Selective functionalisation of Re6 cluster anionic units:from hexa-hydroxo [Re6Q8(OH)6]4− (Q = S, Se) to neutral trans-[Re6Q8L4L′2] hybrid building blocks

The reaction of [Re6Q8(OH)6]4- (Q = S, Se) with p-tertbutylpyridine (TBP) in water leads to neutral trans-[Re6Q8(TBP)4(OH)2] whose hydroxyl reactivity with carboxylic acid and TBP exchange reaction with functional pyridine have been investigated.

Design and application of nanoscale actuators using block-copolymers

Block copolymers are versatile designer macromolecules where a “bottom-up” approach can be used to create tailored materials with unique properties. These simple building blocks allow us to create actuators that convert energy from a variety of sources (such as chemical, electrical and heat) into mechanical energy. In this review we will discuss the advantages and potential pitfalls of using block copolymers to create actuators, putting emphasis on the ways in which these materials can be synthesised and processed. Particular attention will be given to the theoretical background of microphase separation and how the phase diagram can be used during the design process of actuators. Different types of actuation will be discussed throughout.

Base modified peptidic nucleic acids: synthesis and crystallographic analysis of intermediates

Peptidic Nucleic Acids (PNAs) are achiral, uncharged nucleic add mimetics, with a novel backbone composed of N-(2-aminoethyl)glycine units attached to the DNA bases through carboxymethylene linkers. With the aim of extending and improving upon the molecular recognition properties of PNAs, the aim of this work was to synthesjse PNA building block intermediates containing a series of substituted purine bases for subsequent use in automated PNA synthesis. Four purine bases: 2,6~diaminopurine (D), isoGuanine (isoG), xanthine (X) and hypoxanthine (H) were identified for incorporation into PNAs targeted to DNA, with the promise of increased hybrid stability over extended pH ranges together with improvements over the use of adenine (A) in duplex formation, and cytosine (C) in triplex formation. A reliable, high-yielding synthesis of the PNA backbone component N -('2- butyloxycarbonyl-aminoethyl)glycinate ethyl ester was establishecl. The precursor N~(2-butyloxycarbonyl)amino acetonitrile was crystallised and analysed by X-ray crystallography for the first time. An excellent refinement (R = 0.0276) was attained for this structure, allowing comparisons with known analogues. Although chemical synthesis of pure, fully-characterised PNA monomers was not achieved, chemical synthesis of PNA building blocks composed of diaminopurine, xanthine and hypoxanthine was completely successful. In parallel, a second objective of this work was to characterise and evaluate novel crystalline intermediates, which formed a new series of substituted purine bases, generated by attaching alkyl substituents at the N9 or N7 sites of purine bases. Crystallographic analysis was undertaken to probe the regiochemistry of isomers, and to reveal interesting structural features of the new series of similarly-substituted purine bases. The attainment of the versatile synthetic intermediate 2,6-dichloro~9- (carboxymethyl)purine ethyl ester, and its homologous regioisomers 6-chloro~9- (carboxymethyl)purine ethyl ester and 6-chloro-7-(carboxymethyl)purine ethyl ester, necessitated the use of X-ray crystallographic analysis for unambiguous structural assignment. Successful refinement of the disordered 2,6-diamino-9-(carboxymethyl) purine ethyl ester allowed comparison with the reported structure of the adenine analogue, ethyl adenin-9-yl acetate. Replacement of the chloro moieties with amino, azido and methoxy groups expanded the internal angles at their point of attachment to the purine ring. Crystallographic analysis played a pivotal role towards confirming the identity of the peralkylated hypoxanthine derivative diethyl 6-oxo-6,7-dihydro-3H-purlne~3,7~djacetate, where two ethyl side chains were found to attach at N3 and N7,

Synthesis and biological evaluation of potential anti-cancer agents

The new technology of combinational chemistry has been introduced to pharmaceutical companies, improving and making more efficient the process of drug discovery. Automated combinatorial chemistry in the solution-phase has been used to prepare a large number of compounds of anti-cancer screening. A library of caffeic acid derivatives has been prepared by the Knoevenagel condensation of aldehyde and active methylene reagents. These products have been screened against two murine adenocarcinoma cell lines (MAC) which are generally refractive to standard cytotoxic agents. The target of anti-proliferative action was the 12- and 15-lipoxygenase enzymes upon which these tumour cell lines have been shown to be dependent for proliferation and metastasis. Compounds were compared to a standard lipoxygenase inhibitor and if found to be active anti-proliferative agents were tested for their general cytotoxicity and lipoxygenase inhibition. A solid-phase bound catalyst, piperazinomethyl polystyrene, was devised and prepared for the improved generation of Knoevenagel condensation products. This piperazinomethyl polystyrene was compared to the traditional liquid catalyst, piperidine, and was found to reduce the amount of by-products formed during reaction and had the advantage of easy removal from the reaction. 13C NMR has been used to determine the E/Z stereochemistry of Knoevenagel condensation products. Soluble polymers have been prepared containing different building blocks pendant to the polymer backbone. Aldehyde building blocks incorporated into the polymer structure have been subjected to the Knoevenagel condensation. Cleavage of the resultant pendant molecules has proved that soluble linear polymers have the potential to generate combinatorial mixtures of known composition for biological testing. Novel catechol derivatives have been prepared by traditional solution-phase chemistry with the intention of transferring their synthesis to a solid-phase support. Catechol derivatives prepared were found to be active inhibitors of lipoxygenase. Soluble linear supports for the preparation of these active compounds were designed and tested. The aim was to develop a support suitable for the automated synthesis of libraries of catechol derivatives for biological screening.

The synthesis and evaluation of small organic molecules as cholecystokinin antagonists

Cholecystokinin (CCK) is a peptide hormone, present in the alimentary and the CNS. It is the most abundant peptide in the brain. CCK has been implicated in a number of disorders. The link between CCK and anxiety was the basis for this research. A comprehensive discussion on the many types of CCK receptor antagonists is included. For the drug discovery process, a number of synthetic approaches have been investigated and alternative chemical approaches developed. 1,4-Benzodiazepine analogues were prepared, with substitutents In the 1,2 & 3- position of the benzodiazepine scaffold varied, and substituted 3-anilino benzodiazepines exhibited the greatest in vitro activity towards the CCKA receptor subtype. Through extensive screening, pyrazolinone-ureido derivatives were identified, optimised, SAR studied and re-screened. A comprehensive in vivo study on the most active analogue is included, which has a number of common structural features with L-36S, 260 including activity. Pyrazolinone-amide derivatives, bearing the tryptophan moiety were equally active. A number of existing and novel furan- 2(SH)-one building blocks were prepared, from which a selected mini-library of 4- amino-substituted furan-2(SH)-ones were prepared and evaluated. All synthesised compounds were evaluated in a CCK radiolabelled binding assay (CCKA & CCKB), with compounds demonstrating receptor selectivity and lead structures being discovered. The work in this thesis has identified a number of highly active prime structures, from which further investigations are essential in providing more in vitro & in vivo data and the need to prepare more analogues.

Zwitterionic and charge-balanced (polyampholyte) copolymer hydrogels

Zwitterionic compounds, or zwitterions, are electrically neutral compounds having an equal number of formal unit charges of opposite sign. In common polyzwitterions the zwitterionic groups are usually located in pendent groups rather than the backbone of the macromolecule. Polyzwitterions contain both the anion and cation in the same monomeric unit, unlike polyampholytes which can contain the anion and cation in different monomeric units. The use of cationic and anionic monomers (or monomers capable of becoming charged) in stoichiometric equivalent proportions produces charge-balanced polyampholyte copolymers. Hydrogel materials produced from zwitterionic monomers have been proposed for use and are used in many biomaterial applications but synthetic charge-balanced polyampholyte are less common. Certain properties of hydrogels which are important for their successful use as biomaterials, these include the equilibrium water content, mechanical, surface energy, oxygen permeability, swelling and the coefficient of friction. The zwitterionic monomer N,N-dimethyl-N-(2-acryloylethyl)-N-(3-sulfopropyl) ammonium betaine (SPDA) was synthesized with 2-hydroxyethly acrylate (HEMA) as the comonomer to produce a series of polyzwitterion hydrogels. To produce charged-balanced copolymer hydrogels two “cationic” monomers were selected; 2-(diethylamino) ethyl methacrylate (DMAEMA) and 3-(dimethylamino) propyl methacrylamide (DMAPMA) and an anionic monomer; 2-acrylamido 2,2 methylpropane sulphonic acid (AMPS). Two series’ of charge-balanced copolymers were synthesized from stoichiometric equivalent ratios of DMAEMA or DMAPMA and AMPS with HEMA as a terpolymer. The zwitterionic copolymer and both charge-balanced copolymers produced clear, cohesive hydrogels. The zwitterionic and charge-balanced copolymers displayed similar EWC’s along with similar mechanical and surface energy properties. The swelling of the zwitterionic copolymer displayed antipolyelectrolyte behavior whereas the charge-balanced copolymers displayed behaviour somewhere between this and a typical polyelectrolyte. This work describes some aspects of the polymerisation and properties of SPDA copolymers and charge-balanced (polyampholyte) copolymers relevant to their potential as biomedical / bioresponsive materials. The biomimetic nature of SPDA together with its compatibility with other monomers makes it a useful and complimentary addition to the building blocks of biomaterials.

ALEX:mobile language assistant for low-literacy adults

Basic literacy skills are fundamental building blocks of education, yet for a very large number of adults tasks such as understanding and using everyday items is a challenge. While research, industry, and policy-making is looking at improving access to textual information for low-literacy adults, the literacy-based demands of today's society are continually increasing. Although many community-based organizations offer resources and support to adults with limited literacy skills, current programs have difficulties reaching and retaining those that would benefit most from them. To address these challenges, the National Research Council of Canada is proposing a technological solution to support literacy programs and to assist low-literacy adults in today's information-centric society: ALEX© – Adult Literacy support application for EXperiential learning. ALEX© has been created together with low-literacy adults, following guidelines for inclusive design of mobile assistive tools. It is a mobile language assistant that is designed to be used both in the classroom and in daily life, in order to help low-literacy adults become increasingly literate and independent.

Low-loss waveguides fabricated by femtosecond chirped-pulse oscillator

Recent results on direct femtosecond inscription of straight low-loss waveguides in borosilicate glass are presented. We also demonstrate lowest ever losses in curvilinear waveguides, which we use as main building blocks for integrated photonics circuits. Low-loss waveguides are of great importance to a variety of applications of integrated optics. We report on recent results of direct femtosecond fabrication of smooth low-loss waveguides in standard optical glass by means of femtosecond chirped-pulse oscillator only (Scientific XL, Femtolasers), operating at the repetition rate of 11 MHz, at the wavelength of 800 nm, with FWHM pulse duration of about 50 fs, and a spectral widths of 30 nm. The pulse energy on target was up to 70 nJ. In transverse inscription geometry, we inscribed waveguides at the depth from 10 to 300 micrometers beneath the surface in the samples of 50 x 50 x 1 mm dimensions made of pure BK7 borosilicate glass. The translation of the samples accomplished by 2D air-bearing stage (Aerotech) with sub-micrometer precision at a speed of up to 100 mm per second (hardware limit). Third direction of translation (Z-, along the inscribing beam or perpendicular to sample plane) allows truly 3D structures to be fabricated. The waveguides were characterized in terms of induced refractive index contrast, their dimensions and cross-sections, mode-field profiles, total insertion losses at both 633 nm and 1550 nm. There was almost no dependence on polarization for the laser inscription. The experimental conditions – depth, laser polarization, pulse energy, translation speed and others, were optimized for minimum insertion losses when coupled to a standard optical fibre SMF-28. We found coincidence of our optimal inscription conditions with recently published by other groups [1, 3] despite significant difference in practically all experimental parameters. Using optimum regime for straight waveguides fabrication, we inscribed a set of curvilinear tracks, which were arranged in a way to ensure the same propagation length (and thus losses) and coupling conditions, while radii of curvature varied from 3 to 10 mm. This allowed us to measure bend-losses – they less than or about 1 dB/cm at R=10 mm radius of curvature. We also demonstrate a possibility to fabricate periodical perturbations of the refractive index in such waveguides with the periods using the same set-up. We demonstrated periods of about 520 nm, which allowed us to fabricate wavelength-selective devices using the same set-up. This diversity as well as very short time for inscription (the optimum translation speed was found to be 40 mm/sec) makes our approach attractive for industrial applications, for example, in next generation high-speed telecom networks.

Chapter 1 : nucleobases with designed patterns of hydrogen bonding

The chemistry used in key bond-forming steps to prepare nucleobases with designed patterns of hydrogen bonding is surveyed. Incorporation of the nucleobases into DNA and RNA oligomers is achieved either chemically using building blocks such as nucleoside phosphoramidites or enzymatically using nucleotide triphosphates. By varying the hydrogen bonding pattern within nucleobases, and by incorporating additional substituents, new structures have been designed that "reach over" so that contacts with both strands in targeted duplex DNA can be made in antigene strategies to control gene expression. Various new base-pairing systems have been evaluated that expand the genetic alphabet beyond Watson-Crick base pairs A.T and G.C. For example, benzo-homologated analogs of the natural DNA bases represent a new genetic set of orthogonal, size-expanded derivatives that have been shown to encode amino acids of a protein in a living organism.

Investigating polymer-peptide conjugates and electrospinning for the production of advanced materials

This thesis describes the production of advanced materials comprising a wide array of polymer-based building blocks. These materials include bio-hybrid polymer-peptide conjugates, based on phenylalanine and poly(ethylene oxide), and polymers with intrinsic microporosity (PIMs). Polymer-peptides conjugates were previously synthesised using click chemistry. Due to the inherent disadvantages of the reported synthesis, a new, simpler, inexpensive protocol was sought. Three synthetic methods based on amidation chemistry were investigated for both oligopeptide and polymerpeptide coupling. The resulting conjugates produced were then assessed by various analytical techniques, and the new synthesis was compared with the established protocol. An investigation was also carried out focussing on polymer-peptide coupling via ester chemistry, involving deprotection of the carboxyl terminus of the peptide. Polymer-peptide conjugates were also assessed for their propensity to self-assemble into thixotropic gels in an array of solvent mixtures. Determination of the rules governing this particular self-assembly (gelation) was required. Initial work suggested that at least four phenylalanine peptide units were necessary for self-assembly, due to favourable hydrogen bond interactions. Quantitative analysis was carried out using three analytical techniques (namely rheology, FTIR, and confocal microscopy) to probe the microstructure of the material and provided further information on the conditions for self-assembly. Several polymers were electrospun in order to produce nanofibres. These included novel materials such as PIMs and the aforementioned bio-hybrid conjugates. An investigation of the parameters governing successful fibre production was carried out for PIMs, polymer-peptide conjugates, and for nanoparticle cages coupled to a polymer scaffold. SEM analysis was carried out on all material produced during these electrospinning experiments.

Low-loss waveguides fabricated by femtosecond chirped-pulse oscillator

Recent results on direct femtosecond inscription of straight low-loss waveguides in borosilicate glass are presented. We also demonstrate lowest ever losses in curvilinear waveguides, which we use as main building blocks for integrated photonics circuits. Low-loss waveguides are of great importance to a variety of applications of integrated optics. We report on recent results of direct femtosecond fabrication of smooth low-loss waveguides in standard optical glass by means of femtosecond chirped-pulse oscillator only (Scientific XL, Femtolasers), operating at the repetition rate of 11 MHz, at the wavelength of 800 nm, with FWHM pulse duration of about 50 fs, and a spectral widths of 30 nm. The pulse energy on target was up to 70 nJ. In transverse inscription geometry, we inscribed waveguides at the depth from 10 to 300 micrometers beneath the surface in the samples of 50 x 50 x 1 mm dimensions made of pure BK7 borosilicate glass. The translation of the samples accomplished by 2D air-bearing stage (Aerotech) with sub-micrometer precision at a speed of up to 100 mm per second (hardware limit). Third direction of translation (Z-, along the inscribing beam or perpendicular to sample plane) allows truly 3D structures to be fabricated. The waveguides were characterized in terms of induced refractive index contrast, their dimensions and cross-sections, mode-field profiles, total insertion losses at both 633 nm and 1550 nm. There was almost no dependence on polarization for the laser inscription. The experimental conditions – depth, laser polarization, pulse energy, translation speed and others, were optimized for minimum insertion losses when coupled to a standard optical fibre SMF-28. We found coincidence of our optimal inscription conditions with recently published by other groups [1, 3] despite significant difference in practically all experimental parameters. Using optimum regime for straight waveguides fabrication, we inscribed a set of curvilinear tracks, which were arranged in a way to ensure the same propagation length (and thus losses) and coupling conditions, while radii of curvature varied from 3 to 10 mm. This allowed us to measure bend-losses – they less than or about 1 dB/cm at R=10 mm radius of curvature. We also demonstrate a possibility to fabricate periodical perturbations of the refractive index in such waveguides with the periods using the same set-up. We demonstrated periods of about 520 nm, which allowed us to fabricate wavelength-selective devices using the same set-up. This diversity as well as very short time for inscription (the optimum translation speed was found to be 40 mm/sec) makes our approach attractive for industrial applications, for example, in next generation high-speed telecom networks.

Structure of glassy GeO2

The full set of partial structure factors for glassy germania, or GeO2, were accurately measured by using the method of isotopic substitution in neutron diffraction in order to elucidate the nature of the pair correlations for this archetypal strong glass former. The results show that the basic tetrahedral Ge(O-1/2)(4) building blocks share corners with a mean inter-tetrahedral Ge-O-Ge bond angle of 132(2)degrees. The topological and chemical ordering in the resultant network displays two characteristic length scales at distances greater than the nearest neighbour. One of these describes the intermediate range order, and manifests itself by the appearance of a first sharp diffraction peak in the measured diffraction patterns at a scattering vector k(FSDP) approximate to 1.53 angstrom(-1), while the other describes so-called extended range order, and is associated with the principal peak at k(PP) = 2.66( 1) angstrom(-1). We find that there is an interplay between the relative importance of the ordering on these length scales for tetrahedral network forming glasses that is dominated by the extended range ordering with increasing glass fragility. The measured partial structure factors for glassy GeO2 are used to reproduce the total structure factor measured by using high energy x-ray diffraction and the experimental results are also compared to those obtained by using classical and first principles molecular dynamics simulations.

Novel anti-bacterials against MRSA:Synthesis of focussed combinatorial libraries of tri-substituted 2(5H)-furanones

Mucobromic and mucochloric acid were used as building blocks for the construction of a chemical combinatorial library of 3,4,5-trisubstituted 2(5H)-furanones. With these 2 butenolide building blocks, and eight alcohols a sublibrary of 16 dihalogenated 5-alkoxy-2(5H)-furanones was prepared. This sublibrary of 5-alkoxylated furanones was reacted with 16 amines generating a full size focussed combinatorial library of 256 individual compounds. This three dimensional combinatorial library of 3-halogen-4-amino-5-alkoxy-2(5H)-furanones was prepared around the benzimidazolyl furanone lead structure by applying a solution phase combinatorial chemistry concept. Typical representatives of the library were purified and fully characterized and one x-ray structures was recorded, additionally. The 3-bromo-4-benzimizazolyl-5-methoxy-2(5H)furanone, Br-A-l, showed an MIC of 8 μg/ml against the multiresistant Staphylococcus aureus ( MRSA). © 2006 Bentham Science Publishers Ltd.

Modular construction of dynamic nucleodendrimers

Isoguanosine-containing dendritic small molecules self-assemble into decameric nucleodendrimers as observed by 1D NMR spectroscopy, 2D DOSY, and mass spectrometry. In particular, apolar building blocks readily form pentameric structures in acetonitrile while the presence of alkali metals promotes the formation of stable decameric assemblies with a preference for cesium ions. Remarkably, co-incubation of guanosine and isoguanosine-containing nucleodendrons results in the formation of decameric structures in absence of added salts. Further analysis of the mixture indicated that guanosine derivatives facilitate the formation, but are not involved in decameric structures; a process reminiscent of molecular crowding. This molecular system provides a powerful canvas for the rapid and modular assembly of polyfunctional dendritic macromolecules. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis and characterization of silica-supported L-Lysine-based dendritic branches

Two series of novel modified silicas have been prepared in which individual dendritic branches have been attached to aminopropylsilica using standard peptide coupling methodology. The dendritic branches are composed of enantiomerically pure l-lysine building blocks, and hence, the modified silicas have the potential to act as chiral stationary phases in chromatography. In one series of modified silicas, the surface of the dendritic branch consists of Boc carbamate groups, whereas the other has benzoyl amide surface groups. Different coupling reagents have been investigated in order to maximize the loading onto the solid phase. The new supported dendritic materials have been fully characterized with properties of the bulk material determined by elemental analysis, 13C NMR, and IR spectroscopy, whereas XPS provides important information about the surface of the modified silica exposed to the incident X-rays, the key region in which potential chromatographic performance of these materials will take place. Although the bulk analyses indicate that loading of the dendritic branch onto silica decreases with increasing dendritic generation (and consequently steric bulk), XPS indicates that the optimum surface coverage is actually obtained at the second generation of dendritic growth.