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.

Philosophiae Doctor - PhD / Nowadays, the pollution of surface waters with chemical contaminants is one of the most crucial environmental problems. These chemical contaminants enter rivers and streams resulting in tremendous amount of destruction, so the detection and monitoring of these chemical contaminants results in an ever-increasing demand. This thesis describes the search for a suitable method for the determination of platinum group metals (PGMs) in environmental samples due to the toxicity of mercury films and the limitations with methods other than electroanalytical methods. This study focuses on the development of a novel bismuth-silver bimetallic nanosensor for the determination of PGMs in roadside dust and soil samples. Firstly, individual silver, bismuth and novel bismuth-silver bimetallic nanoparticles were chemically synthesised. The synthesised nanoparticles was compared and characterised by cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), ultraviolet-visible spectroscopy (UV-Vis), Fourier-transformed infrared spectroscopy (FT-IR), Raman spectroscopy, and transmission electron microscopy (TEM) analysis to interrogate the electrochemical, optical, structural, and morphological properties of the nanomaterials. The individual silver, bismuth, and bismuth-silver bimetallic nanoparticles in the high resolution transmission electron microscopy results exhibited an average particle size of 10-30 nm. The electrochemical results obtained have shown that the bismuth-silver bimetallic nanoparticles exhibit good electro-catalytic activity that can be harnessed for sensor construction and related applications. The ultraviolet-visible spectroscopy, Fourier-transformed infrared spectroscopy, and Raman spectroscopy results confirmed the structural properties of the novel bismuth-silver bimetallic nanoparticles. In addition the transmission electron microscopy and selected area electron diffraction morphological characterisation confirmed the nanoscale nature of the bismuth-silver bimetallic nanoparticles. Secondly, a sensitive adsorptive stripping voltammetric procedure for palladium, platinum and rhodium determination was developed in the presence of dimethylglyoxime (DMG) as the chelating agent at a glassy carbon electrode coated with a bismuth-silver bimetallic nanofilm. The nanosensor further allowed the adsorptive stripping voltammetric detection of PGMs without oxygen removal in solution. In this study the factors that influence the stripping performance such as composition of supporting electrolyte, DMG concentration, deposition potential and time studies, and pH have been investigated and optimised. The bismuth-silver bimetallic nanosensor was used as the working electrode with 0.2 M acetate buffer (pH = 4.7) solution as the supporting electrolyte. The differential pulse adsorptive stripping peak current signal was linear from 0.2 to 1.0 ng/L range (60 s deposition), with limit of detections for Pd (0.19 ng/L), Pt (0.20 ng/L), Rh (0.22 ng/L), respectively. Good precision for the sensor application was also obtained with a reproducibility of 4.61% for Pd(II), 5.16% for Pt(II) and 5.27% for Rh(III), for three measurements. Investigations of the possible interferences from co-existing ions with PGMs were also done in this study. The results obtained for the study of interferences have shown that Ni(II) and Co(II) interfere with Pd(II), Pt(II) and Rh(III) at high concentrations. The interference studies of Cd(II), Pb(II), Cu(II) and Fe(III) showed that these metal ions only interfere with Pd(II) and Pt(II) at high concentrations, with no interferences observed for Rh(III). Phosphate and sulphate only interfere at high concentrations with Pt(II) and Rh(III) in the presence of DMG with 0.2 M acetate buffer (pH = 4.7) solution as the supporting electrolyte. Based on the experimental results, this bismuth-silver bimetallic nanosensor can be considered as an alternative to common mercury electrodes, carbon paste and bismuth film electrodes for electrochemical detection of PGMs in environmental samples. Thirdly, this study dealt with the development of a bismuth-silver bimetallic nanosensor for differential pulse adsorptive stripping voltammetry (DPAdSV) of PGMs in environmental samples. The nanosensor was fabricated by drop coating a thin bismuth-silver bimetallic film onto the active area of the SPCEs. Optimisation parameters such as pH, DMG concentration, deposition potential and deposition time, stability test and interferences were also studied. In 0.2 M acetate buffer (pH = 4.7) solution and DMG as the chelating agent, the reduction signal for PGMs ranged from 0.2 to 1.0 ng/L. The detection limit for Pd(II), Pt(II) and Rh(III) was found to be 0.07 ng/L, 0.06 ng/L and 0.2 ng/L, respectively. Good precision for the sensor application was also obtained with a reproducibility of 7.58% for Pd(II), 6.31% for Pt(II) and 5.37% for Rh(III), for three measurements. In the study of possible interferences, the results have shown that Ni(II), Co(II), Fe(III), Na+, SO42- and PO43- does not interfere with Pd(II) in the presence of DMG with sodium acetate buffer as the supporting electrolyte solution. These possible interference ions only interfere with Pt(II) and Rh(III) in the presence of DMG with 0.2 M acetate buffer (pH = 4.7) as the supporting electrolyte solution.

As part of the Bagnold Dune campaign conducted by Mars Science Laboratory rover Curiosity, visible/near-infrared reflectance spectra of dune sands were acquired using Mast Camera (Mastcam) multispectral imaging (445-1013nm) and Chemistry and Camera (ChemCam) passive point spectroscopy (400-840nm). By comparing spectra from pristine and rover-disturbed ripple crests and troughs within the dune field, and through analysis of sieved grain size fractions, constraints on mineral segregation from grain sorting could be determined. In general, the dune areas exhibited low relative reflectance, a weak similar to 530nm absorption band, an absorption band near 620nm, and a spectral downturn after similar to 685nm consistent with olivine-bearing sands. The finest grain size fractions occurred within ripple troughs and in the subsurface and typically exhibited the strongest similar to 530nm bands, highest relative reflectances, and weakest red/near-infrared ratios, consistent with a combination of crystalline and amorphous ferric materials. Coarser-grained samples were the darkest and bluest and exhibited weaker similar to 530nm bands, lower relative reflectances, and stronger downturns in the near-infrared, consistent with greater proportions of mafic minerals such as olivine and pyroxene. These grains were typically segregated along ripple crests and among the upper surfaces of grain flows in disturbed sands. Sieved dune sands exhibited progressive decreases in reflectance with increasing grain size, as observed in laboratory spectra of olivine size separates. The continuum of spectral features observed between the coarse- and fine-grained dune sands suggests that mafic grains, ferric materials, and air fall dust mix in variable proportions depending on aeolian activity and grain sorting.

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.

Diagnostic measurements play a vital role in experiments. Without them we would be in the dark with no way of knowing what was happening; of understanding the processes and behaviour occurring; or even of judging the success or failure of our experiments. The development of fusion plasma devices is no different. In this thesis we concentrate on visible spectroscopy based diagnostics: examining the techniques for measurement and analysis; the breadth of plasma parameters that can be extracted from the spectroscopic data; and how the application of these diagnostic techniques gives us a broader picture of the plasma and the events taking place within. Techniques are developed and applied to plasmas in three fusion experiments, EXTRAP T2R, ASDEX Upgrade and JET. The diagnostic techniques exploit different features of the measurements of the emitted photons to obtain various useful plasma parameters. Determination of the ion temperature and rotation velocity of oxygen impurity ions in the EXTRAP T2R plasma is achieved through measurement and analysis of, respectively, the Doppler broadening and the Doppler wavelength shift of visible wavelength atomic spectral lines. The evolution of the temperature and rotation is studied as a function of the discharge parameters, in particular looking at the effect of applying active feedback control schemes to the resistive wall modes and/or pulsed poloidal current drive. Measurements of multiple ionisation stages are used to estimate radial profiles of the toroidal rotation and the ion temperature and correlations between the ion rotations and the rotation velocities of tearing modes are also established. Radial profiles of the emissivity and density (or concentration) of the oxygen ions are obtained by means of measurements of the spectral line intensities on a small array of linesof- sight through the plasma. Changes to the profiles for different plasma schemes and the implications for particle transport are investigated. The derived emissivity profiles are used in the analysis for some of the other spectroscopic diagnostics. Spectral line intensity measurements (in this case of neutral ions) are also the basis for calculations of both the electron temperature and the particle fluxes at the plasma edge. The latter is an indicator of the degree and type of interaction between the plasma and the surrounding surfaces. Particle fluxes of the operating gas hydrogen and of chromium and molybdenum impurities are investigated in EXTRAP T2R for different operating scenarios, in particular changes in the metallic influx with the application of active feedback mode control are examined along with the correspondence between spectroscopic and collector probe results. In the ASDEX Upgrade divertor estimates of the particle flux of the deuterium operating gas are also made through analysis of spectral intensities. Molecular D2 band structure is explored in addition to the Balmer Dα spectral line intensity to acquire both atomic and molecular particle fluxes, investigate the contribution of the dissociating D2 to the Dα line and study the effect of changes in the divertor. Analysis of the D2 molecular band structure (the relative intensities of the rotational lines and vibrational bands) also enables calculation of the upper state rotational and ground state vibrational temperatures. The locations of emitting atomic ions in JET are estimated from Zeeman splitting analysis of the structure of their spectral lines. The measurement and analysis of visible wavelength light is demonstrated to be a sensitive diagnostic tool in the quest for increased knowledge about fusion plasmas and their operating scenarios. / QC 20100810

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.