Chemistry

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This is the collection for the University of Waterloo's Department of Chemistry.

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Supercooling and Freezing of HNO3/H2O Aerosols
(University of Waterloo, 2000) Dickens, Dustin
The freezing kinetics of binary nitric acid/water aerosols is of fundamental importance to the modelling of polar stratospheric clouds and the role they in ozone depletion over the Arctic/Antarctic regions. Cirrus clouds are also often composed of nitric acid solutions, hence an understanding of freezing process in these aerosols also aids in modelling the earth's radiation budget and global warming. This thesis explores the kinetic phase diagram of nitric acid/water aerosols with sizes ranging between 0. 2 and 1. 5 mm in radius and concentrations ranging between pure water and 0. 45 mole fraction HNO3. Although the kinetic phase diagram has now been studied between 0. 46 mole fraction HNO3 and pure water, more data is needed in the region between 0. 18 and 0. 25 mole fraction HNO3 to confirm the results reported. The project described in this thesis are a continuation of a project begun by Allan Bertram. The measurements involving aerosols with compositions greater than 0. 25 mole fraction HNO3 were carried out as part of Allan Bertram's Ph. D. thesis (see ref. 20) These data were later examined using a more comprehensive data analysis method (as presented in this thesis) in an effort to obtain a more complete understanding of this system.
Direct Fitting of Analytical Potential Functions to Diatomic Molecular Spectroscopic Data
(University of Waterloo, 2000) Seto, Jenning
The standard practice of spectroscopic data reduction is generally to fit data to level energy expansions in terms of the vibrational and rotational quantum numbers. However, the utility of such expressions is limited because they extrapolate poorly and they need very large sets of parameters, many of which have no independent physical significance. One method of addressing these problems is to fit the spectroscopic data directly to analytical potential energy functions incorporating the natural physical behaviour of the molecule in question. Although there have been a number of successful applications of this approach, there are still certain problems associated with the types of potential forms being used. This thesis will explore some of these problems and determine how effective the potential forms being used are for a number of specific cases.
Noble Gas Collision Induced Vibrational Relaxation of (v=1) para-H2
(University of Waterloo, 2001) Weir, Douglas
Close coupling scattering calculations have been conducted for the para spin modification of H₂-{He, Ne and Ar}. The XC(fit) potential energy surfaces for H₂-Ne and H₂-Ar have been used for calculations for these two systems, while a newly fitted version of the Schaefer and Kohler potential energy surface was used for the H₂-He system. The fitting procedure employs nine modified Lennard-Jones oscillator functions to describe accurately 90% of the original tabulated potential energy surface to better than 12% error. The scattering calculations for H₂-Arfailed at higher energies due to the presence of a previously undocumented potential energy surface turn-over at R less than 1. 0 Angstroms. Manifold-to-manifold v=1 vibrational relaxation calculations for each of these systems are compared with other experimental and theoretical calculations. These comparisons demonstrate a common discrepancy between previous calculations and the current calculations for each system. The current vibrational relaxation rate constants are generally too small when compared to low temperature values of Audibert et al. and Orlikowski, and the high temperature values obtained by Flower et al. and Dove andTeitelbaum. The current calculations indicate the presence of a dramatic up-turn in the low temperature H₂-He rate constants. Other experimental and theoretical treatments do not exhibit this same up-turn, which is puzzling. A set of follow-up calculations featuring a larger basis set (such as the {16,12,10,8} Flower et al. basis set) and a larger manifold of included relaxation pathways are needed to improve these calculations.
Determining Analytical Potential Energy Functions of Diatomic Molecules by Direct Fitting
(University of Waterloo, 2001) Huang, Yiye
The fully quantum mechanical 'direct-potential-fit' (DPF) method has become increasingly widely used in the reduction of diatomic spectra. The central problem of this method is the representation of the potential energy and Born-Oppenheimer breakdown (BOB) correction functions. There are a number of problems associated with the existing method and potential forms. This thesis delineates these problems and finds solutions to some of them. In particular, it is shown that use of a different expansion variable and a new treatment of some of the expansions resolves most of the problems. These techniques have been successfully tested on the ground electronic states of the coinage metal hydrides and the Rb2 molecule. To address the problem of representing 'barrier' potential curves, a flexible new functional form, the 'double-exponential long-range' (DELR) potential function, is introduced and applied to the B barrier state of Li2. In addition, the Lambda-doubling level splitting which occurs for singlet Pi electronic states has been taken into account by extending the effective Schrodinger equation. The computer program DSPotFit developed in our laboratory for performing DPF analyses has been extended to incorporate the ability to fit the analytical potential energy functions to tunneling predissociation line widths for quasibound levels. Finally, an attempt is made to investigate whether there exists a hump in the ground state rotationless potential curve of beryllium hydride.
Fourier Transform Spectroscopy of Selected Transient Species
(University of Waterloo, 2003) Li, Gang
The procedures and results of experimental and/or theoretical studies of four transient molecules, GeO, WO, BeH, and MgH are reported in the thesis. Two of them, GeO and WO, are diatomic molecules composed of relatively heavy atoms, and the other two are diatomic molecules with hydrogen as one of their component atoms. The GeO species was generated using a high temperature furnace. The rovibrational spectrum of five isotopomers were detected in emission using a Bruker IFS 120 HR Fourier transform spectrometer. Combined-isotopomer Dunham-type molecular constants have been derived for GeO using the DSParFit computer program. Analysis shows that the Born-Oppenheimer approximation is valid, as expected, for a molecule containing heavy atoms. The WO molecule was generated using a microwave discharge cell, and the spectra of electronic transitions of various systems were detected in emission using both the Bruker IFS 120 HR Fourier transform spectrometer at Waterloo and the McMath Pierce One-Meter Fourier transform spectrometer at the National Solar Observatory in Arizona. The ground electronic state has been confirmed to be X³Σ^- based on the analysis of seven 0-0 bands. BeH and MgH are typical molecules with hydrogen as one of their component atoms, and the effects of Born-Oppenheimer breakdown were expected. Both of these molecules have rotational perturbations in their excited electronic states. A 'new' method of data processing was used, i. e. , treating the electronic data as if they were from fluorescence series. Thus the harmful influence of the perturbed upper electronic states on the ground electronic state molecular constants is eliminated. By using the DSParFit computer program, accurate sets of combined-isotopomer Dunham-type molecular constants have been derived for the ground electronic states of the two molecules, and Born-Oppenheimer breakdown correction terms have been obtained.
Combined Use of Models and Measurements for Spatial Mapping of Concentrations and Deposition of Pollutants
(University of Waterloo, 2004) Ambachtsheer, Pamela
When modelling pollutants in the atmosphere, it is nearly impossible to get perfect results as the chemical and mechanical processes that govern pollutant concentrations are complex. Results are dependent on the quality of the meteorological input as well as the emissions inventory used to run the model. Also, models cannot currently take every process into consideration. Therefore, the model may get results that are close to, or show the general trend of the observed values, but are not perfect. However, due to the lack of observation stations, the resolution of the observational data is poor. Furthermore, the chemistry over large bodies of water is different from land chemistry, and in North America, there are no stations located over the great lakes or the ocean. Consequently, the observed values cannot accurately cover these regions. Therefore, we have combined model output and observational data when studying ozone concentrations in north eastern North America. We did this by correcting model output at observational sites with local data. We then interpolated those corrections across the model grid, using a Kriging procedure, to produce results that have the resolution of model results with the local accuracy of the observed values. Results showed that the corrected model output is much improved over either model results or observed values alone. This improvement was observed both for sites that were used in the correction process as well as sites that were omitted from the correction process.
New Calibration Approaches in Solid Phase Microextraction for On-Site Analysis
(University of Waterloo, 2004) Chen, Yong
Calibration methods for quantitative on-site sampling using solid phase microextraction (SPME) were developed based on diffusion mass transfer theory. This was investigated using adsorptive polydimethylsiloxane/divinylbenzene (PDMS/DVB) and Carboxen/polydimethylsiloxane (CAR/PDMS) SPME fiber coatings with volatile aromatic hydrocarbons (BTEX: benzene, toluene, ethylbenzene, and o-xylene) as test analytes. Parameters that affected the extraction process (sampling time, analyte concentration, water velocity, and temperature) were investigated. Very short sampling times (10-300 s) and sorbents with a strong affinity and large capacity were used to ensure a 'zero sink' effect calibrate process. It was found that mass uptake of analyte changed linearly with concentration. Increase of water velocity increased mass uptake, though the increase is not linear. Temperature did not affect mass uptake significantly under typical field sampling conditions. To further describe rapid SPME analysis of aqueous samples, a new model translated from heat transfer to a circular cylinder in cross flow was used. An empirical correlation to this model was used to predict the mass transfer coefficient. Findings indicated that the predicted mass uptake compared well with experimental mass uptake. The new model also predicted rapid air sampling accurately. To further integrate the sampling and analysis processes, especially for on-site or in-vivo investigations where the composition of the sample matrix is very complicated and/or agitation of the sample matrix is variable or unknown, a new approach for calibration was developed. This involved the loading internal standards onto the extraction fiber prior to the extraction step. During sampling, the standard partially desorbs into the sample matrix and the rate at which this process occurs, was for calibration. The kinetics of the absorption/desorption was investigated, and the isotropy of the two processes was demonstrated, thus validating this approach for calibration. A modified SPME device was used as a passive sampler to determine the time-weighted average (TWA) concentration of volatile organic compounds (VOCs) in air. The sampler collects the VOCs by the mechanism of molecular diffusion and sorption on to a coated fiber as collection medium. This process was shown to be described by Fick's first law of diffusion, whereby the amount of analyte accumulated over time enable measurement of the TWA concentration to which the sampler was exposed. TWA passive sampling with a SPME device was shown to be almost independent of face velocity, and to be more tolerant of high and low analyte concentrations and long and short sampling times, because of the ease with which the diffusional path length could be changed. Environmental conditions (temperature, pressure, relative humidity, and ozone) had little or no effect on sampling rate. When the SPME device was tested in the field and the results compared with those from National Institute of Occupational Health and Safety (NIOSH) method 1501 good agreement was obtained. To facilitate the use of SPME for field sampling, a new field sampler was designed and tested. The sampler was versatile and user-friendly. The SPME fiber can be positioned precisely inside the needle for TWA sampling, or exposed completely outside the needle for rapid sampling. The needle is protected within a shield at all times hereby eliminating the risk of operator injury and fiber damage. A replaceable Teflon cap is used to seal the needle to preserve sample integrity. Factors that affect the preservation of sample integrity (sorbent efficiency, temperature, and sealing materials) were studied. The use of a highly efficient sorbent is recommended as the first choice for the preservation of sample integrity. Teflon was a good material for sealing the fiber needle, had little memory effect, and could be used repeatedly. To address adsorption of high boiling point compounds on fiber needles, several kinds of deactivated needles were evaluated. RSC-2 blue fiber needles were the more effective. A preliminary field sampling investigation demonstrated the validity of the new SPME device for field applications.
Surface Chemistry of Hexacyclic Aromatic Hydrocarbons on (2x1) and Modified Surfaces of Si(100)
(University of Waterloo, 2004) Li, Qiang
Room-temperature chemisorption of hexacyclic aromatic hydrocarbons on the 2x1, sputtered, oxidized and H-terminated Si(100) surfaces, as well as those upon post treatments of hydrogenation, oxidization and electron irradiation have been investigated by using thermal desorption spectrometry (TDS), Auger electron spectroscopy (AES) and low energy electron diffraction (LEED). This work focuses on the effects of the functional groups (phenyl, methyl, vinyl, heteroatom, and H atom) in the chemisorbed aromatic hydrocarbons (benzene, toluene, xylene isomers, styrene and pyridine) on organic functionalization of the Si(100) surface, particularly on such surface processes as cycloaddition, dative adsorption, hydrogen abstraction, desorption, dissociation, diffusion, and condensation polymerization. Unlike the earlier notion that hydrogen evolution in the hydrocarbon/Si(100) systems is the result of hydrocarbon dissociation (into smaller hydrocarbon fragments and H atoms) on the surface, condensation polymerization of the adsorbed aromatic hydrocarbons is proposed in the present work, in order to explain the higher-temperature hydrogen evolution feature in the toluene/Si(100) system. This hypothesis is supported by our TDS results for other hydrocarbon adsorbates, especially in the pyridine/Si(100) system where electron-induced condensation polymerization has been observed at room temperature. The improved techniques in the TDS experiments developed in the present work have enabled us to observe condensation polymerization and the effect of H on the surface processes (via surface reconstruction) on Si(100) for the first time. New analysis methods have also been developed to determine the adsorption coverage from the AES data, and this work has not only improved the accuracy of the elemental-coverage evaluation, but also provided a means to estimate the rate and the order of chemisorption. By using the density functional theory with the Gaussian 98 program, the adsorption geometries and the corresponding adsorption energies of various adsorption phases have been calculated. These computational results have provided useful insights into the chemisorption structures on the Si(100) surface. The present work also presents the development of three kinetics models for hydrogen evolution in the aforementioned aromatic-hydrocarbon systems on Si(100). Based on a modified collision theory with consideration of diffusion, these theoretical models have proven to be quite successful in simulating the observed TDS profiles and in estimating the kinetic parameters for the analysis of condensation polymerization in 2-dimensional diffusion systems. The present work illustrates that TDS experiments can be used effectively with quantum computation and theoretical kinetics modelling to elucidate the intricate nature of organosilicon surface chemistry.
Quantitative Modelling of the Shifts and Splitting in the IR Spectra of SF₆ in an Ar Matrix
(University of Waterloo, 2005) Peng, Tao
An infrared active polyatomic molecule has several vibrational modes, each of which has a characteristic frequency. If the molecule is trapped in a matrix of perturbing atoms, those vibrational frequencies will shift, and if the vibrational mode is degenerate, the perturbation may lift the degeneracy. Such shifts and splitting are due to the dependence of the chromophore/matrix-atom interaction potential on the internal vibrational motion of the chromophore. Applying a previously-developed model for the shifting and splitting of the triply degenerate ν₃ mode of SF₆ perturbed by a rare gas atom, we use Monte Carlo simulations to sample the accessible equilibrium configurations of the system and to predict the associated thermally averaged perturbed IR spectra. Since the experimental spectrum has 10 peaks while the triply degenerate ν₃ mode of SF₆ in a particular environment could have at most 3 peaks, the observed spectrum must be a combination of spectra for SF₆ trapped in different types of lattice sites. A fit to experiment of simulated spectra generated from a family of lattice sites is then used to identify the peaks in the experimental spectrum, determine the relative importance of the various lattice sites, and semi-quantitatively reproduce the experimental spectrum.
The Catalytic Intramolecular Friedel-Crafts Acylation of Meldrum's Acid Derivatives and The Total Synthesis of Taiwaniaquinol B
(University of Waterloo, 2005) Fishlock, Daniel
The intramolecular Friedel-Crafts acylation of aromatics with Meldrum?s acid derivatives catalyzed by metal trifluoromethanesulfonates and other Lewis acids is reported. Meldrum?s acids are easily prepared, functionalized, handled, and purified. The synthesis of polysubstituted 1-indanones from benzyl Meldrum's acids was investigated thoroughly, and it was shown that a variety of catalysts were effective, whilst accommodating a diversity of functional groups under mild conditions. The scope, limitations, and functional group tolerance (terminal alkene and alkyne, ketal, dialkyl ether, dialkyl thioether, aryl methyl ether, aryl TIPS and TBDPS ethers, nitrile- and nitro-substituted aryls, alkyl and aryl halides) for a variety of 5-benzyl (enolizable Meldrum?s acids) and 5-benzyl-5-substituted Meldrum?s acids (quaternarized Meldrum?s acids), forming 1-indanones and 2-substituted-1-indanones respectively, are delineated.

This method was further applied to the synthesis of 1-tetralones, 1-benzosuberones, and the potent acetylcholinesterase inhibitor donepezil.

Mechanistic investigations were undertaken to determine the rate-determining step in the acylation sequence using Meldrum?s acid, as well as to examine the role of the Lewis acid catalyst. Enolizable Meldrum?s acid derivatives can react via an acyl ketene intermediate under thermal conditions, while quaternarized Meldrum?s acid derivatives are thermally stable and only act as effective Friedel-Crafts acylating agents in the presence of a Lewis acid catalyst.

The total synthesis of (±)-Taiwaniaquinol B was completed. This natural product was the first ever isolated containing an unusual 6-5-6 fused ring system, and it also contains a hexasubstituted aromatic ring, and two all-carbon quaternary centers. This synthesis was accomplished via an intramolecular Friedel-Crafts acylation/carbonyl a-tert-alkylation reaction that exploits the unique chemistry of Meldrum?s acid. This novel methodology can be used to access a variety of highly substituted fused ring systems of various sizes.
Laser Desorption Solid Phase Microextraction
(University of Waterloo, 2006) Wang, Yan
The use of laser desorption as a sample introduction method for solid phase microextraction (SPME) has been investigated in this research project. Three different types of analytical instruments, mass spectrometry (MS), ion mobility spectrometry (IMS) and gas chromatography (GC) were employed as detectors. The coupling of laser desorption SPME to these three instruments was constructed and described in here.

Solid phase microextraction/surface enhanced laser desorption ionization fibers (SPME/SELDI) were developed and have been coupled to two IMS devices. SPME/SELDI combines sampling, sample preparation and sample introduction with the ionization and desorption of the analytes. Other than being the extraction phase for the SPME fiber, the electro-conductive polymer coatings can facilitate the ionization process without the involvement of a matrix assisted laser desorption/ionization (MALDI) matrix. The performance of the SPME coatings and the experimental parameters for laser desorption SPME were investigated with the SPME/SELDI IMS devices. The new SPME/SELDI-IMS 400B device has a faster data acquisition system and a more powerful data analysis program. The optimum laser operation parameters were 250 μJ laser energy and 20 Hz repetition rate. Three new SPME coatings, polypyrrole (PPY), polythiophene (PTH) and polyaniline (PAN) were developed and evaluated by an IMS and a GC. The PPY coating was found to have the best performance and was used in most of the experiments. The characteristics of the PPY and the PTH SPME/SELDI fiber were then assessed with both IMS and MS. Good linearity could be observed between the fiber surface area and the signal intensity, and between the concentration and the signal intensities.

The ionization mechanism of poly(ethylene glycol) 400 (PEG) was studied with the SPME/SELDI-IMS 400B device. It was found that the potassiated ions and sodiated ions were both present in the ion mobility spectra. The results obtained with quadrupole time-of-flight (QTOF) MS confirmed the presence of both potassiated and sodiated ions. This result suggested that cationization is the main ionization process when polymers are directly ionized from the PPY coated silica surface. Four PEGs with different average molecular weights and poly(propylene glycol) 400 were also tested with this SPME/SELDI device. The differences between the ion mobility spectra of these polymers could be used for the fast identification of synthetic polymers.

The SPME/SELDI fibers were then coupled to QTOF MS and hybrid quadrupole linear ion trap (QqLIT) MS, respectively. Improved sensitivity could be achieved with QqLIT MS, as the modified AP MALDI source facilitated the ion transmission. The application of method for analysis of urine sample and the bovine serum albumin (BSA) digest were demonstrated with both PPY and PTH fibers. The LOD for leucine enkephalin in urine was determined to be 40 fmol μL^-1 with PTH coated fiber; and the LOD for the BSA digest was 2 fmol μL^-1 obtained with both PTH and PPY fibers.

A new multiplexed SPME/AP MALDI plate was designed and evaluated on the same QqLIT MS to improve the throughput, and the performance of this technique. The experimental parameters were optimized to obtain a significant improvement in performance. The incorporation of diluted matrix to the extraction solution improved the absolute signal and S/N ratio by 104X and 32X, respectively. The incorporation of reflection geometry for the laser illumination improved the S/N ratio by more than two orders of magnitude. The fully optimized high throughput SPME/AP MALDI configuration generated detection limit improvements on the order of 1000-7500X those achieved prior to these modifications. This system presents a possible alternative for qualitative proteomics and drug screening.

Laser desorption SPME as a sample introduction method for the fast analysis of non-volatile synthetic polymers was also demonstrated here. The coupling of laser desorption SPME to GC/FID and GC/MS was performed, and the advantage of laser desorption over traditional thermal desorption was demonstrated in this research. Laser desorption PEG 400 was observed more effcient than thermal desorption. Good separation was obtained even with a 1-m or 2-m column. These results demonstrate the potential of laser desorption SPME as a sample introduction method for the fast GC analysis of non-volatile compounds such as synthetic polymers.
Multiple Substituent Effects on the Rate Constants for N(2)-N(3) Restricted Rotation of cis-1,3-Diphenyltriazenes
(University of Waterloo, 2006) Lim, Herlina
Triazenes represent an interesting class of organic photochromic materials based on cis-trans isomerization around a nitrogen-containing double bond, and of potential use in optical memory devices. One structural property of triazenes related to cis-trans isomerization is restricted rotation around the N(2)-N(3) bond. The purpose of the study presented in this thesis is to investigate the influence of aryl substitution on the N(2)-N(3) rotational barrier of meta and/or para substituted cis-1,3-diphenyltriazenes. Rate constants for restricted rotation in cis-triazenes were measured by means of a laser-flash photolysis system, via trans-to-cis photoisomerization of corresponding trans-triazenes (which were synthesized either by classical or non-classical diazonium coupling reactions). A quantitative structure-reactivity correlation analysis of rate constants for restricted rotation of cis-triazenes was carried out in terms of an extended Hammett equation. Resulting Hammett reaction contants for restricted rotation rotation are -1. 88 ± 0. 08 and 0. 70 ± 0. 08 for N(1) and N(3), respectively, indicating that restricted rotation of cis-triazenes is more sensitive to the electronic character of the aryl group at N(1) than to than at N(3). Interestingly, the observed rate constants for restricted rotation in cyano-containing substrates are found to be pH-dependent. The latter is attributed to a change in the ionization state of the substrate, which is supported by solvent isotope effects. Furthermore, the pH dependence observed for unsymmetrical cyano-containing substrates indicates that upon deprotonation of the amino group, the negative charge concentrates either on the 4-CN substituent attached to the phenyl ring at N(3) or on the triazeno moiety. Thus, the primary cis-anionic 4-cyano-containing forms are not the same ions and do not equilibrate rapidly, since they undergo cis-to-trans isomerization. Finally, an extended Hammett equation was employed in the analysis of pKa values of trans-triazenes. The results show that there is a direct mesomeric interaction between the charge at N(3) in the triazeno moiety with 4-CN and 4-NO₂groups in the systerms studied. Consequently, the Yukawa-Tsuno modification of the Hammett equation is introduce to correlate pKa values and Hammett substituent constants
Interfacial Properties of Amphiphilic Dendritic Polymers
(University of Waterloo, 2006) Njikang, Gabriel
The self-assembly behavior of arborescent polystyrene-graft-poly(ethylene oxide) copolymers (PS-g-PEO) at the air-water interface and the solubilization/release properties of arborescent polystyrene-graft-poly(2-vinylpyridine) (PS-g-P2VP) copolymers were investigated. These amphiphilic dendritic molecules are covalently bonded unimolecular micelles incorporating a highly branched hydrophobic polystyrene core surrounded by a hydrophilic poly(ethylene oxide) or poly(2-vinylpyridine) shell. Molecules of PS-g-PEO copolymers spontaneously formed supramolecular assemblies at the air-water interface. The type of superstructures formed was found to depend upon copolymer composition, while the level of association was more directly related to the branching density of the polymers. At low surface pressures the PEO segments apparently remained adsorbed on the water subphase, but desorbed into water at very high surface pressures, in the condensed monolayer state. Controlled degradation of the PEO chains with UV light greatly enhanced molecular association, resulting in the formation of either large clusters or long ribbon-like superstructures. The PS-g-P2VP copolymers were found to efficiently solubilize and release hydrophobic small molecules in aqueous media. The partition coefficient and solubilization capacity of the copolymers for hydrophobic polyaromatic hydrocarbons increased with the polystyrene content of the copolymers, while the rate of solubilization decreased with increasing branching functionality of the copolymers. The release profiles for two model drugs displayed an initial burst in release followed by gradual approach to equilibrium. The diffusion coefficients of the drugs in the micelles increased with the branching functionality and the generation number of the micelles, presumably due to increased electrostatic repulsions of the protonated vinylpyridine units.
Chlorine, Fluorine and Water in the Stratosphere: Chemistry, Transport and Trends based on ACE-FTS measurements
(University of Waterloo, 2006) Nassar, Raymond
The Atmospheric Chemistry Experiment (ACE) is a satellite mission for remote sensing of the Earth's atmosphere using the solar occultation technique. The primary instrument on this satellite is the Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE-FTS). ACE-FTS retrievals are described with a focus on the creation of a priori temperature and pressure profiles. ACE-FTS measurements are then used to investigate the chemistry, transport and trends of chlorine, fluorine and water in the stratosphere, leading to an improved understanding of processes affecting both stratospheric ozone depletion and global climate change.

Total chlorine (Cl_TOT) in the stratosphere is determined using ACE-FTS measurements of eleven chlorine-containing species, supplemented by both other measurements and models, to determine Cl_TOT as a function of altitude in five latitude zones. All resulting Cl_TOT profiles are nearly linear, with a slight slope. Mean Cl_TOT for 2004 is determined to be 3. 65 ppbv for both the northern and southern midlatitudes (with a precision and estimated accuracy of ±0. 09 and ±0. 13 ppbv, respectively). A slightly lower value of mean Cl_TOT is determined for the tropics and slightly higher values at high latitudes. Total fluorine (F_TOT) in the stratosphere is also determined primarily from ACE-FTS measurements using a similar approach, resulting in stratospheric F_TOT profiles which are nearly linear with mean values ranging from 2. 50 to 2. 59 ppbv for each latitude zone (with a precision of 0. 04-0. 07 ppbv and an estimated accuracy of 0. 15 ppbv). The observed slopes and pattern of latitudinal variation are evidence of the beginning of a decline in global stratospheric chlorine and of the continuing increase in global stratospheric fluorine levels.

The abundance of water in the stratosphere is investigated for the northern hemisphere midlatitudes in 2004 using ACE-FTS measurements. Potential water is determined as [H₂O]+2[CH₄] and from [H₂O] versus [CH₄] correlations, resulting in a value of 7. 14±0. 05 ppmv, which is used to determine a value of 3. 65±0. 15 ppmv for the mean abundance of water entering the stratosphere. Both values are compared directly with historical data from the Atmospheric Trace Molecule Spectroscopy (ATMOS) instrument (1985-1994) and show a negligible change, implying that the increases observed by ATMOS and other long-term measurements from that time period have not continued.

The removal of stratospheric water in the Arctic vortex is investigated using ACE-FTS measurements. Using derived quantities from a meteorological data assimilation, northern hemisphere occultations from early 2004 are classified as vortex, vortex edge or extravortex. [CH₄] versus [N₂O] correlations are used to further classify the extravortex occultations as tropical, subtropical or midlatitude. Comparisons between profiles of [N₂O], [CH₄] and [H₂O] inside and outside the Arctic vortex, give estimates of upper stratospheric and lower mesospheric descent rates, indicating that descent in the winter 2004 Arctic vortex was rapid, with evidence of descent at higher altitudes than in past years.

The dehydration of air in the tropical tropopause layer and mechanisms for the entry of water vapor into the stratosphere are investigated by an analysis of ACE-FTS profiles of temperature, water vapor and [HDO]/[H₂O]. Month-to-month comparisons for 2004 and 2005 reveal a clear pattern of seasonal variation and a correlation between minimum temperature and maximum HDO depletion. Further interpretation indicates that the gradual dehydration mechanism accompanied by lofting of ice particles in the tropical troposphere is the most likely explanation for the observed seasonal variation and the shape of the [HDO]/[H₂O] profiles.
Modelling of Atmospheric Mercury Emission, Transport, Transformation and Deposition in North America
(University of Waterloo, 2006) Wen, Deyong
A modelling study was conducted to explore the emission, transport, transformation and deposition behaviour of atmospheric Hg. A detailed natural Hg emission model was developed to estimate the natural Hg emissions from soil, water and vegetation. U. S. Environmental Protection Agency (EPA) Community Multiscale Air Quality (CMAQ) Hg model system was improved by incorporating the detailed treatment of natural Hg emissions, adopting boundary conditions from a global Hg model (Seigneur et al. , 2004) and including the calculation of the dry deposition velocity of elemental Hg. The natural Hg emission model and the improved CMAQ-Hg model were validated with some measurements and then applied to North America for a whole year (2002). A detailed natural Hg emission model was developed in this study. This model made use of detailed soil Hg concentration measurements, meteorological data and soil conditions to estimate Hg emissions from soil, water and vegetation. The influence of snow cover and low temperature was also considered in the model. This model was then applied to simulate one-year natural Hg emissions in North America in 2002. The modelled results, compared to some reported natural Hg emission measurements, demonstrated a strong simulation ability. The spatial and temporal variations of emission fluxes were examined through numerical simulations. A pronounced diurnal cycle and a seasonal cycle were found in the emissions from most land uses. Compared with summer, natural Hg emission was significantly limited in winter. Simulation results showed that about 229 metric tons of total natural Hg emission, 1. 8 times anthropogenic Hg emission, was emitted from the simulation domain in 2002. U. S. EPA CMAQ Hg model system was improved and then applied to simulate the emission, transport, transformation and deposition of atmospheric Hg in North America for the year 2002. The simulated results were compared with measured hourly Total Gaseous Hg (TGM) for 3 sites. The good agreement between them demonstrated the good performance of this improved model in modelling the behaviour of emission, transport, transformation and deposition of atmospheric Hg. Hg budget and net evasion of Hg in North America were also investigated. A sensitivity analysis was conducted to assess the effects of emissions, including Hg and non-Hg emissions, on the air concentration and deposition of atmospheric Hg. The results indicated that ambient concentration of TGM was much more sensitive to Hg emissions than non-Hg emissions. Natural Hg emission was more significant than anthropogenic emission to affect ambient concentration of TGM, illustrating natural Hg emission is a key factor influencing TGM ambient concentration. Unlike TGM concentration, Hg dry deposition was not only sensitive to Hg emissions but also to non-Hg emissions such as VOCs and NO_x. Anthropogenic Hg emission, natural Hg emission and NO_x emission had almost the same effect on total dry deposition of Hg. The results also illustrated that Hg wet deposition was only sensitive to non-Hg emissions such as NO_x and VOCs, especially of VOCs emission. Because of the inverse effect of VOCs on Hg wet deposition, reducing NO_x emission should be an ideal solution to mitigate Hg wet deposition. A possible pathway through which atmospheric Hg was greatly affected by emissions changes was identified: emissions of pollutants, especially VOCs and NO_x, greatly affect the level of OH in the atmosphere; OH influences the concentration and deposition of Hg by significantly affecting the gas phase reaction between Hg(0) and OH.
Biosensing at an individually addressable electrochemical array
(University of Waterloo, 2006) Sun, Wei
In this thesis, a novel electrochemical array is reported. The array consists of two planar halves, each having four carbon screen-printed band electrodes (SPEs), orthogonally facing each other and separated by a spacer to yield 16 two-electrode electrochemical cells with 1 mm² working electrode areas. The 16 counter electrodes were converted to Ag/AgCl by electrodeposition and anodization. These electrodes were stable for at least 30 days with potentials under the current densities used in our experiments. The 16 working electrodes were modified by Au electrodeposition, and were examined by scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS).

Immobilization strategies for biomolecules are of paramount importance for successful fabrication of biosensors. This thesis reports a new immobilization method that is based on patterned deposition of alkyl thiosulfates (Bunte salts). Monolayers were formed through electrochemical oxidation of Bunte salts at Au-modified electrodes. Single-component and mixed monolayers were investigated, where the mixed monolayers involved one component with a terminal carboxylic acid functional group to allow immobilization of biomolecules.

Applications of the newly developed immobilization method to an enzyme-based biosensor and an immunosensor were investigated. Glucose and biotin were chosen as model analytes, respectively. Glucose oxidase (GOx) and avidin were covalently immobilized onto the mixed-monolayer-modified electrodes through the carboxylic acid groups. Under the optimized conditions for the fabrication and operation of the biosensors, the new electrochemical array showed linearity up to 10 mM glucose with a sensitivity of 4. 7 nA mM^-1 and a detection limit of 0. 8 mM (S/N=3), and linearity up to 12. 8 µM biotin with a detection limit of 0. 08 µM (S/N=3).
Biochemistry in Bacterioferritin
(University of Waterloo, 2006) Suttisansanee, Uthaiwan
Bacterioferritin, an iron storage protein having a 24-subunit quaternary structure, was used as a model for the study of host-guest interactions and guest encapsulation, making use of its spherical cage-like structure. A hexahistidine-affinity tag fused to the C-terminus of each bacterioferritin subunit was constructed. The C-terminus of each subunit points toward the inside of the cavity, while the N-terminus is exposed on the surface of the protein. The hexaHistag was able to form strong interactions with a nickel-nitrilotriacetic acid linked dye molecule (guest) and this interaction was used in attempts to develop a principle to control guest molecule encapsulation within the spherical cavity of the 24-mer bacterioferritin protein molecule. The procedure involved (1) subunit dissociation under acidic pH, (2) affinity controlled dye-Histag binding with exposed C-terminal hexahistidine residues and (3) reassociation of the subunits at neutral pH. The encapsulation conditions involving step 1 and 3 were studied preliminarily using laser light scattering to measure size (hydrodynamic radius) of the protein particle with apoferritin as a model system as it resembles the size and structure of bacterioferritin. In order to encapsulate guest molecules, the emptied shell of bacterioferritin was generated by site-directed mutagenesis resulting in ferroxidase- as well as heme-free bacterioferritin mutants (E18A/M52L/E94A), and these mutants were used to examine protein stability before conducting encapsulation experiments. However, wild-type bacterioferritin possessed highest stability in maintaining its multisubunit structure; hence, it was used for the encapsulation studies. It was found that 100% bacterioferritin with hexahistidine tag at the C-terminus, and a combination of 60% bacterioferritin with hexahistidine tag at the C-terminus and 40% bacterioferritin without hexahistidine tag at the C-terminus yielded similar amounts of encapsulated guest molecules. This suggested that all hexahistidine at the C-terminus were not equally available for dye molecule binding.
Asymmetric Synthesis using 3,3'-Disubstituted Binaphthol-modified Boronates
(University of Waterloo, 2006) Wu, Tao
A number of 3,3'-disubstituted binaphthol-modified allylboronates (2. 42a-m) were prepared from the reaction between triallylborane and the corresponding 3,3'-disubstituted binaphthols. These chiral allylboronates could allylate carbonyl compounds to produce chiral homoallylic alcohols in high chemical and optical yields. Chiral ligands were readily recycled through simple acid-base extraction. Among all allylboronates tested, 3,3'-(CF₃)₂-BINOL-modified allylboronate (2. 42b) is an especially effective reagent that allows for allylborations of both aldehydes and ketones in high enantioselectivities (up to 98% yield and >99% ee). Reagent 2. 42b represents one of the best allylation reagents for carbonyl compounds developed thus far.

Allylations of cyclic imines using 3,3'-disubstituted binaphthol-modified allylboronates (2. 42a-j) were carried out at low temperature. 3,3'-Bis[3,5-(CF₃)₂-C₆H₃]-binaphthol-modified allylboronate (2. 42j) gave the best enantioselectivities (91% ee to >99% ee) in the allylation of a variety of cyclic imines. This methodology represents the first successful enantioselective allylboration of cyclic imines. The versatility of the allylation products (chiral a-allyl cyclic amines) was demonstrated through efficient total syntheses of several naturally occurring alkaloids such as coniine, crispine A and corynantheidol.

3,3'-Disubstituted binaphthol-modified alkynylboronates (4. 47a-g) were synthesized according to a reported procedure. It was found that these chiral alkynylboronates add to N-acylaldimines in an enantioselective manner to produce chiral propargylamides in excellent yields and enantioselectivities. Up to >99% ee could be obtained with 3,3'-diphenyl binaphthol-modified alkynylboronates (4. 47f). This represents the first direct asymmetric synthesis of chiral propargylamides. Using this methodology, an antitubulin agent (-)-N-acetylcolchinol (AstraZeneca® ZD6126 phenol) was synthesized in 4 steps from commercially available 3-hydroxybenzaldehyde.

During a study of the asymmetric conjugate alkynylation of enones via chiral alkynylboronates, it was found that achiral dialkyl alkynylboronates could add to enones enantioselectively in the presence of catalytic amounts of chiral bidentate ligands (such as 3,3'-disubstituted binaphthols, diisopropyl tartrate and activated chiral amino acids). A catalytic cycle driven by "ligand-exchange" processes was proposed to rationalize this asymmetric induction. This is the first reported example of an asymmetric reaction that is promoted by a catalytic amount of an exchangeable chiral ligand on the boron reagent. More importantly, we have demonstrated a proof of principle that ligand exchange with boronates can be sufficiently fast that catalytic amounts of chiral ligands can be used to effect high levels of stereoselectivity. This catalytic protocol can potentially be applied to other asymmetric reactions providing the following three requirements are met: (1) the starting achiral boronate does not react with the electrophile (no background reaction); (2) the chiral boronate reacts with the electrophile and (3) ligand exchange or transesterification occurs under the reaction conditions. Potential applications of this principle include asymmetric allylboration, hydroboration, aldol reaction and reduction, just to name a few.
Study of Transition Metal Phosphides as Anode Materials for Lithium-ion Batteries: Phase Transitions and the Role of the Anionic Network
(University of Waterloo, 2006) Gosselink, Denise
This study highlights the importance of the anion in the electrochemical uptake of lithium by metal phosphides. It is shown through a variety of in-situ and ex-situ analytical techniques that the redox active centers in three different systems (MnP₄, FeP₂, and CoP₃) are not necessarily cationic but can rest almost entirely upon the anionic network, thanks to the high degree of covalency of the metal-phosphorus bond and strong P-character of the uppermost filled electronic bands in the phosphides. The electrochemical mechanism responsible for reversible Li uptake depends on the transition metal, whether a lithiated ternary phase exists in the phase diagram with the same M:P stoichiometry as the binary phase, and on the structure of the starting phase. When both binary and lithiated ternary phases of the transition metal exist, as in the case of MnP₄ and Li₇MnP₄, a semi-topotactic phase transformation between binary and ternary phases occurs upon lithium uptake and removal. When only the binary phase exists two different behaviours are observed. In the FeP₂ system, lithium uptake leads to the formation of an amorphous material in which short-range order persists; removal of lithium reforms some the long-range order bonds. In the case of CoP₃, lithium uptake results in phase decomposition to metallic cobalt plus lithium triphosphide, which becomes the active material for the subsequent cycles.
Studies of Interaction of Small Molecules with Water Condensed Media
(University of Waterloo, 2006) Mitlin, Sergey
STUDIES OF INTERACTION OF SMALL MOLECULES WITH WATER CONDENSED MEDIA

The present work reports experimental and theoretical studies of the intermolecular interactions in condensed water media. The chemical objects comprise pristine ice and polar organic substances: acetone, acetaldehyde, methanol and chloroform and bi-component water-organic deposits. The experimental part of the studies includes the Fourier Transform Infrared Reflection Absorption spectral (FTIR RAS) examination of the processes of film growth by vapor deposition on cold metal substrate and subsequent annealing. The theoretical studies include ab initio (MP2) and semi-empirical (B3LYP) calculations on the small water and water-organic clusters and classical molecular dynamics simulations of the adsorption of inert guests (Xe/Rn) on the ice surface. The FTIR RA spectral studies reveal that depending on the deposition conditions condensed water media exist in two principal structural forms: noncrystalline and polycrystalline. The former is characterized by porous structure while the latter exists as a non-porous medium with smooth external interface. On annealing, characteristic spectral changes indicate on a rapid crystallization occurring at a certain temperature range. The initial adsorption of organic molecules is accompanied by the hydrogen-bonded coordination between the functional group of organic species and non-coordinated hydroxyl group of the ice surface, the topology of which depends on the electronic properties of the functional group. The computational studies of small water-organic clusters reveal, in particular, two major coordination minima for carbonyl group: a single hydrogen-bonded in-plane complex and a double hydrogen-bonded in-plane complex. The classical molecular dynamics of Xe/Rn species on the ice interface is consistent with two distinctly different surface adsorption sites: one that delocalized over the entire surface and one that confined to small opening in the top ice layer, disrupted by the thermal molecular motion. The penetration barrier is associated with van der Walls repulsion of guest species from the ordered water hexagonal arrangement. A thermo-disruption of latter leads to a rapid diffusion of guest species inside ice medium.

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