abstract: Cellular redox phenomena are essential for the life of organisms. Described here is a summary of the synthesis of a number of redox-cycling therapeutic agents. The work centers on the synthesis of antitumor antibiotic bleomycin congeners. In addition, the synthesis of pyridinol analogues of alpha-tocopherol is also described. The bleomycins (BLMs) are a group of glycopeptide antibiotics that have been used clinically to treat several types of cancers. The antitumor activity of BLM is thought to be related to its degradation of DNA, and possibly RNA. Previous studies have indicated that the methylvalerate subunit of bleomycin plays an important role in facilitating DNA cleavage by bleomycin and deglycobleomycin. A series of methylvalerate analogues have been synthesized and incorporated into deglycobleomycin congeners by the use of solid-phase synthesis. All of the deglycobleomycin analogues were found to effect the relaxation of plasmid DNA. Those analogues having aromatic C4-substituents exhibited cleavage efficiency comparable to that of deglycoBLM A5. Some, but not all, of the deglycoBLM analogues were also capable of mediating sequence-selective DNA cleavage. The second project focused on the synthesis of bicyclic pyridinol analogues of alpha-tocopherol. Bicyclic pyridinol antioxidants have recently been reported to suppress the autoxidation of methyl linoleate more effectively than alpha-tocopherol. However, the complexity of the synthetic routes has hampered their further development as therapeutic agents. Described herein is a concise synthesis of two bicyclic pridinol antioxidants and a facile approach to their derivatives with simple alkyl chains attached to the antioxidant core. These analogues were shown to retain biological activity and exhibit tocopherol-like behaviour. / Dissertation/Thesis / Ph.D. Chemistry 2011

Subsurface contamination is common at nuclear sites and it is likely that radioactive wastes will be managed in the long-term via burial in a deep Geological Disposal Facility (GDF). The migration of radionuclides in the geosphere from such sites is a major societal concern. In particular, long-lived, redox-active radionuclides (in the case of this thesis: 99Tc and Np) can migrate over large distances due to their high solubility under oxic conditions. Bioremediation has been proposed as a mechanism to limit the migration of 99Tc and Np in the environment. Here, an electron donor is supplied to the subsurface and soluble Tc(VII) and Np(V) are reduced to poorly soluble Tc(IV) and Np(IV), respectively. Reduction occurs via direct microbial action (termed bioreduction) or through radionuclide reaction with the by-products of microbial metabolism (primarily Fe(II)). Given the ubiquity of microorganisms and Fe in the geosphere, similar reactions can be expected in the deep subsurface surrounding a GDF. Once reduced, the long-term stability of the Tc(IV) and Np(IV) phases will significantly impact migration rates. Oxidative dissolution of Tc(IV)- and Np(IV)-bearing solids has been demonstrated in the literature and can be pervasive, thus questioning the efficacy of bioreduction. However, these studies have been conducted over short time-scales and during a single period of oxidation. Given the long half-life of 99Tc and Np and the ephemeral nature of redox conditions in the subsurface, there is a need to better understand 99Tc and Np biogeochemistry during longer time-scales and across multiple redox cycles. In this thesis, microcosm experiments have been used to address this knowledge gap. Sediment and groundwater used in the microcosms were representative of the Sellafield Ltd. nuclear site. For Tc, three successive redox cycles (reduction followed by oxidation with O2) over 2 years, gradually reduced the extent of Tc remobilisation during oxidation, and molecular scale characterisation of solids revealed that sediment associated Tc was always present as Tc(IV). Further, over time sequential extractions and EXAFS revealed an increased significance of Tc-Fe bonding in the sediment at the expense of TcO2. Despite this, a small but significant fraction of Tc(IV) was also found to be stable in solution during the experiments and XAS and TEM analysis suggested this was Tc(IV) associated with magnetite colloids. In other experiments completed with higher concentrations of bioavailable Fe (added as ferrihydrite to sediments, and in pure culture experiments with Geobacter sulfurreducens), the significance of Tc-Fe bonding was again highlighted, and potential Tc(IV) incorporation into biogenic magnetite was also documented. In experiments with Np, virtually all of the Np(V) added to oxic groundwater was removed to the sediment commensurate with microbially mediated Fe(III) reduction. Further, in systems with elevated bioavailable Fe, Np removal from solution was more extensive. Taken together, the data for Tc and Np reveals critical links between redox-active radionuclides and Fe cycling in sediments over periods of years and across multiple redox cycles. Furthermore, these processes help to predict the long-term fate of radioactive contamination at the Sellafield Ltd. nuclear site and have implications for contaminated land worldwide.

Human exposure to arsenic in groundwater is a global concern, and arsenic mobility in groundwater is often controlled by Fe mineral dissolution and precipitation. Additionally, Fe(II)-catalyzed recrystallization of Fe oxides has been shown to enable trace element release from and incorporation into Fe oxides. However, the effect of As(V) on the Fe(II)-catalyzed recrystallization of Fe oxides such as goethite, magnetite, and ferrihydrite remains unclear. Here, we measured the extent of Fe atom exchange between aqueous Fe(II) and magnetite, goethite, or ferrihydrite in the presence of As(V) by reacting isotopically "normal" Fe oxides with 57Fe-enriched aqueous Fe(II). At lower levels of adsorption (≤13.3 μM), As(V) had little influence on the rate or extent of Fe(II)-catalyzed Fe atom exchange in goethite or magnetite. However, Fe atom exchange was increasingly inhibited as As(V) concentration increased above 100 μM. Additionally, adsorbed As(V) may be incorporated into magnetite over time in the presence and absence of added aqueous Fe(II) as indicated by X-ray absorption spectroscopy (XAS) and chemical extraction data, with more rapid incorporation in the absence of added Fe(II). XAS and chemical extraction data are also consistent with the incorporation of As(V) during goethite and magnetite precipitation. Additionally, atom exchange data indicated that low levels of As(V) coprecipitation (As:Fe = 0.0005-0.0155) had little influence on the rate or extent of Fe(II)-catalyzed Fe atom exchange in goethite or magnetite. Atom exchange data indicated that ferrihydrite likely transforms via a dissolution-reprecipitation mechanism both to lepidocrocite at 0.2 mM Fe(II) and to magnetite at 5 mM Fe(II). The presence of 206 μM As(V) slowed the transformation of ferrihydrite to more crystalline iron minerals and slowed the rate of atom exchange between aqueous Fe(II) and ferrihydrite. However, the degree of atom exchange did not directly correlate with the amount of ferrihydrite transformed. In summary, Fe oxide recrystallization processes may affect As(V) uptake and release in the environment, and As(V) may inhibit Fe(II)-catalyzed Fe oxide recrystallization.

This research is directed towards developing a more sensitive and rapid electrochemical sensor for enzyme labeled immunoassays by coupling redox cycling at interdigitated electrode arrays (IDA) with the enzyme label b-galactosidase. Coplanar and comb IDA electrodes with a 2.4 mm gap were fabricated and their redox cycling currents were measured. ANSYS was used to model steady state currents for electrodes with different geometries. Comb IDA electrodes enhanced the signal about 3 times more than the coplanar IDAs, which agreed with the results of the simulation. Magnetic microbead-based enzyme assay, as a typical example of biochemical detection, was done using the comb and coplanar IDAs. The enzymes could be placed close to the sensing electrodes (~10 mm for the comb IDAs) and detection took less than 1 min with a limit of detection of 70 amole of b-galactosidase. We conclude that faster and more sensitive assays can be achieved with the comb IDA. A paramagnetic bead assay has also been demonstrated for detection of bacteriophage MS2, used as a simulant for biothreat viruses, such as small pox. The immunoassay was carried out in a microfluidic format with the IDA, reference and counter electrodes integrated on the same chip. Detection of 90 ng/mL MS2 or 1.5x1010 MS2 particles/mL was demonstrated.

Biosensors are used for the detection of a range of analytes for applications in healthcare, food production, environmental monitoring and biodefence. However, many biosensing platforms are large, expensive, require skilled operators or necessitate the analyte to be labelled. Direct electrochemical detection methods present a particularly attractive platform due to the simplified instrumentation when compared to other techniques such as fluorescence-based biosensors. With modern integrated circuit capabilities electrochemical biosensors offer greater suitability for monolithic integration with any necessary signal processing circuitry. This thesis explores micro- and nanogap devices for both redox cycling and dielectric spectroscopy sensing mechanisms. By using two electrodes with interelectrode separation down to distances in the micro- and nanometre scale, several benefits can be realised. Firstly the close proximity of the two electrodes significantly reduces the interdiffusion time. This allows an electroactive species to be rapidly shuttled across the gap and switched between reduced and oxidised states. The result is feedback amplification of the amperometric response, increasing the signal. The second benefit is that the screening effect caused by electric double layers at the electrode–electrolyte interface is reduced due to the electric double layers occupying a larger fraction of the sensing volume. This significantly improves the sensor suitability for dielectric spectroscopy by increasing the potential drop across the biolayer. These two sensing mechanisms are demonstrated using a large area dual-plate microgap device for the detection of two different analytes. Utilising the first mode, detection of cysteine–cystine, an important redox couple involved in the signalling mechanism for the regulation of protein function, interaction and localisation is shown. The microgap device is then used for dielectric spectroscopy sensing of a mannose-specific uropathogenic Escherichia coli strain whilst also demonstrating the effect of ionic concentration on the capacitive response. The response of these devices is highly dependent on the interelectrode separation as well as the surface area of the electrodes. However, fabrication of large-area nanogap devices presents a significant challenge. This meant that careful optimisation and the development of novel techniques was necessary. This work reports the design, fabrication and characterisation of both a vertical and a horizontal coplanar large area nanogap device. The vertical nanogap device is fabricated using an inductively-coupled plasma reactive ion etching process to create a channel in a silicon substrate. A lower electrode is then optically patterned in the channel before anodically bonding a second identical electrode patterned on glass directly above. The horizontal nanogap device uses a different approach, utilising a state-of-the-art electron-beam lithography system to create a long serpentine nanogap with passivation to reduce fringing effects. The design allows the electron-beam lithography step to be substituted with nanoimprint lithography to reduce cost and improve throughput. Both of these devices have integrated microfluidic channels and provide a capacity for relatively high-throughput production.

No description available.

Mechanistic aspects of carbonaceous aerosol toxicity were examined with respect to the ability of particles to catalyse reactive oxygen species-generating redox cycling reactions. To investigate the role of secondary organic material, we examined two systems. In the first, two-stroke engine exhaust particles were found to increase their ability to catalyse redox cycling in the presence of a reducing agent, dithiothreitol (DTT), when the exhaust was exposed to ozone. This occurred through deposition of redox-active secondary organic aerosol (SOA) onto the particle that was ten times more redox active per microgram than the primary engine particle. In the second system, naphthalene SOA formed highly redox active particles. Activity was strongly correlated to the amount of the 1,4- and 1,2-naphthoquinone measured in the particle phase. However, these species and the newly quantified naphthalene oxidation product 5-hydroxy-1,4-naphthoquinone accounted for only 30% of the observed DTT decay from the particles. Gas-particle partitioning coefficients suggest 1,4- and 1,2-naphthoquinone are not strong contributors to ambient particle redox activity at 25°C. However, a large number of redox active species are unidentified. Some of these may be highly oxidised products of sufficiently low vapour pressure to be atmospherically relevant. DTT activity of diesel particles was found to be high per unit mass. The activity was found to be associated with the insoluble fraction as filtration of the particles nearly eliminated DTT decay. Neither methanol nor dichloromethane extracts of diesel particles exhibited redox activity, indicating that the redox active species are associated with the black carbon portion of the particles. Examination of particle concentration techniques found that use of water condensation to grow and concentrate particles introduced a large organic artefact to the particles. Experiments with concentrated inorganic particles suggest that the source of this artefact is from irreversible uptake of water-soluble volatile organic compounds. Overall, carbonaceous redox active species can be thought of as a continuum from small, water-soluble species to redox active functionalities on elemental carbon backbones. In addition to clearly defined, quantifiable species, future research may need to consider examining broader chemical classes or redox-active chemical functionalities to overcome the inherent complexity of these constituents.

Mechanistic aspects of carbonaceous aerosol toxicity were examined with respect to the ability of particles to catalyse reactive oxygen species-generating redox cycling reactions. To investigate the role of secondary organic material, we examined two systems. In the first, two-stroke engine exhaust particles were found to increase their ability to catalyse redox cycling in the presence of a reducing agent, dithiothreitol (DTT), when the exhaust was exposed to ozone. This occurred through deposition of redox-active secondary organic aerosol (SOA) onto the particle that was ten times more redox active per microgram than the primary engine particle. In the second system, naphthalene SOA formed highly redox active particles. Activity was strongly correlated to the amount of the 1,4- and 1,2-naphthoquinone measured in the particle phase. However, these species and the newly quantified naphthalene oxidation product 5-hydroxy-1,4-naphthoquinone accounted for only 30% of the observed DTT decay from the particles. Gas-particle partitioning coefficients suggest 1,4- and 1,2-naphthoquinone are not strong contributors to ambient particle redox activity at 25°C. However, a large number of redox active species are unidentified. Some of these may be highly oxidised products of sufficiently low vapour pressure to be atmospherically relevant. DTT activity of diesel particles was found to be high per unit mass. The activity was found to be associated with the insoluble fraction as filtration of the particles nearly eliminated DTT decay. Neither methanol nor dichloromethane extracts of diesel particles exhibited redox activity, indicating that the redox active species are associated with the black carbon portion of the particles. Examination of particle concentration techniques found that use of water condensation to grow and concentrate particles introduced a large organic artefact to the particles. Experiments with concentrated inorganic particles suggest that the source of this artefact is from irreversible uptake of water-soluble volatile organic compounds. Overall, carbonaceous redox active species can be thought of as a continuum from small, water-soluble species to redox active functionalities on elemental carbon backbones. In addition to clearly defined, quantifiable species, future research may need to consider examining broader chemical classes or redox-active chemical functionalities to overcome the inherent complexity of these constituents.

L'arsenic est un metalloïde toxique et cancérigène. Ubiquiste dans la pedosphere, il est très sensibleaux fluctuations des conditions redox du sol, ce qui influe significativement sa toxicité et mobilité. Nousétudions le cycle biogéochimique global de l'arsenic, en tenant compte de l'usage croissant des ressources, etpassons en revue l'importance respective de l’arsenic geogénique et anthropogénique dans l’environnement.La contamination à l’arsenic est souvent diffuse dans les bassins sédimentaires de l'Europe. Cependant, desconcentrations dans l'eau interstitielle du sol peuvent être élevées lors de périodes de saturation du solcausées par la monté des eaux souterraines ou les inondations, prévues d'augmenter dû aux changementsclimatiques. La spectrométrie de fluorescence X quantitative et sans standard a été utilisée pour analyserl'arsenic dans des sols relativement contaminés de la plaine alluviale de la Saône au moyen de protocoles depréparation d'échantillons conçus pour optimiser la précision d'analyse et l'exactitude in situ aux bassesconcentrations d'arsenic. L'arsenic dans ces sols est associe aux (hydr)oxydes du fer et de manganèse de lataille d'argile colloïdale. Ceux-ci subissent une dissolution réductrice par les microorganismes lors desinondations, libérant une importante concentration d'arsenic dans la phase aqueuse. Si, par la suite, l'arsenicdégagé n'est pas éliminé avec l'eau de crue évacuée, il est ré-immobilisé pendant l'oxydation du sol et lareprécipitation des oxydes métalliques. Grâce à une combinaison novatrice d'analyses chimiques par voiehumide, d’écologie microbienne, de spectroscopie ainsi que de modélisation thermodynamique et cinétique,nous démontrons que les cycles d'oxydo-réduction séquentiels entraînent une atténuation d'arsenic aqueuxdans des conditions réductrices dû à la coprécipitation croissante, et a une diminution de l'activitémicrobienne causée par l’appauvrissement en matière organique labile. Des processus d'atténuationsimilaires sont observés en l'absence d'activité microbienne pour Cr et As dans des argiles pyriteuses lorsquecelles-ci sont exposés aux oscillations redox provoquées par l'ajout de substances humiques réduites. Ainsi,nous montrons que les effets cumulatifs de cycles redox successifs sont extrêmement importants pour lamobilité de divers contaminants dans l'environnement. / Arsenic is a toxic and carcinogenic metalloid, ubiquitous in the pedosphere and highly sensitive tofluctuations in soil redox conditions which dramatically influence both its toxicity and mobility. We reviewthe global biogeochemical cycle of arsenic in light of increasing resource usage and re-evaluate theimportance of anthropogenic and geogenic arsenic inputs to the exogenic cycle. Arsenic contamination isoften diffuse in European sedimentary basins. Despite this, concentrations in soil pore-water may be highduring periods of soil saturation caused by rising groundwater or surface flooding which is predicted toincrease due to climatic change. Standardless quantitative X-ray fluorescence spectrometry is used toanalyse for arsenic in moderately contaminated soils on the alluvial plain of the Saône River with samplepreparation protocols designed to optimize analytical precision and accuracy in-situ at trace arsenicconcentrations. Arsenic in these soils is shown to be associated with colloidal and clay sized iron andmanganese (hydr)oxides which undergo microbially mediated reductive dissolution during flooding, releasingsubstantial arsenic to the aqueous phase. If released arsenic is not subsequently removed with recedingflood water it is re-immobilized during soil oxidation and re-precipitation of metal oxides. We demonstratethrough a novel combination of wet chemistry, microbial ecology, spectroscopy and thermodynamic andkinetic modelling that sequential reduction-oxidation cycles result in aqueous arsenic attenuation duringreducing conditions due to increased co-precipitation and decreases in microbial activity due to depletion oflabile organic matter. Similar attenuation processes are observed in the absence of microbial activity for Crand As in pyrite-bearing clays when subjected to redox oscillations induced by addition of reduced humicsubstances. We demonstrate that the cumulative effects of successive redox cycling are therefore of greatimportance to contaminant mobility in a variety of environments. / El arsénico es un metaloide tóxico y cancerígeno, ubicuo en la pedosfera y altamente sensible a lasfluctuaciones de las condiciones redox del suelo, las cuales controlan tanto su toxicidad como su movilidad.La presente tesis doctoral tiene como objeto de estudio el ciclo biogeoquímico global del arsénico y examinala importancia de los aportes del arsénico antropogénicos y geogénicos al ciclo exógeno tomando en cuentael uso creciente de recursos.La contaminación con arsénico es generalmente difusa en las cuencas sedimentarias europeas. No obstante,las concentraciones en las aguas intersticiales del suelo pueden ser elevadas durante los periodos desaturación causados por el aumento de aguas subterráneas o inundaciones, cuyo incremento se prevédebido a los cambios climáticos. La espectrometría de fluorescencia de Rayos-X cuantitativa y sin estándar esutilizada para analizar el arsénico en suelos relativamente contaminados en la llanura aluvial del río Saône,mediante protocolos de preparación de muestras diseñados para mejorar la precisión analítica y la exactitudin-situ a bajas concentraciones de arsénico. La presencia de arsénico en estos suelos demuestra estarasociada a los (hidr)óxidos de hierro y de manganeso de tamaño de arcilla coloidal, los cuales experimentanuna disolución reductora por acción microbiana durante las inundaciones, liberando así una importanteconcentración de arsénico en la fase acuosa. Si, posteriormente, el arsénico despedido no se elimina con elagua saliente, éste se vuelve a inmovilizar durante la oxidación del suelo y la re-precipitación de óxidosmetálicos. Gracias a una combinación innovadora de análisis químicos por vía húmeda, ecología microbiana,espectroscopia, así como modelado termodinámico y cinético, demostramos que los ciclos de oxidoreducciónsecuenciales provocan una atenuación de arsénico acuoso durante condiciones de reduccióndebido al aumento de coprecipitacion y disminución de la actividad microbiana causada por el agotamientode materia orgánica lábil. Se observan procesos de atenuación similares en caso de ausencia de actividadmicrobiana para Cr y As en arcillas piritas cuando son sometidos a oscilaciones de redox inducidas mediantela adición de sustancias húmicas reducidas. Es así como demostramos que los efectos acumulativos de ciclossucesivos de redox son muy importantes para la movilidad contaminante en una variedad de ambientes.

Mercury (Hg) is a global pollutant and potent neurotoxin that bioaccumulates in aquatic and terrestrial food webs as monomethylmercury (MeHg). Anaerobic microbes are largely responsible for MeHg production, which depends on the bioavailability of inorganic Hg substrates to methylators. Hg redox cycling pathways such as Hg reduction play a key role in determining Hg’s availability in the environment. Although abiotic photochemical Hg reduction typically dominates in oxic surface environments, Hg reduction pathways mediated by photosynthetic and anaerobic microbes are thought to play an important role in anoxic habitats where light is limited and MeHg production occurs. Currently, the physiological mechanisms driving phototrophic and anaerobic Hg reduction remain poorly understood. The main objective of my thesis is to provide mechanistic details on novel anaerobic and phototrophic Hg reduction pathways. I used a combination of physiological, biochemical and trace Hg analytical techniques to study Hg reduction pathways in a variety of anaerobic and photosynthetic bacteria. I demonstrated that Hg redox cycling was directly coupled to anoxygenic photosynthesis in aquatic purple non-sulphur bacteria that reduced HgII when cells incurred a redox imbalance. I discovered that terrestrial fermentative bacteria reduced Hg through pathways that relied on the generation of reduced redox cofactors. I also showed that sulphur assimilation controlled Hg reduction in an anoxygenic phototroph isolated from a rice paddy. In addition, I developed methods to explore cryptic anaerobic Hg redox cycling pathways using Hg stable isotope fractionation. At its core, my thesis underscores the intimate relationship between cell redox state and microbial Hg reduction and suggests a wide diversity of microbes can participate in anaerobic Hg redox cycling.