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Thesis (Ph. D.)--University of Washington, 2006. / Vita. Includes bibliographical references (leaves 122-136).

This thesis presents the study of organic layers covalently assembled onto carbon surfaces. As a result of their attachment, the properties of carbon surfaces were controllably adjusted so that these surfaces could be used for desired applications. In order that a wide range of properties were imparted onto the carbon surface, many different modifiers were attached and thoroughly characterised. Three applications that the modified carbon surfaces were used for were the subsequent coupling of molecular species, adsorption of protein and assembly of aldehyde/sulfate-functionalised polystyrene (PS) and citrate-capped gold nanoparticles (NPs). Finally, patterning of different organic layers at pre-determined spatially defined locations on the one carbon surface was also investigated. The carbon surfaces used in this work were glassy carbon (GC) and pyrolysed photoresist film (PPF) surfaces. For PPF, methods for the reproducible fabrication of electrochemically suitable surfaces were investigated. The properties of GC and PPF surfaces are very similar apart from the surface roughness. PPF has near atomic smoothness and has RMS roughness values that are approximately four times smaller than GC. The first series of modifier layers attached to the carbon surfaces was via the oxidation of seven different primary amines. The different layers allowed the modulation of the wettability of the surface. Both n-tridecylamine (TDA, monoamine) and 1,12-diaminododecane (DAD, diamine) are able to form multilayers. The stability of TDA and DAD layers were tested by scanning, soaking and sonicating the layers in different media. Changes in the layer were monitored by the probe response of ferrocene monocarboxylic acid (FCA). However, atomic force microscope (AFM) depth profiling experiments showed that changes in the probe response did not indicate cleavage of the covalently attached layer and mechanisms are proposed to account for the changes in the response of the probe. Surface concentrations of the amine modifiers were estimated by the coupling of an electrochemically active species, FCA and nitrobenzoyl chloride (NBC). The electrochemical reduction of the 4-nitrophenylethylamine (NPEA) layer in acid caused the layer to 'shrink'. Surface concentration estimates of NPEA from acid reduction of layers with different thicknesses suggested that only a limited fraction of the p-nitrophenyl groups were reduced in acid. However, in ACN (acetonitrile)/0.1 M [Bu4N]BF4 (tetrabutyl ammonium fluoroborate) the relationship between the concentration of electroactive surface groups and layer thickness was linear. The other series of modifiers that was attached to alter the surface properties was performed by the reduction of aryl diazonium salts. Subsequent coupling reactions of tetraethylene glycol diamine (TGD) to para methylene carboxylic acid phenyl (MCA) and NBC to electrochemically reduced para nitro phenyl (NPh) layers were carried out. Surface concentrations of NPh as estimated from reduction scans was higher when reduction was performed in ethanol/water compared to acid. Four peaks at N1s binding energies were observed in x-ray photoelectron spectroscopy (XPS) spectra for both acid and ethanol/water reduced layers. The ability of attached amine and aryl layers to modulate the adsorption of protein was investigated using fluorescently labelled protein, bovine serum albumin-fluorescein isothiocynate (BSA-FITC) and fluorescence microscopy. TGD, para methyl phenyl (MP), para hexyl phenyl (HP) and para polyethylene glycol phenyl (PEG)-modified GC surfaces promoted protein adsorption relative to as-prepared GC, whereas n-hexylamine (HA) and polyethylene glycol diamine (PGD) layers reduced protein adsorption. The assembly of two types of NPs, aldehyde/sulfate-functionalised PS and citrate-capped gold NPs, onto amine-containing modifiers layers was examined. Citrate-capped gold NPs were synthesised and characterised. The surface coverage of the gold NPs was controlled by using different modifiers of different chemical compositions, tuning the modification conditions and adjusting the immersion time, concentration and pH of gold NP solution. Approaches to creating patterns of modifiers in pre-determined spatially defined locations on GC and PPF surfaces using poly(dimethyl)siloxane (PDMS), poly(vinyl)alcohol (PVA) and thin metal films were investigated. With the "fill-in" approach using PDMS, the smallest pattern of modifiers was the parallel lines with a line width of 20 µm and straight edges and was created by performing electrochemistry in PDMS microchannels which has not been previously investigated. Visualisation techniques, based on optical and scanning electron microscopy, were demonstrated for the molecular patterns.

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Faculty of Science School of Chemistry 0100505x jzeevaart@csir.co.za / The application of homogenous transition metal catalysis to the arylation of enolates to develop new synthetic procedures which are more environmentally benign, atomefficient and economically viable than current methods was the motivation behind the current work. The specific choice of molecules with an aromatic group in the a- position of a ketone, carboxylic acid, amide or other electron-withdrawing group arose from the fact that many natural products, pharmaceutical actives and synthetic intermediates contain such a substructure while the syntheses of these substructures are often cumbersome. The application of homogenous catalysis to various types of enolates was explored and in the process several developments were achieved and discoveries made. These included the use of inorganic bases under phase transfer conditions for the Heck reaction of acrylic acid as well as the synthesis and application of phosphine and phosphite ligands in the Heck reaction of acrylic acid esters. The successful use of low palladium loadings (as low as 0.01mol%) in the arylation of diethyl malonate using aryl chlorides and the application to the synthesis of ketoprofen and phenobarbital was demonstrated. The novel application of palladium catalysis to the arylation of methanesulfonamides and the first example of a bromoindole derivative as the aryl halide partner in an enolate arylation reaction was demonstrated. Ligand-free palladium catalysed phenylation of pinacolone followed by Baeyer Villiger oxidation led to a proposed novel synthetic route to tert-butyl esters of 2-arylacetic acids. The palladium and copper catalysed arylation of acetoacetate esters, with in situ decarbonylation, provided a different route to 2-arylacetic acid esters which are useful in the preparation of non-steroidal anti-inflammatory compounds.

The development of safe and efficient hydrogen storage materials will aid in the transition away from fossil fuels toward a renewable, hydrogen-based energy infrastructure. Boron-nitrogen (BN) containing materials have attracted much attention due to their high hydrogen storage capacity and fast kinetics of hydrogen release. Furthermore, computational studies predict that hydrogen storage materials based on the BN-heterocycle 1,2-azaborine may enable reversible H2 uptake and release, with little additional energy input. This thesis develops the basic science needed for a hydrogen storage platform based on BN-heterocycles such as 1,2-azaborine. Chapter I is a review of recent developments in azaborine chemistry. Chapter II describes a regeneration scheme from a "spent" 1,2-azaborine hydrogen storage material to "fully charged" fuel using molecular H2 and H-/H+ equivalents. Chapter III describes the experimental determination of the resonance stabilization energy of 1,2-azaborines using reaction calorimetry. Chapter IV explores the effect of boron-substitution on the rate and extent of hydrogen release from BN materials. Chapter V describes work on a project unrelated to hydrogen storage, the synthesis and electronic parameter determination of the first 1,2- azaborine-containing phosphine ligand analog. This dissertation includes previously published and unpublished co-authored material.

Dioxins are environmental contaminants that raise concern because they are potent and persistent. The most potent dioxin congener, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), causes a wide variety of biochemical and toxic effects in laboratory animals and in humans. Major toxicities of TCDD are initiated by their binding to the AH receptor (AHR), a ligand-activated transcription factor that regulates expression of numerous genes. However, the specific genes whose dysregulation leads to major toxicities such as wasting, hepatotoxicity, and lethality are unknown. The objective of this thesis research was to identify the molecular mechanisms by which dioxins cause lethality. To this end, a powerful genetic rat model was utilized – the Han/Wistar (Kuopio) rat which is highly resistant to dioxin toxicity due to a major deletion in the AHR’s transactivation domain (TAD) leading to 3 potential AHR variant transcripts. We found that insertion-variant transcripts (IVs) are the dominant forms of AHR expressed in H/W rats, constitutively and after TCDD treatment. Gene expression array analysis revealed that the total number of TCDD-responsive genes in liver was significantly lower in H/W rats (that carry the TAD deletion) than in dioxin-sensitive rats (that carry wildtype AHR). Genes that are well-known to be AHR-regulated and dioxin-inducible  such as CYP1 transcripts  remained responsive to TCDD in H/W rats; thus the TAD deletion selectively interferes with expression of a subset of hepatic genes rather than abolishing global AHR-mediated responses. Genes that differed in response to TCDD between dioxin-sensitive rats and dioxin-resistant rats are integral parts of pathways known to be disrupted by dioxin treatment such as protein synthesis/degradation, fatty acid transport/metabolism, and apoptosis. These genes are worthy candidates for further mechanistic studies to test their role in major dioxin toxicities. Numerous differentially-regulated genes were downregulated; however, microRNAs, which downregulate mRNA levels in other systems, likely play no role in downregulation of mRNAs by dioxins in adult liver and are unlikely to be involved in hepatotoxicity. Findings in this research support the hypothesis that H/W rats are resistant to TCDD lethality because the TAD deletion prevents the AHR from dysregulating specific mRNA transcripts but not hepatic miRNAs.

Many physiological responses to dioxin-like compounds (DLCs), including polychlorinated dibenzodioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) are mediated by the aryl-hydrocarbon receptor (AhR). In birds, activation of the AhR stimulates the transcription of cytochrome P4501A (CYP1A) genes, including CYP1A4 and CYP1A5, and ultimately leads to expression of biotransformation enzymes, including ethoxyresorufin-O-deethylase (EROD). It is well established that potencies of different DLCs range over several orders of magnitude. There is also a wide variation among birds in their responsiveness to DLCs both in efficacy and threshold for effects. A molecular basis for this differential sensitivity has been suggested. Specifically, a comparison of the AhR ligand-binding domain (LBD) indicated that key amino acid residues are predictive of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) sensitivity. Based on sequencing of the AhR LBD from numerous avian species a sensitive classification scheme has been proposed (in order of decreasing sensitivity, chicken (type I; sensitive) > Common pheasant (type II; moderately sensitive) > Japanese quail (type III; insensitive)). A series of egg injection studies with White-leghorn chicken (<i>Gallus gallus domesticus</i>), Common pheasant (<i>Phasianus colchicus</i>) and Japanese quail (<i>Coturnix japonica</i>) were performed to determine whether molecular and biochemical markers of exposure to DLCs are predictive of the proposed classification scheme. In addition, I was interested in determining whether this classification scheme applies to other DLCs, specifically dibenzofurans. Determining which species are "chicken- like", "pheasant-like" and "quail-like" in their responses to DLCs should allow more refined risk assessments to be conducted as there would be less uncertainty about the potential effects of DLCs in those species for which population-level studies do not exist.<p> Several concentrations of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), 2,3,4,7,8-pentachlorodibenzofuran (PeCDF), or 2,3,7,8-tetrachlorodibenzofuran (TCDF) (triolein vehicle) were injected into the air cells of Japanese quail, Common pheasant and chicken eggs. Liver from 14 d post-hatch chicks was harvested for analysis of CYP1A4 and CYP1A5 mRNA abundance by quantitative real-time PCR (Q-PCR), and EROD activity. Lowest observed effective concentration (LOEC) and relative potency (ReP) values for CYP1A mRNA abundance and EROD activity were determined and used to make comparisons of sensitivity between each species and DLC potency within each species.<p> The TCDD is widely considered to be the most potent DLC and this is supported by the rank order of LOEC values for CYP1A5 mRNA abundance in White-leghorn chicken (TCDD > PeCDF > TCDF). CYP1A4 mRNA abundance and EROD activity in White-leghorn chicken were significantly increased in the lowest dose exposure groups of each of the three DLCs, so the potency of these compounds based on these endpoints was not established. Interestingly, TCDD was not the most potent DLC in Common pheasant and Japanese quail. In Common pheasant, PeCDF is the most potent as a CYP1A4 mRNA inducer, followed by TCDD and TCDF. However, TCDF was the most potent EROD activity inducer for Common pheasant, followed by PeCDF, and then TCDD. No significant increases were found in CYP1A5 mRNA abundance in pheasant within the tested dose ranges for all the three DLCs. No significant increases in either CYP1A5 mRNA abundance or EROD activity were found in Japanese quail. In addition, PeCDF and TCDF, but not TCDD, significantly increased CYP1A4 mRNA abundance.<p> According to the predicted relative sensitivity by comparing the AhR LBD amino acid sequences, the White-leghorn chicken is more responsive to DLCs than the Common pheasant which is more responsive than the Japanese quail. By comparing the relative sensitivity calculated based on the LOEC values from my study, the sensitivity order to TCDD and TCDF support the proposed molecular based species sensitivity classification scheme (chicken > pheasant > quail), while pheasant is almost as sensitive as chicken to PeCDF ( pheasant ¡Ý chicken > quail).<p> Taken together, the data suggest that TCDD is the most potent DLC in White-leghorn chicken, but not in Common pheasant, or or Japanese quail. The data suggest that in type II avian species PeCDF may be more potent than TCDD. In addition, I found in my study that different biomarkers have different responses, which depends on species and chemicals as well. These data provide further insight into avian sensitivities to DLCs.</p>