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

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Modulation of Metastable Metal-Semiconductor Junctions

Author: 
File(s): 
Date created: 
2014-09-26
Supervisor(s): 
Hua-Zhong Yu
Department: 
Science:
Thesis type: 
(Thesis) M.Sc.
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

Molecular Modeling of Interfacial Proton Transport in Polymer Electrolyte Membranes

File(s): 
Date created: 
2014-08-27
Supervisor(s): 
Michael Eikerling
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.
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

Characterization of the first stage prototype of the TIFFIN detector

File(s): 
Date created: 
2014-07-16
Supervisor(s): 
Krzyzstof Starosta
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) M.Sc.
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

The reactivity of organometallic diamido-actinide complexes

File(s): 
Date created: 
2013-06-24
Supervisor(s): 
Daniel B. Leznoff
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.
Abstract: 

This thesis explores the coordination chemistry of diamido-actinide complexes and establishes them as active catalysts for a number of transformations. The synthesis, characterization and reactivity studies of a series of diamido-ether actinide complexes are described. The focus of these studies include the use of two different ligand frameworks: a silyl ether backbone of the form [(RNHSiMe2)2O] ([RNON]H2; R = tBu, 2,6-iPr2Ph, 2,4,6-Me3Ph), and an alkyl ether backbone of the form [(RNHCH2CH2)2O] ([RNCOCN]H2; R = 2,6-iPr2Ph). A series of diamido-ether actinide halide complexes supported by these ligands can be prepared through the addition of either [RNON]Li2 or [RNCOCN]Li2 to UCl4 or ThCl4•2DME. These halide complexes can then be alkylated via the addition of appropriate alkylating reagents such as LiCH2SiMe3, LiCH(SiMe3)2 or KCH2Ph. A series of new diamido-actinide alkoxide complexes has also been prepared from the addition of alkoxide reagents such as LiOiPr or KOtBu. These diamido-actinide alkyl complexes are explored as catalysts for ethylene polymerization, lactide polymerization, and intramolecular hydroamination. In all cases, these alkyl complexes are found to be active catalysts, but in each instance, different complexes are established as the most active species. The mixed-donor amido-amino-siloxo ligands [(RN(Li)SiMe2N(R)SiMe2O] ([RNNO]Li2; R = 2,6-iPr2Ph, 2,4,6-Me3Ph), are also used to prepare a series of new actinide-based complexes. The addition of one equivalent of ligand per metal centre yields “ate” complexes that retain solvent and salt in the coordination sphere of the metal while the addition of two equivalents of ligand per metal centre yields bis(amido-siloxo)actinide-based products. These complexes, like their diamido counterparts, can be alkylated through the addition of appropriate alkylating reagents such as LiCH2SiMe3. Lastly, oxidation reactions with {[tBuNON]UCl2}2, [iPr2PhNCOCN]UCl3Li•THF and [Me3PhNNO]2U are described. The preparation of two non-uranyl U(VI) complexes from the oxidation of {[tBuNON]UCl2}2 are reported. Furthermore, the oxidation of [Me3PhNNO]2U yields a new, ligand-activated U(V) complex.

Document type: 
Thesis

Determining local viscoelastic properties of collagen systems using optical tweezers

Author: 
File(s): 
Date created: 
2014-01-13
Supervisor(s): 
Dr. Nancy R. Forde
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.
Abstract: 

In this work, I aimed to develop and apply a technique capable of measuring the viscoelastic properties of collagen at different levels of hierarchy. Collagen is the predominant structural protein in vertebrates, and its self-assembly into well-defined structures including fibrils underlies the formation of a wide variety of biological structures with a broad range of functions. Here, in order to understand the correlation between collagen’s structure and its mechanical properties, the viscoelastic properties of different collagen systems were characterized, ranging from solutions of molecules to self-assembled forms of fibrillar gels and gelatin. To determine rheological properties, optical tweezers were used to trap and monitor thermal fluctuations of an embedded micron-sized particle, producing measurements of viscoelastic response of collagen systems at a high bandwidth (> 10^4 Hz). To validate these measurements, I reproduced results on a previously characterized system (polyethylene oxide). The obtained viscoelastic response is affected by the timescales of the interactions between polymers, which play a critical role in conferring elasticity to the system. To provide guidance to the microrheology experiments, the structure of collagen in acidic solution was probed using dynamic light scattering. My microrheology studies of collagen molecules in acidic solution showed that elastic response becomes comparable to viscous response at the highest concentration studied here, 5 mg/ml. Here, the significant elasticity observed at frequencies above ~200 Hz is due to collagens’ intermolecular interactions, which I found were not due to electrostatic interactions. However, elasticity was found to decrease following the removal of collagen’s telopeptides, consistent with their role in facilitating fibril formation. At the fibrillar level, unlike in solutions of collagen, I observed spatial heterogeneity in viscoelastic properties. The elastic modulus varies by an order of magnitude at different locations within fibrillar collagen gels. By making measurements over 100-minute timescales as collagen self-assembled into fibrils, I probed the development of microscale heterogeneity and concluded that heterogeneity appears during early phases of fibrillar growth and continues to develop further during this growth phase.

Document type: 
Thesis

Examining Structure-Property Relationships of Proton Exchange Membranes through the Study of Model Sulfonated Graft Copolymers

File(s): 
Date created: 
2014-03-24
Supervisor(s): 
Steven Holdcroft
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.
Abstract: 

The role of polymer nanostructure on morphology, crystallinity, water sorption and proton conductivity was investigated using a model solid polymer electrolyte. Poly([vinylidene difluoride-co-chlorotrifluoroethylene]-graft-styrene) [P(VDF-co-CTFE)-g-PS], which consists of a hydrophobic, fluorous backbone and styrenic graft chains of varied length was synthesized with controlled chain architecture and chemical composition. The polystyrene graft chains were sulfonated to different degrees to provide three series of polymers with controlled ion exchange capacity (IEC). Due to chemical dissimilarity of the hydrophobic fluorous segments and the hydrophilic sulfonated polystyrene segments, the copolymers phase separate into ionic and non-ionic domains. The ionic domains allow transport of water and protons; the hydrophobic domains provide mechanical integrity, preventing the membranes from dissolving in water. The design of the model graft copolymers allows systematic examination of the effects of graft length and graft density on water sorption and proton conductivity. One of the major features of this work is that the sulfonated graft copolymers with shortest graft chains exhibit highest degree of crystallinity and highest PVDF content, which restrict excessive swelling and alleviate acid dilution, leading to a wider IEC operating range for high proton conductivity. Furthermore, the short graft copolymers allow access to very high IEC membranes that are insoluble in water. These short graft polymers with high IECs exhibit exceptionally high proton conduction under reduced humidity and elevated temperatures. In addition, for a given PVDF content, the lower graft density copolymers were observed to possess higher crystallinity and more contiguous PVDF domains that allow high IEC membranes to be prepared that possess lower degrees of swelling. Another important finding is that blending fully sulfonated graft copolymers with high molecular weight PVDF yields membranes with overall low IECs that exhibit highly localized ion content. This promotes the interconnection of ionic domains for effective proton transport while the more extended hydrophobic domains significantly reduce excessive swelling which serve to maintain the mechanical property of the membranes. This thesis describes a systematic approach, demonstrating the design, synthesis, characterization of model polymers, followed by the analysis of structure-property relationships in proton exchange membranes.

Document type: 
Thesis

Rational Design of Dithienylethenes with Photoelectrochromic Properties

File(s): 
Date created: 
2014-01-13
Supervisor(s): 
Neil R. Branda
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.
Abstract: 

1,2-Dithienylethene compounds (DTEs) reversibly interconvert between two isomeric forms, referred to as the colourless (ring−open isomer) and coloured (ring−closed isomer). This interconversion can be achieved through photochemical, electrochemical and thermal means. The photochemical toggling of DTEs is well characterized in the literature. However, their electrochromic behaviour is seldom reported and almost all known examples degrade through electropolymerisation. The fully electroactive DTEs are unstable in the coloured form at room temperature and undergo ring−opening in the dark. Depending on the application, DTEs may require a “single time use” (biological application / imaging) or must undergo extensive cycling (ophtalmics, smart windows). The goal of this work was to find the structural demands that allow integration of three desirable features, photo-, electrochemical and thermal stability. The first part of this thesis addresses the synthetic manipulation of the DTE core capable of catalytic oxidative ring−opening reactions. Key functional groups were appended in the α−positions of the electroactive DTE framework. These groups were carefully chosen in the context of thermal stability of the coloured−form and the mitigation of the undesired electropolymerisation. These substituents range from electron donating (through induction) methyl and t-butyl, to electron withdrawing fluorine atoms and electron rich thiophene rings. It was found that the DTEs studied presented an additive driving force, π-π stacking, for the undesired thermal ring−opening in the dark, a first observation among these type of compounds. The second part of the thesis is concerned with the mechanism of the ring−closing reaction triggered by the reduction of the uncoloured form. A new hypothesis regarding the mechanism of the process is presented. The preliminary studies suggest that the intermediate for the ring−closing reaction is the doubly reduced form of the ring−open isomer rather than the mono-reduced form as previously thought.

Document type: 
Thesis

Studies toward the Total Synthesis of Biselides & Radical Fluorination of Aliphatic Compounds

Author: 
File(s): 
Date created: 
2014-01-24
Supervisor(s): 
Robert Britton
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) M.Sc.
Abstract: 

Modern pharmaceuticals originate predominately either from natural products or totally synthetic compounds. The rich variety of marine life found in the Earth’s oceans have especially allowed our access to increasingly more and intriguing biologically active marine natural products, such as haterumalides and biselides. The lack of materialistic return associated with natural product isolation from marine organisms has prompted the need for practical laboratory synthesis. The same demand holds true for synthetic drugs, as more novel synthetic methods are required to complement the increasingly target- and diversity-oriented approach to synthetic drug discovery. Biselides, isolated from the Okinawan ascidian Didemnidae sp., are marine macrolides which have demonstrated potent cytotoxicity towards a variety of human cancer cell lines while being non-toxic towards brine shrimp. They contain a 2,5-disubstituted-3-oxygenated tetrahydrofuran functionality and a (Z,Z)-1,4-diene as part of a 14-membered macrocyclic molecular skeleton. A proposed total synthesis of biselide A involves the cyclization of chloropolyols to form the substituted tetrahydrofuran and metathesis for construction of the (Z,Z)-1,4-diene. Specifically, direct ring-closing metathesis (RCM), relay ring-closing metathesis (RRCM), and cross metathesis (CM) strategies were examined, with only the CM strategy allowing us to construct the 1,4-diene with desired geometry. The second part of this thesis describes the development of a novel methodology for the direct conversion of C(sp3)-H bonds to C(sp3)-F bonds. This radical-based, photocatalytic process yielded monofluorinated products from various small molecule aliphatic substrates, and has showed further potential with other chemical systems. Improvement and expansion of this methodology could hold positive future implications with regards to fluoropharmaceuticals.

Document type: 
Thesis

Fast Detection of Low Volumes of Mouse Antibodies Using a Nanofluidic Bioarray Chip

Author: 
File(s): 
Date created: 
2013-12-20
Supervisor(s): 
Paul Li
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) M.Sc.
Abstract: 

We have developed a novel nanobioarray (NBA) chip for the detection of antibodies (Abs) secreted from mouse immune cells. The NBA chip was constructed by sealing PDMS channel plates with a glass slide, and the intersection approach employed to develop various bioarrays whereby multiple samples each react with multiple probes using a simultaneous liquid delivery method for sample introduction. In our system, we utilized several Ab samples to react with multiple peptide probes. We were able to use the NBA chip to detect samples with a solution volume of 500 nL and of a concentration of 0.05 nM which was lower than what was detected using the conventional ELISA method. This device, when used with human samples, has applications in the detection of antibodies secreted from single immune cells and in the diagnosis of diseases.

Document type: 
Thesis

Inactivation of Micromonospora viridifaciens Sialidase by Fluorinated Sialic Acids; Binding Specificities of the Hydrophobic Pocket

Author: 
File(s): 
Date created: 
2013-12-02
Supervisor(s): 
Andrew Bennet
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) M.Sc.
Abstract: 

The sialidase from Micromonospora viridifaciens (MvS) is inactivated by the sialic acid analogue 5-acetamido-2,3,5-trideoxy-3-fluoro-D-erythro-β-L-manno-non-2-ulopyranoson- yl fluoride (DiFSA), and by the Kdn analogue 2,3-dideoxy-3-fluoro-D-erythro-β-L-manno-non-2-ulopyranosonyl fluoride (DiFKdn). The second-order rate constant for inhibition of MvS by DiFSA at 25 C at a pH of 7.00 is 3.60  106 M–1 s–1. Whereas, the corresponding rate constant for inhibition by the Kdn inactivator is approximately one thousand-fold smaller (2.92  103 M–1 s–1 at 25 C and with a pH of 5.25). This decrease in activity on substitution of an acetamido group (DiFSA) for a hydroxyl functionality (DiFKdn) is remarkably similar to that for MvS-catalyzed hydrolysis of 4-nitrophenyl glycosides of sialic acid and Kdn. These observations are consistent with the difluoro containing inhibitors being 'mechanism-based' inactivators and that the hydrophobic pocket of MvS providing approximately 22 kJ/mol transition state stabilization by virtue of its hydrophobic interaction with the 5-acetamido group.

Document type: 
Thesis