymethylsilane (APDS) and 3-aminopropyl mono-ethoxydimethylsilane (APMS)] and two different methods: water (classical method) or a Tri-phasic Reverse Emulsion (TPRE) using toluene and a surfactant (Triton X-100). It was observed that the materials prepared using the TPRE method produced higher surface amine density values on average. The first application involved bio-catalysis where lipases [Pseudomonas Fluorescens lipase (PFL) and Candida Rugosa lipase (CRL)] were chemically conjugated (covalently linked) via glutaraldehyde-modification onto the amino-functionalised nanoparticles for applications such as: (i) hydrolysis of p-nitrophenyl palmitate to produce palmitic acid and p-nitrophenol (model reaction), (ii) transesterification of ethyl butyrate with n-butanol to produce butyl butyrate and (iii) partial and selective hydrolysis of cis-3,5-diacetoxy-1-cyclopentene to produce pharmaceutically important and expensive chiral intermediate molecules. Various reaction parameters such as (a) water concentration in a bi-phasic solvent mixture and (b) temperature were investigated to determine the optimum conditions. All reactions were carried out using free lipases and the physically adsorbed lipases in order to compare the performance with chemically conjugated nano-biomaterials. It was observed from the bio-catalytic reaction (i) that the conversion values given by lipase-immobilised materials were comparable to those given by free lipases with the added advantage of being re-usable for further catalytic cycles. PFL-immobilised nanoparticles were shown to be more effective catalysts than CRL-immobilised materials. In the bio- catalytic reaction (ii), Lipase-immobilised materials were shown to exhibit reasonable conversion values (maximum 53%) along with easy separability by one-step magnetic separation from the reaction mixture and re-usability. Finally, in the bio-catalytic reaction (iii), lipase-immobilised materials were shown to give lower total conversion values compared to free enzymes, but a higher proportion of desired products [(1S,4R)-cis-4-acetoxy-2-cyclopenten-1-ol and (1R,4S)-cis-4-acetoxy-2-cyclopenten-1-ol]. PFL (both free and immobilised) materials were shown to give higher conversion and enantioselectivity towards the desired (1S,4R)-enantiomer (93-100% ee) than CRL materials (30-40% ee). The second application involved bio-separation and bio-sensing where 5ʹ-NH2-modified oligonucleotide sequences specific to either Listeria Monocytogenes (LM) or Escherichia Coli (EC) were immobilised onto the surface of glutaraldehyde modified nanoparticles to assess the specific capture and enhance the sensitivity of detection of pathogenic bacterial DNAs from food samples. Firstly, the oligonucleotide-grafted nanoparticles were used in a hybrid capture assay (model assay) at UCLan using specific single stranded DNA primers of our interest followed by the application in real food samples at Q-Bioanalytic GmbH, Germany. Capture of the complementary sequences was reasonably high (48-70% for LM-specific materials and 48-55% for EC-specific materials) when calculated as a molar ratio of conjugated oligonucleotides to complementary oligonucleotides captured. Specific capture was determined to be 33-52% for LM-specific oligonucleotide-grafted nano-materials and 59-60% for EC-specific oligonucleotide-grafted nano-materials. Dehybridisation of captured sequences was shown to be efficient for all oligonucleotide-grafted materials (72-97% for LM-specific materials and 86-87% for EC-specific materials), indicating that the materials were ready for real applications using food matrices at Q-Bioanalytic GmbH, Germany. Nucleic acid DNA was extracted from a real food sample inoculated with either LM or EC and the extracted DNA was used for specific capture using the oligonucleotide-grafted materials tested at UCLan. Dehybridised oligonucleotides were amplified and analysed using quantitative real-time PCR (qPCR). The results showed that using a one-step hybrid capture assay, LM-specific oligonucleotide-grafted materials were successful at detecting LM from an undiluted solution of LM only and from a 1:1 mixture of LM and EC. Using a two-step assay where the forward and reverse oligonucleotide-grafted materials were applied for capture separately, only EC-specific materials were successful for the detection of EC from an undiluted solution, and also from a 1:1 mixture of LM and EC.

The selective oxidation of lower alkane components of natural gas, such as ethane, to partial oxygenates remains a major challenge for both industry and academia. At present 60% of industry’s 7.8 Mt annual acetic acid demand is met through the carbonylation of methane, the operation of which is highly energy intensive, leads to formation of corrosive iodide by-products and requires high pressures of CO. Meanwhile ethene, a feedstock of great industrial importance, is produced via steam cracking of alkanes such as ethane, a process which is typically operated at > 800 oC and accounts for ca. 40% of the petrochemical industry’s annual energy consumption. The development of an atom efficient, low temperature, environmentally benign process for the direct conversion of ethane to either of these molecules would circumvent the need for current practices and thereby represent an important milestone in the valorisation of natural gas. The heterogeneous catalyst system explored in this thesis is based upon zeolite (ZSM-5) catalysts, which may be modified via post synthesis deposition of either or both of iron and copper and are shown to selectively transform ethane to a variety of higher value products including but not limited to ethanol, acetaldehyde, acetic acid and ethene under mild, environmentally benign conditions (H2O2 as oxidant, water as solvent, temperatures of < 90oC). C-C scission of C2 products led to formation of carbon centred radicals and yielded C1 products including methylhydroperoxide, methanol and formic acid, whilst deep oxidation yielded CO2, typically at selectivities of < 5%. The method by which catalysts were prepared was shown to impact significantly upon catalyst performance, with chemical vapour impregnation, a novel vapour deposition technique being shown to yield highly active catalysts. Investigations of reaction conditions such as ethane pressure, ethane partial pressure, temperature, oxidant concentration and catalyst mass [Chapter 1] III were conducted in a batch reaction system. All parameters were found to impact significantly upon both catalytic activity and product distributions allowing for directed selectivity to either ethanol or acetic acid as major product. Through extensive mechanistic studies, it was shown that a complex reaction scheme operates with these catalysts, which results in the primary C2 products ethanol, ethylhydroperoxide and ethene. Of these the former two were shown to undergo consecutive oxidation to acetaldehyde and acetic acid, whilst ethene was shown to react under test conditions to yield acetic acid. Additionally, upon deposition of Cu2+ onto ZSM-5 catalysts ethene was shown to become the major reaction product, with selectivities of 45.5% at 1.15% conversion. Following development under batch reaction conditions, the ZSM-5 catalysts were then applied under a continuous flow regime through co-feeding of an aqueous hydrogen peroxide solution and mixed ethane/ argon feed through a custom built fixed bed trickle bed reactor system. Through optimisation of reaction conditions 23% ethane conversion to acetic acid (73% selectivity) was observed. Through varying the catalyst bed makeup, turnover frequencies equal to those observed at comparable conditions under batch reaction conditions were observed, thereby showing the viability for translating this catalyst system to a more industrially viable continuous flow system. High ethene and acetic acid selectivities of 37.8% and 43.0% were observed, respectively at 3.3% ethane conversion upon testing of 1.25% Fe 1.25% Cu/ZSM-5 (30) within this regime at 50 oC. Subsequent studies focused upon elucidating the role played by aluminium sites within the zeolite framework in catalyst activity and determining product selectivities. This has led to the development of Cu/ZSM-5 and FeCu/ZSM-5 catalysts which are not only highly active for the activation of ethane, but also highly selective for the formation of ethene, with productivity to ethene alone shown to reach 25.6 mol (ethene) kg-1 (catalyst) [Chapter 1] IV h-1 (at 50% ethene selectivity). Through studies of ZSM-5 catalysts of varying support composition, headway has been made in decoupling the effects which increased exchange capacity (aluminium content) has upon catalyst performance, thereby paving the way for future development of more active, selective catalysts for the transformation of ethane to higher value products, specifically ethene. An interesting aspect of this work was the discovery that copper oxide particle size and size distribution may be controlled through varying of the ZSM-5 support’s SiO2/Al2O3 ratio due to a metal support interaction.

The role for protein dynamics in the transition states (TS) of enzyme reactions has been debated over decades. Dihydrofolate reductase (DHFR) catalyses the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate and has long been considered a paradigm of enzymology. Numerous studies on DHFR have provided strong evidence that there is no coupling between the long-range motions on nanosecond to millisecond timescales to the chemical coordinate. However, the role of femtosecond (fs) bond vibrations in the TS has not been fully investigated. This investigation focused on understanding how these fast protein vibrations affect enzyme catalysis. A thermophilic DHFR from Geobacillus stearothermophilus (BsDHFR) was investigated kinetically by complete enzyme isotope substitution. Our studies indicated that, whilst protein vibrations do couple to the reaction coordinate, they do not affect the height or width of barrier crossing. Instead, dynamic coupling enhances the frequency of dynamic recrossing. In line with the other DHFR investigations by enzyme isotope substitution, efficient enzymes tend to reduce dynamic coupling as a mean to maximise enzyme catalytic efficiency. The transition state in DHFR was also characterised by α-secondary hydrogen and heavy atom kinetic isotope effects (KIEs). Secondary KIEs were measured for DHFR isolated from Escherichia coli, Moritella profunda and G. stearothermophilus. The high resemblance in the magnitude and temperature dependence of the measured α-secondary KIE implied that the reaction ready configuration is essentially the same among these enzymes. Carbon isotope effect measurements were measured for EcDHFR. The reacting carbon in NADPH showed a profound isotope effect at low temperature. Further analysis by measuring hydride KIE indicated the hypothetical "promoting" motion is unlikely to act via the C4 atom of NADPH. The carbon isotope effect likely reports on the recrossing events or the reorganisation effect that occur along the transition state dividing surface.