Thesis advisor: Marc L. Snapper / Cyclobutadiene cycloadditions provide rapid access to rigid polycyclic systems with high strain energy and unusual molecular geometries. Further functionalization of these systems allows entry into unexplored chemical space. A tricarbonylcyclobutadiene iron complex on solid support enables exploration of these cycloadditions in a parallel format amenable to diversity oriented synthesis. Modeling of the cycloaddition transition states with density functional calculations provides a theoretical basis for analysis of the regioselectivity observed in generation of these substituted bicyclo[2.2.0]hexene derivatives. The high strain energy accessible in cyclobutadiene cycloadducts and their derivatives renders them useful synthons for access to medium-ring natural products through ring expansion. Torilin, a guaiane sesquiterpene isolated from extracts of the fruits of <italic>Torilis japonica</italic>, exhibits a range of biological activities including testosterone 5&alpha;-reductase inhibition, hKv1.5 channel blocking, hepatoprotective, anti-inflammatory and anti-cancer effects. These activities are reviewed and analyzed from the perspective of a common biochemical target. Tandem oxidation and acid-catalyzed rearrangement of a highly strained tetracyclo[5.3.0.0<super>1,5</super>.0<super>2,4</super>]decane in the presence of tetrapropylammonium perruthenate provides the bicyclo[5.3.0]decane core of this natural product with complete control of relevant stereochemistry. The complex precursor required for this rearrangement is rapidly accessed by cyclopropanation of an intramolecular cyclobutadiene cycloadduct. Synthetic studies are reported which provide preliminary access to 8-deoxytorilolone. / Thesis (PhD) — Boston College, 2010. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

No presente trabalho foi estudada a viabilidade da fotometria em fase sólida usando cela de fluxo com caminho óptico de 3 mm e fotômetro de LED, para determinação de cobalto em suplementos vitamínicos digeridos em meio ácido. O método automatizado foi baseado na formação de um composto de cobalto(II) com o reagente cromogênico 1-(2\'-tiazolilazo)-2-naftol (TAN) retido em suporte sólido quimicamente modificado (C18) monitorado em 580 nm. O módulo de análise foi baseado no processo de multicomutação em fluxo. Após a definição das variáveis de controle, as amostras digeridas em meio ácido foram processadas. O procedimento permitiu a determinação de cobalto na faixa linear de 0,05 a 2,0 mg L-1. A precisão analítica, expressa como DPR, foi de 4,2% (n = 9) e freqüência de amostragem de 17 determinações por hora foram observadas. Os limites de detecção e quantificação foram estimados em 0,0166 e 0,055 mg L-1, respectivamente. / In the present work the viability of the solid phase photometry using a flow cell with optical pathway of 3 mm and a LED photometer for the determination o cobalt vitamin supplements digested in acidic medium was studied. The method automated was based on the compound formation of cobalt and the chromomeric reagent 1-(2\'-tiazolilazo)-2-naftol (TAN), which was immobilized on a solid support (C18) and monitored at 580 nm. The analysis module was based on the multicommutation flow analysis process. After definition of the variables control, samples digested in acid medium ware analyzed. The procedure allowed cobalt determination within the linear range 0.0 up to 2.0 mg L-1. The analytical precision, expressed as DPR, was 4.2 %, and the analytical frequency was 17 determinations per hour. Limit of detection and limit of determination were 0.0166 and 0.055 mg L-1, respectively.

Os contaminantes emergentes são considerados compostos onipresentes em águas, portanto investigar a degradação e comportamento dessas substâncias torna-se necessária, pois é reportado que estes compostos causam efeitos adversos em seres vivos. O composto 2-(tiocianometiltio) benzotiazol (TCMTB), considerado um contaminante emergente, é amplamente empregado na indústria do couro como biocida com a finalidade de inibir o desenvolvimento de microrganismos na pele. Sendo assim, o objetivo do presente trabalho foi estudar a degradação do contaminante emergente TCMTB, por meio das técnicas de fotólise direta com radiação UV, radiação solar e oxidação com ozônio. Experimentos de fotólise direta do TCMTB, em soluções aquosas com diferentes concentrações, em efluente do processo de remolho e efluente simulado do remolho, foram conduzidos em reator com lâmpada de vapor de mercúrio (250 W). O teste de hidrólise foi realizado protegido da luz, a temperatura ambiente com diferentes concentrações do TCMTB para observar o comportamento do contaminante na ausência de luz. O maior coeficiente de absorção molar foi medido e identificado em 220 e 280 nm como 20489 e 11317 M-1 cm-1, respectivamente, para pH 5,0. Os resultados experimentais da fotodegradação mostraram que TCMTB foi rapidamente degradado por fotólise direta em soluções aquosas em 30 min de tratamento fotolítico. Os resultados do estudo do pH, demonstraram que pH interfere no processo fotoquímico, uma vez que em condições alcalinas o composto é mais estável e a taxa de fotodegradação diminui. Os ensaios com o efluente do processo de remolho mostraram que a degradação do TCMTB tem comportamento semelhante às soluções aquosas. O efluente simulado do remolho mostrou que uma alta concentração do contaminante leva a um maior tempo de irradiação de luz para a degradação. A aplicação de luz natural evidenciou degradação mais lenta, mas ainda assim, foi possível observar degradação de até 96% para a concentração de 6 mg L-1 em 420 min. A utilização do oxidante ozônio como tratamento, alcançou 40% de remoção do contaminante em 30 min, assinalando a alta estabilidade do composto. Portanto, este trabalho aponta o potencial do uso de fotólise direta (luz v artificial), ou radiação solar (luz natural) para a degradação de contaminantes emergentes como o 2 (tiocianometiltio) benzotiazol (TCMTB). / Emerging contaminants are considered omnipresent compounds in water, thus investigate the degradation and behavior of these substances becomes necessary as it is reported that these compounds cause adverse effects on living beings. The 2- (thiocyanomethylthio) benzothiazole compound (TCMTB), considered an emerging contaminant, is widely used in the leather industry as a microbicide for the purpose of inhibiting the development of microorganisms in the skin and leather. In this context, the purpose of the present work was to study the degradation of the emerging contaminant TCMTB by direct photolysis with UV radiation, solar radiation and ozone. Experiments of direct photolysis of the TCMTB in aqueous solutions with different concentrations, in the effluent from the soaking process were conducted in a reactor with mercury vapor lamp (250 W). The hydrolysis test was performed protected from light at room temperature with different concentrations of TCMTB to observe the behavior of the contaminant in the absence of light. The highest molar absorption coefficient was measured and identified at 220 and 280 nm as 20489 and 11317 M-1 cm -1, respectively, at pH 5.0. The experimental results of photodegradation showed that TCMTB was rapidly degraded by direct photolysis in aqueous solutions in 30 min of photolytic treatment. The results of the pH study showed that pH interfered in the photochemical process, since under alkaline conditions the compound is more stable and the photodegradation rate decreases. Assays of the direct photolysis in effluent from the soaking process have shown that TCMTB degradation behaves similarly to aqueous solutions. The direct photolysis of the the simulated effluent from the soaking showed that a high concentration of the contaminant leads to a longer time of light irradiation for degradation. The application of natural light evidenced slower degradation, however, it was possible to observe degradation of up to 96% for the 6 mg L-1 concentration with 420 min. The use of the ozone oxidant as a treatment, achieved 40% removal of the contaminant for 30 min of treatment, indicating the high stability of the compound. Therefore, this work highlights the potential of the use of direct photolysis (artificial light), or solar radiation (natural light) for the vii degradation of emerging contaminants such as 2 (thiocyanomethylthio) benzothiazole (TCMTB).

Chemical biology can be defined as the area of science where chemical tools are used to study biological systems. The simplest way this can be achieved is in the identification of compounds which inhibit or modulate a biological pathway and the consequences studied. However, novel tools are required to enable, for example, the development of assays to allow simpler screening of difficult targets such as membrane proteins and protein-protein interactions. A series of kisspeptin analogues were synthesised for the development of a screening platform compatible with G-protein coupled receptors and tagged one bead one compound (OBOC) combinatorial libraries. Fluorescently labelled kisspeptin showed good affinity for GPCR54 and an on-bead version of the peptide, with the required C-terminal amide presented away from the bead was prepared and used for testing possible screening methods. GPCR54 was expressed in a number of formats and a kisspeptin based OBOC library designed and synthesised. Investigation into the C-terminal RF-amide motif of Kisspeptin was also carried out in order to assess the importance of the carbonyl moiety. The corresponding peptide amine was synthesised and the compound biologically assessed. This led to the development of a novel acid labile benzofuranone (ALBA) linker for anchoring amines to a solid support. For the preparation of fluorescent kisspeptin ligands, a novel general synthetic route which gives direct access to single isomer functionalised rhodamine dyes from phthalides has been developed. This circumvents the arduous task of isomer separation usually associated with the synthesis of functionalised rhodamines. The route has been demonstrated with a range of linkage groups and rhodamine types. This rhodamine material was used as a reporter group in various multifunctional reagents synthesised using a trifunctional orthogonally protected backbone (TOBa), which was prepared on a solid support and enables rapid synthesis of trifunctional reagents. This resin takes advantage of protecting group orthogonality and the high yields of peptide bond formation. A series of trifunctional reagents for screening use were prepared using this resin. A proof of concept study was carried out involving the simultaneous labelling and immobilisation of a protein for applications in probing protein-protein interactions. Development of a trifunctional hydroxamic acid containing cross-linker was carried out which takes advantage of its reaction with boronic acids to enable reversible capture on solid support for enrichment of cross-linked peptides. A new benzophenone based heterobifunctional reagent was prepared for protein cross-linking and mass spectrometry analysis. This was shown to give complimentary reactivity to existing cross-linkers, allowing more structural information to be extracted from protein samples.

Positron Emission Tomography (PET) has great value in research and clinical applications from oncology to neurodegenerative disorders. However, there is a barrier in translating biological knowledge into new PET applications due in part to the lack of efficient, widely applicable methods for labelling compounds with PET radioisotopes. Herein, a generic approach to radiolabelling is presented which is direct, broadly applicable and potentially adaptable to either of the two most commonly used PET radioisotopes, 11C and 18F. This approach employs the advantages of solid phase synthesis to achieve selective release of only the desired radiolabelled product from a solid support in a single step, simplifying purification and hence improving synthetic efficiency. Polystyrene resin was functionalised with a 1,2-diol group; this allowed the covalent attachment of compounds bearing boronic acid groups via formation of a boronate ester linkage. A Suzuki-Miyaura reaction with methyl iodide was used to cleave a model compound from the resin in 61% conversion after five minutes. This reaction was adapted to develop a fully automated radiosynthesis with [11C]- methyl iodide which generated a radiolabelled model compound in 2 – 7% non-decay-corrected radiochemical yield. This provided proof of concept for the simultaneous cleavage of compounds from the resin and radiolabelling with 11C. A boronic acid precursor of the known radiotracer [11C]-M-MTEB was attached to the resin and successfully radiolabelled with 11C in 2.4% non-decay-corrected radiochemical yield and 96 – 100% radiochemical purity under the same conditions. Furthermore, the potential adaptability of this solid phase approach to 18F radiolabelling was demonstrated by treatment of the resin-bound small molecules and peptides with potassium bifluoride, which released the compounds rapidly as trifluoroborate salts.

[pt] Este trabalho apresenta um estudo sistemático da sorção de índio de meio iodeto, utilizando espuma de poliuretano à base de poliéter comercial como extrator em fase sólida, visando à pré-concentração e/ou separação de índio de diferentes matrizes de amostras. As características físico-químicas de sorção do sistema foram investigadas por processo em batelada, apresentando rápida cinética e máxima sorção numa faixa significativa de meio ácido ou básico, com coeficientes de distribuição acima de 104 L kg-1 ([KI] maior ou igual 0,6 mol L-1). A análise do equilíbrio de sorção indicou o tetraiodo- indato (MinI4) como a principal espécie sorvida na matriz da espuma; os mecanismos de sorção mais prováveis foram discutidos. A isoterma de Langmuir foi ajustada com êxito sendo obtido um valor de (1,55 mais ou menos 0,02)x10-1 mol kg-1 para a capacidade de saturação. O efeito da temperatura foi avaliado indicando um processo espontâneo e exotérmico caracterizado por sorção química. A reextração do índio da espuma com solução de HCl 1,0 mol L-1 em meio etanol 50% apresentou rápida cinética (10 minutos) e eficiência (97%). O sistema pode ser utilizado para a separação de traços de índio de grandes quantidades de Al, Fe, Zn, Ni, Co, Mn e Ga. Cd e Pb são co-extraídos. Ácido cítrico, F- e EDTA interferem na sorção do índio; tiosulfato de sódio (menor 0,1 mol L-1) e ácido ascórbio (até 0,8 mol L-1) não interferem. O sistema foi avaliado na determinaço de In na presença de 105 vezes Zn, Al, Fe pelo método de adição e recuperação de índio. Os elementos determinados por ICP- OES apresentaram fatores de separação, da ordem de 7,0 x 102 para Zn/In, 1,0x105 para Fe/In e de 5,5x104 para Al/In, com eficiente recuperação de índio. A metodologia desenvolvida foi aplicada para determinar índio por ICP- OES em material de referência padrão de zinco metálico (NIST), apresentando concordância compatível com o valor certificado, para um nível de confiança de 95%. / [en] This work shows a systematic study on indium iodide sorption using commercial polyether-based polyurethane foam as a solid phase extractor in order to preconcentrate and/ or separate indium from different sample matrices. The physico-chemical characteristics of the system sorption were investigated for the batch process. The system has shown rapid kinetic and maximum sorption from a meaningful range of either acid or basic medium and achieves distribution ratios above 104 L kg-1 ([KI] maior ou igual 0.6 mol L-1). Sorption equilibrium analysis indicates the tetraiodo- indate (MInI4) as the main species sorbed on the foam matrix; the more probable mechanisms of sorption were discussed. Langmuir isotherm was successfully fitted and a value of (1.55 mais ou menos 0.02)x10-1 mol kg-1 was obtained for the saturation capacity. The temperature effect was evaluated and indicates a spontaneous and exothermic chemisorption process favored at low temperatures. The indium reextraction from the foam using a HCl 0.1 mol L-1 in ethanol 50% medium solution has also shown a rapid kinetic (10 minutes) and efficiency (97%). The system should be used to separate large quantities of Al, Fe, Zn, Ni, Co, Mn and Ga from trace indium. Cd and Pb are coextracted with indium. Citric acid, F- and EDTA interfere on indium sorption; sodium thiosulfate (menor ou igual 0.1 mol L-1) and ascorbic acid (up to 0.1 mol L-1) do not interfere. The system was evaluated in the determination of indium in the presence of 105 times Zn, Al and Fe by indium addition and recovery technique. The elements determination by ICP-OES showed separation factors around 7.0x102 for Zn/In, 1.0X105 for Fe/In and of 5.5x104 for Al/In, with an efficient recovery of indium. The developed methodology was applied to determine indium in metallic zinc standard reference material (NIST) by ICP-OES and has shown compatible agreement with the certified value at a 95% confidence level.

My dissertation work integrates the techniques of microfabrication, micro/nanofluidics, and bioanalytical chemistry to develop miniaturized devices for healthcare applications. Semiconductor processing techniques including photolithography, physical and chemical vapor deposition, and wet etching are used to build these devices in silicon and polymeric materials. On-chip micro-/nanochannels, pumps, and valves are used to manipulate the flow of fluid in these devices. Analytical techniques such as size-based filtration, solid-phase extraction (SPE), sample enrichment, on-chip labeling, microchip electrophoresis (µCE), and laser induced fluorescence (LIF) are utilized to analyze biomolecules. Such miniaturized devices offer the advantages of rapid analysis, low cost, and lab-on-a-chip scale integration that can potentially be used for point-of-care applications.The first project involves construction of sieving devices on a silicon substrate, which can separate sub-100-nm biostructures based on their size. Devices consist of an array of 200 parallel nanochannels with a height step in each channel, an injection reservoir, and a waste reservoir. Height steps are used to sieve the protein mixture based on size as the protein solution flows through channels via capillary action. Proteins smaller than the height step reach the end of the channels while larger proteins stop at the height step, resulting in separation. A process is optimized to fabricate 10-100 nm tall channels with improved reliability and shorter fabrication time. Furthermore, a protocol is developed to reduce the electrostatic interaction between proteins and channel walls, which allows the study of size-selective trapping of five proteins in this system. The effects of protein size and concentration on protein trapping behavior are evaluated. A model is also developed to predict the trapping behavior of different size proteins in these devices. Additionally, the influence of buffer ionic strength, which can change the effective cross-sectional area of nanochannels and trapping of proteins at height steps, is explored in nanochannels. The ionic strength inversely correlates with electric double layer thickness. Overall, this work lays a foundation for developing nanofluidic-based sieving systems with potential applications in lipoprotein fractionation, protein aggregate studies in biopharmaceuticals, and protein preconcentration. The second project focuses on designing and developing a microfluidic-based platform for preterm birth (PTB) diagnosis. PTB is a pregnancy complication that involves delivery before 37 weeks of gestation, and causes many newborn deaths and illnesses worldwide. Several serum PTB biomarkers have recently been identified, including three peptides and six proteins. To provide rapid analysis of these PTB biomarkers, an integrated SPE and µCE device is assembled that provides sample enrichment, on-chip labeling, and separation. The integrated device is a multi-layer structure consisting of polydimethylsiloxane valves with a peristaltic pump, and a porous polymer monolith in a thermoplastic layer. The valves and pump are fabricated using soft lithography to enable pressure-based sample actuation, as an alternative to electrokinetic operation. Porous monolithic columns are synthesized in the SPE unit using UV photopolymerization of a mixture consisting of monomer, cross-linker, photoinitiator, and various porogens. The hydrophobic surface and porous structure of the monolith allow both protein retention and easy flow. I have optimized the conditions for ferritin retention, on-chip labelling, elution, and µCE in a pressure-actuated device. Overall functionality of the integrated device in terms of pressure-controlled flow, protein retention/elution, and on-chip labelling and separation is demonstrated using a PTB biomarker (ferritin). Moreover, I have developed a µCE protocol to separate four PTB biomarkers, including three peptides and one protein. In the future, an immunoaffinity extraction unit will be integrated with SPE and µCE to enable rapid, on-chip analysis of PTB biomarkers. This integrated system can be used to analyze other disease biomarkers as well.

The primary focus of my work has been to prepare new solid adsorbents for solid phase microextraction (SPME) via sputtering of silicon. The orientation of the silica substrates/fibers and the sputtering pressure induced the formation of porous and columnar structures. Sputtering was performed for different times to yield fibers with different thicknesses. Piranha treatment of the surface increased the concentration of silanol groups, which underwent condensation with vapor deposited octadecyldimethylmonomethoxy silane to incorporate octadecyl chains onto the fiber surfaces. Silanized, sputtered fibers were preconditioned for 3 h at 320 °C to remove the unreacted chains. Comparison of the extraction efficiencies of 1.0 and 2.0 µm sputtered, silanized fibers with a commercial fiber (7 µm PDMS) for a series of analyte mixtures, which included alkanes, alcohols, aldehydes, esters, and amines, was demonstrated. The silanized, sputtered fiber performed better than the commercial fiber in extraction of most of the compounds. These fibers demonstrated long life as no degradation was seen even after 300 extractions. Carry-over between runs was not observed. The repeatability of the sputtered fibers was similar to commercial ones. The extraction of more than 50 compounds from a real world botanical sample using the 2.0 µm sputtered, silanized fiber was also demonstrated. In my second project, a facile method for the preparation of superhydrophobic surfaces (SHS) on glass and silicon surfaces was developed. A two-tier topography (needed for an SHS) was created in 60 min by the aggregation of nanosilica during in situ urea-formaldehyde polymerization. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) demonstrated rough topography. Vapor deposition of a low surface energy silane imparted hydrophobicity, which was confirmed by the presence of an F 1s signal in X-ray photoelectron spectroscopy (XPS). The prepared surfaces exhibited water contact angles (WCA) of greater than 150 °C with very low sliding angles. In my third project, a multilayer assembly of nitrilotris(methylene)triphosphonic acid, a corrosion inhibitor, and zirconium was constructed on alumina at room temperature. Attempts to prepare a layer-by-layer assembly at higher temperature (70 °C) was unsuccessful due to etching of the alumina surface. A suite of analytical techniques, XPS, AFM, time-of-flight secondary ion mass spectrometry, and spectroscopic ellipsometry was used to characterize these surfaces. This thesis also contains appendices of tutorial articles I wrote on modeling in ellipsometry, and data analysis tools (classical least squares and multivariate curve resolution).

One of the poly-Si thin-film cells developed at the University of New South Wales (UNSW) is the EVA cell. In this work, SiN films for EVA cells as an antireflection/barrier coating were investigated. In addition, the effect of hydrogenation pre-treatment of solid phase crystallisation (SPC) on grain size and open-circuit voltage (Voc) was investigated. The SiN films deposited by PECVD were examined for uniformity of the thickness and the refractive index of the films across the position of the samples in the PECVD deposition system. A spectrophotometric analysis was used to determine these film properties. It was found that these properties were very uniform over the deposition area. Good repeatability of the depositions was also observed. A series of SiN film depositions by reactive sputtering were also performed to optimize the deposition process. Parameters adjusted during the deposition were nitrogen flow rate, substrate bias, and substrate temperature. By investigating the deposition rate, refractive index, and surface roughness of the films, the three deposition parameters were optimised. The effects of post SiN deposition treatments (a-Si deposition, SPC, RTA, and hydrogenation) on thickness and refractive index of both SiN films deposited by PECVD and reactive sputtering were investigated by using samples which have the same structure as the EVA cells. The thickness of the PECVD SiN films decreased about 6 % after all the treatments. On the other hand, the thickness reductions of the reactively sputtered SiN films were very small. The refractive index of the PECVD SiN films increased about 0.6 % after the treatments, whereas that of the reactively sputtered SiN films decreased 1.3 % after the treatments. As a possible method to improve the performance of EVA cells, hydrogenation of a-Si was investigated as a pre-treatment of SPC process. There were no obvious differences in the grainsize and the Voc of the EVA cells with and without the hydrogenation. Therefore it is likely that the hydrogenation pre-treatment of SPC does not have a beneficial effect on the performance of EVA cells.

<p>This thesis investigates three different surface modifications, and the route to design and synthesize them. The thesis is therefore divided into three sub- projects. (i.) Design and synthesis of a peptide which secondary structure could be controlled by a negatively charged surface. (ii.) Design and synthesis of a cyclic peptide, that would self-organize prior to surface interaction, using the type I anti-freeze protein of a winter flounder as template. (iii.) The use of solid-phase synthesis to make the synthesis of SAM-molecules easier.</p>