Chemistry - Theses, Dissertations, and other Required Graduate Degree Essays

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The Study of ¹¹⁶Sn via Conversion-Electron Spectroscopy and γ-γ Angular Correlations

Date created: 
2017-12-06
Abstract: 

The β– decay of 116m1In (Iπ = 5+), studied using the 8π array at TRIUMF-ISAC, predominantly populated 4+ states in the semi-magic daughter 116Sn, with 50 protons and 66 neutrons. The resulting electromagnetic decays to the ground state were studied through conversion-electron spectroscopy and through angular correlations of coincident gamma rays. Conversion-electron spectroscopy allowed measuring K-shell internal conversion coefficients (αK), and angular correlations of coincident gamma rays allowed determinations of E2/M1 mixing ratios (δ). These values are reported and used to infer aspects of the underlying nuclear structure of 116Sn. In the course of the analysis, several αK values were measured, of which three were measured for the first time in decay spectroscopy. Additionally, ten mixing ratios were measured, eight of which were not previously reported.The 819 keV mixing ratio was re-measured with excellent agreement to literature results, whereas the 931 keV mixing ratio re-measurement indicates that the previously reported measurement requires a sign change. The 138 keV mixing ratio and αK were combined to measure an E0 component, a possible signature of shape coexistence.Measured transition mixing ratios between 4+ states reveal that these highly-mixed states have similar M1 transition strengths among them, but the E2 transition strengths to lower-lying 2+ states suggest underlying wavefunction differences that should be explored and interpreted with current and improved theoretical models of tin nuclei.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Corina Andreoiu
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.

Recoil distance method lifetime measurements of the 2⁺₁ excited states in ⁸⁴Kr and ⁹⁴Sr

Date created: 
2017-12-13
Abstract: 

Intense re-accelerated beams delivered by the Isotope Separator and Accelerator (ISAC-II) facility at TRIUMF, Canada’s national laboratory for particle and nuclear physics, permit access to nuclear structure information for a wide range of radionuclides via in-beam γ-ray spectroscopy with the TRIUMF-ISAC Gamma-Ray Escape Suppressed Spectrometer (TIGRESS), a high-efficiency and Compton-suppressed segmented high-purity germanium (HPGe) detector array. Electromagnetic transition rates measured via Doppler-shift lifetime techniques such as the recoil distance method (RDM) are recognized as a sensitive probe of collective behavior and shape deformation and can be used to discriminate between model calculations. To take advantage of this opportunity, the TIGRESS Integrated Plunger (TIP) has been constructed at Simon Fraser University (SFU). The TIP infrastructure supports Doppler-shift lifetime measurements via the RDM using a 24-element TIP CsI(Tl) wall for charged-particle identification. A commissioning experiment aimed towards a high-precision measurement of the lifetime of the 2⁺₁→ 0⁺₁ transition in ⁸⁴Kr was performed using Coulomb excitation (Coulex) coupled with an RDM lifetimem easurement of the stable ⁸⁴Kr beam. A rare isotope beam (RIB) experiment was also performed to measure the lifetime of the 2⁺₁→ 0⁺₁ transition as well as the reduced transition probability B(E2; 2⁺₁ → 0⁺₁) in ⁹⁴Sr near the shape transition region around A = 100 and N = 60. A Monte Carlo code for simulating γ-ray spectra has been coupled with a likelihood ratio χ2Λ data analysis method in order to determine the lifetime in the two presented experiments. The device, experimental approach, analysis, and results are presented and discussed.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Krzysztof Starosta
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.

Investigation of H atom and free radical behavior in gas hydrates

Author: 
Date created: 
2017-12-15
Abstract: 

Gas hydrates (or clathrate hydrates) are solid crystalline materials composed of a framework of hydrogen-bonded water molecules arranged to form cages which can contain small guest molecules. They have been a subject of research in the oil and gas industry, for carbon dioxide sequestration, gas storage and separation. In order to better understand the applications of hydrates, there is a need to study them at the molecular scale, but there has been relatively little investigation of chemical reactions of the guest molecules. In this thesis project, muon spin spectroscopy was used for the first time to investigate the behavior of muonium (a light isotope of hydrogen) and free radicals in hydrates. Muonium (Mu) and muoniated free radicals were observed in the hydrates of cyclopentene, furan, 2,5- and 2,3-dihydrofuran, pyrrole, thiophene, isoxazole, benzene and acetone. In order to confirm that hydrates were formed, they were characterized by PXRD and solid state 129Xe-NMR and 13C-NMR. The free radicals were formed by addition of Mu to unsaturated organic compounds that reside as isolated guests in the hydrates. Muon and other nuclear hyperfine coupling constants (hfcs) were extracted from μSR spectra of the radicals and compared to liquid-phase data. DFT calculations of hfcs were used to guide the spectral assignments and distinguish between competing radical products where applicable. An extra μ-LCR resonance was seen in the spectra of radicals in the hydrate, indicating that they have restricted motion compared to the liquid state. Muonium and muoniated free radicals were observed simultaneously in the hydrates of acetone and benzene. This was previously only observed in C60 powder and shows that Mu and the radical are in physically separated environments in the hydrates. The Mu amplitude decreases while the radical amplitude increases with temperature. This is consistent with Mu diffusion from the small cage to the large cage in the hydrates, where it can react with the guest. The diffusion occurs at a lower temperature in the acetone hydrate compared to the benzene hydrate.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Paul Percival
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.

Ion Exchange Materials with Enhanced Stability

Author: 
Date created: 
2017-11-21
Abstract: 

Fuel cells are often seen as an alternative to batteries and internal combustion engines to provide electrical power in portable, stationary, or automotive applications. However, several challenges have to be overcome to enable widespread market penetration. One of these challenges is the limited lifetime of fuel cells, or more specifically, the durability and stability of polymer electrolyte membranes. In proton exchange membrane fuel cells, the chemical degradation of widely used perfluorosulfonic acid (PFSA) membranes can be inhibited by radical scavengers. Instead of time-consuming in situ investigations, radicals are widely generated ex situ by Fenton’s reagent, but this also leads to an unrealistic accumulation of iron species. In a newly developed, time saving test protocol, CeO2, ZrO2 and yttria-stabilized zirconia (YSZ) are investigated for their ability to protect PFSA membranes against radical attack and their diverse impact on the membrane properties. In alkaline anion exchange membrane fuel cells, the durability depends on the caustic resistance of the functional groups providing anion conductivity. Theoretical considerations are performed to understand the stability of benzimidazolium and imidazolium with different substituents for steric protection. Limited structural integrity of anion-conducting polymers in challenging environment can lead to restricted usability. The incorporation of crosslinks is investigated as a convenient approach to control ion exchange capacity, prevent dissolution and enhance anion conduction.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Steven Holdcroft
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.

DNA Repair by DNA with Visible Light: Investigations and Implications

Author: 
Date created: 
2017-04-27
Abstract: 

The DNAzyme UV1C was selected previously on the basis of its ability to utilize UV-B light to catalyze the repair of a cis-syn cyclobutane thymine dimer in which no phosphodiester linkage exists between the dimerized thymines. Systematic replacement of each of nine guanines in and around the active site by the guanine analog 6-MI allowed the expansion of the photocatalytic cross section throughout the UV-A and to the edge of the visible. The behaviour of these mutants fell into 3 classes. In one class, replacement of guanines in the quadruplex did not disrupt the wild-type activity. In another class, quadruplex positions, when replaced with 6-MI, led to a decrease in activity in the UV-B but new activity in the UV-A, providing strong evidence for exactly which guanine residues are catalytic in the DNAzyme. Most surprisingly, the G-23 position, thought to be near the active site but not catalytic in UV1C, when replaced with 6-MI, leads to a full retention of activity in the UV-B with the strongest gain of activity in the UV-A. Further modifications to the G-23 position pushed its activity to maximize in the visible, but also ultimately disrupted the quadruplex-dependent activity in the UV-B. While selected against a model thymine dimer substrate, the DNAzyme is also shown to have photocatalytic activity on a bona fide DNA substrate. The continuity of the natural DNA substrate allows us to measure for the first time the effect of the UV1C DNAzyme on the rate of both thymine dimer formation as well as the rate of repair. When compared to double-stranded and single-stranded controls, at its photostationary state, UV1C leads to an overall reduction in fraction of dimerized thymines. Surprisingly, UV1C catalyzes both the repair and formation of thymine dimers in natural DNA, but more slowly than the model substrate that it was selected against. Together, these results shed further light on the emerging field of protein-independent thymine dimer repair. Arguments connecting the self-repair properties of DNA to the RNA world and prebiotic chemistry are offered.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Dipankar Sen
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.

Understanding Milk Protein Adsorption as a Model to Study Sample Loss in Proteomics

Date created: 
2017-08-25
Abstract: 

Non-specific protein adsorption is one of the causes of sample loss in biological experiments. This is a cause of concern in studies where samples are complex and many of the constituent proteins are low abundant, unquantified or unidentified. Since the proteins are irreversibly lost from the samples, it eludes their detection and their role in biological systems cannot be ascertained. This sample loss is unpredictable and non-reproducible which leads to distorted data. On an industrial scale, non-specific adsorption of proteins on machinery may reduce the machine’s efficiency and life. Similarly, unaccounted sample loss due to adsorption during storage contributes to transmission losses to the manufacturer. Various external factors affect protein adsorption that can be exploited to reduce sample loss. In this work, we studied milk proteome adsorption and attempted to quantify the effect of three prominent external factors on the differential adsorption pattern of milk proteins. For this project, we optimized an in-house developed DPA method based on SDS-PAGE, which not only is tag-less and MS compatible but also fast and economical.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Bingyun Sun
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) M.Sc.

Heme-utilizing ribozymes and DNAzymes: Biological impacts, structural aspects, and a kinetic model of activation

Date created: 
2017-08-17
Abstract: 

Guanine-rich RNAs and DNAs that fold into guanine quadruplexes are found to complex tightly with porphyrins such as hemin [Fe(III)-heme]. The generated complex displays robust peroxidase (1 e- oxidation) as well as peroxygenase (2 e- oxidation) activity, greater than that of disaggregated heme itself. They can, thus, be regarded as heme-Utilizing DNAzymes and ribozymes. The folded DNAzymes appear to provide a unique chemical environment to the bound heme that by analogy resembles that of hemoproteins such as horseradish peroxidase (HRP) and cytochrome P450s. This work focuses on three aspects of these ribozymes and DNAzymes. First, we demonstrate that “toxic”, guanine-rich RNAs that accumulate in the cytoplasm of neurons afflicted with the familial forms of two neurodegenerative diseases: Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD), and are indeed thought to be causative of those diseases, efficiently bind and activate heme. Second, we systematically investigate the special status (or not) of guanine quartets in DNA/RNA for the purpose of binding and activating heme. Specifically, we explore whether isoguanine-containing DNAs, which in the presence of certain cations (including Na+, Cs+ and NH4+) form isoG quintets, while in K+, they form isoG quartets, can also bind and activate heme. We make the important observation that while G-quartets and iG-quintets both bind and activate heme, iG-quartets do not. Evidence from the theoretical/computational literature provides a satisfactory explanation for this observation, which in turn helps to illuminate the key structural features of nucleic acids that are necessary for binding and activating heme. Finally, we carry out fast kinetic measurements (using a stopped-flow enabled UV-vis spectrophotometer) to study the identities and formation of hydrogen peroxide-generated activated heme species within the above DNA-heme complexes. With the aid of Pro-KIV software, we perform singular value decomposition and global fitting analysis to formulate with a kinetic scheme for heme activation by these DNAzymes.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Dipankar Sen
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.

Development of a photo-controlled polymeric dry adhesive

Author: 
Date created: 
2017-08-28
Abstract: 

The work presented in this thesis describes the design, synthesis, and analysis of a polymeric donor-acceptor Stenhouse adduct (DASA). This photoswitch was chosen as it switches between two isomeric states, open and closed, that are neutral and zwitterionic respectively. The goal of this project was to manipulate this change in polarity to induce a stronger adhesive response in the polymer, due to an increase in the dipole-dipole interaction between the polymer and a contact piece. While the single molecule exhibits reversibility in solution, the polymer does not appear to reverse in solution or in the solid state. There was a change of 18° in the contact angle, indicating a photoinduced change in the intermolecular forces did occur, however this has no significant effect on the bulk adhesive properties.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Neil Branda
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) M.Sc.

Computational Studies of the Effects of Pressure on Reaction Kinetics and Reaction Mechanisms

Date created: 
2017-10-10
Abstract: 

Both experiment and first principles calculations unequivocally indicate that properties of elements and their compounds undergo a tremendous transformation at ultra-high pressures due to the fact that the difference between intra- and intermolecular interactions disappears under such conditions. Yet, even at much milder pressures, when molecules still retain their individual identity, their chemical properties and reactivity change dramatically. We propose a set of techniques, based on molecular dynamics simulations and quantum mechanical calculations, which can aid in the understanding and prediction of the behavior of chemical systems over a wide range of high pressures.Experimentally, the effects of pressure on reaction rates and equilibrium constants are described by their pressure derivatives, known as volumes of activation and reaction volumes respectively. These quantities are directly linked to partial molar volumes of reactants, transition states, and products. We formulate a molecular dynamics method for the accurate calculation of molecular volumes. This method can be applied to both stable and transient species, which makes it suitable for quantitative analysis of experimental volumes of activation and reaction volumes. The calculated partial molar volumes, as well as reaction and activation volumes obtained from them, agree well with experimental data. To assess the reliability of the experimental activation and reaction volumes, we also present an analysis of the most common empirical analytical functions used to obtain them from pressure dependences of the rate and equilibrium constants. Since mechanisms of chemical reactions are often described in terms of properties of their potential energy surfaces (PES) or Gibbs energy surfaces (GES), we present an analysis of pressure-induced deformations of GES of solvated reaction systems and use quantum mechanical and molecular dynamics simulations to construct energy surfaces and reaction profiles of compressed species, and to analyze how their shapes and topography change in response to compression. We also discuss the important role of volume profiles in assessing pressure-induced deformations of GES.

Document type: 
Thesis
Senior supervisor: 
Michael Eikerling
Noham Weinberg
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.

Towards stable polymer solar cells through crosslinking and sidechain cleavage

Author: 
Date created: 
2017-08-22
Abstract: 

This thesis focuses on the investigation of two strategies for stabilizing the photovoltaic performance of polymer solar cells. Polymer solar cells (PSC) fabricated using solution processable conjugated polymers offer the potential for high-speed production of solar cell modules at low cost. However, achieving high power conversion efficiency (PCE) and long lifetime remains a challenge for PSCs. Photoexcitation of a conjugated polymer generates tightly bound electron-hole pairs (i.e., excitons) that require an electron acceptor (e.g., fullerene) for the dissociation of excitons into free charges. An interpenetrating network of conjugated polymer and fullerene (i.e., bulk heterojunction) is ideal for efficient charge generation due to the existence of a high interfacial area. However, such a morphology is not thermodynamically stable and is subject to large phase segregation in the form of fullerene aggregation provoked by the build-up of excessive heat during the operation of PSCs. Consequently, the PCE of PSCs degrades over time. In this thesis, two strategies for morphological stabilization are investigated using derivatives of poly(benzo[1,2-b:4,5-b′]dithiophene-thieno[3,4-b]thiophene) (PTB). In one strategy, a derivative of PTB having thermally-cleavable tetrahydropyran (THP) sidechains (PTB(THP)) is synthesized. Removal of the THP sidechains by thermal annealing reduces the mobility of PTB, thus retarding the diffusion of fullerene through the polymer matrix to form large aggregates. Photovoltaic (PV) devices made from PTB(THP) after thermal-cleavage of the sidechains exhibited stable PCE over prolonged thermal annealing, which is attributed to the thermally-stable morphology observed by microscopic studies. In the second strategy, a series of PTB derivatives bearing photocrosslinkable chlorooctyl sidechains (PTB-Cl) are synthesized. Photocrosslinking initiated by deep UV is able to insolubilize thin films of PTB-Cls. PV devices having stable PCE over prolonged thermal annealing were demonstrated using photocrosslinked PTB-Cls. However, high-number of photocrosslinkable sidechains and prolonged UV irradiation pose negative effects on the PCE and stability of PV devices made from PTB-Cls. In addition, accurate PCE measurement is of importance for the research of PSC. In Chapter 4, measurement errors of PCE using a simple xenon arc lamp are discussed. Improvements of measurement accuracy are demonstrated following simple modifications of the instruments and the measurement procedure.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Steven Holdcroft
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.