Oxygenic photosynthesis in plants, algae and cyanobacteria converts sunlight into chemical energy. In this process electrons are transferred from water molecules to CO2 leading to the assembly of carbohydrates, the building blocks of life. A cluster of four manganese ions and one calcium ion, linked together by five oxygen bridges, constitutes the catalyst for water oxidation in photosystem II (Mn4CaO5 cluster). This cluster stores up to four oxidizing equivalents (S0,..,S4 states), which are then used in a concerted reaction to convert two substrate water molecules into molecular oxygen. The reaction mechanism of this four-electron four-proton reaction is not settled yet and several hypotheses have been put forward. The work presented in this thesis aims at clarifying several aspects of the water oxidation reaction by analyzing the mode of substrate water binding to the Mn4CaO5 cluster. Time-resolved membrane-inlet mass spectrometric detection of flash-induced O2 production after fast H218O labelling was employed to study the exchange rates between substrate waters bound to the Mn4CaO5 cluster and the surrounding bulk water. By employing this approach to dimeric photosystem II core complexes of the red alga Cyanidoschyzon merolae it was demonstrated that both substrate water molecules are already bound in the S2 state of the Mn4CaO5 cluster. This was confirmed with samples from the thermophilic cyanobacterium Thermosynechococcus elongatus. Addition of the water analogue ammonia, that is shown to bind to the Mn4CaO5 cluster by replacing the crystallographic water W1, did not significantly affect the exchange rates of the two substrate waters. Thus, these experiments exclude that W1 is a substrate water molecule. The mechanism of O-O bond formation was studied by characterizing the substrate exchange in the S3YZ● state. For this the half-life time of this transient state into S0 was extended from 1.1 ms to 45 ms by replacing the native cofactors Ca2+ and Cl- by Sr2+ and I-. The data show that both substrate waters exchange significantly slower in the S3YZ● state than in the S3 state. A detailed discussion of this finding lead to the conclusions that (i) the calcium ion in the Mn4CaO5 cluster is not a substrate binding site and (ii) O-O bond formation occurs via the direct coupling between two Mn-bound water-derived oxygens, which were assigned to be the terminal water/hydroxy ligand W2 and the central oxo-bridging O5. The driving force for the O2 producing S4→S0 transition was studied by comparing the effects of N2 and O2 pressures of about 20 bar on the flash-induced O2 production of photosystem II samples containing either the native cofactors Ca2+ and Cl- or the surrogates Sr2+ and Br-. While for the Ca/Cl-PSII samples no product inhibition was observed, a kinetic limitation of O2 production was found for the Sr/Br-PSII samples under O2 pressure. This was tentatively assigned to a significant slowdown of the O2 release in the Sr/Br-PSII samples. In addition, the equilibrium between the S0 state and the early intermediates of the S4 state family was studied under 18O2 atmosphere in photosystem II centers devoid of tyrosine YD. Water-exchange in the transiently formed early S4 states would have led to 16,18O2 release, but none was observed during a three day incubation time. Both experiments thus indicate that the S4→S0 transition has a large driving force. Thus, photosynthesis is not limited by the O2 partial pressure in the atmosphere.

Manual collection and processing of seawater samples for dissolved gas analyses are technically challenging, time consuming and costly. Accordingly, in situ analysis techniques present attractive alternatives to conventional gas measurement procedures. To meet the demands of sustained, high-resolution chemical observations of the oceans, the University of South Florida and SRI International developed underwater mass spectrometer systems for quantitative measurements of dissolved gases and volatile organic compounds. This work describes the influence of variable in situ conditions on the performance of a membrane introduction mass spectrometer used for measurements in both the water column and sediment porewater. Laboratory experiments to simulate the effects of field conditions on the membrane were performed by varying sample flow rate, salinity, hydrostatic pressure, and chemistry. Data indicate that membrane permeability has a strong dependence on hydrostatic pressure, and a weak dependence on salinity. Under slow flow conditions bicarbonates in solution contributed to carbon dioxide instrument response as a result of carbon system equilibration processes in the boundary layer at the membrane interface. In addition, method development was undertaken to enable underwater sediment porewater analyses and quantitative (calibrated) measurements of total dissolved inorganic carbon (DIC). This work establishes the capability of membrane introduction mass spectrometry to measure two compatible variables (DIC and dissolved CO2) for comprehensive CO2-system characterizations. In addition to laboratory studies three types of field observation were obtained in this work. High-resolution vertical profiles of dissolved gases in the Gulf of Mexico were obtained through system calibration and characterization of the influence of hydrostatic pressure on the behavior of polydimethylsiloxane membranes. In the South Atlantic Bight, sediment porewater profiles of dissolved gases were repeatedly obtained over a 54 hr period. Data trends were in agreement with high remineralization rates facilitated by porewater advection. Finally, time-series underwater DIC measurements that were undertaken proved to be in good accord with results obtained using conventional techniques. These measurements constitute the first quantitative observations of dissolved gas ocean profiles, sediment porewater profiles, and DIC measurements by underwater mass spectrometry.

No description available.

This dissertation presents the development of novel nano-composite membranes as introduction systems for mass spectrometers. These nano-composite membranes incorporate anodic aluminum oxide (AAO) membranes as templates that can be used by themselves or modified by a variety of chemical deposition processes. Two types of nano-composite membranes are presented. The first nano-composite membrane has carbon deposited within the pores of an AAO membrane. The second nano-composite membrane is made by coating an AAO membrane with a thin polymer film. The following chapters describe the transmission properties these nano-composite membranes and compare them to conventional mass spectrometry introduction systems. The nano- composite membranes were finally coupled to the inlet system of an underwater mass spectrometer revealing their utility in field deployments.

Marine nitrogen (N) is an essential nutrient for all oceanic organisms. The cycling of N between biologically available and unavailable forms occurs through numerous reactions. Because of the vast number of reactions and chemical species involved, the N cycle is still not well understood. This dissertation focuses on understanding some of the reactions involved in the cycling of marine N, as well as improving techniques used to measure dissolved N2 gas. The largest loss term for global marine N is a reaction called denitrification. In this work, denitrification was measured in the sandy sediments of the Georgia continental shelf, an area where this reaction was thought to be unlikely because of the physical properties of the sediments. Nitrogen fixation, which is a reaction that produces biologically available N, was detected in Georgia estuarine sediments. N fixation was measured concurrently with denitrification in these sediments, resulting in a much smaller net loss of marine N than previously thought. Lastly, membrane inlet mass spectrometry (MIMS) is a technique that measures dissolved N2, the end product of denitrification and a reactant in N fixation reactions. This study suggests that N2 measurements by MIMS are influenced by O2 concentrations due to pressure differences inside of the ion source of the mass spectrometer. These findings seek to improve denitrification measurements using MIMS on samples with varying O2 concentrations. In conclusion, this dissertation suggests that the marine N cycle is more dynamic than has been suggested, due to the recognition of input and loss reactions in a wider range of marine and estuarine environments. However, improvements in the understanding of MIMS will help with direct measurements with reactions involved in the global marine N cycle.

Over the last few decades, membrane introduction mass spectrometry (MIMS) has been established as a robust tool for the on-line continuous monitoring of trace gases and volatile organic compounds. However, the range of amenable anlaytes has been limited by the need for molecules to pervaporate into a gaseous acceptor phase, or high vacuum environment of a mass spectrometer. This thesis expands the range of amenable analytes for MIMS to include larger, less volatile molecules (e.g., 200 to 500 Da), such as pharmaceuticals, persistent organic pollutants, and small biomolecules. This was achieved through the use of a liquid|membrane|liquid interface. We distinguish the technique from conventional MIMS, which uses a gaseous acceptor phase, by inserting the prefix ‘condensed phase’ to emphasize the use of a solvent acceptor phase – thus yielding CP-MIMS. An initial flow-cell interface with a methanol acceptor phase was characterized, yielding detection limits for model analytes in pptr to ppb, and analyte response times from 1-10 minutes. The flow cell interface was miniaturized into an immersion style CP-MIMS probe (~2 cm), which allowed for analysis of smaller volume samples and improved membrane washing capabilities. Comparable detection limits were observed for the immersion probe, however, it was noticed that significant analyte depletion was observed for samples under 2 mL. In addition, each of the developed membrane interfaces were observed to suffer from ionization suppression effects from complex samples when paired with ESI. Several strategies for mitigating ionization suppression using CP-MIMS are presented, including the use of a continuously infused internal standard present within the acceptor solvent. The developed CP-MIMS system was challenged with the analysis of naphthenic acids (a complex mixture of aliphatic carboxylic acids) directly in contaminated real-world samples. The method used negative ESI to rapidly screen and mass profile aqueous samples for naphthenic acids (as [M-H]-), with sample duty cycles ~20 min. However, it was found that Negative ESI did not differentiate hydroxylated and carboxylated analytes, and both species contributed signal to the total naphthenic acid concentration. To increase method specificity for carboxylic acids, barium ion chemistry was used in conjunction with positive ion tandem mass spectrometry. Common product ions were used to quantify carboxylated analytes, while a qualifier ion was used to confirm the functionality. The increased selectivity afforded by the barium ion chemistry was at the cost of a modest increase in detection limits. CP-MIMS has been established as a technique capable of the direct analysis of real-world samples, and shows promise as a rapid screening method for amenable environmental contaminants and/or biomolecules. / Graduate / 0486 / 0485 / kyle.duncan@viu.ca

A rapidly growing topic of great interest is the adaptation of benchtop analytical instrumentation for use in outdoor harsh environments. Some of the areas that stand to benefit from field instrumentation development include government agencies involved with the preservation of the environment and institutions responsible for the safety of the general public. Detection systems are at the forefront of the miniaturization movement as the interest in analyte identification and quantitation appears to only be accessible through the use of analytical instrumentation. Mass spectrometry is a distinguished analytical technique known for its ability to detect the mass-to-charge (m/z) ratios of gas-phase ions of interest. Although these systems have been routinely limited to research lab-based analysis, there has been considerable development of miniaturized and portable mass spectrometry systems. Membrane Inlet Mass Spectrometry (MIMS) is becoming a common method of sample introduction that is subject to significant development. MIMS allows for minimal sample preparation, continuous sampling, and excludes complicated analyte introduction techniques. Sampling is accomplished using a semipermeable membrane that allows selective analyte passage into the vacuum of the mass spectrometer. MIMS is becoming the preeminent choice of homeland security and environmental monitoring applications with increasing opportunities for the future development of specialized systems. The steadfast development of miniaturized mass spectrometry systems with efficient operation capabilities for a variety of applications gives promise to the further development of MIMS technology as well as other analytical instrumentation.

Ce travail de thèse a eu pour objectif principal l'étude thermodynamique des changements métaboliques dans l'acidogénèse. L'acidogénèse est un procédé anaérobie à double intérêt qui en traitant des résidus organiques, permet de produire des composés chimiques comme l'hydrogène, l'éthanol et les acides organiques. Par conséquent, l'acidogénèse se place comme un procédé biotechnologique dans le concept de bioraffinerie. En outre, ce processus n'a pas besoin de conditions stériles d'opération et fonctionne sur une large gamme de pH. Ces changements métaboliques sont dépendants des modifications dans les conditions opératoires. Afin d'étudier ces changements métaboliques, des expériences basées sur des modifications du ciel gazeux du réacteur par introduction d'azote et sur des changements du pH, ont été menées. Un des résultats les plus intéressants a été l'augmentation du rendement de production d'hydrogène de 1 à 3,2 molH2/molglucose à pH 4,5 et débit de N2 de 58,4 L/d. Ce rendement est proche de la valeur théorique (4 molH2/molglucose). L'étude thermodynamique a permis d'expliquer les mécanismes métaboliques concernant l'hydrogène, dont la production importante, représentée par le rendement de 3,2 molH2/molglucose, est due à la réaction inverse H2/NAD+, qui est thermodynamiquement faisable à faibles pressions partielles d'hydrogène (par exemple 0,02 bar). En outre, les bas rendements en hydrogène ont été expliqués par l'action consommatrice d'hydrogène par la réaction d'homoacetogénèse. Cependant, le modèle n'a pas été capable d'expliquer les changements métaboliques de l'acétate, du butyrate et de l'éthanol lors de la fermentation acidogénique du glucose. / This thesis deals with thermodynamic based modelling of metabolic shifts during acidogenic fermentation. Acidogenic fermentation is an anaerobic process of double purpose: while treating organic residues, it produces chemical compounds, such as hydrogen, ethanol and organic acids. Therefore, acidogenic fermentation arises as an attractive biotechnology process towards the biorefinery concept. Moreover, this process does not need sterile operating conditions and works under a wide range of pH.Changes of operating conditions produce metabolic shifts, inducing variability on acidogenic product yields. In order to study these metabolic shifts, an experiment design was based on reactor headspace N2-flushing (gas phase) and pH step changes (liquid phase). A major result was the hydrogen yield increase from 1 to 3.2 (molH2/molglucose) at pH 4.5 and N2-flushing of 58.4 L/d. This yield is close to the theoretical acidogenic value (4 molH2/molglucose).The thermodynamic model, based on the assumption that acidogenic fermentation is characterised by limited energy available for biological process, allowed to explain the mechanisms that govern hydrogen metabolic shifts, showing that the synthesis of extra hydrogen, i.e. yield of 3.2 (molH2/molglucose), was due to reverse H2/NAD+ redox reaction, which is thermodynamically feasible at low hydrogen partial pressures (e.g. 0.02 bar). Moreover, low hydrogen yields were explained by the action of homoacetogenesis hydrogen consuming reaction. However, the model was not capable to explain the metabolic shifts of acetate, butyrate and ethanol on acidogenic glucose fermentation.