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

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Design and characterization of metal-thiocyanate coordination polymers

Author: 
Date created: 
2018-01-12
Abstract: 

This thesis focuses on exploring the synthesis and chemical reactivity of thiocyanate-based building blocks of the type [M(SCN)x]y- for the synthesis of coordination polymers. A series of potassium, ammonium, and tetraalkylammonium metal isothiocyanate salts of the type Qy[M(SCN)x] were synthesized and structurally characterized. Most of the salts were revealed to be isostructural and classic Werner complexes, but for (Et4N)3[Fe(NCS)6] and (n-Bu4N)3[Fe(NCS)6], a solid-state size-dependent change in colour from red to green was observed. This phenomenon was attributed to a Brillouin light scattering effect by analyzing the UV-Visible spectra of various samples with different sized crystals. Coordination polymers of the type [M(L)x][Pt(SCN)4] were prepared and structurally characterized using a variety of bi- or tri-dentate capping ligands (ethylenediamine, 2,2’-bipyridine, 2,2';6',2"-terpyridine, N,N,N′,N′-Tetramethylethane-1,2-diamine). Overall, structural correlations between the ligand, the metal centre, the coordinating mode of the [Pt(SCN)4]2- building block and the topologies of the coordination polymers were established. Similar systems were synthesized using the ligands N,N’-bis(methylpyridine)ethane-1,2-diamine (bmpeda) and N,N’-bis(methylpyridine)cyclohexane-1,2-diamine (bmpchda) and were revealed to be multidimensional coordination polymers by structural analysis. Five complexes of the type [Cu2(μ-OH)2(L)2][A]x•yH2O (where L = 1,10-Phenanthroline, tmeda and 2,2’-bipyridine) were prepared and have been characterized by spectroscopic and crystallographic structural analyzes and by SQUID magnetometry. Two complexes were revealed to be dinuclear molecular units capped with the SCN- ligand. The complexes involving the [Au(CN)4]- anion were structurally characterized as double salts involving the dinuclear Cu(II) unit with a varying degree of hydration. The complex [Cu2(μ-OH)2(tmeda)2Pt(SCN)4] was revealed to be a 1D coordination polymer with trans- bridging [Pt(SCN)4]2- units. The magnetic susceptibility versus temperature was measured and fitted for each system to obtain J-coupling values that were qualitatively compared to the previously published magnetostructural correlation for dinuclear hydroxide-bridged units. The birefringence and luminescent properties for four new complexes of the type [Pb(4’-R-terpy)(SCN)2] were measured. The complexes presented unique luminescence based on the presence of the SCN unit, whereas the birefringence of the complexes was compared to [Au(CN)2]- analogues and was correlated to the structural properties of the system.

Document type: 
Thesis
Senior supervisor: 
Daniel B. Leznoff
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.

Electronic structure and reactivity of transition metal complexes incorporating pro-radical bis-phenoxide ligands

Date created: 
2018-04-05
Abstract: 

Transition metal complexes with pro-radical ligands have received considerable research attention due to their interesting electronic structures, photophysical properties, and applications in catalysis. The relative ordering of metal and ligand frontier orbitals in a complex incorporating pro-radical ligands dictates whether oxidation/reduction occurs at the metal centre or at the ligand. Many metalloenzymes couple redox events at multiple metal centres or between metals and pro-radical ligands to facilitate multielectron chemistry. Owing to the simplicity of the active sites, many structural and functional models have been studied. One class of pro-radical ligand that has been investigated extensively are bis-imine bis-phenoxide ligands (i.e. salen) due to their highly modular syntheses. In this thesis, projects related to the synthesis, electronic structure, and reactivity of mono and bimetallic complexes incorporating the salen framework are explored. Chapter 2 presents a systematic investigation of the effects of geometry on the electronic structure of four bis-oxidized bimetallic Ni salen species. The tunability of their intense intervalence charge transfer (IVCT) transitions in the near infrared (NIR) by nearly 400 nm due to exciton coupling in the excited states is described. For the first time, this study demonstrates the applicability of exciton coupling to ligand radical systems absorbing in the NIR region. Chapter 3 investigates the ground-state electronic structure of a bis-oxidized Co dimer. Enhanced metal participation to the singly occupied molecular orbitals results in both high spin Co(III) and Co(II)-L• character in the ground state, and no observable band splitting in the NIR due to exciton coupling. Finally, Chapter 4 describes a series of oxidized nitridomanganese(V) salen complexes with different para ring substituents (R = CF3, tBu, and NMe2), demonstrating that nitride activation is dictated by remote ligand electronics. Upon one-electron oxidation, electron deficient ligands afford a Mn(VI) species and nitride activation, whereas an electron-rich ligand results in ligand based oxidation and resistance to N coupling of the nitrides. This study highlights the alternative reactivity pathways that pro-radical ligands impose on metal complexes and represents a key step in the use of NH3 as a hydrogen storage medium. The results presented herein provide a starting point for further efforts in reactivity with the salen platform.

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

Synthesis and characterization of BiFeO3-based multiferroic solid solution systems

Author: 
Date created: 
2018-02-09
Abstract: 

Bismuth ferrite BiFeO3 (BFO) is one of the most studied single-phase multiferroic materials with both ferroelectricity and G-type antiferromagnetism above room temperature. It undergoes a ferroelectric-paraelectric phase transition at TC = 830°C and an antiferromagnetic-paramagnetic phase transformation at Néel temperature TN = 370 °C. Despite these wonderful properties of BFO, there are some drawbacks associated with this material including the formations of impurity phases, weak magnetic properties, weak magnetoelectric coupling, and large leakage current density. Therefore, the appropriate chemical modifications are required to improve the electrical and magnetic properties of BFO. In this work, the substitutions of rare earth (RE) ions, such as Dy3+, Er3+, Yb3+, etc., for the A-site Bi3+ ion have been performed and the structures and physical properties of the resulting solid solutions have been investigated.First, new multiferroic materials (1−x)BiFeO3-xDyFeO3 (denoted BDF-x) and (1-x)BiFe(1-y)Ti(y)O(3+y/2)-xDyFeO3 (denoted BDFT-x-y) were synthesized by solid-state reactions. Compared with pure BFO, the ferromagnetism in the BDF-x solid solution is substantially enhanced by the structural distortion and unpaired electrons due to A-site substitution of Dy3+ for Bi3+. The electrical properties, including the ferroelectric and dielectric properties, are further improved by the substitution of Ti4+ for Fe3+ on the B-site, which substantially diminishes the conductivity and consequently the dielectric loss. Well-developed ferroelectric hysteresis loops are displayed in BDFT-x-y with a large remnant polarization Pr = 23 μC/cm2 at room temperature, which is significantly higher than the previously reported Pr = 3.5 μC/cm2 in pure BiFeO3 ceramic. Moreover, weak ferromagnetism is found in it at room temperature (Ms = 0.1 μB/f.u.). The structure-composition phase diagram of the BiFeO3-DyFeO3 system is established.The chemically modified (1-x)BiFe(1-y)Ti(y)O(3+y/2)-xLuFeO3 ceramics exhibit ferromagnetism with a saturated magnetization (Ms = 0.03 μB/f.u) and a remnant polarization of 0.30 μC/cm2 at room temperature. In the (1−x)BiFeO3-xYbFeO3 solid solution, a calculated spontaneous polarization of 7.7 μC/cm2 is obtained for the x = 0.11 ceramics which exhibit a weak ferromagnetism with Ms = 0.025 μB/f.u at roomivtemperature. Interestingly, an unusual magnetization reversal behavior is discovered in the (1−x)BiFeO3-xErFeO3 solid solution. At x = 0.12, the magnetic pole inversion occurs at 30 K. Lastly, the (1−x)BiFeO3-xEuFeO3 solid solution is found to exhibit an interesting magnetization behavior, with the magnetic properties undergoing a crossover from an antiferromagnetic to ferromagnetic state at x = 0.12.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Dr. Zuo Guang Ye
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.

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.