The motivation for this thesis was to study chemical and dynamical processes in the Arctic stratosphere, using data from two ground-based spectrometers (GBSs). The GBSs took atmospheric trace gas measurements at the Polar Environment Atmospheric Research Laboratory (PEARL), which is located at Eureka, Nunavut, Canada (80.05°N, 86.42°W) and operated by the Canadian Network for the Detection of Atmospheric Change. The University of Toronto GBS took measurements at Eureka on a campaign basis from 1999 2011. The PEARL GBS was installed permanently at Eureka in 2006 and has taken measurements during the sunlit part of the year since then. GBS and other ground based ozone and NO2 column measurements were compared with Atmospheric Chemistry Experiment (ACE) and Optical Spectrograph and Infra Red Imaging System (OSIRIS) satellite measurements above Eureka. Ozone from all instruments agreed within 9.2%, while NO2 from most instruments, including the GBS, agreed to within 20%. On 1 August 2008, a solar eclipse of 98% totality passed over Eureka. GBS NO2 increased to 1.84 times normal levels. This agrees with a ratio of 1.91 that was calculated using a photochemical model, adjusted for reduced sunlight during the eclipse. In spring/winter 2011, up to 47% (250 DU) ozone loss was calculated using GBS and modeled passive ozone. This was the largest ozone loss in the 11 year GBS measurement record. GBS OClO was elevated, indicating chlorine activation and NO2 was low, suggesting denitrification. GBS, satellite, and chemical transport model data were used to investigate the 2011 vortex breakup. NOx transport led to middle stratosphere ozone loss within an anticyclone. Furthermore, isolated, or “frozen-in”, vortex and lower-latitude airmasses were observed following the vortex breakup. Stratospheric BrO was retrieved from spring 2008 GBS zenith sky measurements, using an optimal estimation technique. GBS BrO was compared with OSIRIS and Ozone Monitoring Instrument (OMI) satellite data. Discrepancies are partly attributed to bromine explosions in the boundary layer. New off axis GBS measurements taken in spring 2010 are sensitive to boundary layer bromine. The combination of GBS stratospheric and tropospheric BrO measurements will be useful for future estimates of the Arctic bromine budget.

The motivation for this thesis was to study chemical and dynamical processes in the Arctic stratosphere, using data from two ground-based spectrometers (GBSs). The GBSs took atmospheric trace gas measurements at the Polar Environment Atmospheric Research Laboratory (PEARL), which is located at Eureka, Nunavut, Canada (80.05°N, 86.42°W) and operated by the Canadian Network for the Detection of Atmospheric Change. The University of Toronto GBS took measurements at Eureka on a campaign basis from 1999 2011. The PEARL GBS was installed permanently at Eureka in 2006 and has taken measurements during the sunlit part of the year since then. GBS and other ground based ozone and NO2 column measurements were compared with Atmospheric Chemistry Experiment (ACE) and Optical Spectrograph and Infra Red Imaging System (OSIRIS) satellite measurements above Eureka. Ozone from all instruments agreed within 9.2%, while NO2 from most instruments, including the GBS, agreed to within 20%. On 1 August 2008, a solar eclipse of 98% totality passed over Eureka. GBS NO2 increased to 1.84 times normal levels. This agrees with a ratio of 1.91 that was calculated using a photochemical model, adjusted for reduced sunlight during the eclipse. In spring/winter 2011, up to 47% (250 DU) ozone loss was calculated using GBS and modeled passive ozone. This was the largest ozone loss in the 11 year GBS measurement record. GBS OClO was elevated, indicating chlorine activation and NO2 was low, suggesting denitrification. GBS, satellite, and chemical transport model data were used to investigate the 2011 vortex breakup. NOx transport led to middle stratosphere ozone loss within an anticyclone. Furthermore, isolated, or “frozen-in”, vortex and lower-latitude airmasses were observed following the vortex breakup. Stratospheric BrO was retrieved from spring 2008 GBS zenith sky measurements, using an optimal estimation technique. GBS BrO was compared with OSIRIS and Ozone Monitoring Instrument (OMI) satellite data. Discrepancies are partly attributed to bromine explosions in the boundary layer. New off axis GBS measurements taken in spring 2010 are sensitive to boundary layer bromine. The combination of GBS stratospheric and tropospheric BrO measurements will be useful for future estimates of the Arctic bromine budget.

Photodynamic therapy (PDT) is a cancer treatment method in which a photosensitizer, light of a particular wavelength, and also oxygen are used to destroy cancerous cells. Cancer cells absorb the photosensitizing agent which is injected into the body, and it is triggered to cause cell destruction upon absorption of light. This occurs because of the excitation of the photosensitizer produces reactive oxygen species that induce a cascade of cellular and molecular events in the body. Photosensitizing agents that can photo-cleave DNA at long wavelengths are highly demanded in PDT, because the long wavelengths of light can penetrate through tissue deeply compared to visible light. While most of the photosensitizers are activated at wavelengths less than 690 nm, penetration of light continues to increase at increasing wavelengths. In this thesis, photosensitizers that can be activated to oxidize DNA with long wavelengths of light will be discussed. Using quinoline cyanine dyes, here we report the first example of DNA photocleavage at a wavelength of light above 800 nm.

A ground-based, zenith-sky, UV-visible triple grating spectrometer was installed at the Polar Environment Atmospheric Research Laboratory (PEARL) in the Canadian High Arctic during polar springtime from 2004 to 2007 as part of the Canadian Arctic ACE (Atmospheric Chemistry Experiment) Validation Campaigns. From the solar spectra, ozone, NO2, and BrO vertical column densities (VCDs) have been retrieved using the DOAS (Differential Optical Absorption Spectroscopy) technique. This spectrometer, the UT-GBS (University of Toronto Ground-Based Spectrometer), was also deployed as part of the fourth Middle Atmosphere Nitrogen TRend Assessment (MANTRA) campaign in Vanscoy, Saskatchewan in August and September 2004. A near-identical spectrometer, the PEARL-GBS, was permanently installed at PEARL in August 2006 as part of the refurbishment of the laboratory by CANDAC (Canadian Network for the Detection of Atmospheric Change). Since then, the instrument has been making continuous measurements, with the exception of during polar night. Vertical columns of ozone and NO2 can be retrieved year-round. During the 2007 sunrise campaign, differential slant column densities (DSCDs) of OClO and VCDs of BrO were also retrieved. Ozone and NO2 DSCDs and VCDs from the UT-GBS were compared to the DSCDs and VCDs from three other UV-visible, ground-based, grating spectrometers that also participated in the MANTRA and Eureka campaigns. Two methods developed by the UV-visible Working Group of the NDACC (Network for the Detection of Atmospheric Composition Change) were followed. During MANTRA, the instruments were found to partially meet the NDACC standards. The comparisons from Eureka were an improvement on the MANTRA comparisons, and also partially met the NDACC standards. In 2007, the columns from the UT-GBS and PEARL-GBS were compared, and were found to agree within the NDACC standards for both species. Ozone and NO2 VCDs from the ground-based instruments were also compared to integrated partial columns from the ACE-FTS (ACE-Fourier Transform Spectrometer) and ACE-MAESTRO (ACE-Measurements of Aerosol Extinction in the Stratosphere and Troposphere Retrieved by Occultation) on board the ACE satellite. ACE-FTS partial columns were found to agree with the ground-based total columns, while the ACE-MAESTRO partial columns were found to be smaller than expected for ozone and larger than expected for NO2.

A ground-based, zenith-sky, UV-visible triple grating spectrometer was installed at the Polar Environment Atmospheric Research Laboratory (PEARL) in the Canadian High Arctic during polar springtime from 2004 to 2007 as part of the Canadian Arctic ACE (Atmospheric Chemistry Experiment) Validation Campaigns. From the solar spectra, ozone, NO2, and BrO vertical column densities (VCDs) have been retrieved using the DOAS (Differential Optical Absorption Spectroscopy) technique. This spectrometer, the UT-GBS (University of Toronto Ground-Based Spectrometer), was also deployed as part of the fourth Middle Atmosphere Nitrogen TRend Assessment (MANTRA) campaign in Vanscoy, Saskatchewan in August and September 2004. A near-identical spectrometer, the PEARL-GBS, was permanently installed at PEARL in August 2006 as part of the refurbishment of the laboratory by CANDAC (Canadian Network for the Detection of Atmospheric Change). Since then, the instrument has been making continuous measurements, with the exception of during polar night. Vertical columns of ozone and NO2 can be retrieved year-round. During the 2007 sunrise campaign, differential slant column densities (DSCDs) of OClO and VCDs of BrO were also retrieved. Ozone and NO2 DSCDs and VCDs from the UT-GBS were compared to the DSCDs and VCDs from three other UV-visible, ground-based, grating spectrometers that also participated in the MANTRA and Eureka campaigns. Two methods developed by the UV-visible Working Group of the NDACC (Network for the Detection of Atmospheric Composition Change) were followed. During MANTRA, the instruments were found to partially meet the NDACC standards. The comparisons from Eureka were an improvement on the MANTRA comparisons, and also partially met the NDACC standards. In 2007, the columns from the UT-GBS and PEARL-GBS were compared, and were found to agree within the NDACC standards for both species. Ozone and NO2 VCDs from the ground-based instruments were also compared to integrated partial columns from the ACE-FTS (ACE-Fourier Transform Spectrometer) and ACE-MAESTRO (ACE-Measurements of Aerosol Extinction in the Stratosphere and Troposphere Retrieved by Occultation) on board the ACE satellite. ACE-FTS partial columns were found to agree with the ground-based total columns, while the ACE-MAESTRO partial columns were found to be smaller than expected for ozone and larger than expected for NO2.

The cytochromes P450 (CYPs) are a superfamily of biological catalysts that are ubiquitous throughout the biological domain. CYPs are heme-b containing monooxygenases which oxidize substrates with the help of accessory redox partners. CYP substrates include endogenous compounds required for many biological functions and homeostasis, such as steroids, as well as the majority of clinically used drugs and environmental xenobiotics. The majority of studies that have been performed to date are on P450cam (CYP101) from Pseudomonas putida. Of the numerous reactions catalyzed by CYPs, unactivated carbon-carbon bond cleavage, is one of particular versatility. Being unique in their catalytic mechanisms, the C-C bond cleaving enzymes and in particular CYP51 from Mycobacterium tuberculosis are though to be capable of utilizing multiple reactive oxygen intermediates. During the process of C-C bond cleavage, CYP51 catalyzes two classical hydroxylation reactions. The final reaction culminates in an enigmatic third step which cleaves a C-C bond, liberates formate, and installs a 14,15 double bond within its steroid substrate. The mechanism of CYP51s final step is still unclear and the exact activated oxygen species has yet to be observed. CYP51 is also distinct from most CYPs owing to the fact that the acid functionality of the conserved active site “acid-alcohol pair” found in most CYPs, is replaced by a histidine. This study aimed to trap and characterize dioxygen reactive intermediates, and elucidate the role of the unique acid-alcohol pair in the formation and stabilization of these intermediates. This study demonstrates our success in generating, stabilizing, and spectroscopically characterizing reactive dioxygen intermediates in Mtb CYP51. As the life-time of the oxyferrous intermediate in Mtb CYP51 is extremely short at ambient temperatures, this work has shown the laboratory’s expertise in being able to generate reduced oxyferrous intermediates at cryogenic temperatures. These intermediates have only been generated in a handful of cytochromes P450 and as such this work adds critical information to the small body of work currently reported.

Studies on a series of polymethine cyanine dyes and analogs (1-24) show that certain near-infrared cyanines are capable of damaging DNA in the absence of light and external reducing agents. Experimental results imply that in this DNA thermal cleavage, the cyanine reduces Cu(II) to Cu(I) which reacts with O2 to generate the reactive oxygen species (ROS) O2∙- and ∙OH. The formation of these ROS is also thought to be responsible for the irreversible bleaching of the dyes in aqueous solutions. A correlation between structural features and DNA thermal cleavage activity as well as dye bleaching is suggested. Long polymethine chains appear to confer instability to cyanines in aqueous solutions and further contribute to undesired thermal DNA cleavage. These drawbacks can be overcome by introducing an electron-withdrawing group to the polymethine bridge of the cyanine dye.

Depuis la découverte de la première exoplanète en 1995 par Mayor et Queloz, le nombre de planètes extrasolaires découvertes n'a cessé d'augmenter, pour dépasser les 1000 planètes à la fin de l'année 2013. Depuis le début des années 2000, la détection s'est accompagnée d'une volonté de caractérisation de l'atmosphère des exoplanètes. Les méthodes utilisées jusqu'ici sont la spectroscopie de transit primaire et l'étude des émissions thermiques en transit secondaire ou via l'étude des courbes de phase. L'objet de cette thèse s'inscrit dans cette recherche de caractérisation des atmosphères exoplanétaires, en s'intéressant à une méthode jusqu'ici inexplorée : l'analyse des émissions thermosphériques, i.e. les émissions de la haute atmosphère induites par les entrées énergétiques, flux extrême UV de l'étoile hôte et précipitations électroniques principalement. La première partie de cette thèse s'intéresse aux émissions thermosphériques de la Terre primitive avec une approche basée sur la modélisation. Le but étant la détermination des différentes émissions de la Terre à travers son histoire, afin de disposer de proxies pour la recherche et la caractérisation d'exoplanètes telluriques. Dans un premier temps nous avons calculé l'émission de l'atmosphère primordiale de la Terre irradiée par le Soleil jeune dans la raie Lyman Alpha. Nous avons montré que la raie planétaire, principalement formée par diffusion cohérente, montre un rapport d'émission avec le Soleil de l'ordre de 10-8, inaccessible aux observations, avec les instruments actuels ou de prochaine génération. Ce premier résultat nous à conduit à étudier la faisabilité d'une méthode indirecte de détection d'une couronne dense d'hydrogène autour d'une planète tellurique possédant une atmosphère de CO2 par les émissions des sous-produits de dissociation et d'ionisation de CO2. Les calculs menés sur la raie verte de l'oxygène (état O1S) et le doublet UV de CO2+ (état B2Σu+) ont montré que ces émissions présentaient des contrastes de l'ordre de 10^-12 avec le Soleil dans le cas d'une Terre primitive, et de l'ordre de 10^-6-10^-8 pour une planète tellurique proche d'une naine M. La conclusion générale des ces investigations est que les raies fines (atomiques ou moléculaires) des émissions thermosphériques sont trop faibles pour être détectées par les instruments actuels. Une voie possible serait l'étude des bandes d'émission moléculaires, qui nécessite une meilleure compréhension de la distribution en intensité des différentes bandes à travers le spectre, compréhension qui passe par l'étude expérimentale de ces émissions. C'est dans ce cadre que se situe la deuxième partie de cette thèse, qui s'intéresse à l'analyse spectroscopique de la Planeterrella, simulateur d'aurores boréales initialement développé à des fins pédagogiques. Nous avons réalisé une étude spectroscopique à basse et haute résolution de l'air, afin de caractériser les émissions présentes dans l'expérience d'une part, et aussi de disposer d'un spectre de référence qui servira à terme de test pour un code Monte Carlo développé pour étudier le dispositif expérimental, la caractérisation du dispositif constituant une étape nécessaire pour faire de la Planeterrella un objet d'étude scientifique. Enfin, la spectroscopie basse résolution du CO2 a été réalisée, avec des applications potentielles à Mars. / Since the discovery of the first exoplanet in 1995 by Mayor and Queloz, the number of extrasolar planets discovered has continuously grown up, to overtake 1000 planets at the end of 2013. Since the beginning of the 2000's, came with the detection the will to characterize the atmospheres of these exoplanets. Until now, the methods used are the primary transit spectroscopy and the study of the thermal emissions in secondary transit or using phase curves. The purpose of this thesis belongs to that search for characterizing exoplanetary atmospheres, by looking at a method unexplored until now: the study of the thermospheric emissions, i.e. emissions from the upper atmosphere induced by the energetic entries, mainly the extreme UV flux and the electronic precipitations. The first part of this thesis concerns the thermospheric emissions of the primitive Earth with an approach based on modeling. The goal is the determination of the several emissions of the Earth through its history in order to have proxies for the search and the characterization of telluric exoplanets. Initially we calculated the emission of the primary atmosphere of the early Earth under the young Sun in the Lyman Alpha line. We showed that the planetary line in mainly due to coherent diffusion and that the emission ratio between the planet and the Sun in this line is of about 10-8, far from the capabilities of current or next generation instruments. This first result lead us to study the feasibility of an indirect method to infer the presence of dense hydrogen corona surrounding a telluric planet with a CO2-dominated atmosphere, by studying its influence on the emissions of two CO2 by-products. The calculations carried out on the oxygen green line (O1S state) and the UV doublet of CO2+ (B2Σu+ state) showed that theses emissions present contrasts of about 10^-12 with the young Sun in the case of a primitive Earth, and of about 10^-6-10^-8 for a close-in telluric planet around a M dwarf. The general conclusion of the investigations is that the thermospheric emissions of thin (atomic or molecular) lines are too weak to be detected. A possible way could be the study of the molecular bands, of which emissions need to be better understood, especially concerning the intensity distribution of the several bands through the spectrum. This comprehension implies experimental studies of these emissions. The second part of this thesis lies in this scope and concerns the spectroscopic analysis of the Planeterrella, an aurora borealis simulator initially designed for outreach purpose. We made a spectroscopic study at low and high resolution with air, in order to characterize the emissions existing in the experiment, and also to have a reference spectrum which will be a final test for a Monte Carlo code developed to study the experimental device, the characterization of this device being a necessary step for the Planeterrella to become suitable for scientific purpose. Finally, we made a low resolution spectroscopic study of carbon dioxide, with potential applications to Mars.

Hydrogen is a vital component in several different chemical reactions as well as a potential fuel source for the future. The water gas shift (WGS) reaction converts CO and water to hydrogen and CO2. The objective of this work is to first, characterize the potential benefits of the addition of lanthanum oxide (lanthana) to the iron-chromium-copper (Fe-Cr-Cu) oxide catalysts industrially used in high temperature water gas shift processes, and second, analyze these catalysts using in-situ UV-Visible spectroscopy. The benefits of each component in the catalyst are discussed as well as potential benefits from the addition of lanthana. Lanthana is a rare earth oxide that dramatically increases the surface area of the iron based WGS catalysts, and small concentrations of other rare earth oxides (i.e. cerium) have been shown to increase the rate of desorption of CO2 from iron surfaces (Hu Yanping 2002). Lanthana has similar chemical properties to other rare earth oxides tested and has not been previously tested as an additive to the WGS catalyst. Therefore catalysts with 0, 1, 2, 5, 10, and 20 wt% lanthana were made via a co-precipitation method in order to measure changes in activity, physical stability, and thermal stability. Catalyst characterization techniques utilized include electron dispersive X-ray spectroscopy (EDX), temperature programmed reduction (TPR) with hydrogen, and nitrogen physisorption (BET). The kinetic analysis was performed utilizing both mass spectroscopy (MS) and gas chromatography (GC). The addition of 1 wt% lanthana to the Fe-Cr-Cu catalysts increases WGS reaction rates of the catalyst at 425°C and 350°C, however the 0% La catalyst has the highest rates at 375°C and 400°C. The 0% La catalyst shows significant drop off in rate at 425°C, suggesting that the lanthana provides a small thermal stabilizing, i.e. the addition of lanthana prevents catalyst sintering at higher temperatures. Traditionally, chromia acts as the sole thermal stabilizer in these catalysts. The addition of large amounts of lanthana inhibits the chromia stabilizing effect, however small additions of lanthana appear to have an additional catalyst promotional effect without interfering with the chromia thermal stabilization. The increased WGS reaction rates at higher temperatures could allow for greater throughput of reactants in industrial settings. Higher concentrations of lanthana decrease the activity due to what is believed to be disruption of the chromia stabilizing effect as well as reduced amount of the active phase of catalyst. In-situ UV-Visible analysis shows that the oxidation state of the iron in the catalyst has a direct correlation to the UV-Visible light absorbance of the surface of the iron catalyst. Extent of reduction is traditionally measured with a synchrotron which is significantly more expensive than UV-Vis spectroscopy. This study uses the more economical UV-Vis spectrometer to determine similar information. The lanthana doped catalysts show an over-reduction of iron during WGS conditions (i.e. rapid reduction of Fe2O3 to Fe3O4 and FeO).

The structural and functional roles of lanthana in unsupported iron-based catalysts for the high-temperature water-gas shift reaction and Fischer-Tropsch synthesis were investigated. The performance of the catalysts with varying lanthana contents was based on their activity, selectivity, and stability. With regard to the former reaction, extent of reduction of the iron in Fe2O3/Cr2O3/CuO/La2O3 water-gas shift catalysts is a key parameter that was characterized using UV-visible spectroscopy. Minor addition of lanthana (<0.5 wt%) produces more active and stable catalysts apparently because it stabilizes the iron-chromium spinel, increases the surface area of the reduced catalysts, enhances the reduction of hematite to the magnetite active phase, and facilitates the adsorption of CO on the surface of the catalyst modeled by an adsorptive Langmuir-Hinshelwood mechanism. Statistical 95% confidence contour plots of the adsorption equilibrium constants show that water adsorbs more strongly than CO, which inhibits the reaction rate. A calibration curve that correlates the oxidation state of surface iron domains to normalized absorbance of visible light was successfully generated and applied to the water-gas shift catalysts. UV-visible studies indicated higher extent of reduction for surface Fe domains for the catalysts promoted with 1 wt% of lanthana and showed potential to be a more convenient technique for surface chemistry studies than X-ray absorption near edge spectroscopy (XANES). Lanthana addition to iron-based Fischer-Tropsch catalysts enhances the olefin-to-paraffin ratio, but decreases their activity, stability, and selectivity to liquid hydrocarbons. Adding lanthana at the expense of potassium reduces the water-gas shift selectivity and enhances the activity and stability of the catalysts. Finally, a model that simulates heat and mass transfer limitations on the particle scale for the Fischer-Tropsch reaction applicable at lab-scale suggests optimal operating and design conditions of 256°C, 30 bar, and 80 mirons are recommended for higher selectivity to liquid hydrocarbons. The model considers pressure drop, deactivation, pore diffusion, film heat transfer, and internal heat transfer when solving for the optimal conditions, and maps them as functions of design variables. This model can be up-scaled to provide guidance for optimal design of commercial-size reactors.