Raman spectroscopy has been used to characterise both organic and geological samples in order to build a database for the future characterization of biomarker molecules that are of astrobiological relevance. Characteristic geological features and hydrated minerals recently found on the surface of Mars by the NASA planetary rovers Spirit and Opportunity suggest that a possible biosphere could have once existed there. Analytical instrumentation protocols for the unequivocal detection of biomarkers in suitable geological matrices are critical for future unmanned explorations, including the forthcoming ESA ExoMars mission scheduled for 2018. Several geological features found on the surface of Mars by planetary rovers suggest that a possible extinct biosphere could exist based on similar sources of energy as occurred on Earth. For this reason, analytical instrumental protocols for the detection of isolated biomarkers preserved in suitable geological matrices unequivocally and non-destructively have to be evaluated for future unmanned missions. Raman spectroscopy is currently part of the Pasteur instrumentation suite of the ExoMars mission for the remote detection of extant or extinct life signatures in the Martian surface and subsurface. Terrestrial analogues of Martian sites have been identified and the biogeological modifications resulting from extremophilic survival activity have been studied. Here we present the Raman spectral characterization of several examples of organic compounds which have been recorded using 785 nm, 633 nm and 514 nm laser excitation -polycyclic aromatic hydrocarbons (PAHs), organic acids, chlorophyll and carotenoids. Experimental mixtures of ß-carotene in usnic acid, PAHs in usnic acid and PAHs in mineral matrices have also been investigated. Organic compounds and PAHs located under crystalline minerals samples were identified using a 5x objective lens and 785 nm III excitation. The pure compounds and compound mixtures were also analysed using X-ray powder diffraction and scanning electron microscopy (SEM). The results of this study indicate that near infrared laser at 785 nm provided the clearest and the most informative spectra due to the reduction of fluorescence emission. Higher energy lasers operating in the visible region have resulted in the emission of significant background fluorescence. Few samples fluoresce even with the use of 785 nm excitation and FT-Raman spectroscopy remains the instrument of choice for the analysis of these samples.

<p> Small nitrogen or silicon containing molecules and their ionized counterparts have attracted a great deal of attention from both experimentalists and theoreticians. This is because such species may play an important role in interstellar chemistry. Small nitrogen containing heterocyclic molecules and ions are of biological importance and are of increasing interest to chemists and biochemists. Therefore, studying the chemistry of such species in the gas phase as solitary ions and neutrals is of considerable importance.</p> <p> The ions studied in this thesis were generated in the rarefied gas phase of the mass spectrometer by (dissociative) electron ionization of selected precursor molecules. The characterization of their structure and reactivity was realized using a variety of tandem mass spectrometry based techniques. These include metastable ion spectra to probe the dissociation chemistry of the low energy ions and (multiple) collision experiments to establish the structure (atom connectivity) of the stable ions. The technique of neutralization-reionization mass spectrometry (NRMS) was used to probe the structure and stability of the neutral counterparts of the ions. The results of theoretical calculations involving the CBS-QB3 model chemistry formed an essential component in the interpretation of the experimental findings.</p> <p> The above approach was used to study various isomers of the CH2N2•+ family of ions, in particular the elusive carbodiimide ion HN=C=NH•+. Unlike other isomers including ionized cyanamide H2N-C≡N•+ and nitrilimine HC=N=NH•+, the carbodiimide ion could only be identified by a strategy that involved the use of the technique of collision-induced dissociative ionization (CIDI) mass spectrometry. Guided by the results of the theoretical calculations, the carbodiimide ion, the global minimum on the CH2N2•+ potential energy surface, could also be generated by the molecule-assisted isomerization of its 1,3-H shift isomer H2N-C≡N•+. This occurs through an ion-molecule interaction with a single molecule of H2O under conditions of chemical ionization : a process termed proton-transport catalysis.</p> <p> The amino-substituted carbodiimide ion, H2N-N=C=NH•+, and nine more isomers have all been calculated to be minima on the potential energy surface of the CH3N3•+ family of ions. Four of these, viz. the aminocarbodiimide ion, the aminonitrilimine ion, H2N-C=N=NH•+, the cyclic C-aminoisodiazirine ion, and the ionized biradical, H2N-N=C(H)=N•+, were generated and characterized by tandem mass spectrometry as stable species in the gas phase. Neutralization-reionization experiments show, in agreement with the CBS-QB3 computational results, that aminocarbodiimide and aminonitrilimine are stable species in the gas phase.</p> <p> Next, the α-distonic ions of a number of heterocyclic nitrogen-containing compounds including pyrazole, pyridazine and aminopyrazine, were characterized and differentiated by tandem mass spectrometry. The stabilities of the neutral counterparts of the ylid ions and their conventional isomers were probed by neutralization-reionization experiments. From these experiments, it follows that the ylid ions have stable neutral counterparts, as predicted by the theoretical calculations.</p> <p> The final component of this work deals with the chemistry of a silicon containing species of potential interest in interstellar chemistry. The reactions of protonated silicic acid, Si(OH)3+, and the mechanisms of these reactions were studied using tandem mass spectrometric experiments and CBS-QB3 model chemistry. The low energy (metastable) ions of Si(OH)3+ dissociate by loss of H2O and SiO2 to form O=SiOH+ and H3O+ ions. Neutralization-reionization experiments show that Si(OH)3• is a stable species in the rarefied gas phase.</p> / Thesis / Master of Science (MSc)

<p> The key objective of this research was to study the rates of the chemical cleavage of benzyl-silicon bonds in small model molecules, oligomers, polymers, copolymers, and crosslinked microspheres and microgels.</p> <p> Substrate species including benzyltrimethylsilane (BTMS), p-isopropylbenzyltrimethylsilane (ISO-BTMS), oligomeric and polymeric vinylbenzyltrimethylsilane (VBTMS), and their copolymers with styrene and methyl methacrylate as well as microspheres and microgels of bis(vinylbenzyl)dimethylsilane (BVBDMS) were synthesized using Grignard reaction, free radical polymerization, and precipitation polymerization.</p> <p> Narrow dispersed microspheres were synthesized from bis(vinylbenzyl)dimethylsilane (BVBDMS) by precipitation polymerization in acetonitrile. The reactivities of para/para, meta/meta, and meta/para isomers of BVBDMS in precipitation polymerization were found to be similar and to obey first-order kinetics. Their apparent rate of polymerization is comparable with that of meta and para divinylbenzene isomers under identical polymerization conditions. FT-IR analysis of BVBDMS microspheres shows that there are only few pendant double bonds in the particles. This is likely due to the similar reactivity of isolated double bonds of BVBDMS.</p> <p> Two nucleophilic (hydroxide and fluoride ion) and one oxidative (ceric ammonium nitrate) reagents have been used to cleave the benzylic-silicon bonds of the substrates. The cleavage reactions were quantitatively monitored by 1H-NMR / 29Si-NMR or FT-IR to derive the reaction kinetic parameters. The reaction behavior of most of the substrates differed from that expected based on the Flory's principle of equal reactivity.</p> <p> Among the hydroxide ion initiated cleavage reactions, the small molecules and the oligomeric analogs obeyed first-order kinetics, but the homopolymer and the copolymers deviated from first-order kinetics. This could be due to the low concentration of hydroxide ion in the polymer matrix, arising from the exclusion of polar hydroxide ion from the hydrophobic polymer matrix. The p-isopropylbenzyltrimethylsilane exhibited a lower pseudo first-order rate than benzyltrimethylsilane. This is attributed to an electron releasing substituent effect. Methyl methacrylate can accelerate the reaction on poly(vinylbenzyltrimethylsilane-co-methyl methacrylate) by increasing the overall copolymer polarity. The reverse is true for the corresponding styrene copolymers owing to the steric hindrance offered by the phenyl ring of styrene, and the enhanced hydrophobic repulsion against the access of hydroxide ion into the polymer matrix. An electrophilically assisted process was proposed as a principal reaction mechanism for this cleavage reaction. It was found that the only nucleophile attacking on silicon would be the hydroxide ion in KOH/EtOH/THF promoted reactions.</p> <p> Fluoride ion initiated cleavage reactions of substrates containing benzylic-silicon bonds were found to follow first-order kinetics. The reaction on small molecules was not studied due to their very rapid reaction at room temperature. The homopolymer of vinylbenzyltrimethylsilane exhibited a higher rate of reaction than the corresponding oligomer. However, the change in the reaction rate within a copolymer series, differing in molecular weight and composition, was not significant. Poly(VBTMS-co-MMA) exhibited a rate higher than that of styrene copolymers for polarity or steric reasons.</p> <p> Oxidative cleavage of benzylic-silicon bond by ceric ammonium nitrate (CAN) was found to obey first-order kinetics at 1:3 substrate to cerium(IV) ratio, and did not show any deviation in reaction order even at higher CAN concentration. The electron releasing isopropyl group reduces the oxidation potential of p-isopropylbenzyltrimethylsilane (ISO-BTMS), resulting in an enhanced reaction rate compared to benzyltrimethylsilane (BTMS). This rate accelerating substituent effect, together with a much higher negative value (-5.4) of Hammett reaction constant p is in accordance with the radical-cation mechanism operating in ceric ammonium nitrate promoted oxidation reactions. Significant loss of silane functionality was observed in reactions with polymeric substrates. This is attributed to the benzylic radical coupling reactions. The possibility of polymer backbone cleavage is ruled out for the following reasons: A) lack of significant molecular weight reduction in the oxidation products of polymeric substrates. B) about 100 times easier breaking of benzylic-silicon bond as trimethylsilyl cation than a hydrogen from carbon as proton, and the steric congestion offered by the polymer chain favors the benzylic radical formation only at the primary carbon, not on tertiary methine (C-H) on the chain.</p> / Thesis / Master of Science (MSc)

At ~662 gigatonnes of carbon (GtC), marine dissolved organic matter (DOM) is the largest reduced pool of actively cycling carbon and nitrogen in the oceans1. Operationally defined as smaller than 0.1µm in size, this carbon reservoir comprises all non-living organic matter smaller than a bacterial cell and comprises organic colloids and molecules spanning as a continuum of sizes ranging from marine viruses and large macromolecules (e.g. DNA, enzymes) to small organic molecules (e.g. polymers and monomers)2. With deep apparent 14C-ages ranging between 4900-6400 ybp 3,4, marine DOM is anomalously old given timescales of global ocean ventilation (1000-1500 years). The great age of DOM has remained one of the most elusive lines of scientific inquiry in Chemical Oceanography for decades. The size and molecular composition of DOM has been shown to be a key variable in determining its biological reactivity (e.g. cycling rate) and long-term persistence in the deep ocean5,6. Despite the importance of DOM in the marine carbon and nitrogen cycles, we lack a detailed understanding of the molecular composition of DOM. Due to the high concentration of salts in seawater relative to DOM, it is difficult to analyze the molecular composition of seawater with conventional chemical- or size- fractionation methods without introducing bias (i.e. isolating only hydrophobic and/or high molecular weight DOM). In fact, it is commonly reported that >80% of DOM remains uncharacterized at the molecular level (e.g. not readily identifiable as an individual known biomolecule)5. Nuclear magnetic resonance (NMR) spectroscopy has been used as a tool for several decades to describe the composition of marine DOM isolates7. For example, 13C-NMR of major high molecular weight DOM functional groups at the molecular-level demonstrated that DOM is largely made up of reactive polysaccharides with low aromaticity compared to terrestrial DOM8. To date, all marine DOM NMR measurements have been made on size-fractionated DOM or chemically-fractionated (e.g. solid phase extracted) DOM isolates. In this thesis, I report the first Proton (1H) NMR composition of total seawater DOM from seawater samples collected from 10 stations in Baffin Bay aboard the CCGS Amundsen (2019). Samples were measured using 1H-NMR at uOttawa following a novel water suppression method established by Lam and Simpson9. The use of this method has allowed for the first molecular composition assessment of total seawater DOM to be measured (e.g. without any chemical or size fractionation). I report the % relative abundance of individual biomarkers and determine molar concentrations of two compound classes of interest. These results are shown in Ocean Data View section plots, and are listed within appendix tables, to provide a comprehensive depiction of the changing concentrations of dissolved organic carbon (DOC), total carbohydrates (TCHO), and carboxyl-rich alicyclic molecules (CRAM). In this thesis, I explore changes in the abundance of these unique DOM compound classes and discuss how the composition of DOM directly determines its bioavailability and thus cycling in Baffin Bay 5. The core objective of my thesis was to measure DOM concentrations for TCHO and CRAM, as well as to calculate the production and removal of these key DOM compounds in Baffin Bay due to either physical and/or biological processes. We found that the concentration of both TCHO and CRAM decreased with depth throughout Baffin Bay. This is consistent with previous work suggesting the rapid cycling of carbohydrates, however it contradicts the current paradigm of CRAM cycling. Our results indicate between 21-43% of CRAM produced in the surface is subsequently removed at depth. Rapid cycling of a surface CRAM population suggests that not all CRAM can be considered recalcitrant DOM We live in a time of unprecedented global change. The Arctic Ocean is warming at a rate at least four times faster than the global average10. The impact of a rapidly warming, freshening and increasingly acidified Arctic Ocean on the biogeochemistry of DOM remains unknown. It is imperative that more DOM research be conducted as early as possible in order to better understand these impacts and inform future research directions. The distribution and cycling of CRAM in Baffin Bay provide novel and fundamental knowledge of DOM cycling in a key Arctic region, but could also potentially occur throughout the global ocean. Such data will no doubt be of use in informing future iterations of Earth System Climate models seeking to forecast how the marine carbon cycle will respond to global change.

Computational methods for predicting the binding affinity of small organic molecules tobiological macromolecules cover a vast range of theoretical and physical complexity. Generally, as the required accuracy increases so does the computational cost, thereby making the user choose a method that suits their needs within the parameters of the project. We present how WScore, a rigid-receptor docking program normally consigned to structure-based hit discovery in drug design projects, is systematically ameliorated to perform accurately enough for lead optimization with a set of ROCK1 complexes and congeneric ligands from a structure-activity relationship study. Initial WScore results from the Schrödinger 2019-3 release show poor correlation (R² ∼0.0), large errors in predicted binding affinity (RMSE = 2.30 kcal/mol), and bad native pose prediction (two RMSD > 4Å) for the six ROCK1 crystal structures and associated active congeneric ligands. Improvements to WScore’s treatment of desolvation, myriad code fixes, and a simple ensemble consensus scoring protocol improved the correlation (R² = 0.613), the predicted affinity accuracy (RMSE = 1.34 kcal/mol), and native pose prediction (one RMSD > 1.5Å). Then we evaluate a physically and thermodynamically rigorous free energy perturbation (FEP) method, FEP+, against CryoEM structures of the Machilis hrabei olfactory receptor, MhOR5, and associated dose-response assays of a panel of small molecules with the wild-type and mutants. Augmented with an induced-fit docking method, IFD-MD, FEP+ performs well for ligand mutating relative binding FEP (RBFEP) calculations which correlate with experimental log(EC50)with an R² = 0.551. Ligand absolute binding FEP (ABFEP) on a set of disparate ligands from the MhOR5 panel has poor correlation (R² = 0.106) for ligands with log(EC50) within the assay range. But qualitative predictions correctly identify the ligands with the lowest potency. Protein mutation calculations have no log(EC50) correlation and consistently fail to predict the loss of potency for a majority of MhOR5 single point mutations. Prediction of ligand efficacy (the magnitude of receptor response) is also an unsolved problem as the canonical active and inactive conformations of the receptor are absent in the FEP simulations. We believe that structural insights of the mutants for both bound and unbound (apo) states are required to better understand the shortcomings of the current FEP+ methods for protein mutation RBFEP. Finally, improvements to GPU-accelerated linear algebra functions in an Auxiliary-Field Quantum Monte Carlo (AFQMC) program effect an average 50-fold reduction in GPU kernel compute time using optimized GPU library routines instead of custom made GPU kernels. Also MPI parallelization of the population control algorithm that destroys low-weight walkers has a bottleneck removed in large, multi-node AFQMC calculations.Computational methods for predicting the binding affinity of small organic molecules tobiological macromolecules cover a vast range of theoretical and physical complexity. Generally, as the required accuracy increases so does the computational cost, thereby making the user choose a method that suits their needs within the parameters of the project. We present how WScore, a rigid-receptor docking program normally consigned to structure-based hit discovery in drug design projects, is systematically ameliorated to perform accurately enough for lead optimization with a set of ROCK1 complexes and congeneric ligands from a structure-activity relationship study. Initial WScore results from the Schrödinger 2019-3 release show poor correlation (R² ∼0.0), large errors in predicted binding affinity (RMSE = 2.30 kcal/mol), and bad native pose prediction (two RMSD > 4Å) for the six ROCK1 crystal structures and associated active congeneric ligands. Improvements to WScore’s treatment of desolvation, myriad code fixes, and a simple ensemble consensus scoring protocol improved the correlation (R² = 0.613), the predicted affinity accuracy (RMSE = 1.34 kcal/mol), and native pose prediction (one RMSD > 1.5Å). Then we evaluate a physically and thermodynamically rigorous free energy perturbation (FEP) method, FEP+, against CryoEM structures of the Machilis hrabei olfactory receptor, MhOR5, and associated dose-response assays of a panel of small molecules with the wild-type and mutants. Augmented with an induced-fit docking method, IFD-MD, FEP+ performs well for ligand mutating relative binding FEP (RBFEP) calculations which correlate with experimental log(EC50)with an R² = 0.551. Ligand absolute binding FEP (ABFEP) on a set of disparate ligands from the MhOR5 panel has poor correlation (R² = 0.106) for ligands with log(EC50) within the assay range. But qualitative predictions correctly identify the ligands with the lowest potency. Protein mutation calculations have no log(EC50) correlation and consistently fail to predict the loss of potency for a majority of MhOR5 single point mutations. Prediction of ligand efficacy (the magnitude of receptor response) is also an unsolved problem as the canonical active and inactive conformations of the receptor are absent in the FEP simulations. We believe that structural insights of the mutants for both bound and unbound (apo) states are required to better understand the shortcomings of the current FEP+ methods for protein mutation RBFEP. Finally, improvements to GPU-accelerated linear algebra functions in an Auxiliary-Field Quantum Monte Carlo (AFQMC) program effect an average 50-fold reduction in GPU kernel compute time using optimized GPU library routines instead of custom made GPU kernels. Also MPI parallelization of the population control algorithm that destroys low-weight walkers has a bottleneck removed in large, multi-node AFQMC calculations.

Homocysteine (Hcy) has been identified as a primary risk factor for atherosclerosis as it induces endothelial cell (EC) activation/dysfunction and thus potentially initiating atherosclerotic plaque formation. There is accumulating evidence indicating a key role for oxidative stress in mediating Hcy atherogenic effects. The aim of this study was to evaluate the effects of chronic treatment with Hcy on EC activation and to explore the role of oxidative stress in these effects. Human umbilical vein endothelial cells (HUVEC) were cultured and treated chronically with DL-Hcy for 5-9 days. An in vitro flow system was also used to characterize the different types of interactions between DL-Hcy-treated HUVEC and neutrophils under physiological flow conditions. EC activation was studied by characterizing the activation of the JNK pathway and the up-regulation of different cell adhesion molecules (CAM) and cytokines, using different techniques including western blot, immunohistochemical staining, enzyme-linked immunosorbent assay and polymerase chain reaction. The role of oxidative stress was investigated by measuring the production of ROS and evaluating the efficiency of antioxidants. Furthermore, the role of nitric oxide and nitric oxide synthase in modulating Hcy effects was investigated. Chronic treatment with DL-Hcy did not kill the EC however, it inhibited cell proliferation. Furthermore, this treatment induced EC activation/dysfunction which was characterized by sustained activation of the JNK pathway, which in turn mediated up-regulation of E-selectin, ICAM-1 and to lesser extent P-selectin. Furthermore, DL-Hcy induced production of IL-8 protein. These CAM and chemokines collectively mediated different interactions between DL-Hcy-treated HUVEC and neutrophils under flow conditions including tethering, rolling, adherence and transmigration. DL-Hcy was also shown to induce significant ROS generation which mediated activation of the JNK pathway. Antioxidants restored DL-Hcy-induced interactions under flow to the basal level. DL-Hcy was shown to induce eNOS uncoupling which mediated, at least in part, the DL-Hcy-induced ROS production. Furthermore, short term treatment with NO inhibited DL-Hcy-induced HUVEC:neutrophil interactions in a cGMP-independent manner. In summary, this research showed that DL-Hcy has several proatherogenic effects, mediated at least in part by the JNK pathway, and induces EC activation/dysfunction priming for atherosclerosis initiation. The data supports that oxidative stress mediates the majority of Hcy atherosclerotic effects. Antioxidants tested, JNK inhibitors and NO showed promising results in reversing all DL-Hcy effects and restoring EC normal status. ¿

The fluorination of porous materials often leads to the enhancement of properties such as stability, crystallinity and selective adsorption. Although there has been much interest in the fluorination of many types of porous materials, little research has been done on the fluorination of macrocycles, specifically trianglimine and leaning pillararene based materials. In this work, we introduce for the first time highly fluorinated trianglimine and leaning pillararene and show the enhancement effects brought about by the inclusion of fluorinated-phenyl moieties, such as increased stability, surface area, and tendency for self-assembly in our systems. We then show how our fluorinated macrocycles open the door for the formation of extended macrocycle-based polymetric materials simply and in high yields via nucleophilic aromatic substitution. We show for the first time the formation of a trianglimine-based cross-linked polymer and demonstrate its use for micropollutant and gas separation.

P2X7 receptors are members of the ATP-gated cationic channel family with a preferential localization at the microglial cells, the resident macrophages of the brain. However, these receptors are also present at neuroglia (astrocytes, oligodendrocytes) although at a considerably lower density. They mediate necrosis/apoptosis by the release of pro-inflammatory cytokines/chemokines, reactive oxygen species (ROS) as well as the excitotoxic (glio)transmitters glutamate and ATP. Besides mediating cell damage i.e., superimposed upon chronic neurodegenerative processes in Alzheimer’s Disease, Parkinson’s Disease, multiple sclerosis, and amyotrophic lateral sclerosis, they may also participate in neuroglial signaling to neurons under conditions of high ATP concentrations during any other form of neuroinflammation/neurodegeneration. It is a pertinent open question whether P2X7Rs are localized on neurons, or whether only neuroglia/microglia possess this receptor-type causing indirect effects by releasing the above-mentioned signaling molecules. We suggest as based on molecular biology and functional evidence that neurons are devoid of P2X7Rs although the existence of neuronal P2X7Rs cannot be excluded with absolute certainty.

No description available.

No description available.