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Novel routes to high performance lithium-ion batteries

Drewett, Nicholas E. — 2013-06-26T00:00:00Z

Abstract: This thesis investigates several approaches to the development of high-performance batteries. A general background to the field and an introduction to the experimental methods used are given in Chapters 1 and 2 respectively. Chapter 3 presents a study of ordered and disordered LiNi₀.₅Mn₁.₅O₄ materials produced using an optimised resorcinol-formaldehyde gel (R-F gel) synthetic technique. Both materials exhibited good electrochemical properties and minimal side reaction with the electrolyte. Structural analyses of the materials in various states of discharge and charge were undertaken, and from these the charge / discharge processes were elucidated. In chapter 4 R-F gel synthesised Li(Ni₁/₃Mn₁/₃Co₁/₃)O₂ is studied and found to exhibit a high degree of structural stability on cycling, as well as excellent capacity, cyclability and rate capability. Photoelectron spectroscopy studies revealed that the R-F gel derived particles have highly stable surfaces. A discussion of the results and their significance, with particular regard to the outstanding electrochemical performance observed, is also presented. Chapter 5 sets out an investigation into the nature of R-F gel synthesised 0.5Li₂MnO₃:0.5LiNi₁/₃Mn₁/₃Co₁/₃O₂. The electrochemical data revealed that, after an initial activation stage, the R-F gel derived material exhibited a high capacity, good cyclability and exceptional rate capability. This chapter also considers some initial structural investigations and the electrochemical processes occurring on charge. In chapter 6 the use of ether-based electrolytes, combined with various cathode materials, in lithium-oxygen batteries is examined. The formation of decomposition products was observed, and a scheme suggesting probable reaction pathways is given. It was noted that significant quantities of the desired discharge product, lithium peroxide, were formed on the 1st cycle discharge, implying some electrolyte / cathode combinations do demonstrate a degree of stability. A summary of the results and a discussion of their significance are also included.

Structural basis of Lassa fever nucleoprotein binding pathogen-associated pattern molecule dsRNA

Xue, Jiang — 2012-11-30T00:00:00Z

Abstract: Lassa fever virus (LASV) infects thousands of people and produces more than 5,000 deaths each year in West Africa. This severe virus is a huge threat, as it transmits between human and rodents, and no effective vaccine or drug is available currently. One key of getting control of this disease lies in the nucleoprotein (NP) of LASV, which plays an essential role in viral replication, transcription and immune suppression. The full length NP crystal structure has been solved, showing a novel structural fold and multi-functions with unusual mechanisms in immune suppression and viral RNA transcription. The C-terminal domain of LAVS NP is a 3’-5’ exonuclease, whose activity is essential for viral immune suppression. This domain alone can suppress an immune response and can degrade dsRNAs with specific preference higher than for ssRNAs. However, the detail of the mechanism is unclear. To understand the mechanism while avoiding another domain’s effect (the N-terminal domain), the C-terminal domain of LASV NP was expressed and purified, and pathogen-associated pattern molecular RNAs were synthesized chemically and biologically to carry on crystallization and functional testing. The C-domain crystals in complex with a pathogen-associated pattern molecule, triphosphate 8 nucleotide dsRNA were obtained. The crystal belongs to the space group P3 with unit cell dimension a=b=177.6 Å, c=56.49Å, α =β=90°, γ=120°. This crystal structure showed that the dsRNA binds in the 3’-5’ exonuclease active site with one 3’ end of the dsRNA perfectly sitting for cleavage. We are trying to figure out the detailed mechanism by mutagenesis, fluorescence-labeled RNA gel scan and band shift assays.

Structural insights into the mechanism and inhibition of the beta-Hydroxydecanoyl-Acyl carrier protein dehydratase from pseudomonas aeruginosa

Moynie, Lucile — 2013-01-23T00:00:00Z

Abstract: Fatty acid biosynthesis is an essential component of metabolism in both eukaryotes and prokaryotes. The fatty acid biosynthetic pathway of Gram-negative bacteria is an established therapeutic target. Two homologous enzymes FabA and FabZ catalyze a key step in fatty acid biosynthesis; both dehydrate hydroxyacyl fatty acids that are coupled via a phosphopantetheine to an acyl carrier protein (ACP). The resulting trans-2-enoyl-ACP is further polymerized in a processive manner. FabA, however, carries out a second reaction involving isomerization of trans-2-enoyl fatty acid to cis-3-enoyl fatty acid. We have solved the structure of Pseudomonas aeruginosa FabA with a substrate allowing detailed molecular insight into the interactions of the active site. This has allowed a detailed examination of the factors governing the second catalytic step. We have also determined the structure of FabA in complex with small molecules (so-called fragments). These small molecules occupy distinct regions of the active site and form the basis for a rational inhibitor design program. (C) 2012 Elsevier Ltd. All rights reserved.

Mechanistic insights into the triazolylidene-catalysed Stetter and benzoin reactions : role of the N-aryl substituent

Collett, Christopher J. — 2013-01-01T00:00:00Z

Abstract: The in situ observation, isolation and reversible formation of intermediate 3-(hydroxybenzyl) azolium salts derived from NHC addition to a range of substituted benzaldehydes is probed. Equilibrium constants for the formation of these 3-(hydroxybenzyl) azolium salts, as well as rate constants of hydrogen-deuterium exchange (k(ex)) at C(alpha) of these intermediates for a range of N-aryl triazolinylidenes is reported. These combined studies give insight into the preference of N-pentafluorophenyl NHCs to participate in benzoin and Stetter reaction processes.

An efficient route for the synthesis of phosphorus-selenium macro-heterocycles

Hua, Guoxiong — 2013-01-01T00:00:00Z

Abstract: Four-membered ring [PhP(Se)(mu-Se)](2) (Woollins' reagent, WR) reacts with disodium alkenyl-diols followed by in situ ring-closure reaction with appropriate dibromoalkanes affording a series of unusual nine-to fifteen-membered organoselenophosphorus macrocycles bearing the O-P-Se-C-n-Se-P-O or O-P-Se-C-n-O-P-Se linkage.

Development of novel active site and allosteric inhibitors of enzymes associated with cancer, neurodegenerative diseases and bacterial infections

Pirrie, Lisa — 2013-06-01T00:00:00Z

Abstract: The sirtuins are a family of NAD⁺-dependent deacetylase enzymes which are implicated in various illnesses including cancer and neurodegenerative diseases. Part I of this thesis describes the synthesis and biological evaluation of inhibitors of the SIRT1 and SIRT2 isoforms of this important family of enzymes. Chapter 1 gives an overview of sirtuin biology and the physiological roles of these enzymes. In particular the link between SIRT1 and cancer and SIRT2 and its role in the onset of neurodegenerative diseases is discussed. A review of the most potent and selective inhibitors of SIRT1 and SIRT2 is given including an introduction to the tenovin and cambinol classes of inhibitor. Chapter 2 describes various issues relating to the structure of the important chemical tool tenovin-6. The synthesis of analogues to improve the solubility, determine the preferred conformation and verify the products of metabolism of tenovin-6 is presented including their evaluation by in vitro and in cell methods. Part II of this chapter reports the design and use of a ¹H NMR method used to monitor the sirtuin-mediated deacetylation reaction. This was particularly relevant due to concerns raised about the possibility of false positive results obtained with the commercially available assay kit commonly used by the sirtuin community. This new ¹H NMR method was used to validate the inhibition of SIRT2 by tenovin-6. Chapter 3 describes the parallel synthesis and evaluation of tenovin analogues as inhibitors of SIRT1 and SIRT2. This study identified that replacement of the t-butyl substituent of tenovin-6 with the 3,5-dihalogen-4-alkoxy substitution pattern led to a variety of analogues having SIRT2 selectivity. As well as the collection of valuable SAR data, in cell data is also presented for the analogues. Chapter 4 provides attempts to rationalise the SAR data collected in Chapters 2 and 3 through a computational study. The molecular docking software GOLD was used to predict the binding site of the tenovin scaffold and hence rationalise the observed potencies of various analogues. Chapter 5 reports the synthesis and biological evaluation of triazole and cambinol analogues as SIRT1 and SIRT2 inhibitors. Part I details the synthesis and in vitro testing of a series of ring constrained tenovin analogues based on the 1,4-disubstituted triazole using click chemistry. A series of 1,5-disubstituted analogues were also synthesised. Part II describes the synthesis of S-alkylated cambinol analogues and the effect of N3-methylation upon activity and selectivity towards SIRT1. Part II of this thesis details the synthesis and biological testing of novel potent allosteric inhibitors of RmlA. RmlA is the first enzyme in the L-rhamnose biosynthetic pathway in bacteria. L-rhamnose is an important component of the bacterial cell wall and as such RmlA is therefore an important target in the discovery of novel anti-bacterial compounds. Chapter 7 provides an overview of the RmlA enzyme including its role in L-rhamnose biosynthesis and why it is an attractive target for anti-bacterial drug discovery. No small molecule inhibitors of RmlA have been reported previously. Chapter 8 describes the design and synthesis of pyrimidine-2,4-dione analogues as novel allosteric inhibitors of RmlA. SAR data is generated and rationalised by X-ray crystallographic techniques to study the structures of complexes of RmlA with various analogues. Analogues were also tested for their ability to inhibit the growth of the important human pathogen Mycobacterium tuberculosis.

Carbon monoxide hydrogenation using ruthenium catalysts

Blank, Jan Hendrik — 2012-11-30T00:00:00Z

Synergism between N-heterocyclic carbene and phosphorus-based ligands in ruthenium and palladium catalytic systems

Schmid, Thibault E. — 2012-12-18T00:00:00Z

Abstract: N-heterocyclic carbenes (NHCs) have become a very popular class of ligands, which has found uses in numerous catalytic applications. The use of such compounds in combination with phosphorus-based ligands within metal complexes has enabled the design of very active yet robust catalytic systems. The following chapters will describe the design of novel well-defined palladium- and ruthenium-based pre-catalysts featuring a NHC and a phosphorus-based ligand, referred at as mixed ligand systems. Such species were employed in catalysis where their properties appeared highly beneficial, uses at low catalysts loading and under harsh conditions were then envisioned. The preparation of a series of well-defined palladium mixed NHC/phosphine species is presented in chapter 2. Their catalytic activity in the aqueous Suzuki-Miyaura reaction of aryl chlorides and boronic acids, using low catalyst loadings, is described. The observation of catalytic activity of the latter systems in the hydration of nitriles prompted us to further investigate this reactivity. This reaction appeared to be operative in the absence of palladium species and could be performed under base-catalysed conditions, which was studied in detail and depicted in chapter 3. The combination of a NHC and a phosphite ligand in ruthenium olefin metathesis pre-catalysts has been underexplored. Preliminary results showed that such species could be readily prepared and presented an unusual geometry and a high catalytic activity. Variations in phosphite-containing ruthenium olefin metathesis pre-catalysts are presented. Chapter 4 describes the investigation of various Schrock carbene moieties in such architectures, as well as their implications in structure and catalysis. Chapter 5 depicts attempts to design olefin metathesis Z-selective pre-catalysts by inserting a chelating NHC moiety within phosphite-containing ruthenium species. This dissertation concludes on the potential of such mixed species in catalysis, and armed with the new knowledge provided by this work, proposes potential developments of such chemistry in the design of always more robust and active catalytic systems.

The search for allosteric inhibitors

Brear, Paul — 2013-06-26T00:00:00Z

Abstract: This thesis describes the development of chemical tools that inhibit the sialidases NanA and NanB from Streptococcus pneumonia. The primary focus was on the discovery of allosteric inhibitors of NanA and NanB, however, promising inhibitors that act by binding at the active site of these enzymes were also investigated. Chapter 1 gives an overview of the use of chemical tools in the field of chemical biology. It focuses in particular on chemical tools that function by the allosteric regulation of their target proteins. The uses, advantages and methods of discovery of allosteric tools are discussed. Finally this chapter introduces the use of serendipitous binders for the discovery of allosteric sites. In particular, the use of CHES to identify novel allosteric sites on the sialidase NanB is proposed. Chapter 2 describes how the ‘hits’ from a series of high throughput screens were reanalysed using a wide range of secondary assays to eliminate any false positives that were contaminating the results. This process removed eight of the eleven ‘hits’. Two of the remaining three compounds were then analysed further in an attempt to characterise their binding mode to NanA and/or NanB using modelling and X-ray crystallographic studies. Whilst, it was not possible to confirm the binding mode by X-ray crystallography modelling studies using the modelling software GOLD generated possible binding modes for these inhibitors. A structure activity relationship study was conducted for both compounds in an attempt to generate more potent inhibitors. Chapter 3 moves from the use of high throughput screens to identify hits against NanA and NanB to the use of the serendipitous binding of N-cyclohexyl-2-aminoethanesulfonic acid in the active site of NanB for the development of selective NanB inhibitors. First taurine was identified as the minimum unit of N-cyclohexyl-2-aminoethanesulfonic acid required to bind to the active site of NanB. Taurine was then used as the basis of an optimisation study. This chapter concludes with the identification of 2-(benzylammonio)ethanesulfonate as the next key intermediate in the development of N-cyclohexyl-2-aminoethanesulfonic acid based active site inhibitors of NanB. Chapter 4 follows on from Chapter 3 with the optimisation of 2-(benzylammonio)ethanesulfonate describing the design and synthesis of a wide range of analogues. From these compounds 2-[(3-chlorobenzyl)ammonio]ethanesulfonate was identified as the most potent and selective inhibitor. Detailed analysis of the binding of 2-[(3-chlorobenzyl)ammonio]ethanesulfonate to NanB gave a rationale for its improved inhibitory activity. The increase in inhibition occurred because on binding of 2-[(3-chlorobenzyl)ammonio]ethanesulfonate to the active site of NanB a well coordinated water molecule was displaced. The displacement of this water caused an increase in the flexibility of the enzyme’s 352 loop. A detailed study of the flexibility of this loop in response to various N-cyclohexyl-2-aminoethanesulfonic acid based chemical tools was then conducted. The research in chapters 2 and 3 has recently been published. In Chapter 5 a molecule of N-cyclohexyl-2-aminoethanesulfonic acid that binds serendipitously in a previously unmentioned secondary site is elaborated into a ligand, known as Optactin, that binds strongly and selectively at this secondary site. It was then shown that Optactin inhibited NanB by binding at this secondary site. It was therefore concluded that this secondary site was in fact an allosteric site that could be used for the regulation of NanB. Chapter 6 describes the development of a rationalisation for the inhibition of NanB by Optactin. This study included the X-ray crystallographic analysis of the apo-NanB structure and the NanB-Optactin complex under a range of conditions. This was followed by mechanistic studies that identified the point in the catalytic cycle at which Optactin was inhibiting NanB. This chapter concludes with a hypothesis for the mechanism of inhibition of NanB by Optactin.

Synthesis of porous metal phosphonate frameworks for applications in gas separation and storage

Wharmby, Michael T. — 2012-05-22T00:00:00Z

Abstract: Porous metal phosphonate framework materials were synthesised by solvothermal reaction of bis(α-aminomethylenephosphonic acid) ligands with divalent and trivalent metal cations. The syntheses and characterisation by NMR and, where possible, single crystal X-ray diffraction of seven bisphosphonic acid ligands, including N,N′-piperazinebis(methylenephosphonic acid) (H₄L), its racemic and enantiopure (R) 2-methyl (H₄L′ and R-H₄L′) and 2,5-dimethyl (H₄L′′) derivatives, and N,N′-4,4′-bipiperidinebis(methylenephosphonic acid) (H₄LL) are reported. Syntheses of the known phase Y₂(LH₂)₃·5H₂O and the new phases, STA-13(Y) (St Andrews microporous material No. 13) and Y₂(R-L′H₂)₃·4H₂O, from reactions of Y(AcO)₃ with H₄L, H₄L′ and R-H₄L′ respectively are reported. The as-prepared and dehydrated structures of each phase have been determined from either laboratory or synchrotron powder X-ray diffraction data. Reaction of Y(AcO)₃ and H₄L′′ is shown to form a phase with a different structure. The features determining which structure crystallises are discussed. Syntheses of other rare-earth forms of STA-13 (Sc³⁺, Gd³⁺–Yb³⁺) and the porosity of each phase to N₂ are reported. STA-13(Y) is the most porous form with loadings of ∼3 mmol g⁻¹ and ∼4 mmol g⁻¹ for N₂ and CO₂ respectively. MIL-91(Fe) was synthesised for the first time from reactions of Fe³⁺ cations with H₄L. Its structure was confirmed by Rietveld refinement, but it was not porous. The first syntheses of [Fe₄L₁.₅(AcO)₁.₅(OH,H₂O)₃]·0.5NH₄5.5H₂O (L= L or L′) are reported, from reactions of H₄L or H₄L′ in the presence of an excess of Fe³⁺ cations. The phase is related to a previously reported Co phase. The synthesis of divalent metal bisphosphonate STA-12(Mg) (Mg₂(H₂O)₂L·5.6H₂O) was reported for the first time and its structure determined from single crystal X-ray diffraction. The dehydration behaviour of this material was compared with the known forms of STA-12. STA-12(Mg) is porous to both N₂ (∼5.5 mmol g⁻¹) and CO₂ (~ 8.5 mmol g⁻¹). Reaction of H₄LL with Co²⁺ and Ni²⁺ gave two materials isoreticular with STA-12, labelled STA-16(Co) and STA-16(Ni). The structures of both materials were solved from synchrotron powder X-ray diffraction data. On dehydration, STA-16(Co) undergoes a reversible structural transition to an unknown structure. By contrast, STA-16(Ni) retains the same symmetry in the dehydrated form and its structure was determined from synchrotron powder X-ray diffraction data. Both materials are porous to N₂, with an uptake of up to 22.2 mmol g⁻¹, and CO₂ with maximum loading of 21.7 mmol g⁻¹. NLDFT analysis of N₂ adsorption data confirm the crystallographically determined pore radii. Syntheses of other frameworks with divalent cations and initial reactions of H₄LL with trivalent cations are also reported.

Synthesis of phosphonate and phostone analogues of ribose-1-phosphates

Nasomjai, Pitak — 2009-07-27T00:00:00Z

Abstract: The synthesis of phosphonate analogues of ribose-1-phosphate and 5-fluoro-5-deoxyribose-1-phosphate is described. Preparations of both the alpha- and beta-phosphonate anomers are reported for the ribose and 5-fluoro-5-deoxyribose series and a synthesis of the corresponding cyclic phostones of each alpha-ribose is also reported. These compounds have been prepared as tools to probe the details of fluorometabolism in S. cattleya.

Three step synthesis of single diastereoisomers of the vicinal trifluoro motif

Brunet, Vincent A. — 2009-11-05T00:00:00Z

Abstract: A three step route to single diastereoisomers of the vicinal trifluoromethyl motif is described. The route starts from either syn- or anti-alpha,beta-epoxy alcohols and takes a direct approach in that each of the three steps introduces a fluorine atom in a regio- and stereospecific manner. Starting from either the syn- or the anti-alpha,beta-epoxy alcohol, stereospecific reactions generate two separate diastereoisomeric series of this motif. The route is a significant improvement on an earlier six step strategy.

Crystallization of Ranasmurfin, a blue coloured protein from Polypedates leucomystax

McMahon, Stephen — 2006-11-01T00:00:00Z

Abstract: Ranasmurfin, a previously uncharacterized similar to 13 kDa blue protein found in the nests of the frog Polypedates leucomystax, has been purified and crystallized. The crystals are an intense blue colour and diffract to 1.51 angstrom with P2(1) symmetry and unit-cell parameters a = 40.9, b = 59.9, c = 45.0 angstrom, beta = 93.3 degrees. Self-rotation function analysis indicates the presence of a dimer in the asymmetric unit. Biochemical data suggest that the blue colour of the protein is related to dimer formation. Sequence data for the protein are incomplete, but thus far have identified no model for molecular replacement. A fluorescence scan shows a peak at 9.676 keV, indicating that the protein binds zinc and suggesting a route for structure solution.

Remarkable transition from rocksalt/perovskite layered structure to fluorite/rocksalt layered structure in rapidly cooled Ln2CuO4

Patabendige, Chami Nilasha Kahakachchi — 2013-03-21T00:00:00Z

Abstract: Lanthanide cuprates of formula Ln2CuO4 exist in two principal forms, T and T′ which are renowned for their exhibition at low temperatures of hole and electronic types of superconductivity, respectively. These structures differ primarily in the arrangement of oxygen between the perovskite layers and also in nature of the copper oxygen planes. The Cu-O distance in the T structure (~1.90 Å) is much shorter than the T′ (1.97Å), reflecting a transition between partial Cu+ and partial Cu3+ character. In seeking to find compositions that bridge these two structure/electron carrier types, we observed the transition from a T structure to a T′ type structure, resulting in the metastable form T″ with slightly larger volume but similar character to T′. This transition from T to T″ is associated with 5% increase in a and a 5% decrease in c parameters of the tetragonal unit cells, which results in disintegration of ceramic bodies. Description: This work was supported by EPSRC

Synthesis of ammonia directly from air and water at ambient temperature and pressure

Lan, Rong — 2013-01-29T00:00:00Z

Abstract: The N equivalent to Nbond (225 kcal mol(-1)) in dinitrogen is one of the strongest bonds in chemistry therefore artificial synthesis of ammonia under mild conditions is a significant challenge. Based on current knowledge, only bacteria and some plants can synthesise ammonia from air and water at ambient temperature and pressure. Here, for the first time, we report artificial ammonia synthesis bypassing N-2 separation and H-2 production stages. A maximum ammonia production rate of 1.14 x 10(-5) mol m(-2) s(-1) has been achieved when a voltage of 1.6 V was applied. Potentially this can provide an alternative route for the mass production of the basic chemical ammonia under mild conditions. Considering climate change and the depletion of fossil fuels used for synthesis of ammonia by conventional methods, this is a renewable and sustainable chemical synthesis process for future.

Weak Te,Te interactions through the looking glass of NMR spin-spin coupling

Buehl, Michael — 2013-01-01T00:00:00Z

Abstract: Across the bay: J(125Te,125Te) spin–spin coupling is a highly sensitive probe into the electronic and geometric structure of 1,8-peri-substituted naphthalene tellurium derivatives. The coupling is related to the onset of multicenter bonding in these systems.

Isolable phosphanylidene phosphorane with a sterically accessible two-coordinate phosphorus atom

Surgenor, Brian A. — 2012-10-01T00:00:00Z

Simultaneous control of regioselectivity and enantioselectivity in the hydroxycarbonylation and methoxycarbonylation of vinyl arenes

Konrad, Tina Maria — 2013-01-01T00:00:00Z

Abstract: Using a family of novel mononuclear and dinuclear palladium complexes of phanephos ligands, the simultaneous control of regioselectivity and enantioselectivity in the hydroxycarbonylation and alkoxycarbonylation of styrene derivatives has been realised for the first time.

Iso-seco-tanapartholides : isolation, synthesis and biological evaluation

Makiyi, Edward F. — 2009-11-01T00:00:00Z

Abstract: The isolation, identification and total synthesis of two plant-derived inhibitors of the NF-kappa B signaling pathway from the iso-seco-tanapartholide family of natural products is described. A key step in the efficient reaction sequence is a late-stage oxidative cleavage reaction that was carried out in the absence of protecting groups to give the natural products directly. A detailed comparison of the synthetic material with samples of the natural products proved informative. Biological studies on synthetic material confirmed that these compounds act late in the NF-kappa B signaling pathway. ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)

Polymer electrolytes : synthesis and characterisation

Maranski, Krzysztof Jerzy — 2013-06-26T00:00:00Z

Abstract: Crystalline polymer/salt complexes can conduct, in contrast to the view held for 30 years. The alpha-phase of the crystalline poly(ethylene oxide)₆:LiPF₆ is composed of tunnels formed from pairs of (CH₂-CH₂-O)ₓ chains, within which the Li⁺ ions reside and along which the latter migrate.¹ When a polydispersed polymer is used, the tunnels are composed of 2 strands, each built from a string of PEO chains of varying length. It has been suggested that the number and the arrangement of the chain ends within the tunnels affects the ionic conductivity.² Using polymers with uniform chain length is important if we are to understand the conduction mechanism since monodispersity results in the chain ends occurring at regular distances along the tunnels and imposes a coincidence of the chain ends between the two strands.² Since each Li⁺ is coordinated by 6 ether oxygens (3 oxygens from each of the two polymeric strands forming a tunnel), monodispersed PEOs with the number of ether oxygen being a multiple of 3 (NO = 3n) can form either “all-ideal” or “all-broken” coordination environments at the end of each tunnel, while for both NO = 3n-1 and NO = 3n+1 complexes, both “ideal” and “broken” coordinations must occur throughout the structure. A synthetic procedure has been developed and a series of 6 consecutive (increment of EO unit) monodispersed molecular weight PEOs have been synthesised. The synthesis involves one end protection of a high purity glycol, functionalisation of the other end, ether coupling reaction (Williamson’s type ether synthesis³), deprotection and reiteration of ether coupling. The parameters of the process and purification methods have been strictly controlled to ensure unprecedented level of monodispersity for all synthesised samples. Thus obtained high purity polymers have been used to study the influence of the individual chain length on the structure and conductivity of the crystalline complexes with LiPF₆. The results support the previously suggested model of the chain-ends arrangement in the crystalline complexes prepared with monodispersed PEO² over a range of consecutive chain lengths. The synthesised complexes constitute a series of test samples for establishing detailed mechanism of ionic conductivity. Such series of monodispersed crystalline complexes have been studied and characterised here (PXRD, DSC, AC impedance) for the first time. References: 1. G. S. MacGlashan, Y. G. Andreev, P. G. Bruce, Structure of the polymer electrolyte poly(ethylene oxide)₆:LiAsF₆. Nature, 1999, 398(6730): p. 792-794. 2. E. Staunton, Y. G. Andreev, P. G. Bruce, Factors influencing the conductivity of crystalline polymer electrolytes. Faraday Discussions, 2007, 134: p. 143-156. 3. A. Williamson, Theory of Aetherification. Philosophical Magazine, 1850, 37: p. 350-356.

Chemical biology studies on 5-nitrofurans and sirtuin inhibitors

Zhou, Linna — 2012-12-01T00:00:00Z

Abstract: Part I: Target identification studies are one of the most difficult but rewarding challenges in chemical biology. Part I of this thesis describes target identification studies for 5-nitrofuran containing hits. The 5-nitrofurans used in this study were identified in a phenotypic screen for compounds that induced melanocyte cells death in zebrafish. Chapter 1 provides brief overviews on three related areas of the project: 1) the use of zebrafish as a model organism in drug discovery; 2) phenotypic screening using zebrafish and 3) the strategies used in target identification studies. Chapter 2 describes the synthesis of and SAR studies on two series of 5-nitrofuran containing analogues. The design and preparation of biotinylated chemical probes based on the SAR data is also described. These chemical tools are then used in affinity chromatography studies and genetic validation of a potential target (zebrafish Aldh2) of the 5-nitrofuran compounds is reported. Chapter 3 provides a review of the biological and chemical processes that human ALDHs are known to mediate. In addition, small molecules that modulate ALDH2 activity are reviewed. A detailed study of the interaction between 5-nitrofurans and human ALDH2 including in vitro enzymatic assays is described leading to the conclusion that the 5- nitrofurans under study are substrates of human ALDH2. Further mechanism of action investigations using model reactions are also presented. Chapter 4 introduces the use of 5-nitrofuran containing drugs in the clinic and highlights the reported side-effects. Further investigation of the interaction between ALDH2 and 5- nitrofurans in zebrafish and yeast using ALDH2 inhibitors is described. Based on these results, a combination therapy strategy is proposed. Finally, the trypanocidal activity of the newly synthesised 5-nitrofurans is discussed. Experimental details and future work for Part I are presented in Chapters 5 and 6 respectively. Part II: Human sirtuins are associated with various biological functions and diseases, including cancer and neurodegeneration. Previous work from the Westwood Lab has led to the discovery of the tenovins that act as inhibitors of SIRT1 and SIRT2. Part II of the thesis reports the development of potent fixed ring tenovin analogues with high SIRT2 selectivity. Chapter 7 provides a brief review of the biology of human SIRT2 and the reported SIRT2 inhibitors available to date. This is followed by a short summary of the previous work on the tenovins in the Westwood Lab and the design of the fixed ring tenovin analogues. Chapter 8 describes the synthesis of three series of fixed ring tenovin analogues. SAR data is generated based on in vitro enzymatic assays against both SIRT1 and SIRT2 and the prepared analogues showed relatively high potency and selectivity against SIRT2. Further cell-based deacetylation assay are also discussed. All the experimental details are reported in Chapter 9 and Chapter 10 provides with conclusions and proposed future work.

Supported ionic liquid phase catalysis in continuous supercritical flow

Duque, Ruben — 2013-06-26T00:00:00Z

Abstract: The separation of the expensive catalysts from the solvent and reaction products remains one of the major disadvantages of homogeneous catalytic reactions, which are otherwise advantageous because of their high activity, tuneable selectivity and ease of study. Ideally, the homogeneous reactions would be carried out in continuous flow mode with the catalyst remaining in the reactor at all times, whilst the substrates and products flow over the catalyst. The system we have been studying is one where the catalyst is dissolved in a thin film of an ionic liquid, and this is supported within the pores of a microporous silica. This supported ionic liquid phase (SILP) catalyst is then placed in a tubular flow reactor, similar to that used for heterogeneous reactions. The raw materials are then injected into the rig, pass through the reactor and the products and the raw materials that have not reacted are collected at the other end of the rig. Supercritical CO₂ is used to transport the raw materials and products along the catalyst bed, allowing a continuous flow mode with low leaching for both the catalyst and the ionic liquid. We have applied this procedure first to alkene metathesis catalysed by a ruthenium complex that has been especially designed to dissolve in 1-butyl-3-methyimidazolium triflamide (BMIM NTf₂), which was used as ionic liquid. Activity is observed for the ring closing metathesis of diethyl 2,2-diallylmalonate, but the catalyst is not stable, only allowing about 300 turnovers. This instability is attributed to the formation of Ru=CH₂ moieties, which dimerise to an inactive species. More success is achieved with internal alkenes such as 2-octene and especially methyl oleate. Self metathesis of methyl oleate continues for >10.000 turnovers over 10 h, with only small decreases in activity. The cross metathesis of methyl oleate with dimethyl maleate has also been studied. Cross metathesis dominates in the early stages of the reaction but the cross metathesis products diminish with time. Surprisingly, the catalyst does not deactivate since self metathesis of methyl oleate continues. The phase behaviour of the reaction was monitored and gave us an insight into the reasons for this change in selectivity. Methoxycarbonylation reactions in continuous flow proved to be a much more difficult process than the previous metathesis reactions. Higher catalyst loading was needed to reduce the reaction times. The first continuous flow reactions showed conversion predominantly, if not exclusive, of 1-octene isomerised products. The presence of ionic liquid (IL) in the SILP system was essential, otherwise the catalyst leached out of the reactor very quickly. Batch reactions showed that none of the studied parameters (absence of presence of either BMIM NTf₂, OMIM NTf₂, silica or CO₂) had any influence on the reaction, but when observing the results it was noticed that the reactions that gave the best results were performed in a close range of pressures between 55 and 70 bar, indicating that the reaction might be pressure dependent. Further continuous flow reactions in that range of pressures gave the best conversions to methoxycarbonylation products. Unfortunately, at these pressures and without CO₂ the reaction took place in a liquid phase and thus substantial IL and catalyst leaching was observed, causing a decrease in conversion and making the reaction not feasible under continuous flow conditions. Nevertheless, the catalyst system composed of Pd, 1,2-bis(di-tert-butylphosphinomethyl)benzene (DTBPMB) ligand and acid showed an excellent linear selectivity, usually higher than 90%, both in batch and continuous flow reactions. Hydrogenation reactions of dimethyl itaconate (DMI) and dibutyl itaconate (DBI) using Rh-MeDuPhos showed excellent activity and enantioselestivity in a batch mode. In a continuous flow mode IL leaching caused a decrease of the enantioselectivity. The best results were obtained when CO₂ was not present. On the other hand, the absence of CO₂ implied that the reaction was performed in a liquid phase and therefore abundant IL leaching was observed along with a decrease in the enantioselectivity. A study of the reaction behaviour when using CO₂ in its different phases (liquid, gas and supercritical) was carried out. Under supercritical conditions IL leaching was avoided but conversion was not observed. When using CO₂ in its liquid phase some conversion was observed and full conversion occurred in its gas phase, but abundant IL leaching caused a decrease in the enantioselectivity. Better results were obtained by immobilising a Rh-MeDuPhos catalyst onto alumina via heteropoly acids. The effect of pressure, H₂ flow and substrate flow were studied and the stability of the reaction in the long term was examined under optimal conditions. More than 12,900 TONs were achieved after 4 days of continuous reaction, with conversions higher than 90% during the 3 first days and e.e. higher than 99% during the 2 first days.

Investigation of structure and disorder in inorganic solids using solid-state NMR

Mitchell, Martin R. — 2013-06-26T00:00:00Z

Abstract: The use of solid-state NMR and DFT calculations to study Y₂Sn[subscript(x)]Ti[subscript(2-x)]O₇, Y₂Sn[subscript(x)]Zr[subscript(2-x)]O₇ and Y₂Ti[subscript(x)]Zr[subscript(2-x)]O₇, materials with applications for the safe encapsulation of radioactive actinides is investigated. As a result of cation or anion disorder in these materials, NMR spectra are often complex and difficult to interpret. Therefore, an investigation using a range of NMR active nuclei and measurement of a variety of NMR parameters (isotropic chemical shift, δ[subscript(iso)]; span, Ω and quadrupolar coupling, C[subscript(Q)]) were used to provide a full and detailed picture of each material. The measurement of Ω in these disordered compounds with multiple resonances in the NMR spectra, required the use of 2D CSA-amplified PASS (CAPASS) experiments to enable the separation of each of the spinning sideband manifolds. An experimental assessment of the CAPASS experiment showed that although low ν₁/Ω[subscript(Hz)] ratios (as found in ⁸⁹Y NMR) resulted in distortions in the spectra obtained, a modified fitting procedure could be utilised to compensate for this fact, which allowed the accurate measurement of Ω. Despite the difficulties in acquiring the ⁸⁹Y NMR spectra, they were found to be the most informative of the NMR-active nuclei available. ¹¹⁹Sn NMR spectra, although much easier to acquire than ⁸⁹Y, were more complex and harder to analyse, owing to the overlapping resonances. Therefore, ¹¹⁹Sn NMR could only be used to confirm or support the results obtained using ⁸⁹Y NMR. Although ¹⁷O NMR was found to be useful, a full study could not be implemented due to the lack of ¹⁷O enriched samples; an area where future investigation may prove fruitful. Finally, [superscript(47/49)]Ti and ⁹¹Zr NMR spectra were found to be the most difficult to acquire due to their low receptivities and the quadrupolar broadened lineshapes, and as a result, little additional information was obtained. As a result of this analysis, for the Y₂Sn[subscript(x)]Ti[subscript(2-x)]O₇ pyrochlore solid solution, using primarily ⁸⁹Y δ[subscript(iso)] and Ω, and additionally confirmed with ¹¹⁹Sn δ[subscript(iso)], it was found that the Sn and Ti cations were randomly ordered throughout the B-sites. Additionally, ⁸⁹Y Ω could be used to obtain approximate Y-O[subscript(48f)] and Y-O[subscript(8b)] bond lengths for each type of Y environment. The study of Y₂Sn[subscript(x)]Zr[subscript(2-x)]O₇ using ⁸⁹Y NMR showed that although the end members were single phase, pyrochlore (Y₂Sn₂O₇) or defect fluorite (Y₂Zr₂O₇), the intermediate compositions were mostly two phase mixtures, consisting of an ordered pyrochlore (with an average formula of Y₂Sn₁.₈Zr₀.₂O₇) and a disordered phase, where the proportions of the pyrochlore and disordered phases decreased and increased, respectively, with the Zr content. Additionally, although the coordination states of the Y and Sn cations were easily determined using ⁸⁹Y and ¹¹⁹Sn NMR, respectively, the coordination states of the Zr cations could not be confirmed directly by ⁹¹Zr NMR. However, using indirect analysis from results obtained with ⁸⁹Y and ¹¹⁹Sn NMR, it was determined that 6 coordinate Zr was present in each composition, and it was always present in a greater proportion than 8 coordinate Zr. Finally, although ⁸⁹Y NMR spectra of Y₂Ti[subscript(x)]Zr[subscript(2-x)]O₇ were extremely difficult to analyse, it was tentatively proposed that they could be similar to Y₂Sn[subscript(x)]Zr[subscript(2-x)]O₇ due to some similarities observed between the spectra.

A class of 5-nitro-2-furancarboxylamides with potent trypanocidal activity against Trypanosoma brucei in vitro

Zhou, Linna — 2013-02-14T00:00:00Z

Abstract: Recently, the World Health Organization approved the nifurtimox–eflornithine combination therapy for the treatment of human African trypanosomiasis, renewing interest in nitroheterocycle therapies for this and associated diseases. In this study, we have synthesized a series of novel 5-nitro-2-furancarboxylamides that show potent trypanocidal activity, 1000-fold more potent than nifurtimox against in vitro Trypanosoma brucei with very low cytotoxicity against human HeLa cells. More importantly, the most potent analogue showed very limited cross-resistance to nifurtimox-resistant cells and vice versa. This implies that our novel, relatively easy to synthesize and therefore cheap, 5-nitro-2-furancarboxylamides are targeting a different, but still essential, biochemical process to those targeted by nifurtimox or its metabolites in the parasites. The significant increase in potency (smaller dose probably required) has the potential for greatly reducing unwanted side effects and also reducing the likelihood of drug resistance. Collectively, these findings have important implications for the future therapeutic treatment of African sleeping sickness.

New phosphine-diamine and phosphine-amino-alcohol tridentate ligands for ruthenium catalysed enantioselective hydrogenation of ketones and a concise lactone synthesis enabled by asymmetric reduction of cyano-ketones

Fuentes García, José Antonio — 2012-12-10T00:00:00Z

Abstract: Enantioselective hydrogenation of ketones is a key reaction in organic chemistry. In the past, we have attempted to deal with some unsolved challenges in this arena by introducing chiral tridentate phosphine-diamine/Ru catalysts. New catalysts and new applications are presented here, including the synthesis of phosphine-amino-alcohol P,N,OH ligands derived from (R,S)-1-amino-2-indanol, (S,S)-1-amino-2-indanol and a new chiral P,N,N ligand derived from (R,R)-1,2-diphenylethylenediamine. Ruthenium pre-catalysts of type [RuCl2(L)(DMSO)] were isolated and then examined in the hydrogenation of ketones. While the new P,N,OH ligand based catalysts are poor, the new P,N,N system gives up to 98% e.e. on substrates that do not react at all with most catalysts. A preliminary attempt at realising a new delta lactone synthesis by organocatalytic Michael addition between acetophenone and acrylonitrile, followed by asymmetric hydrogenation of the nitrile functionalised ketone is challenging in part due to the Michael addition chemistry, but also since Noyori pressure hydrogenation catalysts gave massively reduced reactivity relative to their performance for other acetophenone derivatives. The Ru phosphine-diamine system allowed quantitative conversion and around 50% e.e. The product can be converted into a delta lactone by treatment with KOH with complete retention of enantiomeric excess. This approach potentially offers access to this class of chiral molecules in three steps from the extremely cheap building blocks acrylonitrile and methyl-ketones; we encourage researchers to improve on our efforts in this potentially useful but currently flawed process.

The AEROPATH project targeting Pseudomonas aeruginosa : crystallographic studies for assessment of potential targets in early-stage drug discovery

Moynie, Lucile — 2013-01-01T00:00:00Z

Abstract: Bacterial infections are increasingly difficult to treat owing to the spread of antibiotic resistance. A major concern is Gram-negative bacteria, for which the discovery of new antimicrobial drugs has been particularly scarce. In an effort to accelerate early steps in drug discovery, the EU-funded AEROPATH project aims to identify novel targets in the opportunistic pathogen Pseudomonas aeruginosa by applying a multidisciplinary approach encompassing target validation, structural characterization, assay development and hit identification from small-molecule libraries. Here, the strategies used for target selection are described and progress in protein production and structure analysis is reported. Of the 102 selected targets, 84 could be produced in soluble form and the de novo structures of 39 proteins have been determined. The crystal structures of eight of these targets, ranging from hypothetical unknown proteins to metabolic enzymes from different functional classes (PA1645, PA1648, PA2169, PA3770, PA4098, PA4485, PA4992 and PA5259), are reported here. The structural information is expected to provide a firm basis for the improvement of hit compounds identified from fragment-based and high-throughput screening campaigns.

A small-molecule inhibitor of T. gondii motility induces the posttranslational modification of myosin light chain-1 and inhibits myosin motor activity

Heaslip, Aoife T. — 2010-01-15T00:00:00Z

Abstract: Toxoplasma gondii is an obligate intracellular parasite that enters cells by a process of active penetration. Host cell penetration and parasite motility are driven by a myosin motor complex consisting of four known proteins: TgMyoA, an unconventional Class XIV myosin; TgMLC1, a myosin light chain; and two membrane-associated proteins, TgGAP45 and TgGAP50. Little is known about how the activity of the myosin motor complex is regulated. Here, we show that treatment of parasites with a recently identified small-molecule inhibitor of invasion and motility results in a rapid and irreversible change in the electrophoretic mobility of TgMLC1. While the precise nature of the TgMLC1 modification has not yet been established, it was mapped to the peptide Val46-Arg59. To determine if the TgMLC1 modification is responsible for the motility defect observed in parasites after compound treatment, the activity of myosin motor complexes from control and compound-treated parasites was compared in an in vitro motility assay. TgMyoA motor complexes containing the modified TgMLC1 showed significantly decreased motor activity compared to control complexes. This change in motor activity likely accounts for the motility defects seen in the parasites after compound treatment and provides the first evidence, in any species, that the mechanical activity of Class XIV myosins can be modulated by posttranslational modifications to their associated light chains.

Determination of the spring constants of the higher flexural modes of microcantilever sensors

Parkin, John David — 2013-02-15T00:00:00Z

Abstract: A method for the simultaneous calibration of the spring constants of all flexural modes of microcantilevers is presented. It is based on a flow of gas from a microchannel that interacts with the microcantilever. The gas flow causes a measurable shift in the resonance frequencies of thermal noise spectra of the flexural modes. From the magnitude of the frequency shifts of the individual modes the spring constants can be determined with high accuracy and precision. The method is non-invasive and does not risk damage to the cantilever. Experimental data is presented for several V-shaped and rectangular cantilevers with nominal fundamental spring constants in the range of 0.03-1.75 N/m. The spring constants of the fundamental modes compare favorably to those obtained using the Sader method. The higher modes of oscillation are readily calibrated with experimental uncertainties of 5-10%.

Prins fluorination cyclisations : Preparation of 4-fluoro-pyran and -piperidine heterocycles

Launay, Guillaume G. — 2010-04-26T00:00:00Z

Abstract: The Prins reaction was investigated using BF3 center dot OEt2 as a Lewis acid. It has been recently demonstrated, that if BF3 center dot OEt2 is used in stoichiometric amounts then these reactions generate fluorinated products where the BF3 center dot OEt2 contributes fluoride ion to quench the intermediate carbocations. In this study oxa- and aza-Prins reactions for the synthesis of 4-fluoro-pyrans and -piperidines were investigated. The products were obtained in good yields, but only with moderate diastereoselectivity. These Prins fluorination reactions can be accelerated under microwave conditions. The study extends the Prins fluorination methodology for the generation of the C-F bond in heterocycles.

Coordinatively unsaturated ruthenium complexes as efficient alkyne-azide cycloaddition catalysts

Lamberti, Marina — 2012-01-23T00:00:00Z

Abstract: The performance of 16-electron ruthenium complexes with the general formula Cp*Ru(L)X (in which L = phosphine or N-heterocyclic carbene ligand; X = Cl or OCH2CF3) was explored in azide−alkyne cycloaddition reactions that afford the 1,2,3- triazole products. The scope of the Cp*Ru(PiPr3)Cl precatalyst was investigated for terminal alkynes leading to new 1,5-disubstituted 1,2,3-triazoles in high yields. Mechanistic studies were conducted and revealed a number of proposed intermediates. Cp*Ru- (PiPr3)(η2-HCCPh)Cl was observed and characterized by 1H, 13C, and 31P NMR at temperatures between 273 and 213 K. A rare example of N,N-κ2-phosphazide complex, Cp*Ru(κ2-iPr3PN3Bn)Cl, was fully characterized, and a single-crystal X-ray diffraction structure was obtained. DFT calculations describe a complete map of the catalytic reactivity with phenylacetylene and/or benzylazide.

Electron microscopic studies of growth of nanoscale catalysts and soot particles in a candle flame

Zhou, Wuzong — 2012-09-01T00:00:00Z

Abstract: Scanning electron microscopy and high-resolution transmission electron microscopy have been used to investigate non-classic crystal growth of catalytic nanoparticles, such as zeolites, perovskites, metal and alloy particles. Growth mechanisms of some crystals with novel morphologies, for example, BiOBr flower-like particles and ZnO twin-crystals, have also been studied. A development of sampling method for soot particles inside a candle flame allows us to reveal all four well-known carbon forms, amorphous, graphitic, fullerenic and nanodiamond particles. This article demonstrates that electron microscopy is a powerful tool to study the microstructures of small particles, giving us more freedom to develop new materials.

A model for 3-methyladenine recognition by 3-methyladenine DNA glycosylase I (TAG) from Staphylococcus aureus

Zhu, Xiaofeng — 2012-06-01T00:00:00Z

Abstract: The removal of chemically damaged DNA bases such as 3-methyladenine (3-MeA) is an essential process in all living organisms and is catalyzed by the enzyme 3-MeA DNA glycosylase I. A key question is how the enzyme selectively recognizes the alkylated 3-MeA over the much more abundant adenine. The crystal structures of native and Y16F-mutant 3-MeA DNA glycosylase I from Staphylococcus aureus in complex with 3-MeA are reported to 1.8 and 2.2 angstrom resolution, respectively. Isothermal titration calorimetry shows that protonation of 3-MeA decreases its binding affinity, confirming previous fluorescence studies that show that chargecharge recognition is not critical for the selection of 3-MeA over adenine. It is hypothesized that the hydrogen-bonding pattern of Glu38 and Tyr16 of 3-MeA DNA glycosylase I with a particular tautomer unique to 3-MeA contributes to recognition and selection.

Investigating silver coordination to mixed chalcogen ligands

Knight, Fergus Ross — 2012-11-08T00:00:00Z

Abstract: Six silver(I) coordination complexes have been prepared and structurally characterised. Mixed chalcogen-donor acenaphthene ligands L1–L3 [Acenap(EPh)(E'Ph)] (Acenap = acenaphthene-5,6-diyl; E/E' = S, Se, Te) were independently treated with silver(I) salts (AgBF4/AgOTf). In order to keep the number of variables to a minimum, all reactions were carried out using a 1:1 ratio of Ag/L and run in dichloromethane. The nature of the donor atoms, the coordinating ability of the respective counter-anion and the type of solvent used in recrystallisation, all affect the structural architecture of the final silver(I) complex, generating monomeric, silver(I) complexes {[AgBF4(L)2] (1 L = L1; 2 L = L2; 3 L = L3), [AgOTf(L)3] (4 L = L1; 5 L = L3), [AgBF4(L)3] (2a L = L1; 3a L = L3)} and a 1D polymeric chain {[AgOTf(L3)]n 6}. The organic acenaphthene ligands L1-L3 adopt a number of ligation modes (bis-monodentate μ2-η2-bridging, quasi-chelating combining monodentate and η6-E(phenyl)-Ag(I) and classical monodentate coordination) with the central silver atom at the centre of a tetrahedral or trigonal planar coordination geometry in each case. The importance of weak interactions in the formation of metal-organic structures is also highlighted by the number of short non-covalent contacts present within each complex.

Crystallization, dehydration and experimental phasing of WbdD, a bifunctional kinase and methyltransferase from Escherichia coli O9a

Hagelueken, Gregor — 2012-10-01T00:00:00Z

Abstract: WbdD is a bifunctional kinase/methyltransferase that is responsible for regulation of lipopolysaccharide O antigen polysaccharide chain length in Escherichia coli serotype O9a. Solving the crystal structure of this protein proved to be a challenge because the available crystals belonging to space group I23 only diffracted to low resolution (>95% of the crystals diffracted to resolution lower than 4 angstrom and most only to 8 angstrom) and were non-isomorphous, with changes in unit-cell dimensions of greater than 10%. Data from a serendipitously found single native crystal that diffracted to 3.0 angstrom resolution were non-isomorphous with a lower (3.5 angstrom) resolution selenomethionine data set. Here, a strategy for improving poor (3.5 angstrom resolution) initial phases by density modification and cross-crystal averaging with an additional 4.2 angstrom resolution data set to build a crude model of WbdD is desribed. Using this crude model as a mask to cut out the 3.5 angstrom resolution electron density yielded a successful molecular-replacement solution of the 3.0 angstrom resolution data set. The resulting map was used to build a complete model of WbdD. The hydration status of individual crystals appears to underpin the variable diffraction quality of WbdD crystals. After the initial structure had been solved, methods to control the hydration status of WbdD were developed and it was thus possible to routinely obtain high-resolution diffraction (to better than 2.5 angstrom resolution). This novel and facile crystal-dehydration protocol may be useful for similar challenging situations.

PRC1 and PRC2 are not required for targeting of H2A.Z to developmental genes in embryonic stem cells

Illingworth, Robert S. — 2012-04-09T00:00:00Z

Abstract: The essential histone variant H2A.Z localises to both active and silent chromatin sites. In embryonic stem cells (ESCs), H2A.Z is also reported to co-localise with polycomb repressive complex 2 (PRC2) at developmentally silenced genes. The mechanism of H2A.Z targeting is not clear, but a role for the PRC2 component Suz12 has been suggested. Given this association, we wished to determine if polycomb functionally directs H2A.Z incorporation in ESCs. We demonstrate that the PRC1 component Ring1B interacts with multiple complexes in ESCs. Moreover, we show that although the genomic distribution of H2A.Z co-localises with PRC2, Ring1B and with the presence of CpG islands, H2A.Z still blankets polycomb target loci in the absence of Suz12, Eed (PRC2) or Ring1B (PRC1). Therefore we conclude that H2A.Z accumulates at developmentally silenced genes in ESCs in a polycomb independent manner.

Discovery and validation of SIRT2 inhibitors based on tenovin-6 : use of a H-1-NMR method to assess deacetylase activity

Pirrie, Lisa — 2012-10-01T00:00:00Z

Abstract: The search for potent and selective sirtuin inhibitors continues as chemical tools of this type are of use in helping to assign the function of this interesting class of deacetylases. Here we describe SAR studies starting from the unselective sirtuin inhibitor tenovin-6. These studies identify a sub-micromolar inhibitor that has increased selectivity for SIRT2 over SIRT1 compared to tenovin-6. In addition, a H-1-NMR-based method is developed and used to validate further this class of sirtuin inhibitors. A thermal shift analysis of SIRT2 in the presence of tenovin-6, -43, a control tenovin and the known SIRT2 inhibitor AGK2 is also presented.

Structure of WbdD : a bifunctional kinase and methyltransferase that regulates the chain length of the O antigen in Escherichia coli O9a

Hagelueken, Gregor — 2012-11-01T00:00:00Z

Abstract: The Escherichia coli serotype O9a O-antigen polysaccharide (O-PS) is a model for glycan biosynthesis and export by the ATP-binding cassette transporter-dependent pathway. The polymannose O9a O-PS is synthesized as a polyprenol-linked glycan by mannosyltransferase enzymes located at the cytoplasmic membrane. The chain length of the O9a O-PS is tightly regulated by the WbdD enzyme. WbdD first phosphorylates the terminal non-reducing mannose of the O-PS and then methylates the phosphate, stopping polymerization. The 2.2?angstrom resolution structure of WbdD reveals a bacterial methyltransferase domain joined to a eukaryotic kinase domain. The kinase domain is again fused to an extended C-terminal coiled-coil domain reminiscent of eukaryotic DMPK (Myotonic Dystrophy Protein Kinase) family kinases such as Rho-associated protein kinase (ROCK). WbdD phosphorylates 2-a-d-mannosyl-d-mannose (2a-MB), a short mimic of the O9a polymer. Mutagenesis identifies those residues important in catalysis and substrate recognition and the in vivo phenotypes of these mutants are used to dissect the termination reaction. We have determined the structures of co-complexes of WbdD with two known eukaryotic protein kinase inhibitors. Although these are potent inhibitors in vitro, they do not show any in vivo activity. The structures reveal new insight into O-PS chain-length regulation in this important model system.

Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification

Ballester, Pedro — 2012-12-07T00:00:00Z

Abstract: One of the initial steps of modern drug discovery is the identification of small organic molecules able to inhibit a target macromolecule of therapeutic interest. A small proportion of these hits are further developed into lead compounds, which in turn may ultimately lead to a marketed drug. A commonly used screening protocol used for this task is high-throughput screening (HTS). However, the performance of HTS against antibacterial targets has generally been unsatisfactory, with high costs and low rates of hit identification. Here, we present a novel computational methodology that is able to identify a high proportion of structurally diverse inhibitors by searching unusually large molecular databases in a time-, cost- and resource-efficient manner. This virtual screening methodology was tested prospectively on two versions of an antibacterial target (type II dehydroquinase from Mycobacterium tuberculosis and Streptomyces coelicolor), for which HTS has not provided satisfactory results and consequently practically all known inhibitors are derivatives of the same core scaffold. Overall, our protocols identified 100 new inhibitors, with calculated Ki ranging from 4 to 250 μM (confirmed hit rates are 60% and 62% against each version of the target). Most importantly, over 50 new active molecular scaffolds were discovered that underscore the benefits that a wide application of prospectively validated in silico screening tools is likely to bring to antibacterial hit identification.

Environmental effects in quantum chemistry : QM/MM studies of structures, NMR properties and reactivities in extended systems

Bjornsson, Ragnar — 2012-11-30T00:00:00Z

Abstract: Computational modelling of chemical systems is most easily carried out in the vacuum for single molecules. Accounting for environmental effects accurately in quantum chemical calculations, however, is often necessary for computational predictions of chemical systems to have any relevance to experiment. This PhD thesis focuses on accounting for environmental effects in quantum chemical calculations by quantum mechanics/ molecular mechanics (QM/MM) approaches, taking on diverse examples from the solid state, the liquid phase and the protein environment. The methods are applied to compute a variety of properties from transition metal NMR properties of molecular crystals and enzymes, via conformational properties of zwitterions in aqueous solution, to an intramolecular amidation reaction in peptides. Chapter 3 concerns QM/MM calculations of molecular properties in the solid state, both molecular crystals and metalloenzymes, with a focus on transition metal chemical shift and EFG properties. We demonstrate that solid-state effects on such properties in molecular crystals can be accounted for by a simple general black-box QM/MM approach. We also describe preliminary QM/MM calculations of 51V anisotropic NMR properties for a vanadium-dependent enzyme. In Chapter 4 the focus is on solvent effects on the conformational preference of a small zwitterionic molecule, 3F-γ-aminobutyric acid (3F-GABA), calculated using QM/MM molecular dynamics simulations. NMR spin-spin coupling constants in solution are also calculated. Our simulations highlight the difficulty of accounting for solvation effects well enough to achieve agreement with experimental observations. Chapter 5 concerns the reaction mechanism of an intramolecular amidation reaction in a bacterial peptide, predicted by QM/MM calculations. We predict a reaction mechanism that accounts well for the experimental observations both for the wild-type and mutants. We demonstrate that environmental effects can often be satisfactorily accounted for by QM/MM approaches, thus helping to bridge the gap between theory and experiment.

The preferred conformation of erythro- and threo-1,2-difluorocyclododecanes

Wang, Yi — 2012-08-10T00:00:00Z

Abstract: Cyclododecane adopts a square-like structure with corner and edge CH2 groups. In this study erythro- and threo-1,2-difluorocyclododecanes were prepared to explore whether the two vicinal C-F bonds, with different relative configurations, preferably locate at corner/edge or edge/edge locations. Conformational analysis comparing the diastereoisomers was explored by using a combination of F-19{H-1} NMR spectroscopy, computational studies and, in the case of the threo isomer, X-ray structural analysis. In the lowest energy conformers for both diastereoisomers the vicinal C-F bonds are located corner/edge, rather than edge/edge. These structures avoid placing a C-F bond endo into the ring, and appear to benefit from C-CHF-C angle widening, which relaxes 1,4-H, H transannular interactions.

Extending the utility of [Pd(NHC)(cinnamyl)Cl] precatalysts : Direct arylation of heterocycles

Martin, Anthony — 2012-09-27T00:00:00Z

Abstract: The use of [Pd(NHC)(cinnamyl)Cl] precatalysts in the direct arylation of heterocycles has been investigated. Among four different precatalysts, [Pd(SIPr)(cinnamyl)Cl] proved to be the most efficient promoter of the reaction. The C–H functionalization of sulfuror nitrogen-containing heterocycles has been achieved at low catalyst loadings. These catalyst charges range from 0.1 to 0.01 mol % palladium.

A study of metal-organic frameworks for the storage and release of medical gases

Allan, Phoebe Kate — 2012-11-30T00:00:00Z

Abstract: This thesis presents a study of the interaction of medical gases nitric oxide, carbon monoxide and hydrogen sulfide with metal-organic framework materials. Most analysis is performed via single-crystal X-ray diffraction and Rietveld and pair distribution function analysis of powder X-ray diffraction data. A background to the field and the experimental methods used are described in Chapters 1 and 3. The use of a specially designed static environmental gas cell to assess the role of coordinatively unsaturated metal sites in nitric oxide storage in Co-CPO-27 via in situ single-crystal structure determination is described in Chapter 4. Nitric oxide was shown to bind to the Co-centre of the material in a bent geometry in an approximately 1:1 Co:NO ratio. A multi-technique study was conducted on the framework Cu-SIP-3 in Chapters 5 and 6, utilising both single-crystal X-ray diffraction and pair distribution function analysis to obtain complementary information about atomic movements during a thermally active single-crystal to single-crystal transition. These techniques were further applied during in situ gas-loading experiments on the same framework. Application of the pair distribution function technique to metal-organic frameworks is described in Chapter 7, where refinements of both known and unknown metal-organic framework structures are presented. Partial PDFs are used to determine the secondary building block of a new metal-organic framework and verify the structural solution determined from powder X-ray diffraction data. Chapter 8 presents the study of the M-CPO-27 isostructural series for the adsorption and release of hydrogen sulfide and carbon monoxide. Gas adsorption isotherms and release measurements are correlated with the structure of the Ni-CPO-27 hydrogen sulfide-adduct determined by both powder X-ray diffraction and differential pair distribution function methods which reveal the open-metal site as the primary adsorption interaction in the material. The hydrogen sulfide released from Zn-CPO-27 is determined to be biologically active through vasodilatation experiments.

Synthesis, characterisation and adsorption properties of metal-organic frameworks and the structural response to functionalisation and temperature

Mowat, John P.S. — 2012-07-01T00:00:00Z

Abstract: The synthesis of a scandium aluminium methylphosphonate ScAl₃(CH₃PO₃)₆ isostructural to the aluminium methylphosphonate AlMePO-α and with permanent microporosity is reported here for the first time. Structural characterisation of three lanthanide bisphosphonate structures (I,II,III) with the light lanthanides and N,N’-piperazine bis-(methylenephosphonic acid) and its 2-methyl and 2,5-dimethyl derivatives is described. The framework of structure type I shows considerable flexibility upon dehydration with a symmetry change from C2/c, a = 23.5864(2) Å, b = 12.1186(2) Å, c = 5.6613(2) Å, β = 93.040(2)˚) in the hydrated state to P2₁/n, a = 21.8361(12) Å, b = 9.3519(4) Å, c = 5.5629(3) Å, β = 96.560(4)˚ after dehydration. This cell volume reduces by 27% on dehydration and is accompanied by a change in the conformation of the piperazine ring from chair to boat configuration. The structures of type I (hydrated and dehydrated) were refined against synchrotron powder X-ray diffraction data. Despite the reversible hydration and flexibility, the structures possess no permanent porosity. Investigation of the solvothermal chemistry of scandium carboxylates identified routes to 7 framework structures 5 of which were previously unreported in the scandium system. Lower temperature solvothermal reactions using terephthalic acid (80 - 140°C using dimethylformamide and diethylformamide) yielded two scandium terephthalates, MIL-88B(Sc) and MIL-101(Sc), identified by laboratory X-ray powder diffraction. Whereas higher temperature (160 – 220°C), reactions gave MIL-53(Sc) and Sc₂BDC₃. Further study with the tri- and tetra-carboxylate linkers, trimesic acid, 3,3’,5,5’-azobenzenetetracarboxylic acid and pyromellitic acid yielded MIL-100(Sc), Sc-ABTC and Sc₄PMA₃ respectively. Structural identification of MIL-100(Sc) and Sc-ABTC was performed by means of X-ray powder diffraction analysis and of Sc₄PMA₃ by single crystal X-ray diffraction. The structure of a small pore scandium terephthalate Sc₂BDC₃ was investigated as a function of temperature and of functionalization. In situ synchrotron X-ray diffraction data, collected on a Sc₂BDC₃ in vacuo, enabled a phase change from orthorhombic Fddd to monoclinic C2/c and the associated structural effects to be observed in detail. The orthorhombic structure displayed a negative thermal expansivity of 2.4 × 10⁻⁵ K⁻¹ over the temperature range 225 – 523 K which Rietveld analysis showed to be derived from carboxylate group rotation. Motion within the framework was studied by ²H wide-line and MAS NMR on deuterated Sc₂BDC₃ indicating π flips can occur in the phenyl rings above 298 K. The effects of functionalization on the Sc₂BDC₃ framework were investigated by reactions using the 2-amino- and 2-nitroterephthalic acid and gave evidence for a strong structural effect resulting from inclusion of the functional groups. The structure of Sc₂BDC₃ and the functionalised derivatives were solved using Rietveld analysis on synchrotron X-ray powder diffraction data. Sc₂(NH₂-BDC)₃ was solved using the orthorhombic Sc₂BDC₃ framework starting model and, over the temperature range studied, stayed orthorhombic Fddd. Sc₂(NO₂-BDC)₃, was shown to be monoclinic C2/c over the same temperature range, a result of the steric effects of the bulky –NO₂ group in a small pore framework. Partial ordering of the functional groups was observed in both Sc₂(NH₂-BDC)₃ and Sc₂(NO₂-BDC)₃. The strength of interaction for the Sc₂(NH₂-BDC)₃ with CO₂ was higher than that of the parent Sc₂BDC₃ due to the strong –NH₂•••CO₂ interaction. Despite the inclusion of a relatively large –NO₂ group along the walls of a channel ~4 Å in diameter the Sc₂(NO₂-BDC)₃ still showed permanent microporosity to CO₂ (2.6 mmol g⁻¹) suggesting that there must be some motion in the -NO₂ group to allow the CO₂ molecules to diffuse through the channels. The scandium analogue of the flexible terephthalate MIL-53, a competitive phase in the synthesis of Sc₂BDC₃, was prepared and characterised by Rietveld analysis on synchrotron X-ray powder diffraction data using a combination of literature structural models and models obtained from single crystal X-ray diffraction experiments. Experimental solid state ⁴⁵Sc, ¹³C and ¹H NMR data combined with NMR calculations on the structural models produced from diffraction analysis were used to identify the hydrated (MIL-53(Sc)-H₂O), calcined (MIL-53(Sc)-CAL) and high temperature (MIL-53(Sc)-HT) structures of MIL-53(Sc). Further to this the 2-nitroterephthalate derivative, MIL-53(Sc)-NO₂, was prepared and characterised using single crystal X-ray diffraction. The adsorptive properties of the parent terephthalate and the functionalised derivative were compared and in both cases showed a breathing behaviour, exemplified by steps in the adsorption isotherms. MIL-53(Sc)-CAL was found to possess a closed pore configuration in the dehydrated state, a previously unreported structural form for the MIL-53 series, and its presence can be observed in the low pressure region of the CO₂ adsorption isotherm as a non-porous plateau. The selectivity and separation properties of two MOFs, the nickel bisphosphonate, STA-12(Ni) and the scandium carboxylate, Sc₂BDC₃ were measured using breakthrough curves on mixtures of CH₄ and CO₂. The results showed both materials to be highly selective in the adsorption of CO₂ over CH₄. Column testing using a PLOT column of STA-12(Ni) and a packed column of Sc₂BDC₃ showed promising preliminary results with STA-12(Ni) displaying effective, baseline separation on low boiling point hydrocarbon mixtures (C1 – C4) while the smaller pore channels of Sc₂BDC₃ were effective in the size selective separation of higher boiling point branched and straight-chain hydrocarbons (C5 – C7).

Material characterisation, phase transitions, electrochemical properties and possible fuel cell applications of Nd₂₋ₓPrₓCuO₄ and Nd2-x-y LayPrₓCuO₄ systems

Patabendige, Chami N.K. — 2012-03-13T00:00:00Z

Abstract: The well-known lanthanide cuprates exist in two principal forms, T and T´, which behave as p-type and n-type conductors, respectively. In order to understand the structural properties and crystal chemistry from the T to T´ phase, the Nd₁.₈₋ₓLaₓPr₀.₂CuO₄ (NLPCO) system was studied varying the La substitution ratio (0≤x≤1.8) and then characterised using high temperature X-ray powder diffraction. From analysis of the X-ray diffraction patterns obtained at room temperature, there are clearly five distinguishable regions for the NLPCO system. They are, (1) monophasic T´ solid–solution (2) two phase mixture T´ + T´´ (3) monophasic T´´solid–solution (4) two phase mixture T´´ + O and finally (5) monophasic O phase solid–solution. The T´´ form has previously been suggested as an ordered form of T´; however here we show via high temperature X-ray diffraction studies that it is a non-transformable metastable phase formed on quenching of the T phase via an orthorhombically distorted variant. Also neutron diffraction and selected area electron diffraction (SAED) studies confirmed that the T ´´phase is 4- fold Cu coordinated.The structural, magnetic and electrical properties of this NLPCO series have been investigated for the selected compositions using X-ray diffraction, magnetization measurements, thermal analysis and conductivity measurements. The aim of the second half of this work was to discover the basic high temperature electrical characteristics of Nd₂₋ₓPrₓCuO₄ and investigate how this matches with those required for components on the SOFC cathode side to identify which dopant level shows highest conductivity and whether it is stable at different temperatures. The idea was to make a new concept in SOFC cathodes and current collector development, using n-type conductors instead of p- type conductors and to try to produce a high conductivity material which is stable under the chemical and thermal stresses that exist while under load that can be used in cathode or current collector applications. The Nd₂₋ₓPrₓCuO₄ (NPCO) series has been studied over a range of dopant levels (x=0.15 - 0.25) and maximum conductivity of 86.7 Scm⁻¹ has been obtained for the composition where x = 0.25. Also NPCO shows n-type semiconductor behaviour which gives operational advantages when operating at mild oxygen deficiency. AC impedance studies have been carried out on symmetrical cells to investigate the performance of NPCO as a cathode material. These studies mainly focused on polarization resistance and the activation energies of the cells. Low Rp values and low activation energies are obtained for a composite cathode compared to pure cathode material. Two configurations of NPCO as cathode materials were tested, pre-fired and in-siu fired. Pre-fired NPCO exhibited better performance than in-situ fired NPCO. Both in-situ and pre-fired current collecting NPCO still showed lowest activation energies which suggest good catalytic activity. From all of these studies, it is evident that the praseodymium doped neodymium cuprate material shows considerable promise as a potential cathode material for solid oxide fuel cell applications.

Selective incorporation of the C-F bond as a conformational tool in quadruplex DNA ligand design

Smith, Daniel L. — 2012-08-15T00:00:00Z

Abstract: Chapter 1 provides a general introduction to organofluorine chemistry and focuses on recent developments in fluorination techniques. It also details how the C–F bond influences conformational and physiochemical properties of organic molecules. Chapter 2 highlights the biological role of the telomere, telomerase and quadruplex DNA in cells. It discusses the inhibition of telomerase with small molecules that stabilise quadruplex DNA as a treatment for cancer. An overview of the development of structurally related telomerase inhibitors and recent X-ray crystallographic structural data with BSU6039 and BRACO-19 telomeric DNA is presented. Chapter 3 discusses the synthesis of fluorinated BSU6039 analogues for the investigation of the conformational effects of fluorine in 5-membered rings and its influence on binding with quadruplex DNA. These compounds have been successfully co-crystallised with telomeric DNA and their relative stabilisation of telomeric DNA has been assessed. The latter half of this chapter focuses on the co-crystal structures between (S,S)- and (R,R)-144 with Oxytricha nova telomeric DNA, discussing the key differences between the two stereoisomers. Chapter 4 details the synthesis of fluorinated BRACO-19 analogues. The syntheses of such fluorinated analogues were achieved through a base mediated coupling between 3,6-diaminoacridone and an α-fluorinated-β-amino ester. The α-fluorinated-β-amino ester was synthesised through a deoxyfluorination-mediated approach, using the stereochemistry of natural amino acids. Chapter 5 describes the stereo- and regio- selectivity of deoxyfluorination reactions with dipeptides bearing the β-amino alcohol functionality. Understanding this selectivity enabled the development of a method towards α-fluorination of tertiary amides. The application of this fluorination method with an orthogonally protected tertiary amide is described.

Oligonucleotide based ligands in homogeneous transition metal catalysis

Eichelsheim, Tanja — 2012-11-30T00:00:00Z

Abstract: Catalysis plays an important part in our society. Numerous transition metal catalysts have been developed which can convert many different substrates in a wide range of reactions. Catalysis also plays an important role in nature and therefore special catalysts, enzymes, have evolved over time. Enzymes are tremendously efficient giving high yields and selectivities both regio and chemical but have a limited substrate and reaction scope. It was speculated that by combining the two, an ideal catalyst can be obtained. We planned to achieve this by introducing a transition metal, the catalytic centre, into the chiral environment of a double helical oligonucleotide. The transition metals were introduced by coordinating them to a ligand which was located in the chiral environment of a double helix. The ligand was either covalently bound (Chapter 2) or non-covalently bound (Chapter 3) to the oligonucleotide (Figure 1). Figure 1: A) covalent introduction of a transition metal into a nucleotide B) non-covalent introduction of a transition metal into a nucleotide For the covalent approach a phosphine ligand was chosen. A nucleoside was modified with an alkyne to which a phosphine moiety could be coupled via the copper catalysed 1,3-dipolar cycloaddition. The modified nucleoside was incorporated into an oligonucleotide before attempting to attach the phosphine moiety. The monomer was used as a ligand in allylic substitution and hydroformylation. In the non-covalent approach polyamide minor groove binders were functionalised with an amine linker. Phosphine moieties were connected via amide bond formation. Although the coupling worked effortlessly the phosphines oxidised during purification therefore dienes were also investigated.

MtsslWizard : in silico spin-labelling and generation of distance distributions in PyMOL

Hageluken, Gregor — 2012-04-01T00:00:00Z

Abstract: MtsslWizard is a computer program, which operates as a plugin for the PyMOL molecular graphics system. MtsslWizard estimates distances between spin labels on proteins quickly with user configurable options through a simple graphical interface. The program searches for ensembles of possible MTSSL conformations that do not clash with a static model of the protein. Options include restricting the search procedure to published rotamer libraries of MTSSL or scoring for contacts with protein. Once conformations are assigned, distance distributions between two or more sites are calculated, displayed and can be exported to other software. The program's use is evaluated in a number of challenging test cases and its performance discussed. The strength of the program is its accuracy and simplicity.

Revealing the art and science of self-replicating rotaxanes

Hassan, Nurul Izzaty — 2012-01-01T00:00:00Z

Abstract: This Thesis reveals the strategies for the construction and replication of mechanically interlocked molecules, particularly rotaxanes, which consist of a macrocyclic ring that encircles a linear component terminated with bulky groups. The work highlights our recent research activities in exploring the recognition-mediated synthesis of this class of interlocked molecule and its amplification by replication. Our starting point is the minimal model of self-replication. The introductory chapters (Chapter 1 and 2) provide some background and significance to the study, which presents comprehensive review of the published work carried out in the area of self-replication with existing examples from biomimetic and discrete synthetic assemblies. In Chapter 1, we mainly discuss the do and the donʼts in designing successful self-replicating systems based on our own experience in previous work. Our chief concerns in Chapter 2 are the understanding of the chemistry of the mechanical bond and the synthesis of rotaxanes by three means of approaches (clipping, threading and stoppering, and slippage). Attractive and useful examples are illustrated for each mechanism. Moreover, the definition and the roles of templated-synthesis of interlocked molecules are described. Recent advances in the understanding of the nature of the mechanical bond have also been introduced into molecular electronic devices. Emphasis is placed in Chapter 3 upon the essential requirements for the design of self-replicating rotaxanes, namely a recognition site, a reactive site and a binding site. These aspects are explained in the designed minimal model chosen in the past (Replication model 1) and the alternate proposed models (Replication model 2 and Replication model 3). The importance of high association constant to provide substantial amount of pseudorotaxane [L•M] precursors is exemplify in the simple kinetic model of rotaxane formation. The advantages and disadvantages of each independent minimal replication model are also summarized. In the self-replicating rotaxane frameworks, the principal strategy involves a selection of an efficient macrocycle to accommodate the guest unit. Thus, Chapter 4 exclusively describes the design, synthesis and binding properties of a series of macrocycle incorporating the hydrogen bond donors and/or hydrogen bond acceptors motif. In particular, the guests were designed and synthesised based on the mutual interactions with the macrocycle framework and the binding experiments is described in details. An account is provided of the problems faced in the synthetic attempts towards the formation of these macrocycles. The novel macrocycle MEU demonstrated a deficient binding performance with amide and urea compounds, and thus abandoned in later stages. The developed macrocycle MDG and MP have been selected as our workhorse macrocycles, which successfully increase the binding strength in the pseudorotaxanes formation. We have learnt that the association constant, Kₐ can be manipulated by the changing the binding site of the guest or redesign the framework of the macrocycle itself. An exhaustive investigation of the performance of self-replicating rotaxanes focuses on Replication model 1 is demonstrated in Chapter 5. It was evident now that as a consequence of low Kₐ, a substantial amount of thread is present over rotaxane. The implementation of the simple kinetic model of rotaxane formation is prevailed through out this chapter. The position of the central reversible equilibrium in this model effectively resulted in a different reactivity of thread and rotaxane. Therefore, it is concluded that the ratio of rotaxane and thread is sensitive to both the association constant for the [L•M] complex and to the ratio of k[subscript(rotaxane)]/k[subscript(thread)]. The key marker for the efficiency of the rotaxane-forming protocol is the ratio of rotaxane, R to thread, T. In previous chapter, the Kₐ for the [L•M] complex was around 100 M⁻¹ and k[subscript(T)] = 3 k[subscript(R)], which led to an unacceptably small [R]/[T] ratio. We demonstrated for the first time in Chapter 6, that it is possible to manipulate the Kₐ for the [L•M] complex by means of a change in temperature. Yields of a rotaxane can be improved by employing a two-step capture protocol. Cooling a solution of the linear and macrocyclic components required for the rotaxane increases the population of the target pseudorotaxane, which is then captured by a rapid capping reaction between an azide and PPh₃. The resulting iminophosphorane rotaxane can then be manipulated synthetically at elevated temperatures. Following this, these imines could be reduced readily to afford the stable amine rotaxane. Replication model 2 is subsequently proposed as alternate replication framework in Chapter 7, which realised significant advantages over the first model. A number of designs of a potential self-replicating rotaxane have been fabricated in order to integrate self-replication with the formation of rotaxanes. An account is provided of the problems faced with the unanticipated larger cavity of the newly prepared acid recognition macrocycles, and hence, force us to search for a new scaffold of the nitrone structures. Pleasingly, a substantial amount of rotaxane was present, mostly as trans diastereoisomer. It is concluded that the resulting rotaxane structures may be self-replicating through the recognition-mediated pathways from the preliminary kinetic experiments. Nonetheless, the remainder of the full kinetic analysis are prevented given a small quantity of the necessary building block. Chapter 8 reveals our recent efforts to demonstrate the notions behind the final replication scheme, Replication model 3. We have become aware that the reactive site must be placed sufficiently far away from the binding site to inhibit the remote steric effect through the proximity of the macrocyclic component. The design of novel nitrone structures is described in details. We bring together conclusions that can be drawn from three designated replication models in Chapter 9. Experimental and synthetic procedures of the target compounds and appropriate spectroscopic analysis of the products are elaborated in Chapter 10.

Soft routes to inorganic frameworks via assembly of molecular building blocks

Kandasamy, Balamurugan — 2012-01-01T00:00:00Z

Abstract: The assembly of mononuclear and polynuclear molecular building blocks has been investigated as a route to extended metal oxide structures. Various [MX[subscript(y)]]ⁿ⁻ (X = Cl, OMe, OH) and [(RO)M’M₅O₁₈]³⁻ (R = MeO, M’ = Sn, M = W) building blocks have been synthesised. Controlled hydrolysis has been explored for transition and main group metal hexahalides [MCl₆]ⁿ⁻ M=Ti, Sn using ¹⁷O enriched water. An attempted synthesis of [Me₃NCH₂Ph] [Sn(OMe)₆] gave the dinuclear product [Me₃NCH₂Ph] [Sn₂(OMe)₉]. Variable temperature ¹H NMR studies revealed exchange between terminal and bridging alkoxides and the limiting spectrum is consistent with solid state structure. 2,6-lutidinium hydrochloride was synthesised and used to chlorinate the metal alkoxides {M(OR)[subscript(n)]} (M = Nb). A route to monochloro niobium alkoxide {NbCl(OMe)₄} was developed and variable temperature ¹H NMR spectroscopy studies of {NbCl(OMe)₄} in different solvents revealed exchange between bridging and terminal alkoxides and also suggested the presence of different structural isomers in solution. A novel heterometallic Lindqvist type of POM containing Sn has been successfully synthesised by using controlled hydrolytic aggregation. A mixture of (TBA)₂WO₄, WO(OMe)₄ and {Sn(O[superscript(t)] Bu)₄} was partially hydrolysed in a non-aqueous solvent to give (TBA)₃[(MeO)SnW₅O₁₈] (1). ¹¹⁹Sn NMR INEPT and selective tin decoupled proton NMR experiments have been carried out to determine the axial and equatorial ²J {¹¹⁹Sn*¹⁸³W} coupling constants and to estimate ³J{¹¹⁹Sn¹H} and ³J{¹¹⁷Sn¹H} coupling constants. The electrochemistry of (1) was studied by cyclic voltammetry (CV), and was shown to undergo a reversible one electron reduction close to the solvent limit. Hydrolysis of [(MeO)SnW₅O₁₈]³⁻ produced [(OH)SnW₅O₁₈]³⁻ (2) which is stable in the solid state but in solution undergoes a condensation reaction to give [(µ- O)(SnW₅O₁₈)₂]⁶⁻ (3). The chloro stannotungstate [ClSnW₅O₁₈]³⁻ (4) was also obtained during the synthesis of (1) and (2). Compounds (2) and (4) are crystallographically isostructural and Sn hetero site was disordered over all six metal positions in both anions. The redox properties of (4) were studied by CV and showed an irreversible reduction peak at -1.67 V. Compound (4) is stable in air and did not react with H₂O or PhOH but did react with MeOH or NaOMe to give (1). It also reacted with diisopropylamine (DIPA) to produce the H-bonded aggregate [(Prⁱ₂NH₂)₂(µ-O)(SnW₅O₁₈)₂]⁴⁻. The adduct structure is related to a recently characterised titanium analogue [(µ-O)(TiW₅O₁₈H)₂]⁴⁻ , which forms the H-bonded THF adduct [(µ-O)(TiW₅O₁₈H)₂(THF)]⁴⁻ . 2D-¹H EXSY NMR studies of the mixtures of (1) and MeOH did not show any exchange peaks between (1) and methanol which demonstrates that exchange is slow but reactivity studies of (1) have been carried out with various alcohols and phenols to give substituted products. Sterically smaller alkyl groups gave trans disordered structures, but no disorder is present in structures of anion with bulkier aliphatic alkoxide and aryloxide groups. Hydrogen bonding was observed between the POM cage and pendant phenolic OH groups All the alkyl and aryloxido derivatives have been characterised by single crystal X-Ray diffraction, ¹H and multinuclear NMR spectroscopy, infrared spectroscopy and CHN analysis. Preliminary studies to explore the immobilisation of metal alkoxides [Ti(OPrⁱ )₄] and (1) on ~30% OH functionalised Si(111) surfaces have been carried out. The attempted covalent immobilisation of (1) to Si(111) surfaces appeared to be successful from Atomic Force Microscopy (AFM) measurements.

Lewis base organocatalysts for carboxyl and acyl transfer reactions

Woods, Philip A. — 2011-08-15T00:00:00Z

Abstract: This thesis is concerned with the use of Lewis base organocatalysts for carboxyl and acyl transfer reactions. Chapter 1 introduces the ability of organic Lewis bases other than DMAP-type to promote a range of asymmetric O-, N- and C-acyl transfer processes. This chapter summarizes the developments in catalyst architectures and approaches to these processes that have been disclosed to date in this dynamic area of asymmetric organocatalysis. Chapter 2 introduces studies into the synthesis of pyrrolyl carbonates via cyclization of gamma-amino esters and ring closing metathesis (RCM) of N-allylamides. The ability of a range of Lewis bases to promote the regioselective O- to C-carboxyl transfer of pyrrolyl carbonates is also presented. Chapter 3 introduces isothiourea DHPB as an efficient Lewis base catalyst for the diastereoselective C-acylation of silyl ketene acetals with anhydrides or benzoyl fluoride, giving 3-acyl-3-aryl or 3-acyl-3-alkylfuranones in excellent yields and stereoselectivities (up to 99:1 dr). Chapter 4 introduces C(2)-aryl substituted DHPB derived-isothioureas as efficient Lewis base catalysts for the enantioselective C-acylation of silyl ketene acetals with propionic anhydride, giving 3-acyl-3-aryl or 3-acyl-3-alkylfuranones in good isolated yields and enantioselectivities (up to 98% ee). This chapter also demonstrates that these chiral isothioureas are required for high reactivity and asymmetry in related acylation manifolds. Chapter 5 presents and overall conclusion for chapters 2,3 and 4. Chapter 6 contains full experimental procedures and characterization data for all compounds synthesized in Chapters 2, 3 and 4.

Isothiourea-promoted O- to C-carboxyl transfer reactions

Joannesse, Caroline — 2011-11-30T00:00:00Z

Abstract: This thesis describes an extensive investigation of the O- to C-carboxyl transfer of oxazolyl carbonates using isothioureas as Lewis base catalysts. The structural requirements of simple bicyclic amidines and isothioureas to promote this transformation have been investigated, showing that the catalytic efficiency and product distribution of these reactions are markedly affected by the catalyst structure. The optimal isothiourea catalyst was efficiently applied to the rearrangement of a wide range of oxazolyl, benzofuranyl and indolyl carbonates. The structural motif of tetrahydropyrimidine-based isothioureas has then been evaluated in order to develop an asymmetric variant of the O- to C-carboxyl transfer of oxazolyl carbonates. A number of chiral isothioureas bearing stereodirecting groups in C(2) and/or C(3) have been synthesised and used in this rearrangement, showing that a C(2)-stereodirecting unit is essential for high enantioselectivity, with an additional C(3)-substituent increasing the reactivity. The optimal chiral C(2)-substituted isothioureas identified are general and efficient asymmetric catalysts for O- to C-carboxyl transfer of oxazolyl carbonates, generating a quaternary stereocentre with high enantioselectivity (up to 94% ee). The origin of the enantioselectivity of this process has been probed mechanistically and rationalised computationally. Having gained an insight into the structural motifs of isothioureas required to impart good catalytic activity and asymmetric induction in the O- to C-carboxyl transfer of oxazolyl carbonates, the mechanism of this reaction was probed using kinetic and mechanistic experiments. ¹⁹F NMR spectroscopic analysis allowed the evolution of product, by-product and intermediate throughout the reaction to be monitored while a number of crossover and stability experiments gave additional information about the catalytic cycle. Extension to a related system has been demonstrated with the O- to C-carboxyl transfer of furanyl carbonates, producing a mixture of α- and γ-butenolides depending on the nature of the Lewis base employed. DMAP gives a mixture of both regioisomers with a preference for the α-regioisomer, while NHCs lead predominantly to the γ-regioisomer. Chiral isothioureas have been used to promote this rearrangement, giving the major α-regioisomer with good enantioselectivity (up to 83% ee). To quantify the different reactivities observed with these isothioureas, their nucleophilicities and Lewis basicities using the stopped-flow technique have been determined. Finally, model studies toward the synthesis of the natural product calcaridine A, using the methodology developed herein, have been investigated.

Investigations into the role of α-amino acids as chiral modifiers for Ni-based enantioselective heterogeneous hydrogenation catalysts

Wilson, Karen E. — 2011-11-30T00:00:00Z

Abstract: The hydrogenation of β-ketoesters over chirally modified Ni catalysts is a celebrated and thoroughly researched example of an enantioselective heterogeneous catalytic reaction. Enantioselective heterogeneous processes, although extremely attractive in terms of fewer complications in the separation of products from the catalyst, are hindered in their viability as industrial applications due to the lack of detailed knowledge on how chirality is conferred to the metal surface. Surface science techniques have afforded substantial progress into determining mechanisms between modifier, reactant and catalyst to explain the source of enantioselectivity of the system. In this study, a combination of solution and ultra-high vacuum (UHV)-based experiments allow a more realistic interpretation of the surface chemistry underpinning the catalytic reaction as the key step in achieving enantioselective performance is the adsorption of chiral modifiers from solution. The behaviour of (S)-aspartic acid and (S)-lysine on Ni{111} and their interaction with the prochiral β-ketoester methylacetoacetate is investigated in this study to understand their potential as chiral modifiers for the system. In UHV, scanning tunnelling microscopy (STM), reflection absorption infrared spectroscopy (RAIRS), and temperature programmed desorption (TPD) are used to analyse the conformation and order of the amino acids on the metal, and their thermal stability. Additionally, liquid-solid interface RAIRS and X-ray photoelectron spectroscopy (XPS) are used to examine the modified Ni surface, prepared under aqueous conditions, to give an accurate representation of the catalytic studies. It has been found highly likely that, for (S)-aspartic acid modified Ni{111}, enantioselective sites exist at step or step/kink defects, formed by corrosive leaching of the Ni substrate. Conversely, lysine appears to bind with a high sticking probability to Ni, in the form of lysine islands, and does not appear to etch the Ni chirally. Finally, similar experiments have been carried out on Au{111}, where lysine was found to chiral restructure the surface and form nanofingers, and 2D Ni clusters grown on Au{111} in order to investigate the formation of possible metal-organic frameworks.

Synthetic studies into phosphorus and arsenic peri-substituted naphthalene

Somisara, Dhanasekara M. U. K. — 2011-06-08T00:00:00Z

Abstract: The rac- and meso- forms of “all carbon” 1,2-diphosphonium dications with the naphthalene -1,8-diyl backbone were synthesised in good yields and purity by double alkylation of the parent diphosphine (1,2-diphenyl-1,2-diphosphaacenaphthene) using strong alkylating agents. Pure rac- and meso- forms of 1,2-diphosphoniums were obtained diastereospecifically by using methyl triflate and trimethyloxonium tetrafluoroborate respectively. It was found that the equilibrium between the rac- and meso- forms at room temperature in acetonitrile solutions effectively depends on the anion present. A reaction mechanism which proceeds via a P-pentacoordinated intermediate was proposed for the epimerisation observed between the rac- and meso- forms in the presence of F⁻ donors in the solution. Reactivity of the new 1,2-dications towards a range of compounds (nucleophiles, bases) was examined and a series of new compounds including phosphine-phosphoniums and phosphonium-phosphine oxides were obtained. Cyclic and acyclic compounds belonging to a novel group of phosphine-arsine mixed peri-substituted acenaphthenes were synthesised by introducing arsenic and phosphorus to the acenaphthene ring, using stepwise lithiation and carbon-group 15 element coupling. All new compounds were fully characterised including single crystal X-ray diffraction. The effect of the peri-substitution by phosphorus moieties and mixed arsine-phosphine peri-substitution on the naphthalene ring was studied using the detailed structural data obtained for these systems.

Asymmetric hydroformylation : a powerful tool for the synthesis of pharmaceutical intermediates

Noonan, Gary M. — 2011-06-22T00:00:00Z

Abstract: The hydroformylation of unfunctionalised olefins (such as prop-1-ene and oct-1-ene) is an extremely valuable process and is practised on a massive scale industrially in the synthesis of commodity chemicals. In fact, it represents the worlds largest scale application of homogeneous catalysis. As a result, the majority of research carried out on this reaction has been in the study of catalytic systems which provide high rates and selectivity for the production of linear aldehydes from terminal unfunctionalised olefins, with the products finding use in the production of plasticizers and detergents. Asymmetric hydroformylation, the enantioselective variant of this reaction is extremely attractive, as low cost or easily accessible olefins are transformed into highly versatile value-added enantioenriched aldehydes in a single step. However synthetic organic chemists interested in the synthesis of fine chemicals, both in academia and industry, have been slow to adopt this attractive protocol for the production of chiral aldehydes. This is mainly due to the fact that in the past catalysts for this reaction exhibited low activity and/or selectivity in this process. However, the last two decades have seen major advances, mainly in the development of highly effective chiral ligands, and with these developments the time has come to tackle the vastly under-explored area of asymmetric hydroformylation of more functionalised olefins. To set the scene for the research carried out during this project a brief introduction will be given which highlights the historical development of highly efficient catalysts for the hydroformylation of olefins. This will be accompanied by some examples of the use of this methodology in the synthesis of pharmaceutically relevant compounds. It should become apparent from the introduction that the asymmetric hydroformylation of functionalised olefins and in particular nitrogen containing olefins, has received very little attention despite the fact that over half of all medicinal compounds contain at least one nitrogen containing functional group. Firstly we describe hydroformylation as a useful alternative to the classical synthesis of a delicate chiral building block, namely α-formyl amides. These compounds, traditionally only available through multi-step synthetic procedures from enantiopure starting materials, have been accessed by asymmetric hydroformylation of readily accessible and in some cases commercially available acrylamides. By judicious choice of reaction conditions and selection of the appropriately active chiral ligand enantioenriched α-formyl amides (e.e. up to 82%) were produced in high yield. A comparison is made between the classical route and the hydroformylation route to illustrate the potential of this efficient transformation. We have studied the hydroformylation of enamides, a much under-studied substrate class in hydroformylation and developed knowledge of how some more functionalised 1,1- and 1-2-subtituted olefinic amides react under hydroformylation conditions. This research illustrates the work still to be done in terms of development of more active and selective catalysts for this reaction but despite limitations we developed a potential route to gamma amino aldehyde derivatives which could be used in turn in the synthesis of physiologically important gamma amino butyric acid (GABA) derivatives. We provide an example of the highly efficient and selective asymmetric hydroformylation of a bicyclic olefinic lactam, which is of industrial importance in the synthesis of carbocyclic nucleosides. We demonstrate the efficiency of this synthetic methodology by synthesising the central pharmacophore of a potent anti- HSV-1 (herpes simplex virus) carbocyclic nucleoside via a hydroformylationreduction protocol. The classical synthesis of this pharmacophore involves nine synthetic transformations to produce racemic material, whereas the hydroformylationreduction protocol produces highly enantioenriched material in just two steps. We also demonstrate some downstream chemistry of the aldehyde products showcasing the synthetic versatility of the aldehyde functionality in the production of a variety of functionalised cyclopentanes. Finally the synthesis and catalytic testing of a group of novel phosphine-phosphite ligands for use in asymmetric hydroformylation is described, one of which produces unprecedented regioselectivity and state of the art enantioselectivity in the asymmetric hydroformylation of styrene. Highly selective asymmetric hydroformylation of the other two ‘model substrates’ in this reaction namely, vinyl acetate and allyl cyanide is also achieved. Having shown high activity and selectivity over these ‘model substrates’ this ligand takes its place among the small group of highly active and selective ligands available for asymmetric hydroformylation and may also help to broaden the substrate scope of this efficient and atom-economic transformation.

Design and synthesis of wide bite angle phosphacyclic ligands

Gillespie, Jason A. — 2012-06-01T00:00:00Z

Abstract: By examining structure activity relationships for a given catalytic reaction it is possible to discover what ligand features and parameters lead to stable and highly active/selective catalyst systems. With this knowledge in hand it may be possible to rationally design next generation ligands and catalysts to affect improved substrate transformations, with higher selectivities and faster reaction times. The success of Burk’s DuPhos ligands in asymmetric hydrogenation demonstrated that chiral phosphacycles can be a potent source of chiral induction, whilst in a similar vein the work of van Leeuwen and Kamer established the wide bite angle xanthene based ligands as excellent catalysts in a range of reactions including hydroformylation. In a preliminary study with Osborne they showed that combining these wide bite angle ligand backbones with Burk’s phospholane moieties led to a new powerful ligand in asymmetric allylic substitution. To examine the potential of combining these two ligand features further we designed and synthesised nine new C2-symmetric bidentate wide bite angle bisphosphacyclic ligands, featuring phosphetane, phospholane or diazaphospholane rings, aiming at a wide diversity of steric and electronic properties. The application of these ligands as chiral auxiliaries in transition metal catalysed reactions, including; hydrogenation, hydrocyanation, hydroformylation and allylic alkylation has been investigated. Good to excellent enantioselectivities were observed in all reactions, with maximum ee’s of 92.5% observed in hydrogenation, using N-(3,4-dihydro-1-napthalenyl)-acetamide as substrate, and of 96.2% in the alkylation of 1,3-diphenyl-2-propenyl acetate.

Generation of micro/nano metallic nanostructures using self-assembled monolayers as template and electrochemistry

She, Zhe — 2012-06-20T00:00:00Z

Abstract: This thesis studies a scheme to fabricate small-scaled metal structures by electrochemical metal deposition and lift off. The key point is the use of self-assembled monolayers (SAMs) to control both interfacial charge transfer in electrodeposition and adhesion of the deposit to the substrate. Patterned SAMs exhibiting blocking and non-blocking areas are applied as templates in electrochemical deposition of Cu or Au. Thiol SAMs on Au substrates are used, namely alkane thiols and thiols combining an aliphatic chain with a biphenyl or biphenyl analogous pyridine-phenyl moieties. The patterning of SAMs is realised with microcontact printing (μCP) and electron beam lithography. Electrochemical deposition based on defects in the SAMs is optimised towards generating small nanostructures and depending on the system single or stepped potential procedures are applied. Generated metal structures are transferred to an insulator by lift off. Au microstructures (~10 μm) have been made with microcontact printing and transferred onto epoxy glue, which can potentially be used as microelectrodes in electroanalytical chemistry. Sub-100 nm Cu features and sub-40 nm Au features have been created with electron beam lithography respectively. Lift off process has successfully transferred Cu nanostructures onto epoxy glue with high precision. In contrast to the deposition mediated by defects, Cu deposition mediated by discharging Pd²⁺ coordinated to a pyridine terminated SAM directly through the SAM molecules has been explored as a new approach. This new approach has potential to decrease the size of the metal structure further and the preliminary results show possibility of sub-10 nm features. SAMs prepared with a newly synthesised molecule, 3-(4'-(methylthio)-[1,1'-biphenyl]-4-yl)propane-1-thiol, are characterised by STM, XPS and NEXAFS. The metal structures are investigated by SEM, AFM and STM.

The effects of carbon deposition on catalyst deactivation in high temperature Fischer-Tropsch catalysts

Patterson, Veronica A. — 2012-06-01T00:00:00Z

Abstract: In this work, carbonaceous deposits on spent HTFT catalysts were investigated. This research was required in order to better understand the observed loss in productivity observed in the industrial reactors, with the aim of improving the economy of the HTFT process. A host of complementary techniques were employed to systematically determine the composition of a typical catalyst recovered from a reactor. Spent HTFT catalysts are comprised of magnetite and a mixture of iron carbides as well as adsorbed hydrocarbon products (soft carbon) and hard carbon. Reaction initiates at the particle surface and along the promoter-rich grain boundaries toward the core of the grains. A partially reacted particle would therefore have a core-shell structure, with magnetite representing the unreacted region of the catalyst. The reacted region consists of a porous carbonaceous matrix with soft carbon and carbide crystallites nestled in this matrix. The hard carbonaceous species is a mixture of polymeric carbon and polycyclic aromatic hydrocarbons. The particle structure is linked to the sample preparation method and an alternative method yielding catalyst particle with uniformly distributed promoter elements could be beneficial. Investigating carbonaceous species is a complex process, and development of a fresh methodology would aid in the quest for insight into the nature of carbonaceous species in various systems. A new approach which entails a combination of the traditional techniques combined with MALDI-TOF MS enabled a deeper investigation. Additional aspects such as the molecular weight distributions along with known information about crystallinity and morphology of the catalyst provide a comprehensive study of carbonaceous material. Polymeric carbon and very large polycyclic aromatic hydrocarbons constitute hard carbon and can be observed with minimal sample preparation procedures. The evolution of the HTFT catalysts was investigated as a function of time-on-stream. This enabled us to study the effects of increasing amounts of hard carbon on the activity and the chemical and physical properties of the catalysts. The catalyst activity was found to decrease with increasing hard carbon content, although the effect of carbon deposition cannot be distinguished from phase transformation (oxidation) which occurs simultaneously. A method to quantify the amount of hard carbon, which progressively builds up on the catalyst, was demonstrated. This required a great deal of method development, which provides a platform for future investigations of these catalysts. Importantly, it allows predictions of the amounts of carbon that will be deposited after a certain reaction time. This allows more efficient regulation of catalyst replacement. The production of fine carbon-rich particles in the industrial reactor poses a major problem in the process. Carbon deposition leads to an increase in particle diameter with time on-stream. Permissible levels of hard carbon were identified, beyond which the mechanical strength of the catalyst particles deteriorate. This leads to break-up of the particles and therefore fines formation. The surface area and pore volume generally increase with progressive deposition of hard carbon, while the bulk density of the catalyst material exhibits a linear decrease with carbon build-up. A mechanism is proposed for hard carbon formation which apparently occurs through the dissociative adsorption of CO to form a carbon monolayer. This is followed by polymerisation of the carbon atoms. Meta-stable interstitial carbides are formed at the iron-carbon interface. Owing to a carbon concentration gradient between the top of the surface and the bottom of the metal or carbide particle, carbon diffusion across the crystal (carbide decomposition) and grows as a PAH molecule lifting the iron carbide away from the particle. As this corrosion process is intrinsic to iron-based catalysts, a catalyst that contains sulphur is proposed for future development.

NHCs in organocatalysis : azolium enolate generation and synthetic applications

Douglas, James. J — 2012-11-30T00:00:00Z

Abstract: This thesis details investigations into organocatalytic reactions promoted by N Heterocyclic Carbenes (NHCs) that proceed via an assumed azolium enolate intermediate. Initial research focused on the catalytic asymmetric synthesis of β-lactones via an NHC-catalysed formal [2+2] cycloaddition of alkylarylketenes and chloral. This process operated in good yield (typically >70%) and moderate diastereoselectivity (typically ~75:25 dr, anti:syn) for a range of alkylarylketenes. The enantioselectivity was consistently high for the major anti diastereomer (typically >80% ee) and minor syn diastereomer (typically >70% ee). Interestingly, when a ketene bearing a 2 substituent on the aryl ring, or one that included an α-branched alkyl group was used, an exclusive asymmetric chlorination pathway was accessed. This is, to the best of our knowledge, the first use of chloral as an electrophilic chlorination agent. This methodology was found to be applicable to a range of 2-arylsubstituted alkylarylketenes in good yield and enantioselectivity (typically >70% yield and up to 92% ee). The scope of this reaction with respect to the aldehyde moiety was then analysed with 2-nitrobenzaldehyde providing β-lactone products in excellent dr (up to 94:6 syn:anti) and with good yield and enantioselectivity (typically >60% yield and >80% ee). Importantly these β-lactone products were amenable to further derivatisation with transformation to β-amino- and β-hydroxy acids. Following the identification of an NHC-catalysed chlorination reaction using chloral, the development of a general procedure was undertaken. Following a wide screen of electrophilic chlorination sources, 2,3,4,5,6,6 hexachlorocyclohexa 2,4 dienone was identified as optimal, operating in excellent yield (up to 97%) but in moderate to poor levels of enantioselectivity (21−61% ee). Efforts to expand the practicality of azolium enolate processes focused on the use of α-aroyloxyaldehydes as bench stable mono-substituted ketene surrogates. A range of differentially substituted α-aroyloxyaldehydes allowed access to δ-lactones via the NHC-catalysed [4+2] cycloaddition between azolium enolates and β,γ unsaturated α ketoesters. Following initial optimisation the reaction proceeded in exquisite diastereo- and enantiocontrol (typically >95:5 dr and >99% ee).

Effects of pore modification on the templating of guest molecules in a 2D honeycomb network

Raeisaenen, Minna T. — 2012-01-01T00:00:00Z

Abstract: 1,7-Diadamantanethioperylene-3,4:9,10-tetracarboxylic diimide, (Ad-S)(2)-PTCDI, adsorbed on Au (111) from solution was investigated by scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS). (Ad-S)(2)-PTCDI forms a well-ordered monolayer whose structure is described by a (2 root 63 x root 19) R19.1 degrees chiral unit cell containing four molecules. Codeposition of (Ad-S)(2)-PTCDI with 1,3,5-triazine-2,4,6-triamine (melamine) yields a honeycomb network whose (7 root 3 x 7 root 3)R30 degrees unit cell is identical to the unsubstituted PTCDI/melamine analogue. The effect of the adamantyl thioether moieties on the adsorption of guest molecules is investigated using adamantane thiol and C-60. While the thioether units do not affect the packing of adamantane thiol molecules a pronounced influence is seen in the case of fullerene. Pore modification involving different combinations of enantiomers of (Ad-S)(2)-PTCDI give rise to distinctly different arrangements of C-60 molecules. The diversity of patterns is further increased by the presence of unsubstituted PTCDI molecules. Description: This work was supported by the UK Engineering Physical Sciences Research Council (EPRSC) and the EU.

Emergence in complex systems based on synthetic replicators

Huck, Juergen — 2011-11-01T00:00:00Z

Abstract: Biopolymers with defined recognition pattern were used to generate the first artificial replicating systems. Stripping down these systems to their most fundamental properties allowed to move away from the biological origins to construct replicators consisting of simple organic molecules. These systems have proven highly instructive for the in-depth understanding of the main requirements for the targeted development of efficient replicators. With this knowledge at hand, it is now possible to combine several replicators for the formation of molecular networks, and to use the unique properties of replication to manipulate these networks by external stimuli. In the thesis presented, the investigation of a family of self-replicators culminated in the successful construction of several examples of a multicyclic system in which four building blocks are able to react via two autocatalytic and two reciprocal pathways. Owing to the connectivity in this reaction system, it was demonstrated that its outcome can be influenced in a programmable manner by the addition of informational template. Some of the responses can be deduced directly from the functioning of the individual systems, others however are to be classified as emergent properties of the network. Upon elucidation of the multicyclic systems, it became apparent that working in closed reaction systems puts intrinsic boundaries on the possibility to bias the outcome of the reaction network. This limitation prevented the extinction of the inferior type of replicators even under highly unfavourable conditions and instead always led to coexistence for all species.

ALDH2 mediates 5-nitrofuran activity in multiple species

Zhou, Linna — 2012-07-27T00:00:00Z

Abstract: Understanding how drugs work in vivo is critical for drug design and for maximizing the potential of currently available drugs. 5-nitrofurans are a class of pro-drugs widely used to treat bacterial and trypanosome infections, but despite relative specificity 5-nitrofurans often cause serious toxic side-effects in people. Here, we use yeast, zebrafish and human in vitro systems to assess the biological activity of 5-nitrofurans, and identify a conserved interaction between aldehyde dehydrogenase (ALDH) 2 and 5-nitrofurans across these species. In addition, we show that the activity of nifurtimox, a 5-nitrofuran anti-trypanosome pro-drug, is dependent on zebrafish Aldh2 and that nifurtimox is a substrate for human ALDH2. This study reveals a conserved and biologically relevant ALDH2-5-nitrofuran interaction that may have important implications for managing the toxicity of 5nitrofuran treatment.

The role of silver additives in gold-mediated C-H functionalisation

Patrick, Scott R. — 2011-07-01T00:00:00Z

Abstract: The role of silver additives is examined in the context of gold-mediated functionalisation of aromatic C-H bonds. Doubt is cast on the commonly cited route of halide abstraction from gold and evidence of substrate activation is given.

Interactions of trivalent lanthanide cations with a new hexadentate di-Schiff base : new lanthanide(III) complexes from (NE,N ' E)-2,2 '-(ethane-1,2-diylbis(oxy))bis(N-(pyridin-2-ylmethylene)ethanamine)

Tsiouri, Mantha — 2010-01-01T00:00:00Z

Abstract: The novel lanthanide(III) complexes [Ln(NO3)(2)L](NO3)center dot 3MeOH (Ln = La 1, Pr 2) and [Ln(NO3)(3)L](NO3)center dot 2MeOH (Ln = Gd 3, Yb 4), where L = (NE,N'E)-2,2'-(ethane-1,2-diylbis(oxy))bis(N-(pyridin-2-ylmethylene)ethanamine), have been obtained by direct reaction of the Schiff base ligand and the corresponding hydrated lanthanide(III) nitrates in methanol. All complexes were characterized spectroscopically and thermogravimetrically. Complex 4 was also characterized with crystallographic studies: orthorhombic P2(1)2(1)2(1), a = 10.6683(14), b = 13.4752(15), c = 19.3320(26) angstrom. In the molecular structure of 4, Yb(III) is surrounded by all donor atoms of the Schiff base (four nitrogen and two oxygen atoms) and four oxygen atoms belonging to two bidentate chelating nitrato ligands.

The X-ray crystal structures of primary aryl substituted selenoamides

Li, Yang — 2009-02-23T00:00:00Z

Abstract: The X-ray structures of 12 primary selenoamides are reported. Metric parameters are provided, together with an illustration of the range of hydrogen bonding motifs. Description: The authors are grateful to the University of St Andrews and the Engineering and Physical Science Research Council (EPSRC, U.K.) for financial support.

Predicting drug promiscuity using spherical harmonic surface shape-based similarity comparisons

Perez-Nueno, Violeta I. — 2011-01-01T00:00:00Z

Abstract: Polypharmacology is becoming an increasingly important aspect in drug design. Pharmaceutical companies are discovering more and more cases in which multiple drugs bind to a given target (promiscuous targets) and in which a given drug binds to more than one target (promiscuous ligands). These phenomena are clearly of great importance when considering drug side-effects. In the last 4 years, more than 30 drugs have been tested against more than 40 novel secondary targets based on promiscuity predictions. Current methods for predicting promiscuity typically aim to relate protein receptors according to their primary sequences, the similarity of their ligands, and more recently, the similarity of their ligand binding pockets. Here, we present a spherical harmonic (SH) surface shape-based approach to predict rapidly promiscuous ligands and targets by comparing sets of SH ligand and protein shapes, respectively. We present details of our approach applied to a wide range of PDB complexes comprising ligands in a selected subset of the MDL Drug Data Report (MDDR) database which are distributed over 249 diverse pharmacological targets. The shape similarity of each ligand to each target’s ligand set is quantified and used to predict promiscuity. We also analyse the correlation between binding pocket and ligand shapes. We compare our promiscuity predictions with experimental activity values extracted from the BindingDB database.

Synthesis of visible-light-activated yellow amorphous TiO2 photocatalyst

Randorn, Chamnan — 2008-01-01T00:00:00Z

Abstract: Visible-light-activated yellow amorphous TiO2 (yam-TiO2) was synthesised by a simple and organic-free precipitation method. TiN, an alternative precursor for TiO2 preparation, was dissolved in hydrogen peroxide under acidic condition ( pH similar to 1) adjusted by nitric acid. The yellow precipitate was obtained after adjusting pH of the resultant red brown solution to 2 with NH4OH. The BET surface area of this sample was 261 m(2)/g. The visible light photoactivity was evaluated on the basis of the photobleaching of methylene blue (MB) in an aqueous solution by using a 250 W metal halide bulb equipped with UV cutoff filter (lambda > 420 nm) under aerobic conditions. Yam-TiO2 exhibits an interesting property of being both surface adsorbent and photoactive under visible light. It was assigned to the eta(2)-peroxide, an active intermediate form of the addition of H2O2 into crystallined TiO2 photocatalyst. It can be concluded that an active intermediate form of titanium peroxo species in photocatalytic process can be synthesised and used as a visible-light-driven photocatalyst. Copyright (C) 2008 Chamnan Randorn et al.

Studies on palm oil with special reference to interestterification

Kifli, Hamirin Abdul — 1981-01-01T00:00:00Z

Abstract: Interesterification which can be considered as the removal of fatty acids at random from glyceride molecules, the shuffling of these acids and their replacement of the glyceride molecules, has been investigated for palm oil, palm oil fractions and palm oil mixed with other vegetable oils. The reaction has been effected at 90 C in the presence o£ sodium methoxide as a catalyst. Pancreatic lipolysis has been ernployed to check the completeness of the reaction. On complete randomisation, the fatty acid composition of the 2-position is the same as that of the whole fat either before or after interestelification. The changes in the glyceride composition resulting from interesterification have been exarnined by various standard techniques. Silver ion thin layer chromatography which separates glycerides according to their degree of unsaturation has been used extensively. Using luethyl heptadecanoate as an internal standard various component glycerides have been quantified. GLG of glycerides has also been used to study the changes in glyceride composition of fats containing a wide range of fatty acid composition. The application of thin layer chromatography, using methyl heptadecanoate as an interncll standard, has also been extended to deterrnine the esters formed during interesterification when sodium methoxide is used as a catalyst. The changes in physical properties which result from interesterification have been determined by NMR (solids fat content) and DSC (thermal behaviour). Attempts to prepare a mixture of fats and oils containing palm oil and / or palm oil fractions which simulates vanaspati have been made. Many mixtures have been subjected to interesterification and the physical properties of the products have been investigated using NMR for all the mixtures and DSC of selected mixtures. The SFC curve of each mixture has been compared with that of vana spati. useful mixtures are recognised. Some potentially Stereospecific glyceride analysis of various types of palm oils has also been carried out using Brockerhoff's method. This involves partial deacylation of the triacylglycerols, isolation of the a,B-diacylglycerols, conversion of these diacylglycerols to phospholipid derivatives and finally stereospecific hydrolysis by Phospholipase A 2 from snake venom, The possible component glycerides have then been computed as suming a i-random, z- random, 3-random distribution of the fatty acids found in each of these positions. The results have been discussed in tenus of double bond number and of carbon number: The latter has been compared with results obtained by gas chromatography of the whole oil.

Electron-beam patterned self-assembled monolayers as templates for Cu electrodeposition and lift-off

She, Zhe — 2012-02-06T00:00:00Z

Abstract: Self-assembled monolayers (SAMs) of 4'-methylbiphenyl-4-thiol (MBP0) adsorbed on polycrystalline gold substrates served as templates to control electrochemical deposition of Cu structures from acidic solution, and enabled the subsequent lift-off of the metal structures by attachment to epoxy glue. By exploiting the negative-resist behaviour of MBP0, the SAM was patterned by means of electron-beam lithography. For high deposition contrast a two-step procedure was employed involving a nucleation phase around −0.7 V versus Cu2+/Cu and a growth phase at around −0.35 V versus Cu2+/Cu. Structures with features down to 100 nm were deposited and transferred with high fidelity. By using substrates with different surface morphologies, AFM measurements revealed that the roughness of the substrate is a crucial factor but not the only one determining the roughness of the copper surface that is exposed after lift-off.

MACiE (Mechanism, Annotation and Classification in Enzymes) : novel tools for searching catalytic mechanisms

Holliday, Gemma L. — 2007-01-01T00:00:00Z

Abstract: MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms, and is publicly available as a web-based data resource. This paper presents the first release of a web-based search tool to explore enzyme reaction mechanisms in MACiE. We also present Version 2 of MACiE, which doubles the dataset available (from Version 1). MACiE can be accessed from http://www.ebi.ac.uk/thornton-srv/databases/MACIE/.

Is EC class predictable from reaction mechanism?

Nath, Neetika — 2012-04-24T00:00:00Z

Abstract: Background: We investigate the relationships between the EC (Enzyme Commission) class, the associated chemical reaction, and the reaction mechanism by building predictive models using Support Vector Machine (SVM), Random Forest (RF) and k-Nearest Neighbours (kNN). We consider two ways of encoding the reaction mechanism in descriptors, and also three approaches that encode only the overall chemical reaction. Both cross-validation and also an external test set are used. Results: The three descriptor sets encoding overall chemical transformation perform better than the two descriptions of mechanism. SVM and RF models perform comparably well; kNN is less successful. Oxidoreductases and hydrolases are relatively well predicted by all types of descriptor; isomerases are well predicted by overall reaction descriptors but not by mechanistic ones. Conclusions: Our results suggest that pairs of similar enzyme reactions tend to proceed by different mechanisms. Oxidoreductases, hydrolases, and to some extent isomerases and ligases, have clear chemical signatures, making them easier to predict than transferases and lyases. We find evidence that isomerases as a class are notably mechanistically diverse and that their one shared property, of substrate and product being isomers, can arise in various unrelated ways. The performance of the different machine learning algorithms is in line with many cheminformatics applications, with SVM and RF being roughly equally effective. kNN is less successful, given the role that non-local information plays in successful classification. We note also that, despite a lack of clarity in the literature, EC number prediction is not a single problem; the challenge of predicting protein function from available sequence data is quite different from assigning an EC classification from a cheminformatics representation of a reaction.

Structure and functional analysis of LptC, a conserved membrane protein involved in the lipopolysaccharide export pathway in Escherichia coli

Tran, An X. — 2010-10-22T00:00:00Z

Abstract: LptC is a conserved bitopic inner membrane protein from Escherichia coli involved in the export of lipopolysaccharide from its site of synthesis in the cytoplasmic membrane to the outer membrane. LptC forms a complex with the ATP-binding cassette transporter, LptBFG, which is thought to facilitate the extraction of lipopolysaccharide from the inner membrane and release it into a translocation pathway that includes the putative periplasmic chaperone LptA. Cysteine modification experiments established that the catalytic domain of LptC is oriented toward the periplasm. The structure of the periplasmic domain is described at a resolution of 2.2-angstrom from x-ray crystallographic data. The periplasmic domain of LptC consists of a twisted boat structure with two beta-sheets in apposition to each other. The beta-sheets contain seven and eight antiparallel beta-strands, respectively. This structure bears a high degree of resemblance to the crystal structure of LptA. Like LptA, LptC binds lipopolysaccharide in vitro. In vitro, LptA can displace lipopolysaccharide from LptC (but not vice versa), consistent with their locations and their proposed placement in a unidirectional export pathway. Description: This work is supported by a Wellcome Trust Career Development Fellowship to C.D.

Scoring functions and enrichment : a case study on Hsp90

Konstantinou-Kirtay, Chrysi — 2007-01-26T00:00:00Z

Abstract: Background: The need for fast and accurate scoring functions has been driven by the increased use of in silico virtual screening twinned with high-throughput screening as a method to rapidly identify potential candidates in the early stages of drug development. We examine the ability of some the most common scoring functions (GOLD, ChemScore, DOCK, PMF, BLEEP and Consensus) to discriminate correctly and efficiently between active and non-active compounds among a library of similar to 3,600 diverse decoy compounds in a virtual screening experiment against heat shock protein 90 (Hsp90). Results: Firstly, we investigated two ranking methodologies, GOLD(rank) and BestScore(rank). GOLD(rank) is based on ranks generated using GOLD. The various scoring functions, GOLD, ChemScore, DOCK, PMF, BLEEP and Consensus, are applied to the pose ranked number one by GOLD for that ligand. BestScore(rank) uses multiple poses for each ligand and independently chooses the best ranked pose of the ligand according to each different scoring function. Secondly, we considered the effect of introducing the Thr184 hydrogen bond tether to guide the docking process towards a particular solution, and its effect on enrichment. Thirdly, we considered normalisation to account for the known bias of scoring functions to select larger molecules. All the scoring functions gave fairly similar enrichments, with the exception of PMF which was consistently the poorest performer. In most cases, GOLD was marginally the best performing individual function; the Consensus score usually performed similarly to the best single scoring function. Our best results were obtained using the Thr184 tether in combination with the BestScore(rank) protocol and normalisation for molecular weight. For that particular combination, DOCK was the best individual function; DOCK recovered 90% of the actives in the top 10% of the ranked list; Consensus similarly recovered 89% of the actives in its top 10%. Conclusion: Overall, we demonstrate the validity of virtual screening as a method for identifying new leads from a pool of ligands with similar physicochemical properties and we believe that the outcome of this study provides useful insight into the setting up of a suitable docking and scoring protocol, resulting in enrichment of 'target active' compounds. Description: This work was funded by the EPSRC, InsightFaraday (now part of the Chemistry Innovation Knowledge Transfer Network), Arrow Therapeutics Ltd and Unilever plc.

Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes : implications for classification of enzyme function

Almonacid, Daniel E. — 2010-03-12T00:00:00Z

Abstract: Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes) from the MACiE database. Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products. For similarity of mechanisms, sets of bond changes occurring in each mechanistic step were compared; these similarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionally analogous enzymes in the dataset had significantly similar overall reactions. For these enzymes, convergence to the same mechanism occurred in 33% of cases, with most pairs having at least one identical mechanistic step. Using our metric, overall reaction similarity serves as an upper bound for mechanistic similarity in functional analogs. For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3) show neither significant overall reaction similarity nor significant mechanistic similarity. By contrast, the three carboxylic-ester hydrolases (EC 3.1.1) catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms. The large proportion of enzyme pairs that do not show significant overall reaction similarity (56%) suggests that at least for the functionally analogous enzymes studied here, more stringent criteria could be used to refine definitions of EC sub-subclasses for improved discrimination in their classification of enzyme reactions. The results also indicate that mechanistic convergence of reaction steps is widespread, suggesting that quantitative measurement of mechanistic similarity can inform approaches for functional annotation. Description: The authors thank the National Institutes of Health (NIH R01 GM60595 to PCB) and the Scottish Universities Life Sciences Alliance (SULSA to JBOM) for funding.

A novel hybrid ultrafast shape descriptor method for use in virtual screening

Cannon, EO — 2008-02-18T00:00:00Z

Abstract: Background We have introduced a new Hybrid descriptor composed of the MACCS key descriptor encoding topological information and Ballester and Richards' Ultrafast Shape Recognition (USR) descriptor. The latter one is calculated from the moments of the distribution of the interatomic distances, and in this work we also included higher moments than in the original implementation. Results The performance of this Hybrid descriptor is assessed using Random Forest and a dataset of 116,476 molecules. Our dataset includes 5,245 molecules in ten classes from the 2005 World Anti-Doping Agency (WADA) dataset and 111,231 molecules from the National Cancer Institute (NCI) database. In a 10-fold Monte Carlo cross-validation this dataset was partitioned into three distinct parts for training, optimisation of an internal threshold that we introduced, and validation of the resulting model. The standard errors obtained were used to assess statistical significance of observed improvements in performance of our new descriptor. Conclusion The Hybrid descriptor was compared to the MACCS key descriptor, USR with the first three (USR), four (UF4) and five (UF5) moments, and a combination of MACCS with USR (three moments). The MACCS key descriptor was not combined with UF5, due to similar performance of UF5 and UF4. Superior performance in terms of all figures of merit was found for the MACCS/UF4 Hybrid descriptor with respect to all other descriptors examined. These figures of merit include recall in the top 1% and top 5% of the ranked validation sets, precision, F-measure, area under the Receiver Operating Characteristic curve and Matthews Correlation Coefficient. Description: The authors thank the EPSRC and Unilever plc for funding.

Simultaneous feature selection and parameter optimisation using an artificial ant colony : case study of melting point prediction

O'Boyle, NM — 2008-10-29T00:00:00Z

Abstract: Background We present a novel feature selection algorithm, Winnowing Artificial Ant Colony (WAAC), that performs simultaneous feature selection and model parameter optimisation for the development of predictive quantitative structure-property relationship (QSPR) models. The WAAC algorithm is an extension of the modified ant colony algorithm of Shen et al. (J Chem Inf Model 2005, 45: 1024–1029). We test the ability of the algorithm to develop a predictive partial least squares model for the Karthikeyan dataset (J Chem Inf Model 2005, 45: 581–590) of melting point values. We also test its ability to perform feature selection on a support vector machine model for the same dataset. Results Starting from an initial set of 203 descriptors, the WAAC algorithm selected a PLS model with 68 descriptors which has an RMSE on an external test set of 46.6°C and R2 of 0.51. The number of components chosen for the model was 49, which was close to optimal for this feature selection. The selected SVM model has 28 descriptors (cost of 5, ε of 0.21) and an RMSE of 45.1°C and R2 of 0.54. This model outperforms a kNN model (RMSE of 48.3°C, R2 of 0.47) for the same data and has similar performance to a Random Forest model (RMSE of 44.5°C, R2 of 0.55). However it is much less prone to bias at the extremes of the range of melting points as shown by the slope of the line through the residuals: -0.43 for WAAC/SVM, -0.53 for Random Forest. Conclusion With a careful choice of objective function, the WAAC algorithm can be used to optimise machine learning and regression models that suffer from overfitting. Where model parameters also need to be tuned, as is the case with support vector machine and partial least squares models, it can optimise these simultaneously. The moving probabilities used by the algorithm are easily interpreted in terms of the best and current models of the ants, and the winnowing procedure promotes the removal of irrelevant descriptors. Description: The authors thank the BBSRC (NMOB and JBOM – grant BB/C51320X/1), Pfizer (DSP and JBOM – through the Pfizer Institute for Pharmaceutical Materials Science), and Unilever for funding FN and JBOM and for supporting the Centre for Molecular Science Informatics.

CMLSnap : Animated reaction mechanisms

Holliday, G L — 2004-10-26T00:00:00Z

Abstract: Reactions with many steps can be represented by a single XML-based table of the atoms, bonds and electrons. For each step the complete Chemical Markup Language 1 representation of all components is obtained and a snapshot representing the end point of the step is generated. These snapshots can then be combined to give an animated description of the complete reaction, both in "2D" chemical structure diagrams and in three dimensions. Here we demonstrate the method's power with enzymatic reactions. It should be noted that readers of this paper will benefit from having an SVG (Scalable Vector Graphics) viewer plugin. Description: The authors thank the EPSRC for financial support of this project and Unilever for their support of the Centre for Molecular Science Informatics.

Chemistry in Bioinformatics

Murray-Rust, P — 2005-06-07T00:00:00Z

Abstract: Chemical information is now seen as critical for most areas of life sciences. But unlike Bioinformatics, where data is openly available and freely re-usable, most chemical information is closed and cannot be re-distributed without permission. This has led to a failure to adopt modern informatics and software techniques and therefore paucity of chemistry in bioinformatics. New technology, however, offers the hope of making chemical data (compounds and properties) free during the authoring process. We argue that the technology is already available; we require a collective agreement to enhance publication protocols.

Communication and re-use of chemical information in bioscience

Murray-Rust, P — 2005-07-18T00:00:00Z

Abstract: The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste are time-consuming and introduce errors. The meaning of chemical terms and the identity of compounds is often ambiguous. valuable experimental data such as spectra and computational results are almost always omitted. We describe an Open XML architecture at proof-of-concept which addresses these concerns. Compounds are identified through explicit connection tables or links to persistent Open resources such as PubChem. It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective.

Discovery, in vivo activity, and mechanism of action of a small-molecule p53 activator

Lain, Sonia — 2008-05-06T00:00:00Z

Abstract: We have carried out a cell-based screen aimed at discovering small molecules that activate p53 and have the potential to decrease tumor growth. Here, we describe one of our hit compounds, tenovin-1, along with a more water-soluble analog, tenovin-6. Via a yeast genetic screen, biochemical assays, and target validation studies in mammalian cells, we show that tenovins act through inhibition of the protein-deacetylating activities of SirT1 and SirT2, two important members of the sirtuin family. Tenovins are active on mammalian cells at one-digit micromolar concentrations and decrease tumor growth in vivo as single agents. This underscores the utility of these compounds as biological tools for the study of sirtuin function as well as their potential therapeutic interest.

An investigation into the photocatalytic activity of titanium dioxide

Calder, Raymond Michael — 1990-01-01T00:00:00Z

1,2-bis-(ditertbutylphosphinomethyl)benzene in catalysis

Jiménez, Cristina — 2004-01-01T00:00:00Z

Abstract: Different diphosphine ligands having the structure shown below have been studied for carbonylation and hydroformylation reactions. Depending on the substituent on the phosphorus atoms the electronic and steric properties can be tuned to direct the reaction towards the desired products. Palladium methoxycarbonylation of a large variety of unsaturated compounds has been attempted under very different conditions. The outcome of these reactions was the achievement of the linear products with a selectivity higher than 99.5 % under mild conditions of pressure and temperature. Chloroaromatic compounds have also been employed as substrates in methoxycarbonylation reactions. Unexpected results were observed since carbonylation was possible only when a strong electron withdrawing group was present. The origin of the many side products from these reactions has been elucidated. Rhodium hydroformylation was not as successful as palladium Methoxycarbonylation since relatively severe conditions had to be used to get good rates and good selectivity. In no case were there as good as those obtained in the carbonylation reactions. However, unusual factors, such as the presence of chlorine in the reaction media, have been found to influence either the conversion or the selectivity.

The vicinal difluoro motif in organic chemistry : the synthesis and behaviour of compounds derived from 2,3-diflurosuccinic acids

Schueler, Martin — 2006-01-01T00:00:00Z

Abstract: The following work describes the synthesis of compounds carrying a vicinal difluoro motif and the evaluation of this structural element to influence the conformation of organic molecules. The synthesis of erythro and threo 1,2-difluoro-1,2-diphenylethane was achieved by bromofluorination and subsequent halogen exchange from stilbene. Oxidative degradation of the phenyl rings allowed to access erythro and threo 2,3- difluorosuccinic acids and a variety of derivatives thereof. The conformations of these compounds were investigated by means of X-ray analysis and NMR spectroscopy. Conformational analysis of derivatives of 2,3-difluorosuccinic acid was carried out using JHFandJHHNMR coupling constants. A clear preference for the conformations in which the two vicinal C-F bonds are gauche emerged from these calculations, which was confirmed by temperature and solvent dependent NMR analyses. The vicinal difluoro motif was incorporated into small peptide structures. In the solid state, a strong preference to align the vicinal C-F bonds gauche to each other was observed and when adjacent to an amide moiety, the C-F bond was found to prefer an anti periplanar orientation with respect to the carbonyl bond. These effects appeared to override steric and electrostatic interactions. The conformation of these fluorinecontaining peptides showed a clear dependence on the stereochemicaol rientation of the C-F bonds, and this appears to be an effective tool for influencing the secondary and consequently tertiary structure in a predictable manner. In order to access single enantiomerso f peptides having the vicinal difluoro, motif, a stereoselectiver oute to R,R and SS 2,3-difluorosuccinic was developed. This involved nucleophilic fluorination of the cyclic sulfates generated from (R, R)- and (SS)- diethyl tartrates and subsequent deoxofluorination of the intermediate fluorohydrins.

The C-F bond as a conformational probe in agonist receptor interactions.

Chia, Poh Wai — 2012-06-20T00:00:00Z

Abstract: Chapter 1 gives an introduction on the physical and electronic properties of fluorine and the C-F bond. The application of fluorine in organic chemistry, which is mainly attributed to the electronic properties of fluorine is described. The role of fluorine in neuropsychiatric drug development and for influencing the conformational study of bioactive amines is also illustrated. Chapter 2 of the thesis describes the synthesis of the two fluorinated stereoisomers (2R, 3S) and (2S, 3S) 3-fluoro N-methyl–D-aspartate (NMDA). These were prepared as analogues to study the binding conformation of NMDA on the glutameric NMDA receptor. The (2S, 3S)-3-fluoro NMDA D-72 was successfully prepared from diethyl D-tartrate. The (2S,3R)- stereoisomer was prepared by separation of diastereoisomers generated by reaction of a meso- epoxide with an enantiomerically pure amine, followed by fluorination. Both the (2S,3R)- and (2R,3S)- enantiomers were prepared separately, however assignment of the absolute configuration to each enantiomer could not be unambiguously proven. The fluorinated 3F-NMDA stereoisomers were assessed by dose response analysis and TEVC analysis in the rat glutamate receptor. The biological results show that the (2S, 3S)-3F NMDA D-72 is a good agonist, whereas (2R, 3S)- and (2S, 3R)-3-fluoro NMDA are inactive stereoisomers. The result of this study indicates that (2S, 3S)-3F NMDA D-72 is the only relevant agonist that can access a conformation for binding to NMDA receptor. Chapter 3 describes the preparation of fluorinated analogues of the calcium receptor agonist Cinacalcet. The (2R,1’R)-123 and (2S,1’R)-124 fluoro Cinacalcet diastereoisomers were prepared from 3’-(trifluoromethyl)cinnamic acid and 3’’-SF₅-137 Cinacalcet was synthesized from pentafluorosulfanyl benzyl alcohol. The biological assessment in the calcium receptor (CaR) revealed that both (2R,1’R)-123 and (2S,1’R)-124 fluoro Cinacalcet is slightly lower in potency compared to the non-fluorinated Cinacalcet 117. This suggests that the Cinacalcet 117 adopts an extended conformation when bound to the receptor. The 3’’-SF₅-137 Cinacalcet possesses equipotent activity with Cinacalcet 117.

Structural analysis of the potential therapeutic targets from specific genes in Methicillin-resistant Staphylococcus aureus (MRSA)

Yan, Xuan — 2011-11-01T00:00:00Z

Abstract: The thesis describes over-expression, purification and crystallization of three proteins from Staphylococcus aureus (S. aureus). S. aureus is an important human pathogen and methicillin-resistant S. aureus (MRSA) is a serious problem in hospitals nowadays. The crystal structure of 3-Methyladenine DNA glycosylase I (TAG) was determined by single-wavelength anomalous diffraction (SAD) method. TAG is responsible for DNA repair and is an essential gene for both MRSA and methicilin-susceptible S. aureus (MSSA). The structure was also determined in complex with 3-methyladenine (3-MeA) and was solved using molecular replacement (MR) method. An assay was carried out and the molecular basis of discrimination between 3-MeA and adenosine was determined. The native crystal structure of fructose 1-phosphate kinase (PFK) from S. aureus was determined to 2.30 Å and solved using molecular replacement method. PFK is an essential enzyme involved in the central metabolism of MRSA. Despite extensive efforts no co-complex was determined, although crystals were obtained they diffracted poorly. An assay which can be used to test for inhibitors has been developed. Mevalonate Kinase (MK) is another essential enzyme in MRSA and is a key drug target in the mevalonate pathway. Native data diffracting to 2.2 Å was collected. The structure was solved using multiple isomorphorus replacement (MIR) method. A citrate molecule was bound at the MK active site, arising from the crystallization condition. The citrate molecule indicates how substrate might bind. The protein was kinetically characterized. A thermodynamic analysis using fluorescence-based method was carried out on each protein to investigate binding interactions of potential fragments and thus a drug design starting point.

Titanium dioxide nanomaterials as negative electrodes for rechargeable lithium-ion batteries

Gentili, Valentina — 2011-11-30T00:00:00Z

Abstract: Titanium dioxide, TiO₂, materials have received much attention in recent years due to their potential use as intercalation negative electrodes for rechargeable lithium-ion batteries. The aim of this doctoral work was to synthesise and characterise new titanium dioxide nanomaterials and to investigate their electrochemical behaviour. Three morphologies of TiO₂(B) phase: micro-sized (bulk), nanowires and nanotubes, were synthesised. All three exhibit properties which make them excellent hosts for lithium intercalation. The nanotubes show the best capability of accommodating lithium in the structure, being able to host over one molar equivalent of lithium at low current rates (5 mA g⁻¹). The lithium insertion mechanism in the TiO₂(B) was studied using powder neutron diffraction. In addition, the nature of the irreversible capacity of the nanotubes was studied and ways of reducing it proposed. Nanotubes of another titanium dioxide polymorph, anatase, were synthesised and characterised. Their electrochemical performance was compared with that of commercially available counterparts with different morphologies and particle sizes. The interrelation between particle size/morphology and electrochemical properties has been established. The insertion of lithium which leads to phase variations was studied using in situ Raman microscopy and neutron powder diffraction. It has been demonstrated that doping of the TiO₂(B) nanotubes with vanadium improves their electronic conductivity which is essential for practical applications. Remarkably good electrochemical performance is exhibited by the 6% V-doped TiO₂(B) nanotubes.

Enantioselective homogeneous catalysts for the synthesis of fluorinated organic compounds

Jones, Charlotte E.S — 2011-06-01T00:00:00Z

Abstract: This thesis is divided into three main results chapters that reflect the path my research took. In the first results chapter, the first organocatalyst for the carbonyl-ene reaction was discovered and found to give high conversion using 1,3-bis(3,5-bis(trifluoromethyl)phenyl)thiourea. Various carbonyl and alkene precursors were examined in the ene reaction in both catalysed and uncatalysed reactions. It was found that ene reactions using fluoral and ethyl trifluoropyruvate give higher rates of reaction when compared to other carbonyl compounds. A novel enantiopure thiourea was synthesised and the ene reaction was catalysed enantioselectively to 33% e.e. In an attempt to catalyse the reaction to a further extent a new thiourea bonded to a P(=S)R2 group was developed. However, the intramolecular hydrogen bonding of this catalyst was thought to be so strong that this it did not catalyse the reaction. The synthesis of a chiral phosphoric acid was achieved but this was an unsuccessful catalyst in the ene reaction. Two component achiral thiourea and chiral acids were also examined in the ene and Mannich-type reaction. The new easily synthesised thiourea for this reaction has an interesting intermolecular hydrogen bonding coordination in the solid state. Asymmetric fluorination of ketoesters using palladium is a dynamic kinetic resolution. In the 2nd chapter cationic palladium complexes were synthesised and used to determine the optimum parameters for bidentate ligands in this reaction. Four carbon chain phosphines were found to give the highest conversion for this reaction among those ligands tested such as 1,4-bisdiphenylphosphinobutane (bite angle 99º). A new bis-phosphinous amide chiral ligand was developed with a bite angle of 96.7º. The dichloropalladium complex of this phosphine was isolated and structurally characterised. The use of the palladium complex in asymmetric fluorination was attempted however this was found to be unsuccessful. Mechanistic studies reveal that the formation of the desired cationic catalyst did not occur under conditions shown to work well for other palladium phosphine complexes. The ligand was investigated further in hydrogenation reactions. The phosphinous amide was protected as its borane and was used in the rhodium catalysed hydrogenation of alkenes to give high conversion and up to 93% e.e. The borane protected phosphinous amide was also found to catalyse the hydrogenation of acetophenone using copper complexes with up to 84% e.e for the hydrogenation of acetophenone, although conversion was quite low.

Lewis base-promoted organocatalysis : O- to C-carboxyl transfer reactions

Campbell, Craig D. — 2010-11-30T00:00:00Z

Abstract: This work describes the application of a variety of Lewis bases, encompassing predominantly N-heterocyclic carbenes (NHCs), but also the use of imidazoles, aminopyridines, amidines and isothioureas, as effective catalysts in the dearomatisation of heterocyclic carbonates, predominantly the rearrangement of oxazolyl carbonates to their C-carboxyazlactone isomers by means of the Steglich rearrangement. This rearrangement reaction has been investigated extensively, with the development of simplified reaction procedures and the invention of domino cascade protocols incorporating this transformation. In an attempt to understand the mechanism of this O- to C-carboxylation process, a number of interesting observations have been made. Firstly, the class of NHC has an important factor in promoting the rearrangement, with triazolinylidenes being the most effective. Secondly, an interesting chemoselectivity has been delineated using triazolium-derived NHCs, prepared using weak bases (typically Et₃N) or strong metallated bases; both alkyl and aryl oxazolyl carbonates undergo smooth rearrangement with triazolinylidenes derived from strong metallated bases such as KHMDS, while only aryl oxazolyl carbonates undergo rearrangement using Et₃N. Extensive effort has focused towards the development of asymmetric variants of these protocols, primarily towards the design, synthesis and evaluation of chiral NHC precatalysts. To this end, a number of chiral azolium salts have been prepared, encompassing a number of different NHC classes, including C₁- and C₂-imidazolinium salts, C₂-imidazolium salts and a range of triazolium salts. Efforts towards the asymmetric catalysis of the Steglich rearrangement of oxazolyl carbonate substrates have given an optimal 66% ee. Similar rearrangements have been demonstrated with the related furanyl heterocyclic substrate class, producing a mixture of α- and γ-carboxybutenolides. In contrast to the analogous oxazolyl carbonates, the regioselectivity of this rearrangement is dependent upon the nature of the Lewis base employed. Amidines and aminopyridines give a mixture of the α- and γ- regioisomers with generally the α-regioisomer being preferred, while a triazolium-derived NHC gives rise to predominantly the thermodynamically more stable γ-carboxybutenolide. Using amidines or aminopyridines, this rearrangement has been shown to proceed via an irreversible C-C bond-forming process, but in contrast, the rearrangement using the NHC proceeds via an equilibrium process with an optimised regioselectivity of >98:2 for the γ-carboxybutenolide regioisomer over the α-regioisomer. Whilst the asymmetric variant using chiral NHCs has proven unfruitful, rearrangements using a chiral isothiourea have given high levels of regioselectivity towards the α- regioisomer and with excellent levels of enantiodiscrimination (77–95% ee).

SA-CASSCF and R-matrix calculations of low-energy electron collisions with DNA bases and phosphoric acid

Bryjko, Lilianna — 2011-06-22T00:00:00Z

Abstract: The research presented in this thesis was carried out as part of a collaboration between the groups of Dr Tanja van Mourik at the School of Chemistry, University of St Andrews and Professor Jonathan Tennyson at the Department of Physics and Astronomy at University College London. This thesis presents State-Averaged Complete Active Space Self Consistent Field (SA-CASSCF) calculations on nucleic acid bases, deoxyribose and phosphoric acid H₃PO₄). In the case of uracil, for comparison, Multireference Configuration Interaction calculations were also performed. The SA-CASSCF orbitals were subsequently used in R-matrix electron scattering calculations using the close-coupling model. Of major importance for obtaining accurate SA-CASSCF results is the choice of the active space and the number of calculated states. Properties such as the electronic energy, number of configurations, excitation energy and dipole moment were considered in the choice of active space. Electron-collision calculations were performed on two of the most stable isomers of phosphoric acid, a weakly dipolar form with all OH groups pointing up and a strongly dipolar form where one OH group points down. A broad shape resonance at about 7 eV was found for both isomers. Ten-state close-coupling calculations suggest the presence of narrow, Feshbach resonances in a similar energy region. Elastic and electronically inelastic cross sections were calculated for both isomers. The R-matrix calculations on uracil were done by the group from UCL. R-matrix calculations are currently being done on guanine. Scattering calculations on the other DNA bases will be performed in the near future.

Extending ionothermal synthesis

Aidoudi, Farida Himeur — 2012-01-01T00:00:00Z

Abstract: An exploration of some organic-inorganic hybrid metal fluorides and lanthanide containing metal organic frameworks (Ln-MOFs) has been carried out under ionothermal conditions. In this synthesis technique an ionic liquid (IL) or deep eutectic mixture (DES) is used as the solvent and in many cases as the provider of the organic structure directing agent. A wide range of ILs and DESs have been investigated as the reaction solvent for the synthesis of organically templated vanadium fluorides and oxyfluorides (VOFs), and initially this has proved to be successful with the isolation of 13 phases, including eight new materials. In the VOFs synthesis the IL acts as a solvent, however the DES acts as a solvent and also as a template delivery agent, where the expected template is provided by the partial breakdown of the urea derivative component. Interestingly, it has been shown that the same structure can be accessible via two different ways; either by using IL with an added templating source, or simply through the use of a DES without any other additive; since the template is provided by the in situ breakdown of the DES. The synthesis of VOFs with extended structures was achieved by the use of the hydrophobic IL 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (EMIM Tf₂N) as the solvent. [HNC₅H₅][V₂O₂F₅] represents the first VOF with a 2D network that contains exclusively V⁴⁺. This material may be considered as arising via condensation of the previously known ladder-like chains. Furthermore, using imidazole as an added template has produced another layer material that has significant similarities to the [HNC₅H₅][V₂O₂F₅] structure, but with some key differences. Within the same system three other phases were also isolated, including two novel materials displaying the known ladder-type building units. Further investigations in the ionothermal synthesis of VOF using EMIM Tf₂N resulted in a successful synthesis of [NH₄]₂[HNC₇H₁₃][V₇O₆F₁₈], a novel material displaying a unique double layered topology featuring a S = ½ kagome type lattice of V⁴⁺ ions (d¹). Two of the V⁴⁺ based kagome sheets are pillared by V³⁺ ions to form a double layered structure templated by both ammonium and quinuclidinium cations. This compound exhibits a high degree of magnetic frustration, with significant antiferromagnetic interactions but no long range ordering was observed above 2 K. This material presents an interesting comparison to the famous Herbertsmithite, ZnCu₃(OH)₆Cl₂, and may provide an excellent candidate for realising a quantum spin liquid (QSL) ground state. Interestingly, in this system the use of EMIM Tf₂2N as a solvent produces mainly V⁴⁺-containing materials, despite the high reaction temperature (170 °C). This characteristic is unprecedented in VOFs synthesis, as rising the reaction temperature above 150 °C in other techniques (i.e. hydrothermal synthesis) would often result in further reduction of V⁴⁺ to V³⁺. Using the ionothermal technique in the synthesis of hybrid iron fluorides resulted in the isolation of three chain-type materials. Again, the IL acts as the solvent and the DES acts as the solvent and also as the template provider where the expected template is released by the partial breakdown of the urea derivative component of the DES. The synthesis of Ln-MOF using a choline chloride/ 1,3-dimethylurea deep eutectic mixture has produced three novel isostructural materials. Usually, in ionothermally prepared materials (i.e. zeolites) the urea portion of the DES is unstable and breaks down in situ to form ammonium or alkylammonium cations. In the ionothermal synthesis of Ln-MOF, 1,3-dimethyurea (DMU) remains intact and is occluded in the final structure. Using a choline chloride/ethylene glycol deep eutectic solvent led to the isolation of a Ln-MOF with interesting structural properties, however none of the DES components appeared in the final structure. These results demonstrate once more the usefulness and applicability of the ionothermal synthesis method and emphasise how this synthesis technique can be further extended and applied in the preparation of important structures with unique properties and functionalities.

Assessment of density functional methods for computing structures and energies of organic and bioorganic molecules

Cao, Jie — 2011-11-30T00:00:00Z

Abstract: The work in this thesis mainly focuses on the assessment of density functional methods for computing structures and energies of organic and bioorganic molecules. Previous studies found dramatic conformational and stability changes from B3LYP to MP2 geometry optimization for some Tyr-Gly conformers. Possible reasons could be large intramolecular basis set superposition errors (BSSEs) in the MP2 calculations and the lack of dispersion in the B3LYP calculations. The fragmentation method and three kinds of rotation methods were used to investigate intramolecular BSSE. It is concluded that the rotation method cannot be used to correct intramolecular BSSE along a rotation profile. Another methodology is to employ modern density functionals. We focused on M06-L with the Tyr-Gly conformer ‘book6’. Potential energy profiles were determined by computing the energy for geometries optimized at various fixed values of a distance that controls the degree of foldedness of the structure. M06-L manifested itself as a very promising method to investigate the potential energy surface of small peptides containing aromatic residues. To predict Tyr-Gly structures, 108 potential conformers were created with a Fortran program. The geometry optimizations were done using M06-L/6-31G(d) and M05-2X/6-31+G(d). Two schemes were employed and the most stable conformers were compared to the 20 stable conformers found by B3LYP. Both schemes found 10 conformers similar to one of the B3LYP stable conformers, as well as several newly found conformers. The study of a missing B3LYP stable conformer showed that the possible reason of missing conformers may be the lack in dispersion in B3LYP theory. To study the hydration effect, we studied the conformations of neutral and zwitterionic 3-fluoro-γ-aminobutyric acid (3F-GABA) in solution using different solvation models, mainly the explicit water molecule models. Zwitterionic forms of 3F-GABA are preferred in solution. M06-2X performs better in calculating transition energy profiles than MP2.

Nanomaterials for solid oxide fuel cell electrolytes and reforming catalysts

Kosinski, Marcin Robert — 2011-11-28T00:00:00Z

Abstract: In this work, a broad range of analytical methods was applied to the study of the following three materials systems: yttria-stabilised zirconia (YSZ), samarium-doped ceria (SDC) and SDC-supported metal catalysts. YSZ and SDC were studied in the light of their application as solid electrolytes in Solid Oxide Fuel Cells. The SDC-supported metal catalysts were evaluated for application in the reforming of methanol. The conductive properties of YSZ pellets derived from powders of different Y contents and particle size ranges were investigated using Impedance Spectroscopy (IS). Comparative studies of the crystallography (by X-ray Powder Diffraction (XRD)), morphology (by Scanning and Transmission Electron Microscopy (SEM, TEM)), chemical composition (by Energy Dispersive X-ray Spectroscopy (EDX) and Inductively Coupled Plasma Mass Spectroscopy (ICP-MS)) and sintering behaviour (dilatometry) were employed in the overall assessment of the conductivity results collected. Detailed studies of three SDC compositions were performed on nanopowders prepared by a low temperature method developed in the Baker group. Modifications led to a simple and reliable method for producing high quality materials with crystallites of ~10 nm diameter. The products were confirmed by XRD and TEM to be single-phase materials. Thermogravimetric analysis, dilatometry, specific surface area determination, elemental analysis and IS were carried out on these SDC powders. The relationships between particle size, chemical composition, sintering conditions and conductivity were studied in detail allowing optimum sintering conditions to be identified and ionic migration and defect association enthalpies to be calculated. Finally, the interesting results obtained for the SDC nanopowders were a driving force for the preparation of SDC-supported metal catalysts. These were prepared by three different methods and characterised in terms of crystallographic phase, specific surface area and bulk and surface chemical composition. Isothermal catalytic tests showed that all catalysts had some activity for the reforming of methanol and that some compositions showed both very high conversions and high selectivities to hydrogen. These catalysts are of interest for further study and possibly for commercial application.

Catalytic synthesis of organophosphate plastics additives from white phosphorus

Armstrong, Kenneth Mark — 2011-11-22T00:00:00Z

Abstract: Triaryl phosphates were synthesized from white phosphorus and phenols in aerobic conditions and in the presence of iron catalysts and iodine. Full conversion to phosphates was achieved without the use of chlorine or chlorinated solvents, and the reactions do not produce acid waste. Triphenyl phosphate, tritolyl phosphate and tris(2,4-di-tert-butyl)phenyl phosphate were synthesized by this method with 100% conversion from P₄. Various iron(III) diketonates were used to catalyse the conversion. Mechanistic studies showed the reaction to proceed via the formation of phosphorus triiodide (PI₃), then diphenyl phosphoroiodidate (O=PI(OPh)₂) before the final formation of triphenyl phosphate (O=P(OPh)₃). The nucleophilic substitution of O=PI(OPh)₂ with phenol to form O=P(OPh)₃ was found to be the rate determining step. It was found that by modifying the reaction conditions the same catalytic systems could be used to synthesize triphenyl phosphite directly from P₄. Triphenyl phosphite was synthesized in selectivities of up to 60 %. The mechanism of these transformations was also elucidated. Independent syntheses of the intermediate in the reaction mechanism, O=P(OPh)₂I and its hydrolysis products diphenyl phosphate (O=P(OPh)₂OH) and tetraphenyl pyrophosphate ((O)P(OPh)₂-O-P(O)(OPh)₂) were developed from PI₃. The 2,4-di-tert-butyl phenol analogues of these compounds were also prepared. Bis-(2,4-di-tert-butylphenyl) phosphoroiodidate was then reacted with various alcohols to produce a series of mixed triorgano phosphates.

Towards new catalytic systems for the formation of methyl methacrylate from methyl propanoate

Coetzee, Jacorien — 2011-11-30T00:00:00Z

Abstract: The two stage Lucite Alpha Process for the industrial manufacturing of methyl methacrylate (MMA) represents one of the most efficient technologies currently available for the large scale production of this important chemical commodity. The second stage of this process, which involves the condensation of methyl propanoate (MeP) with formaldehyde over a heterogeneous fixed bed catalyst, however, still shows great scope for improvement. Herein the development of a novel homogeneous catalytic system that would promote the condensation of either propanoic acid or MeP with formaldehyde is explored. Since C–C bond forming reactions which proceed via C–H activation pathways typically display high atom efficiency, our efforts were particularly focussed on employing a functionalisation strategy that is mediated by C–H activation. In the case of propanoic acid, the possibility of achieving regioselective α-methylenation by linking the substrate to phosphorus was evaluated. Thus, a series of acyloxyphosphines and acylphosphites derived from either propionic acid or phenylacetic acid was prepared and, where stability allowed, fully characterised. Some of the resultant simple mixed anhydrides posed problems relating to their stability, and the stabilisation of such ligand systems by using electronic and / or steric effects was therefore explored. In addition, the coordination chemistry and in solution behaviour of Rh(I) and Ru(II) complexes containing these ligands was examined. Similar to the free ligands, complexes derived from these mixed anhydrides rearranged in solution via a number of decomposition pathways, with the specific pathway dependent on the nature of the auxiliary ligands. For most of these complexes, however, ligand decarbonylation was the route of preference for decomposition. Despite the instability of these complexes, a selection of Rh(I) mixed anhydride complexes were assessed for their potential as C-H activation catalysts in reactions aimed at the α-methylenation of saturated carboxylic acids. Furthermore, the stabilisation of Rh(I) mixed anhydride complexes with chelating auxilary ligands, such as bisphosphines or N-substituted diphosphinoamines, was explored. In particular, a series of new Rh(I) mixed anhydride complexes containing dppe, dppb and dppbz as secondary ligands were prepared and the effects of these secondary ligands on the in solution stability of these complexes assessed. As MeP represents the final product in the first stage of the Alpha process and not propanoic acid, the utilisation of PNP iridium pincer complexes in the regioselective sp³ C–H activation of MeP and related esters was also examined. The factors that govern the regioselectivity of such reactions were of great interest to us and, in particular, the effects of water on the reactivity and regioselectivity of these reactions were explored. For MeP, preferential C–H activation of the methoxy group was found to proceed under anhydrous conditions and the catalytic functionalisation of this site with ethene using this activation approach was considered. Formaldehyde, employed in the second stage of the Alpha process, is a difficult substance to manufacture and handle, especially on a large scale. A preliminary study on the in situ production of anhydrous formaldehyde via the catalytic dehydrogenation of methanol was therefore performed. During this study, catalytic systems based on carbonate salts and / or transition metal complexes were considered. In the hope of reducing the number of steps required in the production of MMA, a new one-pot cascade reaction for the indirect α-methylenation of MeP with methanol was developed. Although the production of MMA using this system only proceeded with low efficiency, the obtained results serve as an important proof of concept for future developments in this area. Finally, the capacity of a series of simple bases to catalyse the condensation of MeP with formaldehyde was assessed as part of a fundamental study directed towards determining the factors that govern the efficiency of this reaction. In addition, the extent to which each base effects the deprotonation in the α-position of MeP was determined with the aid of deuterium labelling experiments. Similarly, using sodium propanoate as model base a rough estimate of the kinetics of deprotonation could be made based on the degree of deuterium incorporation over time. These studies suggested that the low efficiency of this condensation reaction is not caused by ineffective deprotonation but rather by the weak nucleophilicity of the generated carbanion. For this reason, attempts to increase the electrophilicity of formaldehyde through Mannich-type condensations reactions involving secondary amine and carboxylic acid additives were made.

Exploring novel functionalities in oxide ion conductors with excess oxygen

Zhang, Yaoqing — 2011-06-22T00:00:00Z

Abstract: Functional materials, particularly metal oxides, have been the focus of much attention in solid state chemistry for many years and impact every aspect of modern life. The approach adopted in this thesis to access desirable functionality for enhanced fundamental understanding is via modifying existing materials by deploying reducing synthetic procedures. This work spans several groups of inorganic crystalline materials, but is unified by the development of new properties within host compounds of particular relevance to solid oxide fuel cell technology, which allow interstitial oxide ion conduction at elevated temperatures. The Ca₁₂Al₁₄O₃₂e₂ electride was successfully synthesized by replacing the mobile extra-framework oxygen ions with electrons acting as anions. The high concentration of electrons in the C12A7 electride gives rise to an exceptionally high electronic conductivity of up to 245 S cm⁻¹ at room temperature. Making use of the high density of electrons in Ca₁₂Al₁₄O₃₂e₂ electride, the strong N-N bonds in N₂ was found to be broken when heating Ca₁₂Al₁₄O₃₂e₂ in a N₂ atmosphere. A reaction between silicate apatites and the titanium metal yielded another completely new electride material La₉.₀Sr₁.₀(SiO₄)₆O₂.₄e₀.₂ which was found to be a semiconductor. To fully understand the role of oxygen interstitials in silicate apatites, high-resolution transmission electron microscopy (HRTEM) was employed as the main technique in probing how the oxygen nonstoichiometry is accommodated at the atomic level. Atomic-resolution imaging of interstitial oxygen in La₉.₀Sr₁.₀(SiO₄)₆O₂.₅ proved to be a success in this thesis. Substitution of oxygen in 2a and interstitial sites with fluoride ions in La[subscript(8+y)]Sr[subscript(2- z)](SiO₄)₆O[subscript(2+(3y-2z)/2)] (0

Building complex systems based on simple molecular architectures

Robertson, Craig Collumbine — 2011-11-30T00:00:00Z

Abstract: Over the past twenty years molecules capable of templating their own synthesis, so called self–replicating molecules have gained prominence in the literature. We show herein that mixing the reagents for replicating molecules can produce a network of self–replicators which coexist and that the networks can be instructed by the addition of preformed template upon initiation of the reaction. Whilst self–replicating molecules offer the simplest form of replication, nature has evolved to utilise not minimal self–replication but reciprocal replication where one strand templates the formation of not an identical copy of itself but a reciprocal strand. Efforts thus far at producing a synthetic reciprocal replicating system are discussed and an alternative strategy to address the problems encountered is proposed and successfully implemented. The kinetic behaviour of a self–replicating reaction bears two distinctive time periods. Upon initiation, the reaction proceeds slowly as no template exists to catalyse the reaction. Upon production of the template, the reaction proceeds more rapidly via template direction. During this slow reaction period, the system is prone to mistakes as the reaction is slow and unselective. The creation of an [A•B] binary complex through non–covalent recognition of reagents allows for the reaction to proceed at an accelerated rate upon initiation however products of such a reaction are usually catalytically inert and do not promote further template directed reaction. A strategy to combine the desired behaviour of an [A•B] binary complex with the further template directed autocatalytic self–replicating reaction is described and implemented. Supramolecular polymers consist of repeating monomers which are held together by non–covalent interactions. The strong association of a self–replicating template dimer is comparable to that of supramolecular polymers reported thus far in the literature which are produced by cumbersome standard linear synthetic procedures. Herein the application of self–replication to the field of supramolecular polymer synthesis is discussed. As the autocatalytic reaction to produce the template monomers occurs under the same conditions as required to allow polymerisation to proceed, the polymer is able to spontaneously form in situ by self–replicating supramolecular polymerisation.

Kinetic analysis of homogeneous catalytic reactions

Robb, Lynzi M. — 2011-11-01T00:00:00Z

Abstract: Reaction progress kinetic analysis (RPKA) is a powerful tool for determining kinetic parameters of catalytic reactions. Many of the published articles that have used RPKA have employed reaction calorimetry for obtaining sufficient data to be reliable. The use of gas uptake measurements, in place of calorimetry is explored in this Thesis. Chapter 2 details the use of gas uptake measurements in establishing the order with respect to substrate and gas for the rhodium catalysed hydrogenation of 1-octene. Previous studies have used initial rate measurements to establish these orders and the reaction cycle is well known. The use of RPKA allows the same information to be established in two reactions. Chapter 3 focuses on the rhodium catalysed hydroformylation of 1-octene as it involves the reaction of one substrate with two gases. Using RPKA it is possible to determine the order in substrate and the overall order in gas, but it was found difficult to determine the order with respect to the individual gases using RPKA alone. Chapter 4 shows the palladium catalysed methoxycarbonylation of vinyl acetate. The reaction has two substrate concentrations changing simultaneously as well as a gas. This chapter shows that by careful design of experiments the orders with respect to each of these substrates and CO can be determined in minimal numbers of experiments. Chapter 5 focuses on the methoxycarbonylation of alkynes, which uses RPKA in complex multistep reactions, to establish if RPKA can be used to determine the kinetics with respect to the individual reacting components for each step. This study focuses on the methoxycarbonylation of phenylacetylene to produce methyl cinnamate as well as the methoxycarbonylation of both terminal and internal linear alkynes. These linear alkynes carbonylate to produce an α,β-unsaturated ester. The double bond is isomerised from its conjugated position along the chain to the terminal position where it is trapped and carbonylated to produce an α,ω-dieter product.

The molecular precursor approach to control the morphology of Co₃O₄ on support materials

de Jongh, Leigh-Anne — 2011-11-14T00:00:00Z

Abstract: In this project, the TMP method was employed to produce “active sites.” These active sites are for influencing and controlling the Co₃O₄ growth. One of the aims was to investigate what effect the grafting of the molecular precursor has on the nature and distribution of active sites on the various support materials. The second aim was to investigate the effect an increase in molecular precursor loading, in various impregnation steps, has on the nature and distribution of the active sites. The third aim was to investigate the effect of the steric constraints of ligand groups, by changing the molecular precursor, on the nature and distribution of active sites. The fourth aim was to use the different aspects discussed above and apply them to investigate what effect the above-mentioned modifications have on Co₃O₄ morphology. While another aim was to investigated what effect varying the quantity of Co(NO₃)₂•6H₂O has on Co₃O₄ morphology. Lastly, we investigated what effect varying the impregnation procedure and calcination temperature have on the Co₃O₄ morphology. The effect the support has on the phase of titanium molecular precursor was investigated using molecular precursor, ⁱPrOTi[OSi(O[superscript(t)]Bu₃)]₃. The supports used were Silica 922, NanoDur, Aerosil 200, Stöber spherical silica, SBA-15, mod MCM-41 and sMCM-41. The molecular precursor ⁱPrOTi[OSi(O[superscript(t)]Bu₃)]₃ was revealed to be in the orthorhombic TiO₂ with space group P(cab), normal brookite lattice, on Silica 922 after calcination but only an isolated area displaying this morphology. Generally we do not observe any TiO₂ on the support, which indicates that we have produce site-isolated sites, suggesting the TMP method has been successful on all of the various supports. The emphasis is placed on the effect of this molecular precursor and the respective support has on the Co₃O₄ morphology in Chapter 3. In this Chapter, a unique morphology was observed on Silica 922 which showed Co₃O₄ nanorods of cubic Co₃O₄ in the space group Fd-3m. Silica 922 was used for the remainder of the thesis to investigate the effect the quantity of molecular precursor has on the nature of active sites and Co₃O₄ morphology in Chapter 4. This support was also used to investigate the effect the amount of Co(NO₃)₂•6H₂O has on Co₃O₄ morphology in Chapter 5. This support was lastly used to investigate the steric constraints of the ligand groups, Ti[OSi(O[superscript(t)]Bu)₃]₄ (TiSi4), ⁱPrOTi[OSi(O[superscript(t)]Bu)₃]₃ (TiSi3), (OtBu)₃TiOSi(O[superscript(t)]Bu)₃ (TiSi) and the least sterically constrained Ti(OⁱPr)₄ has on the loading of precursor and Co₃O₄ morphology in Chapter 6.

Homogeneous gold catalysts : development of applications for gold(I) catalysts bearing N-heterocyclic carbene ligands

Müller, Ruben S. Ramon — 2011-11-01T00:00:00Z

Abstract: Recently established as an excellent activator for π-systems, efforts made in gold chemistry have increased enormously, resulting in a new ‘Gold Rush’ in chemistry. This thesis is a small contribution to it. There are two main aspects dominating the following chapters: gold catalysts bearing N-heterocyclic carbenes (NHCs) as supporting ligand, and H₂O assisted catalysis. The initial motivation for the presented work was to specifically demonstrate the potential of [(NHC)AuCl] as suitable catalysts for both known and new organic transformations and to establish these commercially available catalysts in gold chemistry, a field currently dominated by phosphine bearing gold complexes. Water mediated catalysis became the next repeatingly occurring aspect of this thesis by pursuing this initial aim and finding water as a useful solvent or agent, respectively. Various useful applications for gold-NHC complexes are presented, starting with the Meyer-Schuster rearrangement of propargylic alcohols as a continuation of the work realized with propargylic acetates by the Nolan group in early investigations on gold catalysts. Next, a study on alkyne hydration is presented with focus on low catalysts loadings to establish gold catalysts as a powerful choice for such a highly relevant reaction. The catalytic system is then advantageously adapted to a silver-free variation, still active at low catalyst loadings and with further mechanistic insight. Inspired by gold activation of alkynes, a gap of reactivity in gold catalysis is closed by a successful demonstration of nitrile hydration, a functionality previously thought to be inert towards gold activation. In this context, formation and role of dinuclear hydroxy-bridged gold complexes is investigated highlighting these complexes as a possible resting state of gold complexes in the presence of water. Next, the formation of furanones via alkoxylation/lactonization of propargylic propiolates is presented, an observation initially made when exploring the scope of the Meyer-Schuster rearrangement. The dissertation finally closes with the gold-catalyzed formation of amides, this time however achieved from aldoximes reacting via dehydration/hydration mechanism.

Predicting the mechanism of phospholipidosis

Lowe, Robert — 2012-01-26T00:00:00Z

Abstract: The mechanism of phospholipidosis is still not well understood. Numerous different mechanisms have been proposed, varying from direct inhibition of the breakdown of phospholipids to the binding of a drug compound to the phospholipid, preventing breakdown. We have used a probabilistic method, the Parzen-Rosenblatt Window approach, to build a model from the ChEMBL dataset which can predict from a compound's structure both its primary pharmaceutical target and other targets with which it forms off-target, usually weaker, interactions. Using a small dataset of 182 phospholipidosis-inducing and non-inducing compounds, we predict their off-target activity against targets which could relate to phospholipidosis as a side-effect of a drug. We link these targets to specific mechanisms of inducing this lysosomal build-up of phospholipids in cells. Thus, we show that the induction of phospholipidosis is likely to occur by separate mechanisms when triggered by different cationic amphiphilic drugs. We find that both inhibition of phospholipase activity and enhanced cholesterol biosynthesis are likely to be important mechanisms. Furthermore, we provide evidence suggesting four specific protein targets. Sphingomyelin phosphodiesterase, phospholipase A2 and lysosomal phospholipase A1 are shown to be likely targets for the induction of phospholipidosis by inhibition of phospholipase activity, while lanosterol synthase is predicted to be associated with phospholipidosis being induced by enhanced cholesterol biosynthesis. This analysis provides the impetus for further experimental tests of these hypotheses.

An efficient one-step site-directed deletion, insertion, single and multiple-site plasmid mutagenesis protocol

Liu, Huanting — 2008-12-04T00:00:00Z

Abstract: Background: Mutagenesis plays an essential role in molecular biology and biochemistry. It has also been used in enzymology and protein science to generate proteins which are more tractable for biophysical techniques. The ability to quickly and specifically mutate a residue(s) in protein is important for mechanistic and functional studies. Although many site-directed mutagenesis methods have been developed, a simple, quick and multi-applicable method is still desirable. Results: We have developed a site-directed plasmid mutagenesis protocol that preserved the simple one step procedure of the QuikChange (TM) site-directed mutagenesis but enhanced its efficiency and extended its capability for multi-site mutagenesis. This modified protocol used a new primer design that promoted primer-template annealing by eliminating primer dimerization and also permitted the newly synthesized DNA to be used as the template in subsequent amplification cycles. These two factors we believe are the main reasons for the enhanced amplification efficiency and for its applications in multi-site mutagenesis. Conclusion: Our modified protocol significantly increased the efficiency of single mutation and also allowed facile large single insertions, deletions/truncations and multiple mutations in a single experiment, an option incompatible with the standard QuikChange (TM). Furthermore the new protocol required significantly less parental DNA which facilitated the DpnI digestion after the PCR amplification and enhanced the overall efficiency and reliability. Using our protocol, we generated single site, multiple single-site mutations and a combined insertion/deletion mutations. The results demonstrated that this new protocol imposed no additional reagent costs (beyond basic QuikChange T) but increased the overall success rates.

Reversible solid oxide fuel cells as energy conversion and storage devices

Gamble, Stephen R. — 2011-11-30T00:00:00Z

Abstract: A reversible solid oxide fuel cell (RSOFC) system could buffer intermittent electrical generation, e.g. wind, wave power by storing electrical energy as hydrogen and heat. RSOFC were fabricated by thermoplastic extrusion of (La₀.₈Sr₀.₂)₀.₉₅MnO[subscript(3−δ)] (LSM) ceramic support tubes, which were microstructurally stable with 55% porosity at 1350°C. A composite oxygen electrode of LSM-YSZ was applied, providing a homogeneous substrate for a 20 μm - 30 μm thick YSZ electrolyte. A dip-coated 8YSZ slurry, and a painted commercial 3YSZ ink gave sintered densities of 90% and nearly 100% at 1350°C, respectively. A porous NiO/YSZ fuel electrode was also painted on. A Ag/Cu reactive air braze was unsuccessful at forming a void-free joint between the RSOFC and a 316 stainless steel gas delivery tube, as the braze did not penetrate the oxidation layer on the steel. Two alumina-based ceramic cements failed to fully seal the cell to an alumina gas delivery tube, due to thermal expansion coefficient mismatches and porosity after curing. Therefore, the maximum open circuit voltage (OCV) obtained during RSOFC testing was 0.8 V at 440°C. LSM-YSZ symmetrical cell performance measurements with oxygen pressure showed a diffusion polarisation, which was assigned to dissociative adsorption and surface diffusion of oxygen species. A collaborative RSOFC system software model showed ohmic and activation losses dominated the RSOFC, and diffusion losses were insignificant. Pressurisation from 1 to 70 bar increased the RSOFC Nernst voltage by 11% at 900°C, and reduced the entropy of the gases, reducing heat production and increasing electrical efficiency. A 500 kg Sn/Cu phase change heat store prevented the system overheating. Over a 16 h discharge-charge RSOFC cycle in the range 5 mol.% - 95 mol.% hydrogen in steam, at 20.4 A per cell or 3250 A m⁻², the electrical energy storage efficiency was 64.4%.

Altered antibiotic transport in OmpC mutants isolated from a series of clinical strains of multi-drug resistant E. coli

Lou, Hubing — 2011-10-28T00:00:00Z

Abstract: Antibiotic-resistant bacteria, particularly Gram negative species, present significant health care challenges. The permeation of antibiotics through the outer membrane is largely effected by the porin superfamily, changes in which contribute to antibiotic resistance. A series of antibiotic resistant E. coli isolates were obtained from a patient during serial treatment with various antibiotics. The sequence of OmpC changed at three positions during treatment giving rise to a total of four OmpC variants (denoted OmpC20, OmpC26, OmpC28 and OmpC33, in which OmpC20 was derived from the first clinical isolate). We demonstrate that expression of the OmpC K12 porin in the clinical isolates lowers the MIC, consistent with modified porin function contributing to drug resistance. By a range of assays we have established that the three mutations that occur between OmpC20 and OmpC33 modify transport of both small molecules and antibiotics across the outer membrane. This results in the modulation of resistance to antibiotics, particularly cefotaxime. Small ion unitary conductance measurements of the isolated porins do not show significant differences between isolates. Thus, resistance does not appear to arise from major changes in pore size. Crystal structures of all four OmpC clinical mutants and molecular dynamics simulations also show that the pore size is essentially unchanged. Molecular dynamics simulations suggest that perturbation of the transverse electrostatic field at the constriction zone reduces cefotaxime passage through the pore, consistent with laboratory and clinical data. This subtle modification of the transverse electric field is a very different source of resistance than occlusion of the pore or wholesale destruction of the transverse field and points to a new mechanism by which porins may modulate antibiotic passage through the outer membrane.

Crystalline polymer and small molecule electrolytes

Ainsworth, David A. — 2010-06-23T00:00:00Z

Abstract: The research presented in this thesis includes a detailed investigation into factors influencing ionic conductivity in the crystalline polymer electrolyte PEO₆:LiPF₆. It has previously been shown that preparing PEO₆:LiPF₆ with PEO modified with larger –OC₂H₅ end groups increases ionic conductivity by one order of magnitude [¹],primarily due to disruption of the crystal structure caused by the inclusion of the larger end groups. In this study it is shown that by reducing PEO molecular weight in crystalline PEO₆:LiPF₆ ionic conductivity is also increased. This was attributed to an increasing concentration of polymer chain end regions upon lowering molecular weight resulting in the creation of more defects, as well as possible increases in crystallite size resulting in longer continuous pathways for ion transport. Similar results were observed using both polydispersed and monodispersed PEO to prepare complexes. In addition, it is demonstrated here that ionic conductivity in crystalline polymerelectrolytes is not confined to PEO₆:LiXF₆ (X=P, As, Sb)[²][³] type materials. The structures and ionic conductivity data are reported for a series of new crystalline polymer complexes: the alkali metal electrolytes. They are composed of low molecular weight PEO and different alkali metal hexafluoro salts (Na⁺, K⁺ and Rb⁺), and include the best conductor poly(ethylene oxide)₈:NaAsF₆ discovered to date [⁴], with a conductivity 1.5 orders of magnitude higher than poly(ethylene oxide)₆:LiAsF₆. A new class of solid ion conductor is reported: the crystalline small-molecule electrolytes. Such materials consist of lithium salts dissolved in low molecular weight glyme molecules [CH₃O(CH₂CH₂O)[subscript(n)]CH₃, n=1-12], forming crystalline complexes [⁵][⁶]. These materials are soft solids unlike ceramic electrolytes and unlike polymer electrolytes they are highly crystalline, are of low molecular weight and have no polydispersity. By varying the number of repeat units in the glyme molecule, many complexes may be prepared with a wide variety of structures. Here, ionic conductivity and cation transference number (t₊) data for several such complexes is presented [⁷][⁸][⁹].These complexes have appreciable ionic conductivities for crystalline complexes and their t₊ values vary markedly depending on the glyme molecule utilized. The differences in t₊ values can be directly attributed to differences in their crystal structures. [¹] Staunton, E., Andreev, Y.G. & Bruce, P.G. Factors influencing the conductivity of crystalline polymer electrolytes. Faraday Discussions 134, 143-156 (2007). [²] Gadjourova, Z., Andreev, Y.G., Tunstall, D.P. & Bruce, P.G. Ionic conductivity in crystalline polymer electrolytes. Nature 412, 6846 (2001). [³] Stoeva, Z., Martin-Litas, I., Staunton, I., Andreev, Y.G. & Bruce, B.G. Ionic Conductivity in the Crystalline Polymer Electrolytes PEO₆:LiXF₆, X = P, As, Sb. J. Am. Chem. Soc. 125, 4619-4626(2003). [⁴] Zhang, C., Gamble, S., Ainsworth, D., Slawin, A.M.Z., Andreev, Y.G. & Bruce, P.G. Alkali metal crystalline polymer electrolytes. Nature Materials 8, 580-584 (2009). [⁵] Henderson, W.A., Brooks, N.R., Brennessel, W.W. & Young Jr, V.G. Triglyme-Li⁺ Cation Solvate Structures: Models for Amorphous Concentrated Liquid and Polymer Electrolytes (I). Chem. Mater. 15, 4679-4684 (2003). [⁶] Henderson, W.A., Brooks, N.R. & Young Jr, V.G. Tetraglyme-Li⁺ Cation Solvate Structures: Models for Amorphous Concentrated Liquid and Polymer Electrolytes (II). Chem. Mater. 15, 4685-4690 (2003). [⁷] Zhang, C., Andreev, Y.G. & Bruce, P.G. Crystalline small-molecule electrolytes. Angewandte Chemie, International Edition 46, 2848-2850 (2007). [⁸] Zhang, C., Ainsworth, D., Andreev, Y.G. & Bruce, P.G. Ionic Conductivity in the Solid Glyme Complexes [CH₃O(CH₂CH₂O)[subscript(n)]CH₃]:LiAsF₆ (n = 3,4). J. Am. Chem. Soc. 129, 8700- 8701 (2007). [⁹] Zhang, C., Lilley, S.J., Ainsworth, D., Staunton, E., Andreev, Y.G., Slawin, A.M.Z. & Bruce, P.G. Structure and Conductivity of Small-Molecule Electrolytes [CH₃O(CH₂CH₂O)[subscript(n)]CH₃]:LiAsF₆ (n = 8-12). Chem. Mater. 20, 4039-4044 (2008).

Inorganic organic composite polymer coatings based on functionalised polyhedral oligomeric silsesquioxanes

Robertson, Duncan J. — 2011-06-01T00:00:00Z

Abstract: A study has been undertaken with the aim of preparing appropriately functionalised polyhedral oligomeric silsesquioxane (POSS) compounds to be used in ambient-cure chemistry. Numerous epoxy-functionalised compounds have been designed and synthesised and these materials have been characterised in order to determine their chemical structure. These compounds have also been incorporated into existing polymerisation reactions to test whether these materials could be used in the protective coatings industry. A glycidyl-functionalised POSS compound was prepared and reacted with a series of amines to produce ambient-cured polymers which could be used in the coatings industry. There were also a series of experiments undertaken on these polymers to identify the processes at work and to test how they compare to industry standards. As a direct comparator to this work, another set of results was obtained with a cyclic-siloxane material incorporated into the systems in place of the POSS. A linear analogue was also tested. The reactions proved to be a success and an appropriate data-set was yielded. During the synthesis of POSS precursors there are a series of residual materials produced. These materials have also been studied in this project. It was anticipated that these would behave in a similar way to the POSS compounds however the same functionality was never achieved as had been with the POSS. Ambient-cured polymers have also been targeted from a basic hydride-functionalised POSS compound and a polybutadiene system. The appropriate reactions unfortunately never took place as anticipated but there were a series of tests undertaken to identify the processes at work. A study has also been undertaken using near-I.R. to track the curing reactions. From this data, the extent of cure could be studied and the make-up of the reaction could be investigated in more detail.

The assembly of molecular networks at surfaces : towards novel enantioselective heterogeneous catalysts

Jensen, Sean — 2010-01-01T00:00:00Z

Abstract: Understanding the supramolecular interactions governing the self-assembly of molecular building blocks upon surfaces is fundamental to the design of new devices such as sensors or catalysts. Successful heterogeneous enantioselective catalysts have relied upon the adsorption of ‘chiral modifiers’, usually chiral amino acids, onto reactive metal surfaces. One of the most researched examples is the hydrogenation of β-ketoesters using nickel-based catalysts. The stability of the chiral modifiers upon catalyst surfaces is a major obstacle to the industrial scale-up of this reaction. In this study, the replacement of conventional modifiers with porous, chiral and functionalised self-assembled networks is investigated. Perylene-3,4,9,10-tetracarboxylic diimide (PTCDI) and melamine (1,3,5-triazine,-2,4,6-triamine) have been shown to form hydrogen bonded networks on Ag-Si(111)√3x√3R30° in ultra-high vacuum (UHV) and Au(111) substrates in UHV and ambient conditions, these networks are capable of hosting guest molecules. These networks are investigated further in this study. In UHV, the behaviour of the components and network formation on Ni(111) is probed using scanning tunnelling microscopy (STM) and temperature-programmed desorption (TPD). The stability of the PTCDI-melamine network on Au(111) was analysed using TPD. Metal coordination interactions between each of the network components and nickel upon the Au(111) surface were examined by STM before testing the ability of the network to act as a template for metal growth. Finally, a number of polymerisation reactions are investigated with a view to replacing chiral modifiers with porous, chiral, functionalised covalent networks. Periodic covalent networks should possess the greater chemical and thermal stability required for more widespread use. In UHV and ambient conditions, STM is used to monitor the progress of surface-confined reactions on Au(111) and characterise the resultant covalent structures.

Trifluoro alkyl oligo(ethylene glycol)-terminated alkanethiol self-assembled monolayers : synthesis, characterisation, and protein adsorption properties

Bonnet, Nelly — 2010-01-01T00:00:00Z

Abstract: Self-assembled monolayers have been proven to be well-ordered and to give stable ultrathin films. They show a remarkably high diversity with respect to their functionalisation giving rise to many possible applications. This thesis is focused on the potential use of these molecular thin films in life sciences. The reproduction of a membrane-like environment with these tightly packed and organized unimolecular layers has led to important breakthroughs in their nanotechnological application as biomaterials. Their straightforward modification allows the chemical and physical properties of biological interfaces to be altered. In particular, Oligo(ethylene glycol) based alkanethiol self-assembled monolayers were intensively studied as biointerfaces for their ability to resist the non specific adsorption of proteins. The electrostatic repulsion which originates from these monolayers was seen as one of the possible factors causing this protein repulsion. On the other hand proteins adsorb on alkanethiol self-assembled monolayers. This can be partially attributed to an attractive hydrophobic interaction between the biomolecules and the surface. As a result of the understanding of these two driving forces which are relevant for non-specific protein adsorption/repulsion, novel self-assembling molecules were tailored in an attempt to adjust the adsorption of proteins at the SAM-liquid interface. This was conceivable with these newly designed SAMs since they allow a combination of these forces. We have chosen the ionic strength of the liquid environment as the external parameter which could act on the amount of adsorbed proteins because the electrostatic force created by oligo(ethylene glycol) groups depends on it. In addition to the synthesis of six new molecules, the preparation and characterisation of the novel self-assembled monolayers are reported in this thesis. The density of the monolayers was estimated by X-ray photoelectron spectroscopy and ellipsometry, and the wettability properties were studied by measuring the contact angle. The total force acting on proteins from the SAMs was studied with an atomic force microscope, equipped with a tip mimicking proteins, by measuring force-distance curves. An in-situ technique was investigated in order to study the influence of the variation of this total force on the quantity of adsorbed proteins by varying the ionic strength.

N-heterocyclic carbene ligands in palladium and iridium organometallic chemistry

Diebolt, Olivier — 2010-01-01T00:00:00Z

Abstract: The use of ligand in transition-metal catalysed reactions has had a considerable impact. The present manuscript aims at showing the influence of ligands in the palladium catalysed Suzuki-Miyaura cross-coupling reaction. In chapter one, the mechanism of this reaction will be described based on the numerous contribution published in the literature. It will be shown that the electronic and steric properties of the ligands have a huge repercussion on the catalytic activity of the metal. In the second chapter, the electronic and steric properties of the widely used Buchwald-phosphine ligand will be investigated. For this purpose, bis-carbonyl iridium(I) complexes were synthesized and their characterization allowed determining their TEP (Tolman electronic parameter) and their buried volume %V[subscript(bur)]. Then three next chapters of this thesis will focus on the syntheses and characterizations of new palladium complexes bearing N-heterocyclic carbenes (NHC). Their design was made in a view to obtain high activity in cross coupling reaction, particularly in the Suzuki-Miyaura cross coupling. Their activation under the catalytic conditions leads to the formation of palladium(0) species that can be mono- or bis-ligated. The influence of the ligand on the catalyst activity will be discussed. A palladium(II) precatalyst leading to mono-ligated active species will be described. Its activity in cross-coupling is very good, since activated and non-activated aryl chlorides could be coupled with aryl boronic acids at room temperature using low catalyst loadings. Unfortunately, the catalyst activity decreased with temperature. This result showed the fragility of the mono-ligated active species. In a view to obtain more robust catalysts that can perform high turnover numbers, new palladium(II) precatalysts bearing two ancillary ligands were developed. Mixed systems NHC- phosphites and NHC-phosphines are described. NHC-phosphites precatalysts displayed very good activity, but the phosphites are unfortunately sensitive to reaction conditions, limiting their role of active species shield. NHC-phosphine bearing complexes were highly active and could perform up to 10,000 turnovers with unactivated aryl chlorides. Very interestingly, these catalysts were also able to couple benzylchlorides and allyl chlorides with a wide range of boronic acids at very low catalyst loadings. These reactions had also the great advantage to proceed in aqueous solvents at very high substrate concentration. The activation mechanism of these complexes was investigated. Dichloropalladium(II) complexes were reduced under the catalytic conditions to lead palladium(0) species. Therein, it is shown that this reduction step was rate-determining in catalysis. Some palladium(0) intermediates xxiv were synthesized and showed good to excellent activities at low temperature under the exact same conditions. They displayed high reactivity towards oxygen and moisture and have to be handled under inert atmosphere. A particular complex had the ability to react with molecular dioxygen to form a stable peroxo-complex. Interestingly, this complex displayed excellent activity in water under aerobic conditions. This system was of great advantage since the reaction could be set up under air using cheap and user-friendly reagents displaying low toxicity. Moreover, the readily available distilled water used as solvent did not require prior degassing. Symmetrical and unsymmetrical bis-NHC palladium(0) complexes were successfully synthesized. They display excellent activity in the Suzuki-Miyaura cross coupling and turnover frequencies as high as 300 could be obtained at room temperature with unactivated arylchlorides and arylboronic acids. These complexes were also found excellent catalysts for the coupling of benzylchlorides with arylboronic acids. Mechanistic studies showed that no ligand dissociation occurred during the coupling suggesting as bis-ligated active species.

Solvothermal chemistry of luminescent lanthanide fluorides

Jayasundera, Anil — 2009-01-01T00:00:00Z

Abstract: Exploration of novel lanthanide fluoride framework materials in inorganic-organic hybrid systems under solvothermal conditions towards development of new luminescent materials is discussed. X-ray single crystal and powder diffraction methods have been used as crystallographic characterisation techniques. Determination and study of luminescence properties for selected hybrid materials has also been carried out. The first organically templated luminescent lanthanide fluoride framework, [C₂N₂H₁₀]₀.₅ [Ln₂F₇] (Ln= Nd, Tb, Dy, Ho, Er, Yb and Lu), has been synthesised and characterised. This structure type consists of a three-dimensional yttrium fluoride framework incorporating two similar, but crystallographically distinct, yttrium sites. Photoluminescence studies of [C₂N₂H₁₀]₀.₅ [Y₂F₇]: Ln³⁺ (Ln³⁺ = Gd³⁺, Eu³⁺ and Tb³⁺) have been explored and characteristic luminescence emissions are reported. An inorganic-organic hybrid indium fluoride and its scandium fluoride analogue, [C₄H₁₄N₂][MF₅](M=In and Sc) is reported. The structure consists of infinite trans vertex sharing (InF₅)[subscript(∞)] chains, which are linked via H-bonded organic moieties. The scandium and fluorine local environments of [C₄H₁₄N₂][ScF₅] are characterised by ¹⁹F, and ⁴⁵Sc solid-state MAS NMR spectroscopies. A single scandium site has been confirmed by ⁴⁵Sc MAS NMR. ¹⁹F MAS NMR clearly differentiates between bridging and terminal fluorine. The photoluminescence properties of these complexes, [C₄H₁₄N₂][In[subscript(1-x)] Ln[subscript(x)]F₅] (Ln=Tb and/or Eu), have been explored. The optimum composition for Eu³⁺ doped samples occurs at x = 0.05 Eu³⁺ and the “asymmetry ratio” of R = I₅₉₀/I₆₁₅ ( ⁵D₀ → ⁷F₂ and ⁵D₀ → ⁷F₁) gives a clear picture of the sensitivity for crystal field of the compound. For x = 0.08 Tb³⁺, a strong down-conversion fluorescence corresponding to ⁵D₄ → ⁷F₅ (green at 543.5 nm) occurs. In addition, a Tb³⁺/Eu³⁺ co-doped sample exhibits a combination of green (Tb³⁺) and orange (Eu³⁺) luminescence, with Tb³⁺ enhancing the emission of Eu³⁺ in this host. Exploration of novel indium, aluminium, and zirconium fluoride crystal structures with potential luminescent properties has also been undertaken. A chiolite-like phase K₅In₃F₁₄ (space group P4/mnc) has been synthesised. No phase transition occurs over the temperature range 113K< T< 293 K, as has been seen in other chiolite-like structures. An organically templated indium fluoride, [NH₄]₃[C₆H₂₁N₄]₂[In₄F₂₁] has been prepared; this features the trimeric unit [In₃F₁₅]³⁻ which appears to be the first of its type in a metal fluoride. A new hybrid fluoride, Sr[N₂C₂H₁₀]₂[Al₂F₁₂].H₂O has been synthesised. Because the ionic radius of Eu²⁺ is similar to that of Sr ²⁺ this may be a potential host for blue luminescent Eu²⁺. The new material KZrF₅.H₂O shows pentagonal-bipyramidal geometry of Zr⁴⁺ with a polar space group, Pb2₁m, which may potentially have ferroelectric properties.

The development of novel myosin inhibitors

Lawson, Christopher Peter Abiodun Tevi — 2011-06-01T00:00:00Z

Abstract: This thesis describes a structure activity relationship (SAR) study on the recently discovered small molecule tool blebbistatin (S)-21 with particular emphasis on the development of novel synthetic protocols suitable for the rapid synthesis of libraries of blebbistatin analogues. These analogues are potentially of use as novel myosin inhibitors Chapter 1 introduces the concept of chemical biology with particular emphasis on chemical genetics. This approach has rekindled the search for new chemical tools for the investigation of biological systems. The success of blebbistatin (S)-21, which was identified in a chemical genetic study, as a research tool was also discussed. The link between several myosin classes and genetic diseases such as coeliac disease, Crohn’s disease, deafness, dermatitis, familial hypertrophic cardiomyopathy, Griscelli disease and ulcerative colitis indicate that potent inhibitors which show selectivity towards specific myosin isoforms may be of great value as tools for the study of these conditions. The plan for the SAR study around (S)-21 was outlined. Chapter 2 describes the studies undertaken to develop an efficient synthetic route to N1-alkyl analogues of (S)-21 suitable for the parallel synthesis of chemical collections. These studies culminated in the synthesis of an intermediate (S)-66 from which novel N1-alkyl analogues were synthesised. The biological evaluation of these N1-alkyl analogues was discussed. Chapter 3 describes the development of a protocol suitable for the parallel synthesis of collections of N1-aryl analogues of (S)-21 via the intermediate 66. The application of this protocol to the synthesis of a collection of racemic N1-aryl and heteroaryl analogues of (S)-21 and their biological evaluation was presented. Chapter 4 describes the successful rational design and synthesis of a novel fused thiophene ring containing inhibitor of myosin II. The structure of this compound was proposed by modelling of the existing co-crystal structure of (S)-21 bound to the metastable state of Dictyostelium discoideum myosin II (S1dC) and sought to optimise the π-π stacking interaction displayed by (S)-21 with the tyrosine 261 residue within its binding site. The biological evaluation of this novel analogue was discussed. In Chapter 5 the studies conducted to investigate the contribution of ring-C to the binding affinity of (S)-21 were described. The development of alternate routes to (S)-21, in an attempt to avoid difficulties experienced during the synthesis of some analogues of (S)-21, are described. The synthesis and biological investigation of the fluorescent dye PPBA whose binding site has been suggested to overlap with that of (S)-21 was also reported.

Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales

Paytubi, Sonia — 2012-02-14T00:00:00Z

Abstract: Single-stranded DNA binding proteins (SSBs) based on the OB-fold are considered ubiquitous in nature and play a central role in many DNA transactions including replication, recombination and repair. We demonstrate that the thermoproteales, a clade of hyperthermophilic crenarchaea, lack a canonical SSB. Instead, they encode a distinct ssDNA-binding protein that we term "ThermoDBP", exemplified by protein Ttx1576 from Thermoproteus tenax. ThermoDBP binds specifically to ssDNA with low sequence specificity. The crystal structure of Ttx1576 reveals a unique fold and mechanism for ssDNA binding, consisting of an extended cleft lined with hydrophobic phenylalanine residues and flanked by basic amino acids. Two ssDNA-binding domains are linked by a coiled-coil leucine zipper. ThermoDBP appears to have displaced the canonical SSB during the diversification of the thermoproteales – a highly unusual example where a “ubiquitous” protein has been lost in evolution.

Synthesis and evaluation of α-fluoro analogues of capsaicin and 2-(aminomethyl)piperidine derivatives

Moraux, Thomas — 2011-08-09T00:00:00Z

Abstract: Chapter 1 gives an overview of the fluorine chemistry field, from its early developments to recent applications in medicinal chemistry. The development of asymmetric electrophilic or nucleophilic installation of fluorine in organic molecules is highlighten. Chapter 2 of this thesis discusses the enantioselective synthesis of α-fluoroamides. The study is applied to the synthesis of fluoroenantiomers of the bioactive molecule capsaicin and short-chain analogues. The biological activity of these compounds is assayed with the TRPV1 receptor. Results show that enantioselective α-fluoroamides (R)-97, (R)-99 and (S)-99 can generate differentiated biological responses, from TRPV1 agonists to TRPV1 antagonists. Chapter 3 focuses on the optimisation and development of 2-(aminomethyl)piperidine (R)-251 dihydrochloride. The development of 2-(aminomethyl)piperidine (R)-251 as its ditetrafluoroborate salt proved to offer excellent reactivity and solubility for the preparation of derivatives. This tetrafluoroborate salt was used to improve the syntheses of organocatalysts 2,2,2-trifluoro-N-(piperidin-2-ylmethyl)acetamide 363 and 4-methyl-N-(piperidin-2-ylmethyl)benzenesulfonamide 364.The catalytic properties of these latter two molecules for asymmetric Mannich reaction is demonstrated. Both (R)-363 and (R)-364 show up to 86% ee, in a typical 20 mol% loading, but loading of (R)-363 as low as 5 mol% still induces the catalysis.

An atomistic approach to graphene and carbon clusters grown on a transition metal surface

Wang, Bo — 2011-06-01T00:00:00Z

Abstract: In this thesis, graphene (i.e. monolayer carbon film) and carbon clusters supported on a transition metal surface are systematically studied by local probe techniques, with respect to their structures, electronic properties and formation mechanisms. The main tools used are low-temperature scanning tunnelling microscopy and spectroscopy (STM and STS), which are introduced in Chapter 2. The mechanism of the resonance tunnelling at electron energies higher than the work function of the surface is discussed in detail, and a qualitative explanation of the Gundlach oscillations in the corresponding spectroscopy is presented. Epitaxial graphene synthesised on the Rh(111) surface by ethylene dehydrogenation is investigated by STM in Chapter 4. Such carbon film exhibits a hexagonal Moiré pattern due to a lattice mismatch between graphene and the rhodium substrate. The periodicity and local registries of the graphene/Rh(111) superstructure are carefully analysed. Based on a thorough discussion about the “commensurate vs. incommensurate” nature of the Moiré pattern in surface science field, the graphene/Rh(111) system is identified to have a non-simple-commensurate superstructure. The surface electronic properties and geometric buckling of graphene/Rh(111) are investigated by resonance tunnelling spectroscopy (RTS) and density functional theory (DFT) calculations in Chapter 5. Spectroscopy measurements reveal a modulation of the electronic surface potential (or work function Φ) across the supercell of epitaxial graphene. Based on the microscopy/spectroscopy data and the extended DFT calculations, we examined the electronic coupling of the various local C-Rh registries, and identified both experimentally and theoretically the local atomic configurations of maximum and minimum chemical bonding between graphene and the rhodium substrate. We studied in Chapter 6 the growth mechanism of graphene on Rh(111) at elevated temperatures. This part starts by investigating the dehydrogenation of ethylene into ethylidyne. When the dehydrogenation process is complete, monodispersed carbon species, identified as 7C6, are found to dominate the cluster population on the rhodium terraces. A significant coalescence of the 7C6 clusters into graphene islands occurs at temperatures higher than 873 K. The structural and electronic properties of the 7C6 carbon clusters are examined by high-resolution STM and STS, and compared with coronene molecules, i.e. the hydrogenated analogues of 7C6. DFT calculations are further used to explain the stability of 7C6 supported on the Rh(111) surface, and also the structural characteristics of such magic-sized carbon clusters.

Synthesis and structure-property relationships in selected metal fluorides

Reisinger, Sandra A. — 2012-06-01T00:00:00Z

Abstract: There has been an increase in the interest in fluoride materials over the last decade. This interest has focused on multiferroic materials and kagome lattices, to name but a few areas. This thesis focuses on the synthesis and crystallographic characterisation of selected transition metal fluorides and oxyfluorides. Work is presented on the tetragonal tungsten bronze solid solutions of K[subscript(x)]FeF₃, where x = 0.58 and x ≈ 0.5, and the copper analogue, K₃Cu₃Fe₂F₁₅; the kagome structure of Cs₂ZrCu₃F₁₂; and hydrothermal reactions using vanadium, manganese, or molybdenum as the transition metals in the formation of new fluorides and oxyfluorides. The tetragonal tungsten bronze compounds K[subscript(x)]FeF₃ (x = 0.58 and x ≈ 0.5) are both tetragonal at 500 K. In the variant with the lower K-content, there is a clear phase separation into two tetragonal phases even at this temperature. The K₀.₅₈FeF₃ sample separates into two distinct phases below 340 K to possess one tetragonal and one orthorhombic phase. Then at roughly 300 K, both samples undergo a phase transition where the tetragonal phase in the P4/mbm space group in K₀.₅₈FeF₃ changes to an orthorhombic phase with a larger unit cell; and the tetragonal phase in P4₂bc for the K₀.₅FeF₃ sample changes to the same orthorhombic model, whilst the P4/mbm model remains unchanged. The evolution of the lattice parameters and phase fractions is studied in detail using synchrotron powder X-ray diffraction (sPXRD). The kagome structure investigated, Cs₂ZrCu₃F₁₂, possesses the “ideal” kagome lattice at room temperature, but previous work has suggested that there is a phase transition at 225 K. The two structures are determined by single crystal X-ray diffraction at 300 K and 125 K. Variable temperature sPXRD studies are performed between these two temperature ranges to determine the phase evolution as a function of temperature. The structure changes from a rhombohedral to a monoclinic phase at low temperature. This is the result of the buckling of the kagome layers at the phase transition. The Zr⁴⁺ ion changes from 6 to 7 coordinate and this is seen as the main driving force for the distortion of the kagome layer from its “ideal” planar arrangement. ii The phase transition is first-order as seen from the electrical impedance measurements. The hydrothermal reactions presented reveal seven new materials and their crystal structures. Sr₂V₂F₁₀·H₂O is new and found to be isostructural to Sr₂Fe₂F₁₀·H₂O. BaVO₂F₃ is a cubic material that is potentially piezoelectric. Two hybrid organic inorganic manganese compounds are reported. The ladder structure (C₃N₂H₅)[Mn₂F₆(H₂O)₂] crystallises in a polar space group and shows promise as a candidate for multiferroic studies. The second hybrid material, (C₇NH₁₆)₂[MnF₅(H₂O)]·2H₂O, crystallises in a centrosymmetric space group. The Mo hybrid materials are all centrosymmetric and possess isolated molybdenum-centred monomeric or dimeric octahedral units.

Studies on the synthesis of dicaffeoylquinic acid conjugates

Raheem, Kolawole Saki — 2011-11-01T00:00:00Z

Abstract: Dicaffeoylquinic acid (DCQA) is a natural polyphenolic compound widely distributed in plants such as coffee beans, which possesses a range of pharmacological activities. Herein, is reported studies undertaken towards the first total synthesis of 3,5-DCQA conjugates. Two synthetic routes were investigated. The first route involves a seven step sequence beginning from quinic acid. The overall yield via this synthetic approach was 30%. The key steps involved in the sequence were a regioselective benzylation of the C-3-hydroxyl group followed by silyl protection of the C-1 and C-4 hydroxyl groups. Deprotection of the benzyl group by hydrogenolysis and opening of the lactone afforded the 3,5-diol. Esterification of the 3,5-diol with 3,4-tert-butyldimethylsilyl caffeoyl chloride afforded the di-ester. Removal of the protecting groups afforded 3,5-DCQA. The second route involved selective protection of the C-3-hydroxyl group with silyl followed by benzylation of the C-1 and C-3 hydroxyl groups. Saponification of the lactone ring followed by benzylation of the carboxylic acid gave the benzyl ester. Silyl deprotection afforded the 3,5-diol. The 3,5-diol was subsequently esterified by refluxing in toluene with commercially available Meldrum’s acid. In the final step, the synthesis of 3,5-DCQA was achieved by a Knoevenagel condensation of 3,4-dihydroxybenzaldehyde and a malonate ester of quinic acid. An efficient method for the synthesis of possible metabolites of quinic acid conjugates was also described. This protocol employs N-(4-methoxyphenyl)-trifluoroacetimidate glucuronyl as the donor. The key reaction in this sequence was the coupling of N-(4-methoxyphenyl)-trifluoroacetimidate glucuronyl with 4-hydroxy-3-methoxy-benzaldehyde.

Correlating Pt-P bond lengths and Pt-P coupling constants

Waddell, Paul G. — 2010-08-16T00:00:00Z

Abstract: The X-ray structures of (5) cis-PtBr2(P(OMe)(3))(2), (6) cis-PtBr2(P(OMe)(2)Ph)(2), (7) cis-PtBr2(P(OMe)Ph-2)(2), (8) cis-PtBr2(PPh3)(2), (9) cis-PtI2(P(OMe)(3))(2), (10) cis-PtI2(P(OMe)(2)Ph)(2), (11) cis-PtI2(P(OMe)Ph-2)(2) and (12) cis-PtI2(PPh3)(2) are reported and compared with the previously reported chloride analogues. The magnitude of the J{Pt-P} varies linearly with the Pt-P bond length (l(Pt-P) = 2.421 - J/24255) for these 12 complexes.

Design and synthesis of chemical probes for the plekstrin homology domain

Elliott, Thomas S. — 2010-11-30T00:00:00Z

Abstract: The phosphatidylinositol polyphosphates play a fundamental role in intracellular signalling. Of particular importance is phosphatidylinositol 3,4,5-trisphosphate [PtdIns(3,4,5)P₃], which acts by recruiting effector proteins to the cell membrane. PtdIns(3,4,5)P₃ interacts with its protein targets through selective binding domains that include the pleckstrin homology (PH) domain. The PH-domain-containing kinase, protein kinase B (PKB/Akt), which interacts with PtdIns(3,4,5)P₃, is upregulated in ~15 human malignancies. Significantly, inhibition of the PtdIns(3,4,5)P₃-PKB interaction has proved viable as a point of therapeutic intervention.There is currently a lack of small molecule probes that selectively interact with a given PH domain. Consequently, it is impossible to dissect the cellular function of PH-domain-containing proteins at a molecular level. To address this problem, we have designed and synthesised a number of derivatives of the PtdIns(3,4,5)P₃ inositol head-group – Ins(1,3,4,5)P₄. Replacement of the 5-position phosphate with a range of phosphate bioisosteres afforded compounds that displayed no binding affinity for the PH-domain of general receptor for phosphoinositides 1 (GRP1). However, it was shown that the 5-position sulfamate analogue displayed selectivity for the PH-domain of PKB. The methylphosphate biosiostere at the 1-position displayed binding for both the GRP1 PH-domain as well as the PKB PH-domain. These results demonstrate that subtle modification of the Ins(1,3,4,5)P₄ structure allows the synthesis of compounds that interact selectively with a given PH domain. We will now use these results for the synthesis of a second generation of compounds with improved PH-domain affinity and selectivity.

Artificial metalloenzymes : modified proteins as tuneable transition metal catalysts

Deuss, Peter J. — 2011-06-22T00:00:00Z

Abstract: This thesis describes the design, synthesis and application of artificial metalloenzymes for transition metal catalysed reactions not performed by natural enzymes. Unique cysteine containing protein templates were covalently modified with transition metal ligand complexes that generate catalytic activity, which allows for the use of virtually any protein template. SCP-2L was selected as template for the linear hydrophobic tunnel that traverses the protein, which has high affinity for linear aliphatic molecules. The use of catalysts based on this protein to induce increased activity in the biphasic hydroformylation of linear α-olefins is investigated in this work. For this purpose, unique cysteine containing mutants of SCP-2L were modified with phosphine ligands by application of a novel bioconjugation procedure. Application of rhodium adducts of the phosphine modified protein constructs led to up to a 100 fold increase of the turn over numbers was measured compared to a Rh/TPPTS model system which is used in industry. Furthermore, good selectivity towards the linear product was observed. If it can be confirmed that the found catalytic results truly are the result of substrate encapsulation by the protein scaffold, this system represents the first rationally designed artificial metalloenzyme which exploits the shape selectivity of the protein scaffold to direct the outcome of a catalytic reaction. In addition, a study was performed for the development of enantioselective artificial metalloenzymes. Nitrogen ligands were covalently introduced in SCP-2L and the obtained conjugates were applied in the copper catalysed Diels-Alder and Michael addition reaction. A promising 25% ee was found for the Diels-Alder reaction between azachalcone and cyclopentadiene using one of the created constructs. Further development of these catalyst systems with the use of both synthetic (e.g. optimisation of ligand structure) and biomolecular tools (e.g. optimisation of protein environment) for optimisation can lead to very efficient and enantioselective conversions in the future. Description: Electronic version excludes material for which permission has not been granted by the rights holder

Novel lithium-ion host materials for electrode applications

Lyness, Christopher — 2011-06-22T00:00:00Z

Abstract: Two novel lithium host materials were investigated using structural and electrochemical analysis; the cathode material Li₂CoSiO₄ and the LiMO₂ class of anodes (where M is a transition metal ion). Li₂CoSiO₄ materials were produced utilising a combination of solid state and hydrothermal synthesis conditions. Three Li₂CoSiO₄ polymorphs were synthesised; β[subscript(I)], β[subscript(II)] and γ₀. The Li₂CoSiO₄ polymorphs formed structures based around a distorted Li₃PO₄ structure. The β[subscript(II)] material was indexed to a Pmn2₁ space group, the β[subscript(I)] polymorph to Pbn2₁ and the γ₀ material was indexed to the P2₁/n space group. A varying degree of cation mixing between lithium and cobalt sites was observed across the polymorphs. The β[subscript(II)] polymorph produced 210mAh/g of capacity on first charge, with a first discharge capacity of 67mAh/g. It was found that the β[subscript(I)] material converted to the β[subscript(II)] polymorph during first charge. The γ₀ polymorph showed almost negligible electrochemical performance. Capacity retention of all polymorphs was poor, diminishing significantly by the tenth cycle. The effect of mechanical milling and carbon coating upon β[subscript(II)], β[subscript(I)] and γ₀ materials was also investigated. Various Li[subscript(1+x)]V[subscript(1-x)]O₂ materials (where 0≤X≤0.2) were produced through solid state synthesis. LiVO₂ was found to convert to Li₂VO₂ on discharge, this process was found to be strongly dependent on the amount of excess lithium in the system. The Li₁.₀₈V₀.₉₂O₂ material had the highest first discharge capacity at 310mAh/g. It was found that the initial discharge consisted of several distinct electrochemical processes, connected by a complicated relationship, with significant irreversible capacity on first discharge. Several other LiMO₂ systems were investigated for their ability to convert to layered Li₂MO₂ structures on low voltage discharge. While LiCoO₂ failed to convert to a Li₂CoO₂ structure, LiMn₀.₅Ni₀.₅O₂ underwent an addition type reaction to form Li₂Mn₀.₅Ni₀.₅O₂. A previously unknown Li₂Ni[subscript(X)]Co[subscript(1-X)]O₂ structure was observed, identified during the discharge of LiNi₀.₃₃Co₀.₆₆O₂.

Hypervalent adducts of chalcogen-containing peri-substituted naphthalenes; reactions of sulfur, selenium, and tellurium with dihalogens

Knight, Fergus Ross — 2010-08-16T00:00:00Z

Abstract: A range of structurally diverse compounds 1-15 {Nap[SPh]2•Br4 (Nap = naphthalene-1,8-diyl); Nap[SePh][EPh]•Br4 (E = Se, S); Nap[SePh]2•I2; Nap[SePh][EPh]•3/2I2 (E = Se, S); Nap[TePh][G]•X2 (G = SePh, SPh, Br, I; X = Br, I); and [Nap(PPh2OH)(SPh)]+Br3-} formed from the reactions between peri-substituted naphthalene chalcogen donors D1-D8 {Nap[ER][E0R] (ER/E0R = SPh, SePh, TePh); Nap[TePh][X] (X = Br, I); and Nap[PPh2][SPh]} and dibromine and diiodine were characterized by X-ray crystallography and where possible by multinuclear NMR, IR, and MS. X-ray data for 1-15 were analyzed by naphthalene ring torsions, peri-atom displacement, splay angle magnitude, peri-distance, aromatic ring orientations, and quasi-linear three-body arrangements. The hypervalent linear moieties are considered in the context of the charge-transfer model and the 3c-4e model introduced by Pimentel and Rundle. In general, the conformation of the final products obeyed the rule based on charge-transfer that “seesaw” (X-ER2-X, 10-E-4) adducts arise when the halogen (X) is more electronegative than the chalcogen (E), and if the converse is true then, CT “spoke” (X-X-ER2, 8-E-3) adducts are formed. Upon treatment with dibromine, selenium donor compounds D2 {Nap[SePh]2} and D3 {Nap[SePh][SPh]} afford unusual tribromide salts of bromoselenyl cations containing a hypervalent X-E---E` 3c-4e type interaction. Upon treatment with diiodine, D2 and D3 form “Z-shaped”, “extended spoke” adducts containing an uncommon 2:3 donor/chalcogen ratio and incorporating chains of I2 held together by rare I---I interactions. As expected, “seesaw” 10-E-4 adducts are formed following the reaction of Te donors D4-D7 {Nap[TePh][X] (X = Br, I); Nap[TePh][EPh] (E = Se, S)} with the dihalogens. Naphthalene distortion in general is comparable between respective donor compounds and products 1-15. Ionic species 2 and 3 display a noticeable reduction in molecular distortion explained by the relief of steric strain via weak peri-interactions and the onset of 3c-4e bonding.

Enantioselective hydrogenation using ruthenium complexes of tridentate ligands

Phillips, Scott D. — 2011-06-22T00:00:00Z

Abstract: This thesis describes the development of the [RuCl₂(P^N^N)L] catalytic system for asymmetric hydrogenation. It has been demonstrated that the current system is efficient in preparing a range of bulky chiral alcohols in good enantioselectivity, many of which are likely to be inaccessible using the more classic [RuCl₂(P^P)N^N)] system developed by Noyori and coworkers. It has been shown that the current system is tolerant of a range of substrate electronic effects as well as the presence of heteroaromatic functionality, thus showing its applicability in synthesis. This has been extended to prepare a number of bulky derivatives of synthetically important molecules. The demonstration of this is significant as in drug design, for example, studies that aim to extend lipophilicity or steric bulk make the ability to prepare alcohols across the full range of steric properties important. We have shown that chiral alcohols with adjacent gem-dimethyl groups can be prepared in high enantioselectivity and their conversion into other valuable molecules, such as chiral lactones has been demonstrated. Detailed mechanistic studies have been undertaken for the present system in order to aid rational design of new, more active and selective catalysts. A number of achiral variants of the original system have been prepared and the key features of ligand structure for efficient catalysis have been identified. This was accomplished by rigorous kinetic analysis of each complex, using specialist gas-uptake monitoring equipment. The key features of catalyst structure and optimal reaction conditions for efficient asymmetric hydrogenation have been identified. Our greater understanding of the present system allowed us to rationally design new catalysts of for enantioselective hydrogenation. Our aim was to be able to tune the catalyst structure to carry out hydrogenation of a greater variety of ketone substrate with high activity and selectivity. We have successfully prepared second generation catalysts that show enhanced enantioselectivity for a variety of substrates, many of which were problematic with the Noyori system.

Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus

Overton, Ian M. — 2011-05-12T00:00:00Z

Abstract: Background: Staphylococcus aureus is a major human pathogen and strains resistant to existing treatments continue to emerge. Development of novel treatments is therefore important. Antimicrobial peptides represent a source of potential novel antibiotics to combat resistant bacteria such as Methicillin-Resistant Staphylococcus aureus (MRSA). A promising antimicrobial peptide is ranalexin, which has potent activity against Gram-positive bacteria, and particularly S. aureus. Understanding mode of action is a key component of drug discovery and network biology approaches enable a global, integrated view of microbial physiology, including mechanisms of antibiotic killing. We developed a systems-wide functional association network approach to integrate proteome and transcriptome profiles, enabling study of drug resistance and mode of action. Results: The functional association network was constructed by Bayesian logistic regression, providing a framework for identification of antimicrobial peptide (ranalexin) response modules from S. aureus MRSA-252 transcriptome and proteome profiling. These signatures of ranalexin treatment revealed multiple killing mechanisms, including cell wall activity. Cell wall effects were supported by gene disruption and osmotic fragility experiments. Furthermore, twenty-two novel virulence factors were inferred, while the VraRS two-component system and PhoU-mediated persister formation were implicated in MRSA tolerance to cationic antimicrobial peptides. Conclusions: This work demonstrates a powerful integrative approach to study drug resistance and mode of action. Our findings are informative to the development of novel therapeutic strategies against Staphylococcus aureus and particularly MRSA.

Exploring and exploiting benzylic regioselectivity in rhodium-catalysed hydroformylation

Martin, Nicola — 2011-06-22T00:00:00Z

Abstract: This project involves a study into the hydroformylation of substituted alkenes and ways to exploit “benzylic regioselectivity”. It was our aim to develop a clean, selective hydroformylation reaction which takes advantage of the tendency for benzylic regioselectivity in styrene-type molecules; in doing so, providing a potential route to important biologically active molecules. In Chapter Two, hydroformylation of methyl cinnamate is explored since we envisaged that a regioselective hydroformylation of this substrate would serve as a step in an efficient route to γ-amino acids derivatives; which are important building blocks for the synthesis of important drug molecules. Most Rh-phosphine catalysts install the formyl group α- to the ester group however, we found that certain reaction conditions and appropriate choice of phosphorus containing ligands led to highly chemoselective and regioselective hydroformylation. Regioselectivities of up to 25 : 1 favouring the benzylic aldehyde were observed. However, as will be explained, this reaction is hindered by significant hydrogenation under hydroformylation conditions. Using a novel ligand this side reaction was lowered to 5% with reasonable regioselectivity, however overall conversion to the desired aldehyde was low. As a means to synthesise γ-amino acid derivatives, enamine formation using the aldehyde products was also attempted. An alternative alkenyl arene substrate is studied in Chapter Three. High benzylic regioselectivity was observed using a variety of chiral and achiral ligands and again reaction conditions were optimised with the aim to develop an efficient process for the synthesis of γ-amino alcohol derivatives. It was found that PPh₃, tris(3,4,5-trifluorophenyl)phosphine and a phosphaadamantane cage phosphine ligand gave the most promising results with moderate to high regioselectivity observed. Asymmetric hydroformylation was not possible due to low activity using a variety of state-of-the-art chiral ligands.

Novel metal organic frameworks : synthesis, characterisation and functions

Haja Mohideen, Mohamed Infas — 2011-05-20T00:00:00Z

Abstract: The synthesis and properties of novel Metal Organic Frameworks were investigated and reported in this thesis. Thirteen new materials have been synthesized and their properties have been discussed with nine of the structures being solved. The most interesting and useful MOF among the thirteen materials is STAM-1, a copper-based Metal Organic Framework in which the starting linker (Benzene-1,3,5-tricarboxylic acid) undergoes selective in situ monoesterification during the synthesis. The monoesterified BTC can be recovered easily from the MOF, opening up MOF synthesis as a “protection” tool for unexpected selectivity in preparative chemistry that is difficult to accomplish using standard organic chemistry approaches. The selective linker derivatisation leads to the formation of a porous MOF with two types of accessible channel; one hydrophilic lined by copper and the other hydrophobic, lined by the ester groups. The unique structure of the pores leads to unprecedented adsorption behaviour, which reacts differently to gases or vapours of dissimilar chemistry and allows them to access different parts of the structure. The structural flexibility of STAM-1 shows significant differences in the kinetics of O₂ and N₂ adsorption, showing potential for new materials to be developed for air separation. Having two types of channel systems, adsorption can be switched between the two channels by judicious choice of the conditions; a thermal trigger to open the hydrophilic channel and a chemical trigger to open the hydrophobic channel. The storage and release capability of NO in STAM-1 was investigated for use in biomedical applications. Successful studies showed the strength of the antibacterial effects of NO loaded STAM-1, by using three different bacterial strains as a test of performance and were found to be bactericidal. Furthermore the antibacterial effects of NO free STAM-1 were also probed and found to be bactericidal even with low concentrations of the material such as 5 wt%. STAM-1 showed some complex magnetic behaviour by displaying strong antiferromagnetic properties at room temperature and ferromagnetic properties at lower temperatures. The antiferromagnetic coupling was observed within the dimer and ferromagnetic coupling between the dimers. This property of ferromagnetism can only be attributed to the corporation of magnetic dimers in the framework. STAM-2 displays a different magnetic behaviour than STAM-1 which shows paramagnetic properties at room temperature and antiferromagnetic properties at lower temperatures. Other novel MOFs were also successfully characterised and their properties were investigated for potential applications.

Stereospecific dehydroxyfluorination and the synthesis of trifluoro D-hexose sugar analogues

Bresciani, Stefano — 2011-06-22T00:00:00Z

Abstract: This thesis describes stereospecific fluorination reactions, and addresses the synthesis of fluorosugars. In Chapter 1, the influence of fluorine on the physical properties of organic molecules, as well as its stereoelectronic effects, are introduced. Furthermore, an overview of nucleophilic and electrophilic fluorination reactions is given. Chapter 2 describes the dehydroxyfluorination of allylic alcohol diastereoisomers 155a and 155b, which can proceed either by direct or allylic fluorination. The regio- and stereo- selectivities were also assessed. Chapter 3 outlines the synthesis of the novel trifluoro D-glucose analogue 193 and trifluoro D-altrose analogue 216. The transport of these hexose analogues across the red blood cell membranes was then explored, to investigate the influence of polarity versus hydrogen bonding ability in carbohydrate-protein interactions. Chapter 4 describes the development and optimisation of Bio’s methodology, to promote stereospecific dehydroxyfluorination of benzylic alcohols (R)-213 and (R)-227 by addition of TMS-amine additives 226 and 229. And finally Chapter 5 reports the experimental procedures as well as the characterisation and the crystallographic data of the molecules prepared in this thesis.

Continuous flow homogeneous hydroformylation of 1-octene over supported ionic liquid phase rhodium catalysts using supercritical CO₂

Gong, Zhenxin — 2011-01-01T00:00:00Z

Abstract: The hydroformylation of 1-octene with supported ionic liquid phase catalyst was demonstrated when using a system involving the substrate, reacting gases and products in CO₂ and N₂ flow over a fixed bed supported ionic liquid phase catalyst (silica gel and carbon aerogels as solid support respectively) at different system pressures. Yields, reaction rates, selectivities and rhodium leaching were all monitored. A pressure of CO₂ flow just below the critical point of the flowing mixture (106 bar at 100 °C if no 1-octene has been converted) was the best condition for the hydroformylation. It gave the highest acitivity (conversion to aldehyde up to 70 %), fastest reaction (TOF up to 575.3 h⁻¹) and best stable selectivity ( l:b ratio reaching 3.37 ). The utilization of scCO₂ as reaction media leads to remarkable stability of the catalyst. The supercritical or near critical (expanded liquid) system completely overcame the progressive decrease in activity of catalyst at 50, 75 bar with liquid phase transport and also showed much better results than when using other gas flows such as N₂ flow at 100 bar. In the high pressure scCO₂ phase, the concentration of 1-octene at the catalyst bed was reduced so that the conversion to aldehyde was reduced. The pore size and surface groups of the solid support should be suitable for the SILP catalyst consisting of metal complex, excess ligand and ionic liquid. Using microporous carbon aerogels as the supports, whether activated or not, gave disappointing results.

Hydrogen generation from alcohols catalyzed by ruthenium-triphenylphosphine complexes : multiple reaction pathways

Sieffert, Nicolas — 2010-06-16T00:00:00Z

Abstract: We report a comprehensive density functional theory (DFT) study of the mechanism of the methanol dehydrogenation reaction catalyzed by [RuH2(H2)(PPh3)3]. Using the B97-D dispersion-corrected functional, four pathways have been fully characterized, which differ in the way the critical beta-hydrogen transfer step is brought about (e.g., by prior dissociation of one PPh3 ligand). All these pathways are found to be competitive (Delta G double dagger = 27.0-32.1 kcal/mol at 150 degrees C) and strongly interlocked. The reaction can thus follow multiple reaction channels, a feature which is expected to be at the origin of the good kinetics of this system. Our results also point to the active role of PPh3 ligands, which undergo significant conformational changes as the reaction occurs, and provide insights into the role of the base, which acts as a "co-catalyst" by facilitating proton transfers within active species. Activation barriers decrease on going from methanol to ethanol and 2-propanol substrates, in accord with experiment.

Cu/Ce[subscript(x)]Zr[subscript(1-x)]O₂ catalysts for solid oxide fuel cell anodes

Kearney, Jonathan — 2010-06-01T00:00:00Z

Abstract: Ce[subscript(x)]Zr[subscript(1-x)]O₂ mixed oxides of varying compositions were prepared by a sol-gel citrate complexion technique. In order to improve the catalytic activity of the oxides they were impregnated with copper using two different impregnation techniques. The bare oxides and copper impregnated samples were investigated using a range of Temperature Programmed (TP) techniques, in an attempt to establish their effectiveness as anode materials for solid oxide fuel cells (SOFCs) run on hydrocarbon fuels. In order to conduct the TP experiments a novel system was designed and constructed. The high Ce containing mixed oxides were shown to be reduced at lower temperature than high Zr content samples. TPRx experiments were employed to investigate which of the oxides was most prone to carbon deposition when reacted in methane, with the high ceria sample displaying the lowest level of carbon deposition. Lightoff experiments were undertaken to establish which oxide composition was the most active for methane oxidation. The activity of the oxides increased with ceria content up to 75 mole% (ZCe75), before decreasing for ZCe90. All the mixed oxides were shown to be more active for methane oxidation than CeO₂.

Novel cambinol analogues as potential anticancer agents : an improved understanding of sirtuin isoform selectivity

Medda, Federico — 2011-06-22T00:00:00Z

Abstract: SIRT1 and SIRT2 are two NAD⁺-dependent deacetylases which negatively modulate the activity of p53, a protein which is involved in cell cycle arrest, senescence and apoptosis following genotoxic stress. Part I of the thesis describes the exploration of the chemical space around a reported unselective and modest inhibitor of SIRT1 and SIRT2 with the aim of improving the selectivity and potency of the inhibitor against the two isoforms. Particular emphasis is placed upon understanding the mode of binding of the novel analogues within the active site of the enzymes. Chapter 1 reviews the physiological roles of class III NAD⁺-dependent deacetylases, also known as sirtuins. In particular, the application of SIRT1 and SIRT2 inhibitors as potential anticancer agents is described. Amongst these, only cambinol and the tenovins showed in vivo activity in a mouse xenograft model. Previously only one analogue of cambinol had been reported in the literature. Chapter 2 describes the development of a small collection of novel cambinol analogues (First Generation Studies). The role played by different substituents at the phenyl group and at the N-1 of the thiouracil core is discussed. Along with the synthesis and structure activity relationship (SAR) associated with the core structure, in-cell experiments intended to confirm the activity of the most active compounds are reported. Chapter 3 provides a rationalisation for the SAR discussed in Chapter 2. Based on computational molecular modelling studies (GOLD), the activity of the most potent and selective SIRT2 inhibitors is explained. Two series of novel cambinol analogues were designed (Second and Third Generation Analogues) in order to assess further the proposed binding mode. Chapter 4 focuses on the development of the “Second Generation” analogues, characterised by the presence of lipophilic substituents at the sulfur atom and at the N-3 position of the thiouracil core. The synthesis, biological evaluation and SAR are discussed in detail. Chapter 5 reports the development of the “Third Generation” analogues, characterised by either a benzyl group or para-alkoxy-substituted benzyl group at the N-1 position of cambinol. Once again, the synthesis, biological evaluation and SAR data are presented. An improved understanding of the mode of binding of the novel compounds is proposed based on molecular dynamics (MD) studies. Indole-based alkaloids, such as Vincristine and Vinblastine, are well known for their anticancer activity. Recently, the anticancer activity of members of the calycanthaceous family of alkaloids has been discovered. Part II of the thesis focuses on model studies aimed at developing the total synthesis of one of these compounds, perophoramidine. Chapter 7 provides an overview of the calycanthaceous alkaloid family of natural products, including their biological properties. The structural features of perophoramidine, along with the previously reported synthetic studies are outlined. Chapter 8 describes the synthesis of an advanced intermediate in the total synthesis of dehaloperophoramidine, a structural analogue of perophoramidine Problems encountered, optimisation studies and the synthesis of a re-designed intermediate are also reported in this chapter.

A complementary study of perovskites : combining diffraction, solid-state NMR and first principles DFT calculations

Johnston, Karen Elizabeth — 2010-01-01T00:00:00Z

Abstract: Perovskites, ABX₃, and their associated solid-solutions are a particularly important and attractive area of research within materials chemistry. Owing to their structural and compositional flexibility and potential physical properties they are one of the largest classes of materials currently under investigation. This thesis is concerned with the synthesis and structural characterisation of several perovskite-based materials using a combined approach of high-resolution synchrotron X-ray and neutron powder diffraction (NPD), solid-state Nuclear Magnetic Resonance (NMR) and first-principles Density Functional Theory (DFT) calculations. Initial investigations concentrated on room temperature NaNbO₃, a perovskite widely debated in the literatue. Published crystallographic data indicate NaNbO₃ possesses two crystallographically distinct Na sites in space group Pbcm. Whilst some of our materials appear in agreement with this (notably a commercially purchased sample) many of our laboratory-synthesised samples of NaNbO₃ routinely comprise of two phases, which we show to be the antiferroelectric Pbcm and polar P2₁ma polymorphs. Several different synthetic methods were utilised during this investigation and the quantity of each phase present was found to vary as a function of preparative method. ²³Na, ⁹³Nb and ¹⁷O DFT calculations were used in conjunction with experiment to aid in spectral analysis, assignment and interpretation. In addition, ab initio random structure searching (AIRSS) was utilised in an attempt to predict the most stable phases of NaNbO₃. This proved to be both successful and highly informative. A series of NaNbO₃-related solid-solutions, namely K[subscript(x)]Na[subscript(1-x)]NbO₃ (KNN), Li[subscript(x)]Na[subscript(1-x)]NbO₃ (LNN) and Na[subscript(1-x)]Sr[subscript(x/2)]□[subscript(x/2)]NbO₃ (SNN) have also been synthesised and characterised. The substitution of K⁺ , Li⁺ and Sr²⁺ cations onto the A site appears to produce the same polar P2₁ma phase initially identified in the room temperature NaNbO₃ investigation. The abrupt change in cation size in the KNN and LNN series, and the introduction of vacancies in the SNN series, is thought to result in a structural distortion which, in turn, causes the formation of the P2₁ma phase. A low temperature synchrotron X-ray powder diffraction study (12 < T < 295 K) was completed for a sample of NaNbO₁ composed of the P2₁ma polymorph (~90%) and a small quantity of the Pbcm phase (~10%). A region of phase coexistence was identified between the P2₁ma, R3c and Pbcm phases over a relatively large temperature range. Full conversion of the P2₁ma phase to the low temperature R3c phase was not possible and, consistently, the P2₁ma phase was the most abundant phase present. Factors such as structural, strain, crystallite size and morphology are thought to be crucial in determining the exact phases of NaNbO₃ produced, both at low and room temperature. The solid-solution La[subscript(1-x)]Y[subscript(x)]ScO₃ was also investigated. Compositions x = 0, 0.2, 0.4, 0.6, 0.8 and 1 were successfully synthesised and characterised. Refined high-resolution NPD data indicates that an orthorhombic structure, in space group Pbnm, was retained throughout the solid-solution. Using ⁴⁵Sc and ⁸⁹Y MAS NMR each sample was found to exhibit disorder, believed to result from both a distribution of quadrupole and chemical shifts. NMR parameters were calculated for several model Sc and Y compounds using DFT methods to determine the feasibility and accuracy of ⁴⁵Sc and ⁸⁹Y DFT calculations. These proved successful and subsequent calculations were completed for the end members LaScO₃ and YScO₃. DFT calculations were also utilised to gain insight into the disorder exhibited in the La[subscript(1-x)]Y[subscript(x)]ScO₃ solid-solution.

Development of artificial metalloenzymes via covalent modification of proteins

Popa, Gina — 2010-01-01T00:00:00Z

Abstract: Development of selective artificial metalloenzymes by combining the biological concepts for selective recognition with those of transition metal catalysis has received much attention during the last decade. Targeting covalent incorporation of organometallic catalysts into proteins, we explored site-selective covalent coupling of phosphane and N–containing ligands. The successful approach for incorporation of phosphane ligands we report herein consists of site-specific covalent coupling of a maleimide functionalized hydrazide into proteins, followed by coupling of aldehyde functionalized phosphanes via a hydrazone linkage. Site selective incorporation of N–containing ligands was obtained by coupling maleimide functionalized N–ligands to proteins via Michael addition to the maleimide double bond. These two methods can be easily applied to virtually any protein displaying a single reactive cysteine and allows a wide range of possibilities in terms of cofactor design. Site-specific covalent incorporation of transition metal complexes of phosphane ligands into proteins was successfully obtained. The success of the approach is influenced by several factors like the metal precursor, the phosphane type and the protein scaffold. Metal complexes of 5–maleimido–1,10–phenanthroline modified proteins were formed in situ, via addition of a metal precursor to the phenanthroline modified proteins or by coupling preformed metal complexes to proteins via Michael addition of the thiol group from a cysteine residue to the maleimide double bond of the N-ligand. These successful coupling methods enable the use of a wide range of protein structures as templates for the preparation of artificial transition metalloenzymes, which opens the way to full exploration of the power of selective molecular recognition of proteins in transition metal catalysis.

Electric field gradients of transition metal complexes from density functional theory : assessment of functionals, geometries and basis sets

Bjornsson, Ragnar — 2010-06-01T00:00:00Z

Abstract: Electric field gradients (EFGs) were computed for the first-row transition metal nuclei in Cr(C6H6)(CO)(3), MnO3F, Mn(CO)(5)H, MnCp(CO)(3), Co(CO)(4)H, Co(CO)(3)(NO) and VCp(CO)(4), for which experimental gas-phase data (in form of nuclear quadrupole coupling constants) are available from microwave spectroscopy. A variety of exchange-correlation functionals were assessed, among which range-separated hybrids (such as CAM-B3LYP or LC-omega PBE) perform best, followed by global hybrids (such as B3LYP and PBE0) and gradient-corrected functionals (such as BP86). While large basis sets are required on the metal atom for converged EFGs, smaller basis sets can be employed on the ligands. In most cases, EFGs show little sensitivity toward the geometrical parameters.

Crystallization and preliminary diffraction analysis of Wzi, a member of the capsule export and assembly pathway in Escherichia coli

Bushell, Simon R. — 2010-12-01T00:00:00Z

Abstract: External polysaccharide capsules provide a physical barrier that is employed by many species of bacteria for the purposes of host evasion and persistence. Wzi is a 53 kDa outer membrane beta-barrel protein that is thought to play a role in the attachment of group 1 capsular polysaccharides to the cell surface. The purification and crystallization of an Escherichia coli homologue of Wzi is reported and diffraction data from native and selenomethionine-incorporated protein crystals are presented. Crystals of C-terminally His(6)-tagged Wzi diffracted to 2.8 A resolution. Data processing showed that the crystals belonged to the orthorhombic space group C222, with unit-cell parameters a = 128.8, b = 152.8, c = 94.4 A, alpha = beta = gamma = 90 degrees. A His-tagged selenomethionine-containing variant of Wzi has also been crystallized in the same space group and diffraction data have been recorded to 3.8 A resolution. Data processing shows that the variant crystal has similar unit-cell parameters to the native crystal. Description: Supported by a grant from The Wellcome Trust (081862/Z/06/Z)

cis-Dichloridobis(dimethoxyphenylphosphine)palladium(II)

Slawin, Alexandra M. Z. — 2010-03-01T00:00:00Z

Abstract: The title compound, [PdCl2(C8H11O2P)(2)], has a comparable structure to those of related palladium dichloride complexes containing trimethyl phosphinite and methyl diphenyl phosphinite. The Pd atom is located on a crystallographic twofold rotation axis: thus, there is just one half-molecule in the asymmetric unit. The structure is isomorphous with the platinum analogue cis-[PtCl2{P(OMe)(2)Ph}(2)].

1-(3-Phenylpropyl)urea

Li, Yang — 2009-10-01T00:00:00Z

Abstract: In the crystal of the title compound, C10H14N2O, double supramolecular layers of PhCH2CH2CH2NHC(O)NH2 are formed parallel to the bc plane by intermolecular N-H center dot center dot center dot O hydrogen bonding, with R-2(2)(8) and R-2(1)(6) motifs in the b- and c-axis directions, respectively. The mean plane of the C-ar-C-C group makes a dihedral angle of 84.8 (2)degrees with the benzene ring.

2,2 '-o-Phenylenediacetonitrile

Li, Yang — 2009-11-01T00:00:00Z

Abstract: In the title compound, NCCH2C6H4CH2CN, the bond lengths and angles are within normal ranges. The benzene ring makes dihedral angles of 4.94 (8) and 77.04 (8)degrees with the C-C-C-N mean planes. Weak non-conventional C-H center dot center dot center dot N hydrogen bonds are effective in the stabilization of the crystal structure. The weak C-H center dot center dot center dot N contacts form antiparallel chains running in the a + c direction, and ring systems with two N-atom acceptors and four H-atom donors.

Bis(phenylphosphonic) anhydride

Li, Yang — 2009-11-01T00:00:00Z

Abstract: The asymmetric unit of the title compound, C12H12O5P2, contains four independent molecules, generating two dimers via pairs of intermolecular O-H center dot center dot center dot O hydrogen bonds, forming R-2(2) (8) rings. The two aryl rings of each molecule form dihedral angles of 108.6 (1), 103.2 (1), 12.5 (2) and 8.1 (2)degrees in the four molecules.

cis-Dichloridobis(triisopropoxyphosphine)platinum(II)

Slawin, Alexandra M. Z. — 2009-11-01T00:00:00Z

Abstract: The title compound, [PtCl2(C9H21O3P)(2)], was obtained from a solution of PtCl2(COD) ( COD = 1,5-cyclooctadiene) and triisopropylphosphite in dichloromethane. The complex features a Pt(II) atom coordinated by two Cl and two P atoms, yielding a slightly distorted cis square-planar geometry.

cis-Dichloridobis(trimethoxyphosphine)palladium(II) at 125 K

Slawin, Alexandra M. Z. — 2009-11-01T00:00:00Z

Abstract: The title compound, [PdCl2(C3H9O3P)(2)], which is isotypic with its platinum analogue, adopts a slightly distorted cis square-planar geometry for the Pd centre.

Tris(ethylenediamine)zinc(II) hexafluoridosilicate

Li, Yang — 2009-12-01T00:00:00Z

Abstract: The title compound, [Zn(C2H8N2)(3)](SiF6), was synthesized ionothermally using choline chloride-imidazolidone as solvent and template provider. In the crystal structure, the anions and cations are located on special positions of site symmetry 3.2 and show a typical octahedral geometry. The Zn-II ion is coordinated by six N atoms from three ethylenediamine molecules. The crystal structure displays weak hydrogen bonding between [SiF6](2-) anions and the ethylenediamine NH hydrogen atoms.

Selenocarbonyl synthesis using Woollins Reagent

Bhattacharyya, Pravat — 2001-08-20T00:00:00Z

Abstract: [PhP(Se)(mu -Se)](2) selenates secondary and tertiary amides to the corresponding selenoamides in 30-70% yields at 130 degreesC in toluene and indolizine-3-aldehydes to selenoaldehydes in 40-59% yield at 25 degreesC. (C) 2001 Elsevier Science Ltd. All rights reserved.

1,2-Bis(2-bromobenzyl)diselane

Hua, Guoxiong — 2010-10-01T00:00:00Z

Abstract: In the title compound, C14H12Br2Se2, the Se-Se bond length [2.3034 (9) angstrom] is similar to those in diphenyl diselenide [2.3066 (7) and 2.3073 (10) angstrom] and shorter than that in 1,8-diselenonaphthalene [2.0879 (8) angstrom]. The molecule adopts a classical gauche conformation.

Di-mu-chlorido-bis[chlorido(dimethoxyphenylphosphine)palladium(II)]

Slawin, Alexandra M. Z. — 2010-05-01T00:00:00Z

Abstract: The title compound, [Pd2Cl4(C8H11O2P)(2)], is binuclear and disposed about a crystallographic centre of symmetry with a Pd center dot center dot center dot Pd distance of 3.4662 (17) angstrom. It has a similar geometry to that observed in the triphenylphosphite and triphenylphosphine analogues. The Pd-P bond length is ca 0.04 angstrom shorter than those in mononuclear PdCl2(P(OMe)(2)Ph)(2), possibly due to the lower trans-influence of the bridging Cl- compared to a single-bonded Cl- atom.

(Disulfur dinitrido)triphenylantimony(V)

Slawin, Alexandra M. Z. — 2010-04-01T00:00:00Z

Abstract: The title compound, [Sb(C6H5)(3)(N2S2)], contains a molecular entity that is very similar to that of the known polymorph of Sb(S2N2)Ph-3 [Kunkel et al. (1997). Z. Naturforsch. Teil B, 52, 193-198], differing only in the orientation of the phenyl rings. The bond order in the SNSN unit is S-N=S=N, consisting of one long S-N bond, an intermediate length N=S bond and a short S=N bond.

Synthesis of novel 2,5-diarylselenophenes from selenation of 1,4-diarylbutane-1,4-diones or methanol/arylacetylenes

Hua, Guoxiong — 2010-04-07T00:00:00Z

Abstract: Reaction of 2,4-bis(phenyl)-1,3-diselenadiphosphetane-2,4-diselenide [PhP(Se)(mu-Se)](2) (Woollins' reagent, WR) with one equivalent of 1,4-diarylbutane-1,4-diones 1a-g in refluxing toluene affords the corresponding 2,5-diarylselenophenes 2a-g in excellent yields (up to 99%). Alternatively, the 2,5-diarylselenophenes (2a and 2b) can be obtained in 70-80% yields from the reaction of arylacetylene with an equivalent of O-methyl Se-hydrogen phenylphosphonodiselenoate; the latter was derived from WR and methanol. The first X-ray structure of 2,5-diarylselenophenes is presented along with characterisation of their redox properties.

From phenylalkylcyanamides to heterocyclic selenazadiphospholaminediselenides and carbamidoyl(phenyl) phosphinodiselenoic acids

Hua, Guoxiong — 2008-11-01T00:00:00Z

Abstract: The reaction of 2,4-bis(phenyl)-1,3-diselenadiphosphetane-2,4- diselenide (Woollins' Reagent, WR) with phenylalkyl-cyanamides (RR'NC N, R = PhCH2CH2, R' = CH3 and R = PhCH2CH2CH2, R' = H) in refluxing toluene led to novel heterocyclic selenazadiphospholaminediselenides 1 and 2 (43% and 42% yields), the latter being hydrolyzed to the unusual zwitterionic carbamidoyl(phenyl) phosphinodiselenoic acids 3 and 4 in excellent yields (96% and 98%).

Automated chemical crystallography

Fuller, Amy — 2010-04-28T00:00:00Z

Abstract: The first fully automated small-molecule robotic X-ray diffractometer is described. After demonstrating the utility of the instrument using multiple samples of ammonium bitartrate, we investigated the conformational chirality of diphenyl dichalcogenide (E2Ph2, where E = S, Se, or Te). Structural and computational studies suggest that the two enantiomers are energetically indistinguishable. Therefore, it was unsurprising that we found (in 35 suitable data collections) the proportion 0.51:0.49 of M-S2Ph2 to P-S2Ph2 in the bulk sample. Interestingly, after 65 data collections of Te2Ph2, (46 provided suitable data sets), we found the proportion 0.72 +/- 0.13 of M-Te2Ph2, suggesting there could be a statistically significant preference for the M-enantiomer in the sample examined here. We found that Se2Ph2 underwent homochiral crystallization, with all 24 crystals being M. Our experiments may represent a salutary lesson in statistical analysis.

Synthesis and X-ray structures of new phosphorus-selenium heterocycles with an E-P(Se)-E ' (E, E ' = N, S, Se) linkage

Hua, Guoxiong — 2010-08-01T00:00:00Z

Abstract: Refluxing a toluene solution of Woollins' reagent, WR, with difunctional aromatic substrates (aryldiamines and aryldithiols) leads to a series of novel five-to seven-membered heterocycles 2a-e, 4a, 4b and 6a-c with an E-P(Se)-E' (E, E' = N, S, Se) linkage in 7-98% isolated yields. This method offers a new approach to the library of phosphorus-selenium heterocyclic compounds. All new compounds have been characterized by IR, H-1, C-13, P-31, Se-77 NMR, mass spectrometry and elemental analysis or accurate mass measurement. Four representative X-ray structures are reported.

Five-membered arsenic-sulfur-nitrogen heterocycles, RAs(S2N2) (R = Me, Et, iPr, tBu, Ph, Mes)

Matuska, Vit — 2010-03-15T00:00:00Z

Abstract: A series of 5-alkyl/aryl-1,3 lambda(4)delta(2),2,4,5-dithiadiazarsoles RAs(S2N2) (R = Me, Et, Pr-i, Bu-t, Ph, Mes) were prepared by a ligand exchange between [(Bu2Sn)-Bu-n(S2N2)](2) and the corresponding organodihalogenoarsines RAsX2 (X = Cl, I). All products were characterized by NMR, IR, and Raman spectroscopies and mass spectrometry. The crystal structures of the aryldithiadiazarsoles (R = Ph, Mes) were determined.

Synthesis and structural study of (8-phenylsulfanylnaphth-1-yl)diphenylphosphine metal complexes

Knight, Fergus R. — 2010-05-27T00:00:00Z

Abstract: A series of three platinum(II) halide complexes 2-4 [Pt(X)(2)(Nap(PPh2)(SPh))] (Nap = naphthalene-1,8-diyl: X = Cl, Br, I) and a ruthenium(II) p-cymene complex 5 [Ru(eta(6)-(MeC6H4Pr)-Pr-i)(Cl){Nap(PPh2)(SPh)}]Cl-+(-) of the sterically crowded pen-substituted naphthalene phosphine 1 have been prepared. The compounds were fully characterised by multinuclear NMR. IR and MS and X-ray data for 1-5 are compared. Molecular structures are analysed by naphthalene ring torsions, pert-atom displacement, splay angle magnitude, P center dot center dot center dot S interactions, aromatic ring orientations and geometry around the metal centre. Platinum adopts a strictly square planar geometry which increases the distortion of the naphthalene skeleton in 2-4. Conversely, the classical-piano stool conformation of 5 results in a pseudo-octahedral conformation around the ruthenium atom which influences the naphthalene geometry to a much lesser extent with distortion of a similar magnitude to the free ligand 1. (c) 2010 Elsevier Ltd. All rights reserved.

Preparation and compounds of (8-methoxynaphth-1-yl)diphenylphosphine

Knight, Fergus R. — 2010-05-10T00:00:00Z

Abstract: Reaction of 8-methoxy-1-naphthyllithium (2) with one equivalent of chlorodiphenylphosphine gives the novel (8-methoxynaphth-1-yl)diphenylphosphine (3) which was oxidised to the corresponding sulfide (4) and selenide (5) by reaction with sulfur and selenium, respectively. The P center dot center dot center dot O peri distance is significantly increased in 4 and 5 at 2.819(3)[2.793(3)] and 2.827(3) [2.806(3)] angstrom [values in square brackets are for the second independent molecules in each case] relative to the value in 3 of 2.678(2) angstrom. There are short E center dot center dot center dot O interactions ie O(1)center dot center dot center dot S(1) 3.165(3) [3.124(3)], 0(1)center dot center dot center dot Se(1) 3.247(3) [3.200(2)] angstrom and these may be repulsive and responsible for the increased P center dot center dot center dot O separation. The use of the naphthalene backbone in the synthesis of a potential hemilabile ligand is demonstrated by the synthesis and X-ray structure of (8-methoxynaphth-1-yl)diethoxyphosphine ruthenium p-cymene dichloride (6). (C) 2010 Elsevier Ltd. All rights reserved.

Controlling Cu•••Cu distances using halides: (8-phenylthionaphth-1-yl)diphenylphosphine copper halide dimers

Knight, Fergus R. — 2009-01-01T00:00:00Z

Abstract: In the isomorphous binuclear Cu2X2L2 systems (L = (8-phenylthionaphth-1-yl)diphenylphosphine the Cu center dot center dot center dot Cu separation is reduced as the halide size increases.

V-51 NMR chemical shifts calculated from QM/MM models of peroxo forms of vanadium haloperoxidases

Geethalakshmi, K. R. — 2009-04-02T00:00:00Z

Abstract: QM/MM models of the peroxo forms of vanadium-containing haloperoxidases (VHPOs) are critically assessed in terms of active site geometries, hydrogen bonds within the active site, isotropic and anisotropic V-51 NMR chemical shifts, and TD-DFT excitation energies. The geometric stability within the active site of the protein is comparable to the respective native forms, as indicated by low standard deviations in bond lengths across a number of local minima sampled along MID trajectories. There is a significant calculated upfield shift in delta(V-51) upon formation of the peroxo from the respective native forms for both the vanadium-containing chloroperoxidase (VCPO) and vanadium-containing bromoperoxidase (VBPO) models, which is in qualitative agreement with V-51 NMR experiments of VBPO in solution. The models show appreciable differences between the anisotropic chemical shifts of the different protonation states of the peroxo form of VHPO. The most likely candidates for the peroxo forms of the VHPO enzymes appear to be unprotonated or have a single proton on either of the equatorial oxygen ligands, based on QM/MM modeling in combination with X-ray, V-51 NMR, and UV-vis data.

Geometries of third-row transition-metal complexes from density-functional theory

Buehl, Michael — 2008-09-01T00:00:00Z

Abstract: A set of 41 metal-ligand bond distances in 25 third-row transition-metal complexes, for which precise structural data are known in the gas phase, is used to assess optimized and zero-point averaged geometries obtained from DFT computations with various exchange-correlation functionals and basis sets. For a given functional (except LSDA) Stuttgart-type quasi-relativistic effective core potentials and an all-electron scalar relativistic approach (ZORA) tend to produce very similar geometries. In contrast to the lighter congeners, LSDA affords reasonably accurate geometries of 5d-metal complexes, as it is among the functionals with the lowest mean and standard deviations from experiment. For this set the ranking of some other popular density functionals, ordered according to decreasing standard deviation, is BLYP > VSXC > BP86 approximate to BPW91 approximate to TPSS approximate to B3LYP approximate to PBE > TPSSh > B3PW91 approximate to B3P86 approximate to PBE hybrid. In this case hybrid functionals are superior to their nonhybrid variants. In addition, we have reinvestigated the previous test sets for 3d- (Buhl M.; Kabrede, H. J. Chem. Theory Comput. 2006, 2, 1282-1290) and 4d- (Waller, M. P.; Buhl, M. J. Comput. Chem. 2007,28,1531-1537) transition-metal complexes using all-electron scalar relativistic DFT calculations in addition to the published nonrelativistic and ECP results. For this combined test set comprising first-, second-, and third-row metal complexes, B3P86 and PBE hybrid are indicated to perform best. A remarkably consistent standard deviation of around 2 pm in metal-ligand bond distances is achieved over the entire set of d-block elements.

Noncovalent interactions in a transition-metal triphenylphosphine complex : a density functional case study

Sieffert, Nicolas — 2009-06-01T00:00:00Z

Abstract: The binding enthalpy of a triphenylphosphine ligand in Ru(CO)Cl (PPh3)3(CH=CHPh) is studied with "standard" (BP86 and B3LYP), dispersion-corrected (B3LYP-D and B97-D), and highly parametrized (M05 and M06 series) density functionals. An appropriate treatment of noncovalent interactions is mandatory because these turn out to account for a large fraction of the metal-ligand interaction energy. Among the tested methods, B97-D and the M06 series of functionals best reproduce the experimental binding enthalpy value of Sponsler et al. (Inorg. Chem. 2007, 46, 561).

Structure and stability of aquotetrafluorouranyl(VI) in the solid state - Density functional study of [UO2F4(H2O)][NMe4]2·2H2O1,2

Buehl, Michael — 2009-07-01T00:00:00Z

Abstract: Periodic density functional computations have been performed for solid [UO2F4(H2O)][NMe4]2·2H(2)O at the BLYP level. A model with disordered fluoro and aquo ligands in the uranyl anion is significantly lower in energy than one with a symmetrical assignment of these sites, which was favored in the original X-ray crystallography study. According to optimized energies and Car-Parrinello molecular dynamics (CPMD) simulations, the [UO2F4(H2O)]2- ion in the solid is stable with respect to loss of the coordinated water molecule. In contrast, CPMD simulations had found this ligand to be unbound in aqueous solution. The role of the counterions in stabilizing the higher coordination number in the crystal is discussed.

Dodeka(ethylene)octamine

Buehl, Michael — 2011-03-21T00:00:00Z

Effect of counterions on the structure and stability of aqueous uranyl(VI) complexes. A first-principles molecular dynamics study

Buehl, Michael — 2009-11-02T00:00:00Z

Abstract: The inclusion of NH4+ as counterions in Car-Parrinello molecular dynamics (CPMD) simulations of anionic uranyl(VI) complexes is proposed as a viable approach to modeling "real" aqueous solutions. For [UO2F4(H2O)](2-) in water, it is shown that the inclusion of two NH4+ ions strengthens the bond between uranyl and the water ligand by ca. 2 kcal/mol, improving the accordance with experiment. According to CPMD simulations for [UO2X5]-[NH4](3) (X = F, OH) in water, the fifth fluoride is bound much stronger than the fifth OH-. Implications for a recently proposed model for oxygen exchange in uranyl hydroxide are discussed.

Oxygen exchange in uranyl hydroxide via two "nonclassical" ions

Buehl, Michael — 2010-04-19T00:00:00Z

Abstract: A recently proposed pathway for the scrambling of axial (uranyl) and equatorial 0 atoms in [UO2(OH)4]2- (1) is refined using Car-Parrinello molecular dynamics (CPMD) simulations in an explicit solvent (water) and with model counterions (NH4+). According to constrained CPMD/BLYP simulations and thermodynamic integration, 1 can be deprotonated to [UO3(OH)3]3- with a T-shaped UO3 group (Delta A = 7.1 kcal/mol), which in turn can undergo a solvent-assisted proton transfer via a cis-[UO2(OH)4]2-center dot OH- complex and a total overall barrier of Delta A(double dagger) = 12.5 kcal/mol. According to computed relative energies of trans- and cis-[UO2(OH)4]2- in the gas phase and in a polarizable continuum, "pure" functionals such as BLYP underestimate this overall barrier somewhat, and estimates of Delta A(double dagger) approximate to 16 and 17 kcal/mol are obtained at the B3LYP and CCSD(T) levels, respectively, in excellent agreement with the experiment.

Adsorption of adenine and phenylglycine on Cu(110) surfaces studied using STM and RAIRS

Cheng, Lanxia — 2010-11-19T00:00:00Z

Abstract: The adsorption of biologically active molecules, such as the DNA bases, amino acids, on solid surfaces has been the subject of a number of experimental and theoretical studies in the past years. The understanding of the self-assembly mechanism of bioactive molecules on surfaces not only is fundamentally important in the preparation of bioactive surfaces, but also provides us insight into the origins of life and homo-chirality in nature. In this thesis, the adsorption behaviour of adenine and phenylglycine molecules on the Cu(110) surface has been investigated in order to understand the effect of experimental parameters like coverage, annealing temperature etc. on the molecular orientation and the ordering of the adlayer structures. The thesis is organised in six parts: Chapter I gives an introduction to the relevance of surface sciences studies, describing the phenomena of surface chirality and molecular adsorption behaviours on surfaces. Chapter II gives an overview of the experimental techniques and introduces basic concepts of theoretical calculation. Chapter III investigates the effect of experimental parameters, e.g. surface coverage, annealing temperature and substrate temperature on molecular diffusion, molecular orientation and ordering of the adlayer structures. LT-STM examination of the contrast variations of adenine chains and isolated adsorbate as a function of the tip-sample bias voltage is also presented with the aim to understand the tunnelling mechanism. Chapter IV shows RAIR spectra studies of the evolution of phenylglycine molecular orientation as a function of surface coverage at room temperature. The adsorption geometry and binding nature of phenylglycine is discussed. Chapter V concerns with the adsorption behaviours of phenylglycine and adenine on Cu(110) surface pre-covered with oxygen. Chapter VI summarises the conclusions and describes the outlook of some future work.

Synthesis and characterisation of materials for photoelectrochemical applications

Randorn, Chamnan — 2010-01-01T00:00:00Z

Abstract: The preparation of visible light driven photocatalysts for photocatalytic water splitting has been achieved by a CO₂ free, low cost and simple novel method. Combination of peroxide based route with organic free solvent and titanium nitride, carbon free precursor and air and moisture stable, would be useful. Clear red-brown solution of titanium peroxo species was obtained by dissolution of TiN in H₂O₂ and HNO₃ acid at room temperature without stirring. The resultant red brown solution is then used as a titanium solution precursor for yellow amorphous and yellow crystalline TiO₂ synthesis. Visible light photoactivity of the samples was evaluated by photooxidation of methylene blue and photoreduction producing hydrogen from water splitting. The high surface area of yellow amorphous TiO₂ exhibits an interesting property of being both surface adsorbent and photoactive under visible light for photodecolourisation of aqueous solution of methylene blue. However, it might not appropriate for hydrogen production. Nanoparticulate yellow crystalline TiO₂ with defect disorder of Ti³⁺ and oxygen vacancies depending upon synthesis conditions has been characterised by ESR, XPS, CHN analysis and SQUID. Single phase rutile can be produced at low temperature. It is stable at high temperature and the red shift of absorption edge increases with the treatment temperature. Yellow crystalline TiO₂ exhibits an interesting property of being photoactive under visible light. The best photocatalytic performance was observed for 600°C calcination, probably reflecting a compromise between red shift and surface area with changing temperature. Moreover, overall water splitting into hydrogen and oxygen might be obtained by using this material even in air atmosphere. Photoactivity can be improved by testing under anaerobic atmosphere and/or adding sacrificial agent. Quantum efficiency under visible light is still low but comparable to other reports. The maximum efficiency varies from 0.03 % to 0.37 % for hydrogen production and from 0.03 % to 0.12 % for oxygen production, depending on photon energy and sacrificial agents.

Applications of ordered mesoporous metal oxides : energy storage, adsorption, and catalysis

Ren, Yu — 2010-11-30T00:00:00Z

Abstract: The experimental data and results demonstrated here illustrate the preparation and application of mesoporous metal oxides in energy storage, adsorption, and catalysis. First, a new method of controlling the pore size and wall thickness of mesoporous silica was developed by controlling the calcination temperature. A series of such silica were used as hard templates to prepare the mesoporous metal oxide Co₃O₄. Using other methods, such as varying the silica template hydrothermal treatment temperature, using colloid silica, varying the materials ratio etc., a series of mesoporous β-MnO₂ with different pore size and wall thickness were prepared. By using these materials it has been possible to explore the influence of pore size and wall thickness on the rate of lithium intercalation into mesoporous electrode. There is intense interest in lithium intercalation into titanates due to their potential advantages (safety, rate) replacing graphite for new generation Li-ion battery. After the preparation of an ordered 3D mesoporous anatase the lithium intercalation as anode material has been investigated. To the best of our knowledge, there are no reports of ordered crystalline mesoporous metal oxides with microporous walls. Here, for the first time, the preparation and characterization of three dimensional ordered crystalline mesoporous α-MnO₂ with microporous wall was described, in which K+ and KIT-6 mesoporous silica act to template the micropores and mesopores, respectively. It was used as a cathode material for Li-ion battery. Its adsorption behavior and magnetic property was also surveyed. Following this we described the preparation and characterization of mesoporous CuO and reduced Cu[subscript(x)]O, and demonstrated their application in NO adsorption and delivery. Finally a series of crystalline mesoporous metal oxides were prepared and evaluated as catalysts for the CO oxidation.

Synthesis and stereochemical assignment of (+)-chamuvarinin

Florence, Gordon John — 2011-02-04T00:00:00Z

Abstract: A stereocontrolled total synthesis of (+)-chamuvarinin, isolated from the root extract of Uvaria Chamae, utilizes a convergent modular strategy to construct the adjacently linked C15−C28 ether array, followed by a late-stage Julia−Kocienski olefination to append the butenolide motif. This constitutes the first total synthesis of (+)-chamuvarinin, defining the relative and absolute configuration of this unique annonaceous acetogenin. Description: Supported by grants from EPSRC (EP/F011458/1) and The Wellcome Trust (086658).

1,5,6-Triphenyl-8-oxa-7-selena-6-phosphabicyclo[3.2.1]octane-6-selone

Hua, Guoxiong — 2008-01-01T00:00:00Z

Abstract: The structure of the title compound, C23H21OPSe2, consists of fused puckered five- and six-membered rings, PSeC2O and C5O, respectively, with a C2O bridgehead. The C5O ring adopts a chair conformation, whilst the C2PSeO ring has an envelope conformation.

Substituent effects on Ni-61 NMR chemical shifts

Buehl, Michael — 2009-01-01T00:00:00Z

Abstract: Ni-61 chemical shifts of Ni(all-trans-cdt) L (cdt = cyclododecatriene, L = none, CO, PMe3), Ni(CO)(4), Ni(C2H4)(2)(PMe3), Ni(cod)(2) (cod = cyclooctadiene) and Ni(PX3)(4) (X = Me, F, Cl) are computed at the GIAO (gauge-including atomic orbitals), BPW91, B3LYP and BHandHLYP levels, using BP86-optimised geometries and an indirect referencing scheme. For this set of compounds, substituent effects on delta(Ni-61) are better described with hybrid functionals than with the pure BPW91 functional. On going from Ni(all-trans-cdt) to Ni(all-cis-cdt) the computations predict substantial shielding of the Ni-61 nucleus by nearly 700 ppm, as well as a sharp increase of the electric field gradient at this position. The latter result is predicted to afford an undetectably broad Ni-61 NMR line for the all-cis-cdt complex, rationalizing the apparent failure to record the NMR spectrum experimentally.

The crystal structure of the Y140F mutant of ADP-L-glycero-D-manno-heptose 6-epimerase bound to ADP-beta-D-mannose suggests a one base mechanism

Kowatz, Thomas — 2010-07-01T00:00:00Z

Abstract: Bacteria synthesize a wide array of unusual carbohydrate molecules, which they use in a variety of ways. The carbohydrate L-glycero-D-manno-heptose is an important component of lipopolysaccharide and is synthesized in a complex series of enzymatic steps. One step involves the epimerization at the C6 '' position converting ADP-D-glycero-D-manno-heptose into ADP-L-glycero-D-manno-heptose. The enzyme responsible is a member of the short chain dehydrogenase superfamily, known as ADP-L-glycero-D-manno-heptose 6-epimerase (AGME). The structure of the enzyme was known but the arrangement of the catalytic site with respect to the substrate is unclear. We now report the structure of AGME bound to a substrate mimic, ADP-beta-D-mannose, which has the same stereochemical configuration as the substrate. The complex identifies the key residues and allows mechanistic insight into this novel enzyme. Description: Supported by Wellcome Trust grant 081862/Z/06/Z

Nuclear magnetic resonance spectroscopy and computational methods for the characterization of materials in solution and the solid state

Carnevale, Diego — 2010-01-01T00:00:00Z

Abstract: Nuclear Magnetic Resonance (NMR) and computational methods increasingly play a predominant and indispensable role in modern chemical research. The insights into the local nuclear environment that NMR can provide is unique information which allows the structural characterization of novel materials, as well as the understanding and explanation of their relevant properties on an atomic scale. Computational methods, on the other hand, can be used to support experimental findings, providing a rigorous theoretical basis. Furthermore, when more complex chemical systems are considered, calculations can prove to be invaluable for the interpretation of experimental data and often allow an otherwise impossible spectral assignment. This thesis presents a series of studies in which NMR spectroscopy, in combination with computational methods, is utilized to investigate a variety of chemical systems both in solution and the solid state. An overview of the thesis and experimental and computational details are given in Chapter 1. In Chapter 2, the quantum mechanical basis necessary for the description of the NMR phenomenon is presented. Chapter 3 explores the main experimental techniques employed routinely for the acquisition of NMR spectra in both solution and the solid state. Chapter 4 describes the main features of density functional theory (DFT) and its implementation in computational methods for the calculation of relevant NMR parameters. Chapter 5 reports an experimental solution-phase NMR study and a parallel computational investigation of the poly(CTFE-co-EVE) fluoropolymer. In Chapter 6, the combination of [superscript(14/15)]N solution-phase NMR techniques and DFT methods for the study of alkylammonium cationic templates used in the synthesis of microporous materials is presented. The characterization of a boroxoaromatic compound in the solid state and the study of its reactivity are described in Chapter 7. In Chapter 8, two experimental NMR methods for the study of the anisotropic chemical shift interaction in the solid state are compared and used to characterize a range of materials. Cross-polarization and nutation of quadrupolar nuclei are computationally investigated under both static and spinning conditions in Chapter 9. A general conclusion and a summary are given in Chapter 10.

Novel electrocatalytic membrane for ammonia synthesis

Klinsrisuk, Sujitra — 2010-01-01T00:00:00Z

Abstract: Novel ceramic membrane cells of BaCe₀.₅Zr₀.₃Y₀.₁₆Zn₀.₀₄O[subscript(3-δ)] (BCZYZ), a proton-conducting oxide, have been developed for electrocatalytic ammonia synthesis. Unlike the industrial Haber-Bosch process, in this work an attempt to synthesise ammonia at atmospheric pressure has been made. The membrane cell fabricated by tape casting and solution impregnation comprises of a 200 μm-thick BCZYZ electrolyte and impregnated electrode composites. Electrocatalysts for anode and cathode were investigated. For the anode, the co-impregnation of Ni and CeO₂ provided excellent electrode performance including high catalytic activity, sintering stability and compatibility with the BCZYZ electrolyte. The best composition was the mixture of 25 wt% NiO and 10 wt% CeO₂. A symmetrical cell prepared with this electrode composition revealed low polarisation resistances of 1.0 and 0.45 Ωcm² in humidified 5% H₂/Ar at 400 and 500 °C, respectively. For the cathode, 25 wt% of impregnated Fe oxide provided a satisfactory performance in non-humidified N₂ atmosphere. Significant amounts of ammonia were produced from the single cell with Ni-CeO₂ anode and Fe oxide cathode at 400-500 °C under atmospheric pressure. Ammonia formation rate was enhanced by Pd catalyst addition and electrochemical performance was improved by Ru addition. The highest ammonia formation rate of 4 x 10⁻⁹ mols⁻¹cm⁻² was attained using the cell with a Pd-modified Fe cathode at 450 °C. The formation reaction of ammonia typically consumed around 1-2.5 % of total applied current while most of the applied current was employed in H⁺ reduction. The total current efficiency of around 90-100 % could be obtained from the membrane cells. Description: Electronic version does not contain associated previously published material

TarO : a target optimisation system for structural biology

Overton, I M — 2008-07-01T00:00:00Z

Abstract: TarO (http://www.compbio.dundee.ac.uk/taro) offers a single point of reference for key bioinformatics analyses relevant to selecting proteins or domains for study by structural biology techniques. The protein sequence is analysed by 17 algorithms and compared to 8 databases. TarO gathers putative homologues, including orthologues, and then obtains predictions of properties for these sequences including crystallisation propensity, protein disorder and post-translational modifications. Analyses are run on a high-performance computing cluster, the results integrated, stored in a database and accessed through a web-based user interface. Output is in tabulated format and in the form of an annotated multiple sequence alignment (MSA) that may be edited interactively in the program Jalview. TarO also simplifies the gathering of additional annotations via the Distributed Annotation System, both from the MSA in Jalview and through links to Dasty2. Routes to other information gateways are included, for example to relevant pages from UniProt, COG and the Conserved Domains Database. Open access to TarO is available from a guest account with private accounts for academic use available on request. Future development of TarO will include further analysis steps and integration with the Protein Information Management System (PIMS), a sister project in the BBSRC Structural Proteomics of Rational Targets initiative. Description: This work was funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC) Structural Proteomics of Rational Targets (SPoRT) initiative, (Grant BBS/B/14434). Funding to pay the Open Access publication charges for this article was provided by BBSRC.

Studies in cyclic ether synthesis: Part one: Domino cyclisations to cyclic ethers -- Part two: Synthetic studies towards neopeltolide

Cadou, Romain F. — 2010-11-01T00:00:00Z

Abstract: Tetrahydrofuran (THF) and tetrahydropyran (THP) rings are commonly found in a wide range of natural products and biologically active compounds. In total synthesis, the formation of THF/THP motifs is often the key step but existing methods often involve numerous steps and low overall efficiencies. Part one of this thesis details the development of a practical method for the synthesis of THF rings by the controlled mono-addition/cyclisation of organolithium species to C2-symmetric diepoxides (Scheme A-1). This method can also be applied to the synthesis of bis-THF rings from triepoxides and has potential applications in more complex cascade reactions. A similar cyclisation process providing THF rings from epoxyaldehydes is also described.Part two of this thesis details our efforts towards the synthesis of the marine macrolide neopeltolide. Wright and co-workers reported the isolation of neopeltolide 211 from a deep-water sponge of the family neopeltidae off the north coast of Jamaica. The structure, which was assigned by NMR and HRMS studies and reassigned by total synthesis, contains a 14-membered macrolactone, a 2,6-cis THP ring and an unsaturated oxazole side-chain. Chapter four describes the synthesis of the C2-C8 and C9-C16 fragments (Scheme A-2). Chapter five details our initial attempts in the coupling of subunits 268 and 320, as well as a revised synthetic strategy that allowed us to successfully couple C2-C9 alkyne 347 with C10-C16 aldehyde 348 and the preparation of an advanced intermediate 364 (Scheme A-3).

Synthesis and characterisation of ordered mesoporous materials

Dougherty, Troy Allen — 2010-06-23T00:00:00Z

Abstract: Ordered mesoporous materials have attracted much attention recently for use in a wide range of applications. The oxidising materials, ceria (CeO₂) and CGO (Ce₀.₉Gd₀.₁O[subscript(2-δ)]) have both been synthesised with ordered mesopores, but a method for the simple fabrication of these materials in high yields with crystalline pore walls has not yet been reported in the literature. This thesis details the development of the vacuum impregnation method for the synthesis of ordered mesoporous materials with emphasis on ceria and CGO. Using the vacuum impregnation method both materials were successfully prepared. The materials exhibited the porous single crystal morphology in high yields, with unusual crystallographic features. Nitrogen physisorption, transmission electron microscopy (TEM), TEM tomography and temperature programmed studies were employed. Temperature programmed studies showed the materials to be catalytically active at lower temperatures than traditionally-prepared ceria. Photovoltaic studies showed that the materials exhibited efficient exciton quenching. The observation of nanowire extrusion during the synthetic procedure assisted in the postulation of a mechanism for product formation in the vacuum impregnation method. The vacuum impregnation method was subsequently shown to be applicable to the synthesis of other materials, with encouraging results presented for ordered mesoporous carbon and Zr₀.₈₄Y₀.₁₆O[subscript(2-δ)]. The syntheses of ordered mesoporous La₀.₈₅Sr₀.₁₅GaO[subscript(3-δ)] and La₀.₇₆Sr₀.₁₉CoO[subscript(3-δ)] were unsuccessful.

Pd catalysed C-C & C-O bond formation using bis-(dialkyl/diarylphosphino)ferrocene ligands

Milton, Edward J. — 2010-06-23T00:00:00Z

Abstract: A brief introduction explaining phosphine ligand properties, Pd catalysed cross-coupling reactions; the importance of the steps involved in the catalytic cycle (oxidative addition, transmetalation & reductive elimination), mechanistic studies and a comparison of various reactions will give an overview of important cross-coupling reactions and their limitations.The development of a “super-concentrated” (5M) Pd catalysed Kumada type coupling reaction has been developed for coupling a range of aryl bromide and chloride substrates with the Grignard reagents ((p-CF₃-C₆H₄)MgBr)) and PhMgBr in methyl-tetrahydrofuran (Me-THF). Using a range of bidentate ligands such as bis-phosphinoferrocenyl ligands, good conversions were achieved using small amounts of solvent; up to 10 times less than typical procedures in THF. The unsymmetrical Pt complexes of the form [Pt(P-P)Br₂], [Pt(P-P)(Ph)Br] and [Pt(P-P)Ph₂] have been synthesised and characterised. The variations of substituents on the ligand system and the steric bulk have been shown to have a dramatic effect on the rate of transmetalation. The results provide one explanation why 1,1’-bis(di tert-butylphosphino)ferrocene (dtbpf), an excellent ligand for certain Suzuki reactions, is quite poor in reactions where transmetalation is more difficult. Palladium dichloride complexes of the ferrocenylphosphine based ligands 1,1’-bis- (diphenylphosphino)ferrocene (dppf), 1,1’-bis-(diisopropylphosphino)ferrocene (dippf) and 1,1’-bis-(di-tert-butylphosphino)ferrocene (dtbpf) have been shown to be active in the Hiyama cross-coupling of p-bromoacetophenone and vinyltrimethoxysilane (CHCH₂Si(OMe₃)) in the presence of TBAF under thermal heating and microwave conditions. Ligands with the optimum balance for promoting the transmetalation, oxidative addition and reductive elimination steps along the reaction pathway have been identified. Competition experiments are consistent with slow transmetalation being an issue with the Hiyama reaction relative to the Suzuki coupling.A novel protocol has been developed for the synthesis of aryl-alkyl ethers via C-O bond activation under Pd catalysed conditions. Utilising the unsymmetrical 1-bis-(ditertbutyl-1’- bis-diphenylphosphino)ferrocene (dtbdppf) under optimised conditions with silicon based nucleophiles and NaOH or TBAF as an activator, the formation of methyl, ethyl, n-propyl and n-butyl ethers with a range of aryl halides was achieved in good yield.

Porous anodic metal oxides

Su, Zixue — 2010-01-01T00:00:00Z

Abstract: An equifield strength model has been established to elucidate the formation mechanism for the highly ordered alumina pore arrays and titanium oxide nanotubular arrays prepared via a common electrochemical methodology, anodisation. The fundamentals of the equifield strength model was the equilibrium between the electric field driven oxidation rate of the metal and electric field enhanced dissolution rate of oxide. During the anodic oxidation of metal, pore initiation was believed to generate based on dissolution rate difference caused by inhomogeneity near the metal/oxide interface. The ionic nanoconvection driven by the electric force exerted on the space charge layer in the vicinity of electrolyte/oxide interface is established to be the main driving force of the pore ordering at the early stage of the anodisation. While the equifield strength requirement governs the following formation of the single pore and the self-ordering of random distributed pore arrays during the anodisation process. Hexagonal patterned Al2O3 nanopore arrays and TiO2 nanotubular arrays have been achieved by anodisation of corresponding metal substrates in proper electrolytes. The two characteristic microstructural features of anodic aluminium oxide (AAO) and anodic titanium oxide (ATO) were investigated using scanning electron microscopy (SEM) and high resolution transmission electron microscopy (HRTEM). The observations of the hemispherical electrolyte/oxide and oxide/metal interfaces, uniform thickness of the oxide layer, as well as self-adjustment of the pore size and pore ordering can be well explained by the equifield strength model. Field enhanced dissociation of water is extremely important in determination of the porosity of anodic metal oxide. The porosity of AAO and ATO films was found to be governed by the relative dissociation rate of water which is dependent on anodisation conditions, such as electrolyte, applied voltage, current density and electric field strength. Using an empirical method, the relations between the porosity of the AAO (ATO) films and the anodisation parameters, such as electric field strength, current density and applied voltage, have been established. Besides, the extent that an external electric field can facilitate the heterolytic dissociation of water molecule has been estimated using quantum-chemical model computations combined with the experimental aspect. With these achievements, the fabrication of anodic metal oxide films can be understood and controlled more precisely. Additionally, the impacts of other factors such as the electrolyte type and the temperature effect on the morphology of the anodic products were also investigated. Some important experimental evidences on the pore diameters variation with applied voltage in the anodisation of aluminium and the titanium were obtained for future investigation of the anodic metal oxide formation processes.

Probing the influence of bimetallic composition on the Pd/Au catalysed synthesis of vinyl acetate monomer

Haire, Andrew Richard — 2010-06-01T00:00:00Z

Abstract: Scanning Tunnelling Microscopy (STM) was utilised together with the high resolution depth-profiling capabilities of Medium Energy Ion Scattering (MEIS), a technique traditionally associated with single crystal substrates, to probe the mean size and depth dependent composition profile of bimetallic PdAu nanoparticles on planar oxide surfaces as functions of the starting composition and annealing temperature. In order to fit composition profiles to experimental MEIS data, a new analysis tool has been designed that models the particles as flat-topped structures with a hexagonal base which can be divided into a number of shells, each shell corresponding to a particular ion pathlength inside the material. The reliability of this method will be discussed in detail. Fitting results show that the surface layers are always significantly enriched in Au compared to the bulk alloy composition. By comparing MEIS data for clean surfaces data for modified surfaces it was found that Pd generally segregates towards the particle surface on adsorption of acetic acid. The interaction of potassium acetate with Au/Pd{111} alloy surfaces of varying composition has been investigated using Temperature Programmed Desorption (TPD) and Reflection Absorption Infra Red Spectroscopy (RAIRS). At lower coverage, potassium acetate reacts reversibly with the surface to form CO and carbonate. Formation of surface acetate is observed on Pd-rich surfaces only. At higher coverage, acetate is the major surface species formed on all samples examined.

Adenylate forming enzymes involved in NRPS-independent siderophore biosynthesis

Schmelz, Stefan — 2010-06-23T00:00:00Z

Abstract: Activation of otherwise unreactive substrates is a common strategy in chemistry and in nature. Adenylate-forming enzymes use adenosine monophosphate to activate the hydroxyl of their carboxylic substrate, creating a better leaving group. In a second step this reactive group is replaced in a nucleophilic elimination reaction to form esters, amides or thioesters. Recent studies have revealed that NRPS- independent siderophore (NIS) synthetases are also adenylate-forming enzymes, but are not included in the current superfamily description. NIS enzymes are involved in biosynthesis of high-affinity iron chelators which are used for iron acquisition by many pathogenic microorganisms. This is an important area of study, not only for potential therapeutic intervention, but also to illuminate new enzyme chemistries. Here the structural and biochemical studies of AcsD from Pectobacterium chrysanthemi are reported. AcsD is a NIS synthetase involved in achromobactin biosynthesis. The co-complex structures of ATP and citrate provide a mechanism for the stereospecific formation of an enzyme-bound citryl-adenylate. This intermediate reacts with L-serine to form a likely achromobactin precursor. A detailed characterization of AcsD nucleophile profile showed that it can not only catalyze ester formation, but also amide and possibly thioester formation, creating new stereospecific citric acid derivatives. The structure of a N-citryl-ethylenediamine product co-complex identifies the residues that are important for both recognition of L-serine and for catalyzing ester formation. The structural studies on the processive enzyme AlcC, which is involved in the final step of alcaligin biosynthesis of Bordetella pertussis, show that it has a similar topology to AcsD. It also shows that ATP is coordinated in a manner similar to that seen in AcsD. Biochemical studies of a substrate analogue establish that AlcC is not only capable of synthesizing substrate dimers and trimers, but also able to assemble the respective dimer and trimer macrocycles. A series of docked binding models have been developed to illustrate the likely substrate coordination and the steps along dimerization and macrocyclization formation. Structural and mechanistic comparison of NIS enzymes with other adenylate-forming enzymes highlights the diversity of the fold, active site architecture, and metal coordination that has evolved. Hence, a new classification scheme for adenylate forming enzymes is proposed.

Modified nucleosides and oligonucleotides as ligands for asymmetric reactions

Nuzzolo, Marzia — 2010-06-23T00:00:00Z

Abstract: Development of chiral ligands capable of achieving high selectivity for various asymmetric catalytic reactions has been an important aim of both academia and industry. Nature is capable to selectively catalyze chemical reactions by using enzymes. An ideal catalyst would combine the selectivity of nature and the reactivity of man-made catalysts based on transition metal complexes. The two biomolecules chosen to achieve this are DNA and PNA. DNA is a chiral molecule with high binding selectivity towards small molecules and has been used as ligand for asymmetric catalysis. PNA is an achiral structural analogue of DNA that can form duplexes with DNA. To produce DNA based catalysts it is necessary to introduce a ligand such as a phosphine that will strongly coordinate to transition metals. To achieve this, functionalized linkers need to be introduced into a DNA strand, to covalently couple the phosphine moiety at a specific location of the DNA strand. Amine linkers and several modified nucleosides have been prepared containing thiol and amine functionalities and some of them were successfully introduced into DNA strands to function as linkers for the introduction of phosphine functionalities. Those strands were purified and an adequate procedure was developed for their analysis by MALDI-TOF. Diphenylphosphino carboxylic acids have been coupled to amine modified deoxyuridines by amide bond formation. The same coupling method has been used for oligonucleotides. DNA strands containing phosphine moieties were characterized by MALDI-TOF and ³¹P NMR spectrometry. ³¹P NMR spectroscopy was also used to confirm coordination of a phosphine modified 15-mer to [PdCl(η³-allyl)]₂. The phosphine modified nucleobases were also tested as ligands for palladium catalyzed allylic alkylation and allylic amination with diphenylallyl acetate as substrate although no enantioselectivity was observed. A PNA monomer was also modified with a bidentate sulfur protected phosphine and successfully introduced into a short PNA strand using manual solid phase synthesis. This strand was analyzed by MALDI-TOF. Moreover, preliminary studies were performed to test the use of aptamers as scaffolds for targets containing a ligand functionality.

Structural and functional studies of bacterial outer membrane proteins

Lou, Hubing — 2010-02-01T00:00:00Z

Abstract: This thesis studies two particular bacterial outer membrane proteins called OmpC and Wzi, focusing on their expression, purification, crystallization and X-ray structure determination. A series of four naturally occurring OmpC mutants were isolated from a single patient with an E. coli infection of liver cysts. The isolated E. coli strains progressively exhibited increasing breadth of antibiotic resistance in which OmpC was predicted to take a partial role. We carried out an assay in which a strain of E. coli lacking OmpC was used to express the first (antibiotic sensitive) and the last (antibiotic resistant) of the clinical OmpC mutants and drug permeation assessed. Single channel conductance measurements were carried out and the X-ray structures for all the isolates were determined. Protein stability was assessed. With these data we propose that changes in the transverse electric field, not the pore size, underlie the clinically observed resistance to the antibiotics. This is the first demonstration of this strategy for antibiotic resistance. Wzi is a novel outer membrane protein involved in the biosynthesis and translocation mechanism of the K30 antigen from E. coli. The mechanism is a complicated process that requires several proteins including outer and inner membrane proteins. The protein Wzi was expressed, purified and crystallized. Initial crystals were tested and diffracted to 15Å. After optimization, a crystal diffracting to 2.4Å has been obtained.

Studies and application of the enzymes of fluorometabolite biosynthesis in Streptomyces cattleya

Onega, Mayca — 2009-01-01T00:00:00Z

Abstract: This thesis focuses on studies investigating the structure of intermediates involved in fluorometabolite biosynthesis, and the potential applications of the fluorinase enzyme in positron emission tomography (PET). Chapter 1 introduces the rare natural occurrence of fluorinated compounds. The bacterium Streptomyces cattleya is known to biosynthesise two fluorinated secondary metabolites: the toxin fluoroacetate (FAc) and the antibiotic 4-fluorothreonine (4-FT). The enzymes and intermediates identified on this fluorometabolite biosynthetic pathway in S. cattleya, prior to this research, are discussed in detail. Chapter 2 presents studies towards the unambiguous structural identification of (3R,4S)-5- deoxy-5-fluoro-D-ribulose-1-phosphate (5-FRulP) as the third fluorinated intermediate on the biosynthetic pathway to fluoroacetate and 4-fluorothreonine in S. cattleya. Chapter 3 describes the synthetic routes to key molecules, necessary as reference compounds and substrates, to underpin the subsequent studies in this thesis. In particular, synthetic routes to 5'-deoxy-5'-fluoroadenosine (5'-FDA), 5'-deoxy-5'-fluoroinosine (5'-FDI), 5-deoxy-5-fluoro-D-ribose (5-FDR) and 5-deoxy-5-fluoro-D-xylose (5-FDX) are described. Chapter 4 describes the use of the fluorinase enzyme from S. cattleya as a tool for the synthesis of new [¹⁸F]-labelled sugars with potential application in positron emission tomography (PET). A new route to 5-deoxy-5-[¹⁸F]fluoro-D-ribose ([¹⁸F]FDR) is developed in a two-step enzymatic synthesis. A total of three potential radiotracers ([¹⁸F]FDA, [¹⁸F]FDR and [¹⁸F]FDI) are synthesised using fluorinase-coupled enzyme reactions. In addition, in vitro studies are reported with these [¹⁸F]-labelled sugars to investigate their uptake and potential as PET radiotracers in cancer cells. A preliminary rat imaging study with [¹⁸F]FDA is reported. Chapter 5 details the experimental procedures for the compounds synthesised in this research and the biological procedures for chemo-enzymatic syntheses and protein purification.

Metal-chalcogen-nitrogen ring complexes and crystallographic studies

Waddell, Paul G. — 2010-06-23T00:00:00Z

Abstract: 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.

Target identification and validation studies in chemical biology & Synthesis of medium-sized ring containing compounds via oxidative fragmentation

Liu, Gu — 2010-06-23T00:00:00Z

Abstract: Part I of this thesis describes the development of bioactive small molecules of relevance to the study of the apicomlexan parasite Toxoplasma gondii into useful chemical tools. The research includes the target identification and validation studies, using both chemical and biological methods. Chapter 1 provides an overview of chemical genetics with a particular emphasis on methods for the identification of the protein targets of bioactive small molecules. The concept of biochemical protein target identification techniques was introduced with a detailed discussion of interesting applications from the literature. Chapter 2 focuses on the development of a tetrahydro-β-carboline based lead molecule into a chemical tool through target identification studies. The structure activity relationship (SAR) data associated with this core structure, the design of a chemical inducer of dimerisation (CID) and the synthesis of this CID are discussed in detail. Chapter 3 described work done to identify the potential protein target(s) of Conoidin A. Experiments to assess whether Conoidin A can inhibit a proposed target in vitro are also included. Further optimisation of this structural class to develop more potent inhibitors is discussed in the second part of this chapter. Part II of this thesis describes the development of methods for the synthesis of medium-sized ring containing compounds using oxidative fragmentation and rearrangement strategies. Chapter 5 provides an overview of the existing oxidative fragmentation methodology, with an emphasis on the use of oxidative fragmentation reactions for the synthesis of medium-sized ring systems (8-11 ring atoms). Chapter 6 focuses on using the established oxidative fragmentation method in the oxizino carbazolone system to investigate the diasteroselectivity of this reaction. Possible mechanisms for this transformation are investigated and discussed using both chemical and computational methods. An interesting rearrangement reaction has also been observed during this study. Chapter 7 focuses on developing an asymmetric oxidative fragmentation method, for use in the diazabenz[e]aceathrylenes system. Asymmetric oxidative fragmentation reactions using [Ru(pybox)(pydic)] catalysts are discussed. Attempts to optimise the enantiomeric excesses of the reaction by varying reaction conditions and substituents in the substrate are also included.

Continuous flow homogeneous catalysis using ionic liquid/supercritical fluid biphasic systems

Martins, Tânia Isabel Quintas — 2010-01-01T00:00:00Z

Abstract: Ionic liquid/scCO₂ biphasic systems have been studied as a possible solution to the main problems concerning homogeneous catalysis reactions such as, the product/catalyst separation, the catalyst retention in the reaction medium and the use of organic solvents. The hydroformylation of long chain alkenes (1-octene) has been carried out as a continuous flow reaction using [OctMIM]Tf₂N (OctMIM = 1-octyl-3-methylimidazolium, Tf = CF₃SO₂) as the reaction solvent and scCO₂as the mobile phase to extract the products. The performance of the rhodium complexes formed with the ionic ligands [PentMIM][TPPTS] (1-pentyl-3- methylimidazolium tri(m-sulfonyl)triphenylphosphine) and [OctMIM][TPPTS] (1-octyl-3- methylimidazolium tri(m-sulfonyl)triphenylphosphine) is described under different sets of experimental conditions. Continuous flow hydroformylation of 1-octene was also carried out using a SILP (Supported Ionic Liquid Phase) catalyst formed with the TPPTS-based ionic ligands named above. The SILP system described in this work has the peculiarity of introducing the “without gases” approach: syn gas was synthesised in situ by the decomposition of formaldehyde. The performance of both systems is compared in the end. The extension of the continuous flow ionic liquid/scCO₂ biphasic system is shown with the optimisation of the silver-catalysed heterocyclisation of furans. A comparison is carried out with a previously developed and optimised continuous flow heterogeneous system.

Cathode development for solid oxide electrolysis cells for high temperature hydrogen production

Yang, Xuedi — 2010-01-01T00:00:00Z

Abstract: This study has been mainly focused on high temperature solid oxide electrolysis cells (HT-SOECs) for steam electrolysis. The compositions, microstructures and metal catalysts for SOEC cathodes based on (La₀.₇₅Sr₀.₂₅)₀.₉₅Mn₀.₅Cr₀.₅O₃ (LSCM) have been investigated. Hydrogen production amounts from SOECs with LSCM cathodes have been detected and current-to-hydrogen efficiencies have been calculated. The effect of humidity on electrochemical performances from SOECs with cathodes based on LSCM has also been studied. LSCM has been applied as the main composite in HT-SOEC cathodes in this study. Cells were measured at temperatures up to 920°C with 3%steam/Ar/4%H₂ or 3%steam/Ar supplied to the steam/hydrogen electrode. SOECs with LSCM cathodes presented better stability and electrochemical performances in both atmospheres compared to cells with traditional Ni cermet cathodes. By mixing materials with higher ionic conductivity such as YSZ(Y₂O₃-stabilized ZrO₂ ) and CGO(Ce₀.₉Gd₀.₁O₁.₉₅ ) into LSCM cathodes, the cell performances have been improved due to the enlarged triple phase boundary (TPB). Metal catalysts such as Pd, Fe, Rh, Ni have been impregnated to LSCM/CGO cathodes in order to improve cell performances. Cells were measured at 900°C using 3%steam/Ar/4%H₂ or 3%steam/Ar and AC impedance data and I-V curves were collected. The addition of metal catalysts has successfully improved electrochemical performances from cells with LSCM/CGO cathodes. Improving SOEC microstructures is an alternative to improve cell performances. Cells with thinner electrolytes and/or better electrode microstructures were fabricated using techniques such as cutting, polishing, tape casting, impregnation, co-pressing and screen printing. Thinner electrolytes gave reduced ohmic resistances, while better electrode microstructures were observed to facilitate electrode processes. Hydrogen production amounts under external potentials from SOECs with LSCM/CGO cathodes were detected by gas chromatograph and current-to-hydrogen efficiencies were calculated according to the law of conservation of charge. Current-to-hydrogen efficiencies from these cells at 900°C were up to 80% in 3%steam/Ar and were close to 100% in 3%steam/Ar/4%H₂. The effect of humidity on SOEC performances with LSCM/CGO cathodes has been studied by testing the cell in cathode atmospheres with different steam contents (3%, 10%, 20% and 50% steam). There was no large influence on cell performances when steam content was increased, indicating that steam diffusion to cathode was not the main limiting process.

New gas-phase cascade reactions of stabilising phosphorus ylides leading to ring-fused indoles and quinolines

Murray, Lorna — 2010-01-01T00:00:00Z

Abstract: Synthesis and flash vacuum pyrolysis (FVP) of stabilised phosphorus ylides containing an o-amino functionalised benzene ring has been examined for the first time. Model studies using N-methyl-N-tosyl and N-mesyl-N-methyl ylides showed that the ylides could be prepared, although yields were variable, and had the expected spectroscopic properties. Upon FVP, however, the expected loss of Ph₃PO and the sulfonyl group was accompanied by unexpected transfer of the reactive site from nitrogen to carbon giving 3- substituted quinolines rather than the expected indole products. Moving to ylides with an α-cinnamoyl group (or heterocyclic analogue) did, however, result in the originally planned tandem cyclisation leading to ring-fused carbazole products. N-Benzyl was also found to be a suitable thermally labile group and a series of α-cinnamoyl N-benzyl-N-methyl ylides were prepared and characterised. For their synthesis, use of N-cinnamoylbenzotriazoles was found to be preferable to cinnamoyl chloride, requiring only half the amount of amino-functionalised phosphonium salt. While FVP of some of these ylides led to benzo-, furo- and thienocarbazoles in good yield, others again gave quinoline-type products pointing to a fine balance between the two alternative modes of cyclisation. It was noted that one of the furocarbazole products was very similar to a natural product, Eustifoline D, isolated from the medicinally active shrub Murraya euchrestifolia from Taiwan and its synthesis was planned. With a view to producing the required N-H carbazole, N,N-dibenzylamino amino ylides were prepared and were found to exhibit restricted rotation leading to broad NMR signals. Their FVP again led to both quinoline and carbazole products, with the former having usually, but not always, lost a phenyl group. Mechanistic pathways for the formation of the various products are proposed. Complete assignment of the complex ¹H NMR spectra of the various fused-ring heterocyclic products was achieved, assisted by simulations in many cases. The ylide precursor required for Eustifoline D was prepared in five steps and 10% overall yield from 5-methylanthranilic acid. The final FVP step gave a quinoline as the major product, but the minor product was Eustifoline D, spectroscopically identical to the natural product.

The synthesis and biological evaluation of d-myo-inositol 1,4,5-trisphosphate receptor ligands

Keddie, Neil S. — 2010-06-01T00:00:00Z

Abstract: The intracellular second messenger InsP₃ is a vital molecule in the regulation of Ca²⁺ signalling. Ca²⁺ mediates a wide range of cellular activities from fertilisation and cell differentiation through to apoptoisis. Using X-ray crystal structure data and molecular modelling, a series of novel InsP₃ analogues were designed as selective InsP₃R-antagonists. Two novel synthetic routes have been developed for the synthesis of these analogues. The first route uses a Ferrier-II rearrangement to provide enantiopure inositol intermediates, whereas, the second route employs a diastereomeric resolution to obtain the enantiopure inositols. The successful synthesis of InsP₃ and a series of 5-position modified analogues are reported herein.

Synthesis and structural studies of group 16 peri-substituted naphthalenes and related compounds

Knight, Fergus Ross — 2010-06-23T00:00:00Z

Abstract: Understanding how atoms interact is a fundamental aspect of chemistry, biology and materials science. There have been great advances in the knowledge of covalent and ionic bonding over the past twenty years but one of the major challenges for chemistry is to develop full understanding of weak interatomic/intermolecular forces. This thesis describes fundamental studies that develop the basic understanding of weak interactions between heavier polarisable elements. The chosen methodology is to constrain heavy atoms using a rigid naphthalene backbone. When substituents larger than hydrogen, are positioned at close proximity at the peri-positions of a naphthalene molecule they experience steric strain; the extent of which is dictated by intramolecular interactions. These interactions can be repulsive due to steric hindrance or attractive due to weak or strong bonding. In efforts to understand the factors which influence distortion in sterically crowded naphthalenes and study possible weak intramolecular interactions between peri-atoms, investigations focussed on previously unknown mixed 1,8-disubstituted naphthalene systems. Mixed phosphorus-chalcogenide species were initially studied; three mixed phosphine compounds of the type Nap[ER][PPh2] were prepared along with their chalcogenides and a series of metal complexes. The study of interactions between heavy atoms was progressed by investigations into a series of mixed chalcogenide compounds of the type Nap[EPh][E’Ph] (E = S, Se, Te). Subsequent reaction of the chalcogenide systems with the di-halogens, dibromine and diiodine, afforded a mixture of charge transfer and insertion adducts displaying an array of different geometries around the chalcogen atom. From molecular structural studies, a collection of intramolecular peri-interactions were found, extending from no interaction due to repulsive effects, weak attractive 3c-4e type interactions and one example containing a strong covalent peri-bond. Further weak intramolecular interactions observed include CH-π and E•••E’ type interactions plus π-π stacking between adjacent phenyl rings. It was discovered that the bulk of the peri-atoms is influential on the distance between them, but this is not the only factor determining the naphthalene geometry. Inter- and intramolecular interactions can also have an impact and furthermore the number, size and electronic properties of substituents attached to the peri-atoms can determine molecular distortion.

Novel catalysts for the hydroxymethylation of allyl alcohol : a convenient synthetic route to 1, 4-butanediol

Boogaerts, Ine Ida Françoise — 2009-11-01T00:00:00Z

Abstract: Hydroxymethylation catalysis provides a valuable strategy for the high volume production of alcohols from α-alkenes. Generally this involves a hydroformylation-hydrogenation sequence, but the capacity to optimise selectivity for each transformation is limited. Condensation reactions between aldehyde products and alcohol products frustrate process economics. By an alternative scheme, all relevant bond-forming reactions occur in a single mechanism. This thesis describes several approaches to catalyst development and the application of derived systems for the hydroxymethylation of allyl alcohol. A review of auto-tandem hydroxymethylation and domino hydroxymethylation is presented in Chapter 1. In Chapter 2 the synthesis of bis-(diethylphosphine) ligands based on a modular series of chiral alicyclic scaffolds is described. High pressure NMR studies have shown that the catalytically active complex [RhH(CO)₂(L-L)] adopts preferentially ea geometry, with [Rh(CO)(L-L)(μ-CO)]₂ as the primary competing species. Catalyst performance can be correlated with the flexibility of the chelating ring; this favoured a high monomer/dimer ratio which enhances activity, but could not rigidify the configuration of the diethylphosphine groups which inhibits linear selectivity. Deuterium labelling studies were suggestive of a domino hydroxymethylation scheme. From the rhodium-hydroxyalkyl-hydride-carbonyl cation, a reductive elimination furnishes the diol derivatives and a β-hydride abstraction furnishes the hydroxyaldehyde derivatives. Up to 53 mol% selectivity to 1, 4-butanediol was attained. The catalysts could be recycled via biphasic separation, however poisoning by methacrolein caused a decline of activity upon reuse of the solution. An investigation of enhanced specific activity via the meta-effect is the subject of Chapter 3. The effect of systematic meta-substitution in triphenylphosphine upon physicochemical properties was investigated by IR spectroscopy and electrochemistry, both of which showed no significant structural impact on the uncoordinated triarylphosphine. Variable temperature ¹H NMR studies however revealed a change in the solution dynamics of the corresponding Vaska complex. The activation barrier to phosphorus-(ipso)carbon rotation increases as a function of meta-substitution, with rotation of substituted aryl rings past each other being more strained. This should create a well-defined coordination sphere around rhodium, and is proposed to account for the high linear selectivity observed in the hydroformylation of allylic alcohols with [RhH(CO){(3, 5-Me₂Ph)P}₃]. Linear-selectivity reached 96 mol%. Catalyst recycling was executed via biphasic separation, retaining on over twelve cycles an average of ~ 94 % efficiency. The kinetics of allyl alcohol hydroformylation with [RhH(CO){(3, 5-Me₂Ph)P}₃] was found to be well represented by Equation 11 (Section 3.6) A detailed analysis of how substrate-specific the influence of the meta-effect remains to be performed. In Chapter 4 domino hydroxymethylation by multi-component L-L/PEt3/Rh systems is described. The regioselective performance of a diphosphine rhodium catalyst in hydroformylation was translated for hydroxymethylation upon introduction of triethylphosphine at a L-L/PEt3 molar ratio ≥ 1. The highest observed selectivity to 1, 4-butanediol was 66 mol%. Competitive activity of triethylphosphine-modified rhodium species presumably accounts for the reduced linear selectivity observed when L-L/PEt3 molar ratio < 1. Despite aggravated catalyst decomposition at higher triethylphosphine concentrations, heterogeneous hydrogenation does not appear to take place. Deuterium labelling studies also discount a sequential homogeneous hydrogenation. There is evidence for the activation of a tris-phosphine-modified rhodium-acyl-carbonyl complex, but such a species could not be isolated from complexation reactions with a variety of precursors. It would be of interest to determine alternative promotors and to establish whether it is preferential to employ a high concentration of mildly acidic species or a low concentration of highly acidic species. The self-assembly of DNA base pair analogues 2-N-pivaloylaminopyridyl phosphine and isoquinolyl phosphine, each modified with diphenylphosphine, diethylphosphine, dicyclohexylphosphine and bis(3, 5-dimethylphenyl)phosphine, is described in Chapter 5. In the presence of a rhodium precursor, exclusive formation of the heteroleptic complex was observed. Although the intramolecular hydrogen-bonding network is sensitive to temperature and free hydroxyl functionalities, highly regioselective catalysts were generally afforded under the appropriate operating conditions. Only the catalyst based on the bis(dicyclohexylphosphine)-heterodimer performed poorly, presumably due to the formation of mono-phosphine complexes. High chemoselectivity was correlated with the heterodimer acidity constant, however this is rendered non-linear by a trans influence when electronic distinction between the platforms is high. Overall, complexes based on the assembly of a dicyclohexylphosphine platform and a bis(3, 5-dimethylphenyl)phosphine platform were found to be optimal; up to 73 mol% selectivity to 1, 4-butanediol was reached. It has been demonstrated in this thesis that in order to effect linear-selective domino hydroxymethylation of allyl alcohol, two distinct transition state structures must be optimised. High regioselectivity demands an asymmetric rhodium-hydride-dicarbonyl complex, which can be generated by an asymmetric chelate or by rigidifying the configuration of the substituents on phosphorus. Interestingly, chelation geometry in this transition state has little impact on this parameter. It has been shown that domino hydroxymethylation is activated by an electron-rich rhodium-acyl-dicarbonyl. The state of electron density on rhodium can be controlled by the substitution pattern on the phosphorus donors, but can also be changed by the inclusion of a suitable promoter. The chelation geometry in this transition state is more significant; placing the acyl functionality trans to a phosphorus donor concentrates the electronic effect in the rhodium-alkyldiol-hydride-carbonyl cation to such an extent as to impede hydride migration and reductive elimination of the diol, favouring β-hydride abstraction and reductive elimination of the hydroxyaldehyde.

N-hydroxyguanidines and related compounds as nitric oxide donors

Kulczynska, Agnieszka — 2009-01-01T00:00:00Z

Abstract: The design of new, improved NO-donor drugs is an important pharmacological objective due to the biological importance of nitric oxide. N-Hydroxyguanidines represent a useful class of NO donors where the mechanism of action is based on the biosynthetic pathway for NO. Thirty new N-arylalkyl-N’-hydroxyguanidines were synthesized and their vasodilatation activity examined by myography in rat aortic rings. The observed relaxations were reversed by ODQ, which is an inhibitor of the guanylate cyclase, implying that this was an NO dependent vasodilatation. The most active compounds were also tested in the isolated perfused kidney (IPK) giving the vasodilatation properties. Preliminary results indicated that N-phenyl-N’- hydroxyguanidine showed the best pharmacological profile with EC₅₀= 19.9 μM and ca. 100% reversibility with ODQ. A series of N-phenylalkyl-N’-hydroxyguanidines were synthesised. NO donor activity was found to be fairly constant up to three methylene groups, and then decreased. Substitutions in the benzene ring of N-phenylethyl-N’-hydroxyguanidine demonstrated that various electron-withdrawing and electron-donating groups in the para position did not significantly affect the NO donor activity of this series of analogues. The nitro and trifluoromethyl substituted compounds gave the best biological profiles. Additionally, a novel heterocyclic, N–furfuryl-N’–hydroxyguanidine possessed very promising vasodilatation properties. In general, almost all the N-arylalkyl-N’-hydroxyguanidines behaved as potent NO donors in the rat aorta assay. In order to establish the influence of the free NH₂ group in the hydroxyguanidine functionality on the vasodilatation properties, N,N-dimethyl and N-methyl-N’- hydroxyguanidines were successfully synthesised. Unfortunately, they have not been tested yet in the biological assay. However, their NMR spectra showed some unusual features and their detailed analysis and X-ray data are presented herein. In addition a series of hydroxamic acids was synthesised and the NO donor activity investigated using the same biological methodology. It was found that the 3-phenylpropionohydroxamic acid was the most potent compound with EC₅₀ = 6 μM and ODQ = 96%. However, behavior in the IPK indicated that hydroxamic acids did not undergo the same biological pathway as in the rat aorta. Two different types of enzyme-activated pro-drugs were designed using N-hydroxyguanidines as the NO donating molecule. Synthetic studies towards these targets were carried out using various synthetic approaches. The desired molecules have not yet been synthesised but the chemistry explored so far has indicated potentially more successful approaches that could be attempted.

The effect of high pressure gasses on heterogeneous catalysts

Mitchell, Robert G. L. — 2009-01-01T00:00:00Z

Abstract: Several heterogeneously catalysed reactions have been studied at pressures above and below the critical pressure of carbon dioxide in both carbon dioxide and nitrogen. The purpose of this study was to ascertain if carbon dioxide above its critical pressure and temperature would have a beneficial effect on the active life time of the catalysts When the Beckmann rearrangement of cyclohexanone oxime was studied it was discovered that using carbon dioxide above its critical pressure and temperature was beneficial to catalyst lifetime at both 250°C and 300°C, however the beneficial effect was also observed in nitrogen under the same conditions. It is proposed that the benefits at higher pressures are due to an increased residence time in the reactor or increased competition for active sites. When the process was performed at 380°C, a previously unreported impurity was observed in the collected samples. This was shown to be N-ethyl caprolactam, it is proposed that this is formed by a Ritter style reaction with 5-cyanopent-1-ene known to be formed during the reaction When the Fries rearrangement of phenyl acetate was studied it was discovered that increasing reactor pressure appeared to have little or no effect on the catalyst; it is thought this is because the reaction temperature of 150°C is below the boiling point of phenyl acetate, and that the reaction being observed occurs purely in the liquid phase. When the Diels-Alder addition of isoprene to methyl acrylate was studied, it was discovered that using carbon dioxide above its critical pressure had the effect of improving catalyst lifetime and conversion to desired product, with the greatest effect being at 50 bar. It was discovered that using nitrogen under the same conditions led to a greater improvement in conversion and catalyst lifetime. It is thought that the reactions in carbon dioxide are in a near critical state at 50 bar leading to the maximum effect at this pressure, and at higher pressures the reactions are bi- or multi-phasic, leading to the decrease in the effect. In the process of studying the above reactions an effective rig for the study of high pressure heterogeneously catalysed reactions was built.

Synthesis and characterisation of electronically active species

Mahenthirarajah, Thushitha — 2009-01-01T00:00:00Z

Abstract: An exploration of some early transition metal (oxy) fluoride systems using solvothermal techniques has been carried out. 30 novel materials have been synthesised, which fall into three classes based on different metal centres; vanadium (21), molybdenum (5) and niobium (4). Some of these also contain secondary metal centres, namely copper (22) and zinc (1). Simultaneously, the relationship between the SHG values and the crystal structures of the hilgardites family members Pb₂B₅O₉Cl, Pb₂B₅O₉Br, Sr₂B₅O₉Cl and Ba₂B₅O₉Cl was investigated. In particular, the Pb–containing members of the hilgardite family of borate halides exhibit an abnormally large non–linear optical response, which was analysed based on neutron powder diffraction. Using solvothermal synthesis in HF–containing media, 21 novel vanadium oxyfluorides containing interesting structural features, were synthesised at 160˚C using a range of organo-amine compounds as a ligand, template, linker or structure directing agent. The architectures of the crystal structures may be categorised into; four clusters including monomeric vanadium units, five clusters including vanadium dimers, eight 1–D chains, two 2–D layers and two 3–D networks. ‘Composition–space’ diagrams with three components were used to study the effect of stoichiometry changes of reactants and to map out the crystallisation fields. The combination of early (Nb⁵⁺, Mo⁶⁺) and late (Cu²⁺) transition metals with different organo-amines produced nine novel compounds incorporating monomers, chains and 2– D interpenetrated networks. The chains and layers were synthesised from a systematic series of reactions at 160˚C and can be subdivided into four pairs, the topologies of which are essentially unique to each ligand, containing in each case a Cu–based cationic species, but alternately either [MoO₂F₄]²⁻ or [NbOF₅]²⁻, in an isomorphous manner, as the anionic moiety. The overall structures of these materials reflect the influence of the organo–amine ligands. The materials have been studied for their magnetic properties and characterised by thermogravimetric analysis, Rietveld refinement and elemental analysis where relevant.

Studies toward the synthesis and structural elucidation of chamuvarinin

Vanga, Raghava Reddy — 2009-01-01T00:00:00Z

Abstract: Chamuvarinin (22) is a unique annoanceaeous acetogenin isolated from the roots of Senegalese medicinal plant Uvaria chamae by Laurens and co-workers in 2004. It displays highly potent cytotoxicity towards the cervical cancer cell lines (KB 3-1, IC₅₀= 0.8 nM). Structurally, chamuvarinin is the first reported acetogenin to contain an adjacently linked bis-THF-THP ring system spanning the C15-C28 carbon backbone. However, initial efforts to assign the relative and absolute configuration within this stereochemical array, on the basis of ¹H and ¹³C NMR analysis, provided only partial information pertaining to the relative configuration of C15-C19 region. As a consequence, 32 diastereomeric structural possibilities exist for the highly unusual structure of chamuvarinin; an unrealistic target for total synthesis. The synthesis of the central core tricyclic (BCD) intermediate represents the most challenging aspect in the entire synthesis, which in turn will aid ultimate structural proof. At the outset of the project the stereochemical configuration of C15-C28 (BCD) of chamuvarinin was uncertain and a library approach was proposed to enable structure elucidation (Scheme A-1). Chapter 2 and Chapter 3 detail the synthesis of possible diastereomers of the C9-C21 (51) and C22-C34 fragments (52). Chapter 4 details the intial strategy to couple the key diastereomeric fragments in a series of model studies. Chapter 5 describes the successful coupling strategy via an revised synthetic approach to reach the advanced C9-C34 intermediate 251 (Scheme A-2).

New nitric oxide releasing materials

McKinlay, Alistair C. — 2010-06-23T00:00:00Z

Abstract: The aim of this thesis was to examine the ability of metal organic frameworks (MOFs) to store and controllably release biologically significant amounts of nitric oxide (NO). Initial work involved the synthesis of a series of isostructural MOFs, known as M-CPO-27, which display coordinatively unsaturated metal sites (CUSs) when fully activated (guest solvent molecules both coordinated and uncoordinated to the metal atom are removed). Two of these frameworks (Ni and Co CPO-27) displayed exceptional performance over the entire cycle of activation, storage and delivery showing the largest storage and release of NO of any known porous material (up to 7 mmolg⁻¹). These frameworks would therefore be considered for initial research into the formulation of MOFs, for possible use in medical applications. It was shown that they still release large amounts of NO even when placed inside porous paper bags, creams or hydrocolloids. The other versions of M-CPO-27 also displayed significant adsorption of NO however they show poor total NO release. It was also shown that it is possible to synthesise both Ni and Co CPO-27 using microwave synthesis without any detrimental effect to the porous structure. Several iron-based MOFs were also investigated for NO storage and release. The results showed that Fe MIL-88 based structures adsorb good amounts of NO but only release a small amount of the irreversibly adsorbed NO. Two successfully amine grafted giant pore MOFs were then investigated to attempt to improve the NO adsorption and release. This result was not observed however, due to the poor total amine grafting coverage and pore blockage resulting from the amines. In-situ IR studies reveal that when exposed to NO, activated Fe MIL-100 forms a chemical bond with the NO. The studies also displayed that when water is then allowed to attempt to replace the NO that only a small amount of NO is actually released, the majority of the NO either remains chemically bonded to the Fe atom or forms N₂O in conjunction with a Fe-OH group. Other MOFs were also successfully synthesised and characterised for NO storage and release. Both Ni succinate and Ni STA-12 display good adsorption and excellent release of NO. This indicates that Ni based MOFs show the best results for NO adsorption and release. In the conclusion of the thesis I am able to categorise the NO release ability of MOFs based on composition and formulate a theory as to why this happens.

Characterisation of the ceria and yttria co-doped scandia zirconia; produced by an innovative sol-gel and combustion process

de Carvalho Tomás, Eduarda M. S. — 2010-06-23T00:00:00Z

Abstract: In the last decade new materials appeared that are candidates to be used as an electrolyte in a Solid Oxide Fuel Cell, SOFC. Some materials show high ionic conductivity but lack in important properties, such as mechanical stability or chemical compatibility with other materials in the fuel cell. Scandia Stabilised Zirconia, SSZ, became a possibility when the scandia price dropped with the opening of the Chinese and Russian markets. In the starting system Ce[subscript(x)]Y[subscript(0.2-x)]Sc₀.₆Zr₃.₂O[subscript(8-δ)], (0≤x≤0.2), scandia is introduced to improve conductivity and stabilise the cubic phase; yttria is introduced to fully stabilise the cubic phase and ceria to enhance conductivity lost with the introduction of yttria. The aim of this project is to develop a reliable new method to produce quality ceramics that are not strongly composition dependent, then to prepare a range of compositions and compare intrinsic properties without having to be concerned that poor sintering dominates conduction properties. This project can be divided in two sections, the first section the powder production method, the characteristics of the powders and its final products are in focus. In the second section the relation between electric characteristics and microstructure of the material is reported. In the first section, the effect of different compositions of the system Ce[subscript(x)]Y[subscript(0.2-x)]Sc₀.₆Zr₃.₂O[subscript(8-δ)], (0≤x≤0.2) is studied, in terms of structure, phase and microstructure. The nature, size and shape of the powders are discussed, and their effect on the final product. The sol-gel and combustion method gives the formation of hard agglomerates (shells), during the combustion, a wide range of grain sizes, between less than 1µm and 200 µm, and the formation of grains with non spherical shape. In this project, the sol-gel and combustion process and solid state method are also compared. In the second section of this project, AC Impedance measurements, as a function of temperature, oxygen partial pressure and time are discussed. The Arrhenius plot for all compositions shows two regions (high and low temperature) and the change of region occurs at 580 °C. At low temperatures there is a slight difference between compositions but this difference is less at high temperatures. The obtained ionic conductivity, at 350 °C, varies from 3.84×10⁻⁶ to 5.53×10⁻⁵ S/cm; at 700 °C, ionic conductivity from 0.013 to 0.044 S/cm. At low temperatures, the activation energy associated with bulk process is generally lower than grain boundary process; for example, the composition Ce₀.₁Y₀.₁Sc₀.₆Zr₃.₂O₇.₆₅ has an activation energy, for the bulk process, of 1.05 eV and an activation energy, for the grain boundary process, of 1.17 eV. For compositions with higher ceria content, activation energy, for bulk and grain boundary, have similar values. The AC impedance as function of oxygen partial pressure show that the amount of ceria introduced as an effect on the conductivity at low oxygen partial pressure. For the sample with no ceria in its composition, Y₀.₂Sc₀.₆Zr₃.₂O₇.₆₀, the conductivity does not vary significantly as the oxygen partial pressure is decreased; for oxygen partial of 0.21 atm, conductivity is 0.018 S/cm and when oxygen partial pressure is approximately 10⁻²⁴ atm conductivity is 0.018 S/cm. For the sample with a higher content of ceria, Ce₀.₁₂Y₀.₀₈Sc₀.₆Zr₃.₂O₇.₆₆, there is a decrease in conductivity while oxygen partial pressure decreases; and there is also the appearance of a semi-circle for lower oxygen partial pressures. For oxygen partial pressure approximately 0.21 atm, conductivity is 0.019 S/cm, but when oxygen partial pressure is decreased to 10⁻²⁴ atm conductivity decreases to 0.011 S/cm. AC impedance measurements as a function of annealing time at 600 °C were performed. Total conductivity is fairly stable, for all compositions, until 1800 hours but after this time, conductivity slowly decreases. Some compositions show a second semi-circle in the AC impedance spectra, either from the beginning, time equals 0 hours, or after some working hours. Here, the changes in conduction and conduction processes with time are discussed.

Towards the development of selective hydrocarbon oxygenation catalysts

Guisado Barrios, Gregorio — 2010-03-09T00:00:00Z

Abstract: The synthesis of pure tris(6-hydroxymethyl-2-pyridylmethyl)amine (H₃L₁₁) is reported for the first time. New complexes of H₃L₁₁ with copper(II), manganese(II) and iron(III) have been characterised by X-ray crystallography. Linear [Fe₃(L₁₁)₂](ClO₄)₃ reveals the tightest Fe-O-Fe angle (87.6°) and shortest Fe...Fe distance (2.834 Å) presently found for a weakly antiferromagnetically-coupled high spin alkoxide-bridged polyiron(III) system. H₃L₁₁ provides a route to various hydrophobic peralkylated TPA ligand derivatives for creating a hydrophobic pocket for the assembly of iron catalysts for the novel 1-hydroxylation of n-alkanes. New 6-py substituted TPA ligands containing methyl (L₁₅) and n-octyl (L₁₆) ether linkages were synthesised via alkylation. Two further novel 6-py substituted ligands were synthesized incorporating n-hexyl substituents on one (L₂₁) and two (L₂₂) of the py moieties. Here a urea spacer group was used to promote hydrogen–bond assisted heterolytic O-O cleavage (generation of the potent FeV=O oxidant) within the hydroxoperoxoiron(III) precursor. High spin [FeII(L)(CH₃CN)[subscript(x)]](CF₃SO₃)₂ complexes (x = 0–2, L = L₁₅,₁₆,₂₁,₂₂) were characterised in solution by ¹H NMR. The structure of [Fe(L₂₂)](CF₃SO₃)₂ reveals a distorted iron(II) centre bound to four N atoms and two urea carbonyls. Iron(II) complexes of H₃L₁₁, L₁₅,₁₆,₂₁,₂₂ and tris(6-Br)-TPA (L₂₄), were investigated for catalysis of the oxygenation of cyclohexane by H₂O₂. Reaction of the iron(II) complexes with H₂O₂ and [superscript(t)]BuOOH was followed by time-resolved EPR and UV-VIS spectrophotometry. A correlation between the observed catalytic activity and the nature of the FeIII(L)-OOR intermediates generated is apparent. A convenient ‘one-pot’ synthesis of benzene-1,3,5-triamido-tris(l-histidine methyl ester) is reported along with attempts at preparing N,N’-bis(pyridylmethyl)-1,3- diaminopropane-2-carboxylic acid (L₂₅), a new water soluble pyridine-amine ligand. The final demetallation step resulted in ligand hydrolysis to the novel amino acid; 1,3-diaminopropane- 2-carboxylic acid which was characterised as its HCl salt by X-ray crystallography.

New approaches for C-F bond formation in organic chemistry

Launay, Guillaume — 2010-06-23T00:00:00Z

Abstract: The importance of fluorinated organic molecules has grown over the last 50 years, particularly in the pharmaceutical and agrochemical industries. Therefore the development of new methods for fluorination is a very attractive research area. In Chapter 1, the properties and impact of the fluorine atom on organic molecules are overviewed. Existing electrophilic and nucleophilic fluorination methods are reviewed, and new developments in asymmetric fluorination are discussed. The emergence of the Prins fluorination reaction as a side product in BF₃.OEt₂ catalysed processes has been investigated as a synthesis method in Chapter 2. Indeed, it is possible to form 4-fluorotetrahydropyrans with some diastereoselectivity from an allylic alcohol and an aldehyde with a stoichiometric amount of BF₃.OEt₂. During this study, formation of 4-fluoropiperidines from N-tosyl-4-butenylamine was achieved. Optimisation of reaction conditions was investigated such as the solvent, the reaction temperature and the influence of substituents on the alcohol and the aldehyde reagents. A ring-opening reaction of 4-fluoro-2-phenyltetrahydropyran was successfully performed. Both oxa-Prins and aza-Prins fluorination reactions were investigated under microwave conditions, allowing reduced reaction times, a process that had a minimum impact on the diastereoselectivity. Attempt to form γ-hydroxy-α-vinylfluorides by the reduction-fluorination of propargylic alcohols with aluminium hydride, or by Horner-Emmons reaction with diethyl (fluoromethyl)phosphonate are reported in Chapter 3. Unfortunately these approaches were unsuccessful in the preparation of γ-hydroxy-α-vinylfluorides. Attempts to fluorinate epoxides by α-lithiation and then treatment with electrophilic fluorination reagents gave encouraging results, but the products could not be purified and characterised due to an apparent instability.

Integrating replication processes with mechanically interlocked molecules

Vidonne, Annick — 2009-11-30T00:00:00Z

Abstract: In the last twenty years, chemists have devised numerous synthetic chemical systems in which self-replication operates, demonstrating that molecules can replicate themselves without the aid of enzymes and that self-replication is not a prerogative of nucleic acids only. However, the coupling of replication to other recognition-mediated events and its exploitation in the amplification of large supramolecular assemblies, such as mechanically interlocked molecules, have remained unexplored areas. Among mechanically interlocked molecules, rotaxanes represent particularly attractive targets because of their application as molecular switches. This thesis describes how the recognition-mediated synthesis of a rotaxane can be combined to the amplification of its structure by replication. Kinetic models for the integration of self-replication with the formation of a rotaxane are presented. The logical steps required to convert these models into molecular structures through consideration of the design criteria highlighted by the models are discussed and executed. The macrocyclic component is an essential part of a rotaxane. The synthesis of several novel macrocycles is presented. Their ability to bind guests in their cavities through hydrogen bonds was probed. The best macrocycle/guest pairs were integrated in the formation of rotaxanes. Further investigations on the stoppering reaction and on the various recognition processes involved in the system lead ultimately to the construction of self-replicating rotaxanes.

Pd catalysed synthesis of phosphines for homogeneous catalysis

Damian, Karen Serena — 2009-01-01T00:00:00Z

Abstract: The synthesis of ligands has been identified as the limitation for wider application of catalytic asymmetric synthesis. Indeed, synthesis of phosphorus-based ligands, has been often shown to be challenging and not always efficient. It has also been observed that subtle changes in the ligand structure can lead to big differences in the catalytic activity of the ligand when coordinated to a metal. Therefore, it was considered useful to develop a methodology in order to obtain a library of phosphines. The first chapter of the thesis is a review of recent development in catalytic phosphine synthesis. In the second chapter of this thesis, the microwave mediated Suzuki cross coupling reaction has been investigated. In particular, attention has been focussed on the coupling of different arylboronic acids to chloroarylphosphine oxides, which are, in general, considered challenging coupling partners for this type of reaction. The reaction conditions have been optimised starting from the coupling of phenylboronic acid to tris(4-chlorophenyl)phosphine oxide. Different solvents, bases, and catalysts have been then tested and the better conditions have been developed for this substrate. Indeed, it was shown that the coupling occurs in only 30 minutes at 140°C, leading to reasonably high yields. These conditions were then applied to two other different chloroarylphosphine oxides with a range of boronic acids, with the aim to verify if the optimised reaction conditions could be applied to other substrates and it was noticed that good yields could be attained. This methodology led us to obtain a library of phosphine oxides. It was then decided to investigate the reduction of phosphine oxides under microwave irradiation. This reaction occurs under conventional heating but it can take several hours. It was observed that reaction times could be importantly reduced when reducing some phosphine oxides under microwave heating. It was found that some phosphine oxides are reduced rapidly under conventional conditions but for more difficult substrates to reduce there are significant advantage to microwave method. We decided to investigate the microwave mediated P-C bond forming reaction, with the aim to rapidly synthesise a library of phosphines cleanly. The conditions were optimised at first using o- trifluoromethylbromobenzene as the substrate. Once the appropriate reaction conditions and catalyst were identified, the reaction was run on other substrates to verify that this could be a general methodology for the synthesis of phosphines. It was found that it is indeed a general method for the synthesis of monophosphines. However, the synthesis of diphosphines with the microwave assisted P-C bond forming reaction on dibromo- and diiodo- aryl compounds proved to be very challenging. The fourth chapter presents different attempts for the synthesis of the new ligand Ph-DuPHOS. The synthesis of this ligand was considered interesting because of the previous results of other phospholane-based ligands, such as Ph-BPE and Me-DuPHOS. However, the synthesis of this ligand has proven to be elusive. A monodentate P-N phospholane-based ligand was prepared and its catalytic activity was tested in the rhodium catalysed hydrogenation of alkenes. Moreover, a bidentate (1,2-bisphospholano)xylene ligand was also prepared and its catalytic activity was also tested in the rhodium catalysed hydrogenation of alkenes. This latter ligand was also used in the hydroxycarbonylation of styrene, since for this reaction bulky diphosphines are required to give branched selectivity. In hydroxycarbonylation it is very rare to give good branched selectivity and there were no examples of substantial enantioselectivity prior to this work. The high regioselectivity and moderate e.e.’s observed suggest promise for future studies. Finally, mechanistic studies on the hydroxycarbonylation of styrene have been carried out in order to investigate the intermediates involved in the reaction as well as the role of the promoters. The possibility of (1-chloroethyl)benzene was proposed as the active intermediate of the reaction. Our results have disproved this possibility, suggesting that the reaction is likely to proceed through the hydride mechanism.

The rechargeable lithium/air battery and the application of mesoporous Fe₂O₃ in conventional lithium battery

Bao, Jianli — 2009-01-01T00:00:00Z

Abstract: By replacing the intercalation electrode with a porous electrode and allowing lithium to react directly with O₂ from the air, the new rechargeable Li/O₂ battery system was studied. The porous cathode is comprised of carbon, catalyst and binder. The effect of every component was investigated. The catalyst was believed to play an important role in the performance of the electrode. A number of potential materials have been examined as the catalyst for the O₂ electrode. It suggests that the nature of the catalyst is a key factor controlling the performance of the O₂ electrode. Several catalysts based on first row transition metal oxides each with three different morphologies, bulk, nanoparticulate and mesoporous were studied. The influence of the morphology on the discharge and charge voltage, discharge capacity and cyclability were examined. Among all the catalysts studied, α-MnO₂ nanowires was found to be the best candidate. The reversible capacities of 3000 mAhg⁻¹(normalised by the mass of carbon) or 505 mAhg⁻¹ (based on the total mass of cathode + O₂ ) was obtained. Some of other factors, such as type of carbon, type of binder, type of electrolyte, the construction of cathode and the modification of the catalyst were also investigated, even just in the early stage. Capacity fading during cycling is the main problem in all the cases. A number of experiments were carried out to understand and attempt to avoid the fading problem. After successful synthesis of mesoporous α-Fe₂O₃ with unique properties (by Jiao et al.), the application of these materials in conventional Li battery was studied. Mesoporous α-Fe₂O₃ with ordered walls, mesoporous α-Fe₂O₃ with disordered walls and Fe₂O₃ nanoparticles were examined. It was also applied to examine the different factors that influence the rate of conversion electrodes, i.e., Li⁺ and e⁻ transport to and within the particles, as well as the rate of the two-phase reaction, demonstrating that for this conversion reaction electron transport to and within the particles is paramount.

Development of new proton conducting materials for intermediate temperature fuel cells

Xu, Xiaoxiang — 2010-02-22T00:00:00Z

Abstract: The work in this thesis mainly focuses on the preparation and characterization of several phosphates and solid oxide systems with the aim of developing new proton conducting materials for intermediate temperature fuel cells (ITFCs). Soft chemical methods such as sol-gel methods and conventional solid state methods were applied for the synthesis of these materials. Aluminum phosphate obtained by a solution method is single phase and belongs to one of the Al(H₂PO₄)₃ allotropies with hexagonal symmetry. The material is stable up to 200°C and decomposes into Al(PO₃)₃ at a higher temperature. The electrical conductivity of pure Al(H₂PO₄)₃ is on the order of 10⁻⁶-10⁻⁷ S/cm, very close to the value for the known proton conductors AlH₃(PO₄)₂•3H₂O and AlH₂P₃O₁₀•2H₂O. Much higher conductivity is observed for samples containing even a trace amount of excess H₃PO₄. It is likely that the conduction path gradually changes from grain interior to the surface as the acid content increases. The conductivity of Al(H₂PO₄)₃-0.5H₃PO₄ exhibited a good stability over the measured 110 hours. Although tin pyrophosphate (SnP₂O₇) has been reported to show a significantly high conductivity (~10⁻² S/cm) at 250°C in various atmospheres, we observed large discrepancies in the electrical properties of SnP₂O₇ prepared by different methods. Using an excess amount of phosphorous in the synthetic procedure generally produces SnP₂O₇ with much higher conductivity (several orders of magnitude higher) than samples with stoichiometric Sn:P ratios in their synthetic procedure. Solid state ³¹P NMR confirmed the presence of residual phosphoric acid for samples with excess starting phosphorous. Transmission Electron Microscope (TEM) confirmed an amorphous layer covered the SnP₂O₇ granules which was probably phosphoric acid or condensed phases. Thereby, it is quite likely that the high conductivity of SnP₂O₇ results mainly from the contribution of the residual acid. The conductivity of these samples exhibited a good stability over the measured 80 hours. Based on the observations for SnP₂O₇, we developed a nano core-shell structure based on BPO₄ and P₂O₅ synthesised by solid state methods. The particle size of BPO₄ using this method varied between 10-20 nm depending on the content of P₂O₅. TEM confirmed the existence of an amorphous layer that is homogeneously distributed. The composite exhibits the highest conductivity of 8.8×10⁻² S/cm at 300°C in air for 20% extra P₂O₅ and demonstrates a good stability during the whole measured 110 hours. Polytetrafluoroethylene (PTFE) was introduced into the composites in order to increase malleability for fabrication. The conductivity and mechanical strength were optimized by adjusting the PTFE and P₂O₅ content. These organic-inorganic composites demonstrate much better stability at elevated temperature (250°C) over conventional SiC-H₃PO₄-PTFE composites which are common electrolytes for phosphoric acid fuel cells (PAFCs). Fuel cells based on BPO₄-H₃PO₄-PTFE composite as the electrolyte were investigated using pure H₂ and methanol as fuels. A maximum power density of 320 mW/cm² at a voltage of 0.31 V and a maximum current density of 1.9 A/cm² at 200°C were observed for H₂/O₂ fuel cells. A maximum power density of 40 mW/cm² and maximum current of 300 mA/cm² 275°C were observed when 3M methanol was used in the cell. Phosphoric acid was also introduced into materials with internal open structures such as phosphotungstic acid (H₃PW₁₂O₄₀) and heteropolyacid salt ((NH₄)₃PW₁₂O₄₀), for the purpose of acquiring additional connections. The hybrids obtained have a cubic symmetry with enlarged unit cell volume, probably due to the incorporation of phosphoric acid into the internal structures. Solid state ³¹P NMR performed on H₃PW₁₂O₄₀-xH₃PO₄ (x = 0-3) showed additional peaks at high acid content which could not assigned to phosphorus from the starting materials, suggesting a strong interaction between H₃PW₁₂O₄₀ and H₃PO₄. The conductivity of hybrids was improved significantly compared with samples without phosphoric acid. Fourier transform infrared spectra (FT-IR) suggest the existence of large amount of hydrogen bonds (OH••••O) that may responsible for the high conductivity. A H₂/O₂ fuel cell based on H₃PW₁₂O₄₀-H₃PO₄-PTFE exhibited a peak power density of 2.7 mW/cm² at 0.3 V in ambient temperature. Solid oxide proton conductors based on yttrium doped BaZrO₃ were investigated by introducing potassium or lanthanum at the A-sites. The materials were prepared by different methods and were obtained as a single phase with space group Pm-3m (221). The unit cell of these samples is slightly smaller than the undoped one. The upper limit of solid solution formation on the A-sites for potassium is between 5 ~ 10% as introducing more K results in the occurrence of a second phase or impurities such as YSZ (yttrium stabilized zirconium). K doped Barium zirconates showed an improved water uptake capability even with 5% K doping, whereas for La doped ones, water uptake is strongly dependent on particle size and synthetic history. The conductivity of K doped BaZrO₃ was improved by a factor of two (2×10⁻³ S/cm) at 600°C compared with undoped material. Fuel cells based on Pt/Ba₀₋₉₅K₀₋₀₅Zr₀₋₈₅Y₀₋₁₁Zn₀₋₀₄O[subscript(3-δ)]/Pt under humidified 5% H₂/air conditions gave a maximum power density 7.7 mWcm⁻² at 718°C and an interfacial resistance 4 Ωcm⁻². While for La doped samples, the conductivity was comparable with undoped ones; the benefits of introducing lanthanum at A-sites may not be so obvious as deficiency of barium is one factor that leads to the diminishing conductivity. Description: Electronic version excludes material for which permission has not been granted by the rights holder

Novel methodology for the synthesis of ¹³C-Labelled phenols and its application to the total synthesis of polyphenols

Marshall, Laura J. — 2010-06-23T00:00:00Z

Abstract: The base-catalysed reaction of 4H-pyran-4-one with a range of nucleophiles, namely diethyl malonate, ethyl acetoacetate, nitromethane, acetylacetone and ethyl cyanoacetate, was developed as a reliable, high yielding method for the preparation of para-substituted phenols. The methodology was extended to include the use of the substituted pyranones, maltol, 2,6-dimethyl-4H-pyran-4-one and diethyl chelidonate. Reactions were studied using conventional heating methods and microwave irradiation. Microwave irradiation had definite beneficial effects, with improved yields, reduced reaction times and cleaner reaction profiles. The potential of this methodology was examined for the regioselective placement of ¹³C-atoms into benzene rings using ¹³C-labelled nucleophiles or ¹³C-labelled 4H-pyran-4-ones. [3,5-13C₂]4H-Pyran-4-one and [2,6-13C₂]4H-pyran-4-one were prepared from various ¹³C-labelled versions of triethyl orthoformate and acetone. This methodology was applied to the synthesis of [1,3,5-¹³C₃]gallic acid, via the base-catalysed reaction of [3,5-¹³C₂]4H-pyran-4-one with diethyl [2-¹³C]malonate, followed by subsequent transformations to yield [1,3,5-¹³C₃]gallic acid. The preparation of [2-¹³C]phloroglucinol was carried out via [2-¹³C]resorcinol, with regioselective placement of a single ¹³C-atom into the aromatic ring. This was accomplished from non-aromatic precursors, with the source of the ¹³C-atom being [¹³C]methyl iodide. The key step in this synthesis was the introduction of the third hydroxyl group, which was achieved using a modified iridium-catalysed C-H activation/borylation/oxidation procedure. The scope of an existing C-H activation/borylation reaction was modified and expanded to include a range of protected resorcinol derivatives. A catalyst system was developed which allowed high conversion to the intermediate arylboronic acids, followed by oxidation using aqueous Oxone® to yield the corresponding phenols. Finally, to demonstrate the potential of these new methods for application in the synthesis of isotopically labelled natural products and polyphenols, the syntheses of ¹³C-labelled anthocyanins were studied. A route was developed that could be applied to the synthesis of either cyanidin-3-glucoside or delphinidin-3-glucoside. Only the final coupling/cyclisation step to yield the desired anthocyanin targets remains to be carried out. Description: Electronic version excludes material for which permission has not been granted by the rights holder

Molecular probes for the evaluation of three isomerase enzyme mechanisms in secondary metabolism

Nasomjai, Pitak — 2010-01-01T00:00:00Z

Abstract: This thesis is focused on an investigation of the mechanisms of three enzymatically mediated carbon skeleton isomerisation reactions. Chapter 1 provides an overview of some representative examples of the carbon skeleton rearrangement reactions in enzymology. Chapter 2 describes the preparation and use of fluorolittorines to explore the mechanism of the rearrangement of the tropane alkaloid littorine to hyoscyamine which is a reaction mediated by the cytochrome P450 enzyme. Chapter 3 describes the synthesis of D-ribose-1-phosphonates and the cyclic phosphonates (phostone) that are candidate inhibitors of the enzymatic isomerisation of 5-fluoro-5-deoxy-ribose-1-phosphate (5-FDRP) to 5-fluoro-5-deoxy-ribulose-1-phosphate (5-FDRulP), an important step in fluorometabolite biosynthesis pathway in Streptomyces cattleya. Chapter 4 describes the synthesis of 5-hydroxy-3,4-dioxohexylphosphonate and [5-13C]-5-hydroxy-3,4-dioxohexylphosphonate. These compounds are proposed as candidates for the transition state of the retro-aldol/aldol mechanism of the enzymatic isomerisation of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methylerythitol-phophate-2-phosphate (MEP) in the biosynthesis of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). The influence of pH on tautomerisation of [5-13C]-5-hydroxy-3,4-dioxohexylphosphonate is also described. Chapter 5 describes the general chemical and biochemical methodologies utilised in this research project.

Evolving complex systems from simple molecules

Sadownik, Jan — 2009-01-01T00:00:00Z

Abstract: Until very recently, synthetic chemistry has focussed on the creation of chemical entities with desirable properties through the programmed application of isolated chemical reactions, either individually or in a cascade that afford a target compound selectively. By contrast, biological systems operate using a plethora of complex interconnected signaling and metabolic networks with multiple checkpoint controls and feedback loops allowing biological systems to adapt and respond rapidly to external stimuli. Systems chemistry attempts to capture the complexity and emergent phenomena prevalent in the life sciences within a wholly synthetic chemical framework. In this approach, complex phenomena are expressed by a group of synthetic chemical entities designed to interact and react with many partners within the ensemble in programmed ways. In this manner, it should be possible to create synthetic chemical systems whose properties are not simply the linear sum of the attributes of the individual components. Chapter 1 discusses the role of complex networks in various aspects of chemistry- related research from the origin of life to nanotechnology. Further, it introduces the concept of Systems chemistry, giving various examples of dynamic covalent networks, self-replicating systems and molecular logic gates, showing the applications of complex system research. Chapter 2 discusses the components of replicator design. Further, it introduces a network based on recognition mediated reactions that is implemented by length- segregation of the substrates and displays properties of self-sorting. Chapter 3 presents a fully addressable chemical system based on auto- and cross- catalytic properties of product templates. The system is described by Boolean logic operations with different template inputs giving different template outputs. Chapter 4 introduces a dynamic network which fate is determined by a single recognition event. The replicator is capable of exploiting and dominating the exchanging pool of reagents in order to amplify its own formation at the expense of other species through the non-linear kinetics inherent in minimal replication. Chapter 5 focuses on the development of complex dynamic systems from structurally simple molecules. The new approach allows creating multicomponent networks with many reaction pathways operating simultaneously from readily available substrates.