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

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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): 
Senior supervisor: 
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): 
Senior supervisor: 
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): 
Senior supervisor: 
Paul Li
Paul Schaffer
Department: 
Science:
Thesis type: 
(Thesis) M.Sc.

Chlorine as an auxiliary in asymmetric aldol reactions and photocatalytic fluorination of C-H bonds

Date created: 
2015-01-20
Abstract: 

Organohalides are ubiquitous in organic chemistry, with broad utility ranging from their use as building blocks in multistep syntheses, to fluoropharmaceuticals that can oftentimes provide more favourable properties to drug molecules. In this regard, two new synthetic methods have been developed that involve the use or preparation of organohalides: chlorine as an auxiliary for asymmetric aldol reactions, and the photocatalytic fluorination of C-H bonds. The aldol reaction is an important carbon-carbon bond forming reaction in organic chemistry, the product of which is a β-hydroxyketone, which is a functionality often encountered in drugs and natural products. As many pharmaceuticals, agrochemicals and bioactive compounds have increased activity as single enantiomers, asymmetric variants of aldol reactions are sought. Herein, an auxiliary strategy is demonstrated for the stereoselective addition of lithium enolates to aldehydes in which the auxiliary itself is not chiral, but a single chlorine atom introduced via organocatalytic asymmetric α-chlorination. The stereodirecting influence of the chloromethine is then exploited prior to its removal by radical reduction. This strategy is demonstrated in the synthesis of various optically enriched β-hydroxyketones (92-99% ee), as well as the natural products (+)-dihydroyashabushiketol and (+)-solistatin. Fluorination reactions are essential to modern medicinal chemistry, and can provide a means to block site-selective metabolic degradation of drugs and access radiotracers for positron emission tomography imaging. Despite current sophistication in fluorination reagents and processes, the fluorination of unactivated C-H bonds remains a significant challenge. Reported herein is a convenient and economic process for direct fluorination of C-H bonds that exploits the hydrogen abstracting ability of a decatungstate photocatalyst in combination with the mild fluorine atom transfer reagent N-fluorobenzenesulfonimide. This operationally straightforward reaction provides direct access to a wide range of fluorinated organic molecules, including structurally complex natural products, acyl fluorides, and fluorinated amino acid derivatives.

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

Mechanistic Insights into Transition States of Sialidases

Date created: 
2013-08-14
Abstract: 

Sialic acids, a family of nine carbon sugars, are important components of many biomolecules, and they play important roles in many biological processes. For example, they modulate cellular responses such as differentiation, proliferation and apoptosis. These critical carbohydrates are usually positioned on glycoconjugates as the terminal sugar and they are removed by a family of enzymes called sialidases. In mammals, there are several sialidases that are involved in various biological pathways; however, some human sialidases such as NEU3 have shown to be up-regulated in cancer. Also, certain viruses, bacteria, and trypanosomes have developed sialidases as part of their weaponry. Therefore, it is crucial to design selective and potent inhibitors against these enzymes, with minimal side effects. Development of such selective therapeutics involves a comprehensive understanding of the mechanism by which sialidases catalyze the removal or transfer of sialic acid moieties from glycoconjugates. A key component when studying enzymes mechanisms involves characterization of the transition state(s) (TS) through which the enzyme:substrate complex (ES) is converted to the enzyme:product complex (EP). Hence, the focus of this thesis involves characterization of the transition states (TSs) for sialidase-catalyzed cleavage of alpha-sialosides (sialic acid residues covalently attached to glycoconjugates), by employing three distinct mechanistic tools. These techniques include Brønsted analysis, linear free energy relationship (LFER), and kinetic isotope effects (KIEs). Of note, chapter 4 of this thesis describes the development of a new 2D-NMR technique for measuring multiple kinetic isotope effects simultaneously as a first step in the process of solving transition state structure(s) of sialidase-catalyzed reactions.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Andrew J. Bennet
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.

Elucidating the Electronic Structure of Transition Metal Complexes Featuring Redox Active Ligands

Date created: 
2014-10-30
Abstract: 

In this thesis a number of projects involving the design and characterization of complexes bearing redox active ligands are described. Focusing on the phenolate containing ligands, the properties and electronic structure of their corresponding metal complexes were studied by a series of experimental (i.e. electrochemistry, UV-Vis-NIR, EPR, rR etc.) and theoretical (DFT) methods. Specifically, the redox processes of these metal complexes were tuned by varying the para-ring substituents. In one study, nickel-salen (salen is a common abbreviation for N2O2 bis-Schiff-base bis-phenolate ligands) complexes were investigated, where the oxidation potentials of the ligand were predictably decreased as the electron donating ability of the para-ring substituents was increased (NMe2 > OMe > tBu > CF3). Interestingly, the oxidation of these geometrically-symmetric complexes afforded an asymmetric electronic structure in a number of cases, in which the ligand radical was localized on one phenolate rather than delocalized across the ligand framework. This difference in electronic structure was found to be dependent on the electron donating ability of the substituents; a delocalized ligand radical was observed for electron-withdrawing substituents and a localized ligand radical for strongly donating substituents. These studies highlight that para-ring substituents can be used to tune the electronic structure (metal vs. ligand based, localized vs. delocalized radical character) of metallosalen complexes. To evaluate if this electronic tuning can be applied to the metal center, a series of cobalt complexes of these salen ligands were prepared. Indeed, the electronic properties of the metal center were also significantly affected by para-ring substitution. These cobalt-salen complexes were tested as catalysts in organometallic radical-mediated polymerizations, where the most electron rich complexes displayed the best conversion rates. With a firm understanding of the role that the para-ring substituent can play in influencing the electronic structure and reactivity of metallosalen complexes in catalysis, two novel iron complexes, which contain a number of redox active phenolate fragments, were prepared. In addition, these iron-complexes feature a chiral bipyrrolidine backbone. Ligands with this chiral diamine backbone bind metals ions diastereoselectively owing to its increased rigidity, which is critical to stereoselectivity in catalysis. A symmetric (with two phenolates) ligand was prepared by reported methods, and a novel route to synthesize an asymmetric ligand (one phenolate and one pyridine) from symmetric starting materials was established. The neutral iron-complexes were found to be high spin (S = 5/2), and can undergo ligand based oxidation to form an antiferromagnetically-coupled (Stotal = 2) species. The results presented will serve as the basis for catalyst development using complexes of similar ligands.

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

Controlling Photochemistry Using Molecular Switches and Upconverting Nanoparticles

Author: 
Date created: 
2014-09-30
Abstract: 

Because light can be tuned, focused and has a ‘on-off’ control, the use of light to drive photolabile compounds to unmask bioactive molecules provides spatial and temporal control required to evaluate how a specific chemical species will affect the cells in living organisms and to potentially deliver therapeutiecs on demand. However, there are still questions need to be answered when using light as a tool for applications. The research described in this thesis addresses issues related to how light can be used to release small molecules from ‘masked’ forms in complex environments such as in living cells of organisms. Four inter-related questions concerning different aspects of the topic listed below are answered in the thesis. (1) How does the user know when and where the photorelease has occurred? In Chapter 2, a ‘release and report’ concept is demonstrated using a novel photolabile compound. The compound absorbs two UV photons and undergoes two sequential reactions. The first reaction releases the protected molecule and the second reaction produces a visible colour that can be conveniently monitored without any special techniques therefore the successful release process is reported.(2) How does one deliver light that is less-damaging but still capable of inducing photoreactions? And (3) How can one maintain photoreactivity of organic compounds in an aqueous environment?In Chapter 3, a ‘plug and play’ method demonstrates the simplicity of creating a water-dispersible nanosystem through co-encapsulation of hydrophobic upconverting nanoparticles and photoactive compounds by an amphiphilic organic polymer shell. More importantly, the photoreactivity of the encapsulated compounds is well maintained in aqueous medium. (4) How are unwanted photo reactions avoided? Chapter 4 decribes how to use a UV-blocking polymer shell to encapsulate upconverting nanoparticles that prevents a one-photon driven photoreaction while still allowing multi-photon driven processes. Data will be presented to show how the isomerization of diarylethenes in the assembly can be triggered by irradiation of Near-Infrared light but not by UV light or ambient light.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Neil Branda
Department: 
Science:
Thesis type: 
(Thesis) Ph.D.

Modulation of Metastable Metal-Semiconductor Junctions

Author: 
Date created: 
2014-09-26
Abstract: 

The feasibility of modulating the electrical properties of metal-semiconductor (MS) junctions was examined via the preparation of self-assembled monolayers (SAMs) at the interface. In this thesis, metal-monolayer-semiconductor junctions were prepared using a hanging mercury (Hg) drop electrode in contact with an oxide-free silicon substrate (H-Si≡), where the mercury drop was subsequently modified with alkanethiolate SAMs. It has been demonstrated that the electrical properties of an Hg-S-C18|H-Si≡ junction can be tuned from rectifying to ohmic or vice versa by manual manipulation of the size and shape of the Hg drop. Evaluation of the rectification ratio (R), ideality factor (η) and barrier height (qɸeff) enables the determination of the threshold value of the surface area change of the mercury contact. In addition, the effect of variation of the alkyl chain length of the alkanethiolate SAMs on the Hg electrode was studied. Both qɸeff and R were found to depend on the alkyl chain length and changed gradually upon aging. This augments the potential for molecularly tuning the electrical properties of classical MS junctions without complicated materials assembly or device fabrication.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Hua-Zhong Yu
Department: 
Science:
Thesis type: 
(Thesis) M.Sc.

Molecular Modeling of Interfacial Proton Transport in Polymer Electrolyte Membranes

Date created: 
2014-08-27
Abstract: 

The proton conductivity of polymer electrolyte membranes (PEMs) plays a crucial role for the performance of polymer electrolyte fuel cells (PEFCs). High hydration of Nafion-like membranes is crucial to high proton conduction across the PEM, which limits the operation temperature of PEFCs to <100o C. At elevated temperatures (>100o C) and minimal hydration, interfacial proton transport becomes vital for membrane operation. Along with fuel cell systems, interfacial proton conduction is of utmost importance in biology and materials science; yet experimental findings of ultrafast proton transport at densely packed arrays of anionic surface groups have remained controversial and unexplained. In the main part of this thesis work, ab initio simulations were performed on a minimally hydrated, densely packed array of sulfonic acid surface groups (SGs). This system served as a model to study the mechanism of interfacial proton transport in perfluorosulfonic acid membranes. Specifically, simulations were performed to explore the impact of the density of SGs on the mechanism of interfacial proton transport. Results reveal a mechanism of highly collective proton motion at a critical SG separation of 6.6 Å. The activation free energy of proton translocations exhibits a high sensitivity to the SG density. A spontaneous concerted proton transition was observed with low activation barrier at a surface group separation of 6.8 Å. When protons translocate concertedly, the activation barrier of the transition drops by more than a factor of two to the value of 0.25 eV compared to the case of disconcerted proton transfer. Results show that the hydrogen-bond network with long-range order that forms upon densification of SGs at the interface enables highly effective proton transport under minimal hydration conditions. These results were then incorporated in a soliton theory for describing collective proton transport through minimally hydrated and highly charged interfaces.

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

Characterization of the first stage prototype of the TIFFIN detector

Date created: 
2014-07-16
Abstract: 

A single-sided, gridded, gas ionization chamber with digital read-out and a dedicated gas-flow control system was built as the first stage prototype of the Twin Ionization chamber for Fission Fragment Investigation (TIFFIN) detector. The detector was tested with an α-particle source, and the operating parameters of the detector were probed to establish its response. Investigation of the operating parameters of the prototype led to an energy resolution of 8.69(1)% when running the detector with a gas mixture of 90% argon and 10% methane (referred to as P10) at a gas pressure of 1800 Torr. Digital read-out of the signal allowed signal risetimes to be successfully evaluated on an event-by-event basis. However, electric field inconsistencies limited the energy resolution achievable. An electric field cage should be installed to encourage a uniform field between the detector plates. The Nuclear Science Laboratories at Simon Fraser University are embarking upon a program of research to address various topics of interest to modern science such as the origin, production, composition and structure of exotic, neutron-rich isotopes. The study of fission fragments is an effective way to investigate neutron-rich nuclei. Ionization chambers are an appropriate and versatile tool with which to study fission fragments, and can be built in such a way as to allow energy, mass and charge measurements of both fragments. The single-sided prototype is a crucial first step towards the final design which will allow such measurements.

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