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

Receive updates for this collection

Optimizing the Processability of Selenium Nanowires and Their Chemical Transformation into Polymer Coated Semiconductor Materials

Date created: 
2014-04-07
Abstract: 

This thesis seeks out to optimize the sonochemically-induced synthesis and the ease of handling high-aspect-ratio selenium nanowires. Understanding the selenium nanowire’s surface chemistry is crucial to controlling their dimensions during growth and to facilitate the manipulation of these materials. The surface chemistry of the nanowires was analyzed with a variety of surface sensitive techniques and electron microscopy. This knowledge of the surface chemistry of selenium nanowires was utilized to increase their colloidal stability. A stable dispersion of selenium nanowires improves the ease of handling and processing these materials for subsequent assembly or use in templated reactions. For example, surfactant stabilized nanowires enhanced their colloidal stability in media that are otherwise poor at stabilizing the nanowires and improved the uniformity of products from templated reactions on the nanowire surfaces. We also discovered that dispersions of selenium nanowires in a low dielectric constant solution could be organized by electrokinetic techniques into fibers that oriented along the electric field. We developed a general method for the assembly of the selenium nanowires into either macroscopic fibers or an array of fibers of various lengths over large areas. Isolated fibers of selenium nanowires could reversibly bend in response to electrostatic charges. These flexible selenium fibers also exhibited a photoconductive response when illuminated with white light. These properties of selenium nanowires can degrade over time as these nanowires are susceptible to oxidative damage, but we were able to demonstrate the first passivation of selenium nanowires with a thin layer of polystyrene. The thin layer of polystyrene was grafted onto the selenium surfaces by a surface-initiated atom transfer radical polymerization reaction. These encapsulated nanostructures demonstrate an enhanced resistance towards oxidative damage, such as corrosion. We were also able to synthesize polystyrene encapsulated copper selenide nanowires by a similar route in a template-engaged reaction in conjunction with a surface-initiated atom transfer radical polymerization reaction.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Byron D. Gates
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.

Development of a neutron generator facility at Simon Fraser University

Date created: 
2015-04-27
Abstract: 

A new neutron generator facility at Simon Fraser University (SFU) utilizes a commercial deuterium-tritium neutron generator (Thermo Scientific P 385) to produce 14.2 MeV neutrons at a nominal rate of 3E8 neutrons/s. The facility will be used to produce radioisotopes to support a research program including nuclear structure studies and neutron activation analysis. As a prerequisite for regular operation of the facility and as a personnel safety consideration, dose rate predictions for the facility were implemented via the GEANT4 Monte-Carlo framework. Dose rate predictions were compared at two low neutron energy cutoffs: 5 keV and 1 meV, with the latter accounting for low energy thermal neutrons but requiring significantly more computation time. As the SFU facility geometry contains various openings through which thermal neutrons may penetrate, it was necessary to study their contribution to the overall dose rate. A radiation survey of the facility was performed as part of the commissioning process, consisting of a neutron flux measurement via copper foil activation and dose rate measurements throughout the facility via a 3He gas filled neutron detector (Thermo Scientific WENDI-2). When using the 1 meV low neutron energy cutoff to account for thermal neutrons in the dose rate predictions, the predictions and survey measurements agree to within 30% or better in most survey locations.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Krzysztof Starosta
Department: 
Science:
Thesis type: 
(Thesis) M.Sc.

Modeling of Water Sorption and Swelling in Polymer Electrolyte Membranes: Diagnostic Applications

Date created: 
2015-04-23
Abstract: 

The polymer electrolyte membrane (PEM) fulfills vital functions as separator, proton conductor, and electronic insulator in a polymer electrolyte fuel cell (PEFC). The well-studied and practically used solid polymer electrolyte membranes are perfluorosulfonic acid (PFSA) polymer membranes such as Nafion. These membranes offer high proton conductivity, high mechanical strength and good chemical stability. The efficiency of the chemical-to-electrical energy conversion in a PEFC critically depends on the ability of the PEM to transport protons from the anode to the cathode. Proton conductivity of the PEM is a key parameter to achieve high power density and performance. The main variable to characterize the state of a PEM and determine its transport properties is its water content. In particular, the proton conductivity is highly sensitive to the level of hydration. Membranes experience continuous stresses and consequently continuous loss of performance throughout their operational life. Chemical degradation alters the chemical structure of the PEM, which affects the water distribution in it. A consistent description of water sorption and swelling under conditions relevant for the PEFC operation lies at the heart of understanding transport properties, performance and degradation phenomena. This work expands on a previously developed poroelectroelastic model of water sorption in PEMs [Soft Matter 7, 5976 (2011)]. The theory relates the charge density at the pore walls to a microscopic swelling parameter. Extended to the water sorption equilibrium in a pore ensemble, the model reconciles microscopic swelling in a single pore with macroscopic swelling of the membrane. This work provides a generalized treatment of elastic effects in PEMs. Different deformation modes of polymeric pore walls are used to derive stress-strain relationships that determine the law of swelling. Moreover, this work enhances the diagnostic capabilities of the model; it provides the statistical pore size distribution as well as a statistical distribution of microscopic fluid and elastic pressures inside the PEM. Thereafter, the model is applied to different sets of water sorption data for PEMs that had undergone either hygrothermal aging or chemical degradation. The model-based analysis provides mechanistic explanations of structural changes and their impact on microscopic distributions of charge density and elastic properties in PEMs.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Michael Eikerling
Department: 
Science:
Thesis type: 
(Thesis) M.Sc.

Total synthesis of 5,5-spiroacetal natural products and studies toward the total synthesis of eleutherobin

Date created: 
2015-04-20
Abstract: 

A novel chlorohydrin-based spirocyclization reaction has been developed that complements contemporary approaches to spiroacetals. The discovery and optimization of a silver(I)-promoted cyclization of ketochlorohydrins enabled the synthesis of a wide range of 5,5-, 5,6-, and 5,7-spiroacetal compounds. In addition, this strategy was applied in the total syntheses of (+)-cephalosporolide E and (−)-cephalosporolide F, which were accomplished in six steps. Further extension of this methodology culminated in the first total synthesis and full stereochemical assignment of (+)-ascospiroketal A. Specifically, a silver(I)-promoted cyclization cascade was developed that effected both a spirocyclization as well as an oxetane rearrangement, and generated a quaternary all-carbon stereogenic centre with complete stereocontrol. This unique reaction sequence was a critical component of the eventual total synthesis of (+)-ascospiroketal A and several diastereomers that were made available in fourteen steps. An additional study detailing efforts geared toward the total synthesis of eleutherobin, an anti-cancer natural product, is also presented. By utilizing a cyclobutanone α-arylation/Haller-Bauer fragmentation/Friedel-Crafts acylation strategy, a tetralone intermediate for the synthesis of eleutherobin was made available on multi-gram-scale. Efforts to convert this material into the bicyclo[8.4.0]tetradecane core of eleutherobin are described including the identification of an intramolecular aza-Michael strategy that secured the carbon complement of eleutherobin.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Robert Britton
Department: 
Science: Chemistry
Thesis type: 
(Thesis) Ph.D.

Investigation of Protein-ligand Interactions by Molecular Dynamics and Saturation Transfer Difference NMR Spectroscopy

Author: 
Date created: 
2015-03-26
Abstract: 

Protein-ligand interactions form the molecular basis of many biological processes. The study of their interactions from a structural perspective can provide not only insights into the molecular recognition between the protein and the ligand but also clues to the design of better ligands that can serve to mediate the biological events. This thesis investigates such interactions for four proteins that are (potential) therapeutic targets. Techniques used in this thesis include molecular dynamics (MD) simulations, saturation transfer difference (STD) NMR spectroscopy, and complete relaxation and conformational exchange matrix (CORCEMA) analysis that calculates theoretical STD effects. MD simulations are employed to study the binding of two designed glycopeptides with SYA/J6, a monoclonal antibody specific for the O-polysaccharide of the Shigella flexneri Y bacterium, as well as the binding dynamics and strengths of a series of inhibitors against human lactate dehydrogenase A (LDHA), an enzyme implicated in the cell energy metabolism of various cancers. The computational results from both cases are consistent with experimental data, predicting that neither glycopeptide would bind to SYA/J6, and clarifying ambiguities in the binding modes of two well-known LDHA inhibitors. Furthermore, binding models of two inhibitors against the enzyme UDP-galactopyranose mutase (UGM), a potential target for the treatment of tuberculosis, and two substrates of UDP-N-acetylgalactopyranose mutase (UNGM), a potential target against diarrheal disease, are constructed by a protocol that combines MD, STD NMR, and CORCEMA calculations. The collective results indicate a unique binding mode for a UGM inhibitor and explain the bifunctionality of UNGM.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Gary Leach
Department: 
Science:
Thesis type: 
(Thesis) Ph.D.

An in-depth examination of the properties and behaviour of Au(III)-based [AuX2(CN)2]- (X = Cl, Br, I) as a coordination polymer building block

Date created: 
2014-11-27
Abstract: 

This thesis primarily focuses on the synthesis and characterization of [AuX2(CN)2]- (X = Cl, Br, I), a square planar Au(III)-based compound, and its use as a coordination polymer building block. K+, nBu4N+ and PPN+ salts of [AuX2(CN)2]- and the Au(I/III)-based double salts K3[Au(CN)2]2[AuBr2(CN)2]-H2O and K5[Au(CN)2]4[AuI2(CN)2]-2H2O were prepared and structurally characterized. All compounds exhibited many structure-defining weak interactions such as X-X, Au-X (X = Br, I) and Au(I)-Au(I) interactions, as well as a rare Au(I)-Au(III) interaction with an intermolecular distance of 3.58 A; no Cl-Cl interactions were observed. [AuX2(CN)2]- was introduced to solutions containing a variety of divalent metals (Mn, Fe, Co, Ni, Cu, Zn, Pb) and ancillary N-donating chelating ligands such as 1,10-phenanthroline or bridging ligands such as 4,4'-bipyridine. In most cases, an ionic material resulted, containing a metal cation coordinatively saturated by ligand and an unbound [AuX2(CN)2]- (X = Cl, Br) anion. In some cases, [AuX2(CN)2]- did bind, but in a pendant, non bridging fashion. With ethylenediamine and 4,4'-bipyridine ligands, and Ni(II) and Co(II) or Zn(II), respectively, an [AuBr2(CN)2]--bridged coordination polymer resulted; no [AuCl2(CN)2]--bridged materials were observed with added ancillary ligands. In the absence of ancillary ligand, several [AuX2(CN)2]--bridged (X = Cl, Br) formed; all reactions involving [AuI2(CN)2]- resulted in decomposition of the [AuI2(CN)2]- molecule. Exposing [AuX2(CN)2]- to temperatures above 80 C or UV light resulted in the reductive elimination of halogen, yielding [Au(CN)2]-. Kinetics (thermal and photochemical) studies revealed pseudo first-order rate kinetics with. Heating some [AuBr2(CN)2]--containing coordination polymers to 125 C converted them to analogous [Au(CN)2]--containing materials. The ligand-free Cu[AuX2(CN)2]2 materials exhibited a vapochromic response when exposed to H2O, DMF, DMSO, pyridine, 1,4-dioxane and ethyleneglycol; they also exhibited distinct IR and Raman vCN patterns. Using Raman analysis, these vCN patterns can be effectively used to detect and identify between DMF, DMSO and pyridine. A series of Cu(I) and Ag(I)-based coordination polymer materials containing bridging [AuX2(CN)2]-, [Au(CN)4]- and [Au(CN)2]- were synthesized and characterized. M[Au(CN)4] (M = Cu, Ag) exhibit negative thermal expansion with expansion coefficients between -11e-6 and -24e-6 K-1. M[Au(CN)2] are isomorphous to known AuCN, and exhibit turquoise (Ag) and red (Cu) emission. Incorporating pyridine, THT, PPh3 and Me2S in the Cu(I)/[Au(CN)2]- reaction yielded materials with distinct emissive properties; Cu(SMe2)[Au(CN)2] emits white light. Thus, Cu[Au(CN)2] shows potential as a sensor for P- or S-donor solvents.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Daniel Leznoff
Department: 
Science: Chemistry
Thesis type: 
(Thesis) Ph.D.

Method Development for an Easy and Direct Quantitation of Protein Adsorption by Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE)

Date created: 
2014-11-20
Abstract: 

The current proteomic approach is to identify and analyze proteins of interest, which can potentially be disease biomarkers. However, these important proteins usually exist in very low concentration, making them vulnerable to sample loss by adsorption during any laboratory manipulations. A simple method, sodium dodecyl sulfate polyacrylamide gel electrophoresis coupled with direct protein adsorption analysis (SDS-PAGE/DPA), is presented here for the quantitation of adsorption-caused protein loss. No complicated steps and expensive equipment are involved; this method for protein study enables measurement of proteins adsorbed on vials at extremely low concentrations (in pg/μl). We used this method to characterize the effects of concentration, time, and volume on adsorption. We also applied this method to discover differential sample loss in protein mixtures and its utility in developing preventive strategies of adsorption. This method is further being employed for studying different aspects of adsorption-caused peptide loss.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Bingyun Sun
Department: 
Science:
Thesis type: 
(Thesis) M.Sc.

Ab Initio Studies on 2D Array Of Acidic Surface Groups as a Model For Polymer Electrolyte Membranes.

Date created: 
2014-08-25
Abstract: 

Polymer electrolyte fuel cells (PEFCs) are touted as the next generation of energy delivering devices. Within a decade, PEFC-driven powertrains are expected to become a viable alternative to internal combustion engines in vehicles. Moreover, PEFCs could provide power to a plethora of portable and stationary applications. The critical component in a PEFC is the polymer electrolyte membrane (PEM). Current PEMs require a high level of hydration in order to provide sufficient proton conduction. Of particular interest in this field is the synthesis of advanced functional membranes that could attain high proton mobility at minimal hydration and at elevated temperature (> 100ºC). At these temperatures, structural correlations and proton dynamics at acid-functionalized polymer aggregates could be vital for membrane operation. Theoretical predictions should guide the efforts in the design of advanced PEMs. Our model system consists of a minimally hydrated interfacial array of acid-terminated surface groups. The density of these surface groups is the main variable parameter of the model; moreover, we have evaluated different chemical architectures of surface groups. We have employed ab initio calculations based on density functional theory to study interfacial energies, structural correlations and transitions in the hydrogen bonded network of hydronium ions and protogenic surface groups.The first part of this thesis focuses on rationalizing the effect of various parameters of highly acid-functionalized interfaces in PEMs, such as density, chemical architecture, and conformational flexibility of acidic surface groups on interfacial structural correlations and transitions. At high surface group density and under minimal hydration, with one water molecule per surface group, sulfonic acid head groups are perfectly dissociated. They assemble into a highly ordered condensed surface state with two sublattices; one of them is formed by hexagonally ordered sulfonate anions; the other sublattice corresponds to interstitial hydronium ions. Sulfonate anions and hydronium ions form a hydrogen bonded network. The saturation of hydrogen bonds renders the network in a superhydrophobic state. Lowering the surface group density triggers a sequence of transitions to states with decreasing long range order, decreasing the number of interfacial hydrogen bonds and the degree of dissociation. Moreover, the interface becomes hydrophilic. The same sequence of transitions was found for arrays with varying length and chemical structure of surface groups. These findings emphasize the importance of 2D correlation effects at polymer-water interfaces in PEMs. The second part of the thesis focuses on the impact of a second monolayer of water molecules on stability, interfacial structural correlations and and transitions of the hydrated array of acidic surface groups. Upon increasing the surface group spacing, the bonding energy of additional water increases, undergoing a transition from superhydrophobic to hydrophilic wettability. At sufficiently large surface group separation, a hydronium ion is seen to transfer from the minimally hydrated interfacial network to the second water layer, where it is then observed to form a Zundel ion.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Michael, Eikerling
Department: 
Science:
Thesis type: 
(Thesis) Ph.D.

The Cyclotron Production and Cyclometalation Chemistry of 192-Ir

Date created: 
2014-12-11
Abstract: 

The goal of this thesis is to demonstrate the cyclotron production, radiochemical isolation, and cyclometalate chemistry of radio-iridium isotopes. In recent work, Luminescence Cell Imaging (LCI) has been combined with radioisotopes leading to compounds that can be imaged with both optical microscopy and nuclear techniques. Radiometals excel in this multifunctional setting, providing ideal chemical and nuclear properties for luminescence, biological targeting, nuclear diagnostics, and therapy. Iridium cyclometalate compounds have demonstrated potential in LCI with excellent photophysical properties. Independently, low specific activity 192-Ir has been successfully applied in brachytherapy as a high-intensity beta (-) emitter. Despite this, radio-iridium has not been applied to cyclometalate chemistry, nor a radiochemical isolation method developed for its cyclotron production. Herein is demonstrated the feasibility of the production and isolation of radio-iridium, and its application to cyclometalate chemistry as a potential tool for nuclear medicine research. Natural osmium was electroplated onto a silver disc from basic media, and the thin deposits obtained were weighed and characterized with scanning electron microscopy. These targets were irradiated using the TRIUMF TR13 cyclotron, delivering 12.7 MeV protons to the target disc to access the A-Os(p,n)A-Ir reaction channels. Three irradiations were performed at 5 microamps for 1 hour, and one at 20 microamps for 2 hours. Gamma spectra of the targets were collected and the range of iridium isotopes (186-190, 192) identified and quantified. The irradiated material was then oxidized, dissolved from the target backing, and separated via anion exchange. Once isolated, the isotopes were applied to an adapted cyclometalation procedure, and the compounds were identified and quantified against non-radioactive standards using high performance liquid chromatography with coupled gamma-ray and ultraviolet detectors. The procedure developed here has enabled the study of radio-iridium cyclometalates, a potentially new class of theranostic compounds for nuclear medicine.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Corina Andreoiu
Paul Schaffer
Department: 
Science:
Thesis type: 
(Thesis) M.Sc.

Pre-concentration of positron-emitting [18F]fluoride and radiosynthesis of fluoride-based prosthetic compounds for PET imaging using magnetic droplet microfluidics (MDM)

Date created: 
2014-12-09
Abstract: 

The radioisotope 18F is often considered the best choice for PET imaging, owing to its desirable chemical and radiochemical properties. However, nucleophilic 18F fluorination of large, water soluble biomolecules, based on C-F bond formation, has been difficult. Thus, several aqueous fluorination approach have been developed which offers significant development in radiopharmaceutical synthesis. Furthermore, since 18F decays rapidly, production of these 18F-labelled compounds requires an automated process to reduce production time, reduce radiation exposure and also minimize transfer of reagents during tracer synthesis to reduce sample transfer loss. Herein, a method called magnetic droplet microfluidics (MDM) has been developed which aims to conduct [18F]fluoride pre-concentration and synthesis of 18F-labeled compound on a microfluidic platform. Using this method, we have demonstrated 18F pre-concentration in a small-volume droplet through the use of anion exchanging magnetic particles. By using MDM, the pre-concentration step took approximately 5 min. and the [18F]fluoride solution was pre-concentrated by 15-fold from a volume of 1 mL to 0.05 mL. After the pre-concentration step, an 18F-labelling reaction was performed on the MDM platform using the S-F bond formation in aqueous conditions to produce an arylsulfonyl [18F]fluoride which can be used as a prosthetic group to label PET targeting ligands. The high radiochemical purity of 95 ± 1% was comparable with 96% which was previously reported using conventional method. In addition, when using MDM, the total synthesis time was improved to 15 min. with lower reagent volumes (50-60 µL) used. The MDM method was also used to produce an 18F-labelled aryltrifluoroborate through B-F bond formation. The synthesis of aryltrifluoroborate compound at low activities (~5 mCi), gave radiochemical purities which were low for both MDM (5.8%) and conventional method (6.0%).

Document type: 
Thesis
File(s): 
Supervisor(s): 
Paul Li
Paul Schaffer
Department: 
Science:
Thesis type: 
(Thesis) M.Sc.