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

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

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

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

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

Synthesis and Characterization of Piezo-/ferroelectric Lead Zirconate-Titanate (PZT) Single Crystals and Related Ternary Ceramics

Author: 
Date created: 
2013-10-17
Abstract: 

PbZr1-xTixO3 (PZT) single crystals with compositions across the morphotropic phase boundary (MPB) have been successfully grown by a top-seeded solution growth (TSSG) technique. The growth conditions are optimized in terms of chemical, thermodynamic and kinetic parameters. The growth temperature is found to be the key factor for controlling the composition of the crystals. The PbZr0.54Ti0.46O3 crystals exhibit the best properties, with a piezoelectric coefficient d33=1223pC/N, an electromechanical coupling factor k33=0.8, a high coercive field Ec=7kV/cm and a high Curie temperature TC=395°C, making them a potentially material for high temperature and high power electromechanical transducer applications. The availability of the PZT single crystals has allowed us to perform a series of characterization of their physical properties. Dielectric measurements of the PbZr0.80Ti0.20O3 crystal show that the phase transition between rhombohedral octahedron-tilted (R3c) and untilted (R3m) phases is of the first order, which is evidenced by a thermal hysteresis upon heating and cooling. The tricritical behaviour of this composition is revealed by the birefringence measurements, showing a slightly discontinuous phase transition in (001)cub platelet and a continuous phase transition in the (110)cub platelet. The domain structures and phase transitions of the PZT single crystals with compositions near the MPB are investigated by polarized microscopy (PLM). Continuous polarization rotation within the (110)cub plane was observed in both PbZr0.58Ti0.42O3 and PbZr0.54Ti0.46O3 crystals. Tetragonal nanodomains observed in the PbZr0.54Ti0.46O3 crystal can be explained by Imry and Ma's random field theory, which suggests that quenched random field related to structural disorder can break the system into nanodomains that are more energetically favored. In our search for new lead-reduced piezoelectric materials, the ternary ceramics of Bi(Zn1/2Ti1/2)O3-PbZrO3-PbTiO3 [BZT-PZ-PT] were synthesized and investigated. The introduction of BZT into the PZT binary system brings the MPB to a lower PT content and enlarges the composition range of the MPB region. Enhanced piezoelectric and ferroelectric properties are obtained in the MPB region with the highest BZT content (=15mole%), with d33=275pC/N, Pr=33μC/cm2 and Ec=26 kV/cm.

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

Modeling of Ultrathin Catalyst Layers in Polymer Electrolyte Fuel Cells: Proton Transport and Water Management

Date created: 
2013-08-09
Abstract: 

Ultrathin catalyst layers (UTCLs) are emerging as a promising alternative to conventional catalyst layers in polymer electrolyte fuel cells. In comparison, UTCLs have dramatically reduced Pt loading and thicknesses and are ionomer–free. We explore two open questions in the theory of UTCLs (1) the proton transport mechanism within the ionomer–free layer and (2) water management in membrane electrode assemblies (MEAs) with UTCLs. To investigate (1), we present a UTCL model, which assumes the protons are drawn into the UTCL via their interaction with the metal surface charge. We consider a continuum model of a water–filled, cylindrical nanopore with charged walls. We derive the relation between metal potential and surface charge density from a Stern double layer model. The model suggests the proton concentration and reaction current density to be highly dependent on the charging properties of the metaljsolution interface, which are parameterized primarily by the potential of zero charge. Therefore, materials for UTCLs should be selected not only for their intrinsic mass activities and durability, but also for their charging properties. A systematic evaluation of the interplay of electrostatic, kinetic, and mass transport phenomena in UTCL demanded an impedance variant of the model. Based on the general set of transient equations, we have derived analytical impedance expressions and equivalent circuit representations in 4 limiting cases. While the UTCL model suggests the charging of the metaljsolution interface to be crucial to performance, theoretical studies on the charging behaviour of platinum are limited. We present a generalised computational hydrogen electrode that enables the ab initio simulation of metaljsolution interfaces as a function of pH and potential. To address (2), we present a water balance model to MEAs with UTCLs. The model relates the current densities, capillary pressure distributions, and fluxes of vapor and liquid water. Analysis of the model suggests that UTCLs require efficient liquid transport paths out of the MEA at low and moderate temperature. We discuss strategies for increasing the current density for the onset of GDL flooding, via enhanced liquid permeabilities, vaporization areas, and gas pressure differentials.

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

Modification of metal / semiconductor junctions with molecular monolayers: structural analysis and electrical characterization

Date created: 
2013-08-09
Abstract: 

Metal/semiconductor (MS) junctions are fundamental in classical microelectronic devices. With device fabrication size approaching atomic scales, electronic performance will become unpredictable as a result of quantum effects becoming relevant in charge transport. The objective of this thesis is to investigate the potential application of thin organic films to modify MS junctions and to modulate their electrical properties. Knowing how the electronic parameters in a device change over time is necessary for commercial viability. I therefore studied the long-term structural and electronic stability of metal-monolayer-silicon junctions, with respect to silicon oxide formation (monitored by x-ray photoelectron spectroscopy (XPS)). Simple straight-chain n-alkyl (CH3-(CH2)11-Si≡) and phenyl-terminated (C6H5-(CH2)3-Si≡) monolayers were compared. Both samples had a significant change in surface, optical and electronic properties upon oxide formation. Although phenyl-terminated samples oxidized quicker than n-alkyl ones, their electrical properties were more similar to its original measurement before oxidation. There is a wide variety of deposition techniques available for placing metal contacts onto organically modified semiconductors, which are complex and costly. The investigation on monolayers that could withstand simple and inexpensive physical vapour deposition provides an alternative, molecular approach to overcome this technical challenge I discovered that phenyl-terminated monolayers have a significantly greater density than n-alkyl monolayers, based on XPS. This correlated with reducing metal penetration into the monolayer and improvements in electronic properties preservation of the molecular junctions, as observed with ballistic electron emission spectroscopy. In fact, molecular dipole moment (perpendicular vector to the surface) can also alter the charge transport in an MS junction. I have prepared a diverse series of monolayers on silicon (n-alkyl, thioether, phenyl and ether) and discovered a linear relationship between dipole moment, and both the barrier height and ideality factor. The calculated dipole moment has been normalized to account for the monolayer density on silicon which greatly improved the aforementioned linear correlation. A simple mathematical model to predict experimental current versus voltage behavior was then proposed. It was determined that relatively negative dipole moment (parallel to the direction of R-S≡) affect the charge transport pathways to a greater extent than neutral ones.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Hua-Zhong Yu
Department: 
Science: Department of Chemistry
Thesis type: 
(Thesis) Ph.D.

Liquid crystals from linked discs

Author: 
Date created: 
2013-08-21
Abstract: 

In the burgeoning field of organic semiconducting devices, molecules able to self-assemble into columnar liquid crystal phases are being investigated due to the unique directional conductivity of their structures. Knowledge of how molecule-level structural features impact the formation of the larger columnar assemblies is of considerable interest. Studies of liquid crystal phases are already informally divided into shape categories, arising from molecules that are either rod-shaped or disc-shaped. Our interest lay in the middle ground where the basic disc-shape is elongated to a more elliptical one. In pursuit of this goal, a series of rigid dimers were prepared by condensation of 3,3’-diaminobenzidine with various 2,3,6,7-tetralkyloxyphenanthrene-9,10-diones. Investigation revealed that these dimers assemble into a number of unusual phases, including nematic and columnar oblique mesophases. In addition, a series of monomeric amide derivatives were synthesized by amidation of 2,3,6,7-Tetrakis(heptyloxy)dibenzo[a,c]phenazine-11-carboxylic acid. These molecules were found to spontaneously align in a homeotropic manner. They also supercooled into persistent glassy phases that preserved their alignment.

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

Coordination and organometallic diamido-donor iron and cobalt complexes

Author: 
Date created: 
2013-04-02
Abstract: 

The structures, reactivity and magnetic properties of high-spin iron and cobalt complexes of diamido donor ligands were investigated. Unusual multinuclear Fe(II) and Co(II) complexes with the basic dinuclear unit M2X2[tBuNON] (X= Br, M= Fe (1), Co (2); X= Cl, M= Fe (3), Co (4)), ([tBuNON]2−= [Me3CN(SiMe2)]2O2−) were synthesized and characterized. The reduction reaction of 3 with KC8 and addition of CO and dmpe (Me2P(CH2)2PMe2) generated {Fe2[tBuNON]}2 and, with dmpe also FeCl2(dmpe)2. However, the addition of 1,3-bis-(2,4,6-trimethylphenyl)imidazol-2-ylidene (NHC) carbene to 3 resulted in the new {[NHC]FeCl2}2. Alkyl for halide metathesis via the reaction of LiCH2SiMe3 in 1-4 generated rare high-spin alkyl/halide {[tBuNON]M2X(CH2SiMe3)2}2 (8-11) complexes and unusual high-spin dialkyl iron and cobalt complexes of the form {M2(CH2SiMe3)2[tBuNON]} (M = Fe (6) and Co (7)); reaction with MeLi to form the dimethyl analogue was not successful, while addition of one equivalent of methyl reagent per dinuclear unit in 3 and 4 resulted in {Fe2Br(Me)[tBuNON]}2 and {Co2Cl(Me)[tBuNON]}2. Neither 6 nor 7 act as polymerization catalysts for ethylene; addition of B(C6F5)3 as a cocatalyst was found to further hinder any activity of 6 and 7 by the formation of {Co2(C6F5)2[tBuNON]} and {Fe2Cl(C6F5)[tBuNON]}2. Upon exposing 6 to excess CO, a rare dicarbamoyl trinuclear iron complex was obtained, which results from CO binding, isocarbonyl binding and Fe-C and Fe-N CO insertions. Attempts towards obtaining high oxidation state iron and cobalt complexes showed that the [NON] ligand did not support such systems. Addition of benzyl bromide to {Fe[Me3PhNON]}2 resulted in {FeBr[Me3PhNON]}2 and reaction of {FeCl[tBuNON]}2 with dmpe led to a rare tetrahedral iron(III) complex {FeCl[tBuNON]}2(µ-Me2PCH2CH2PMe2). To overcome potential difficulties with limited Si-N bond stabilities, carbon-backbone diamido {M[iPrNN′N]}2 and {M[iPrNO′N]}2 (M= Fe, Co) [MeN((CH2)2N−iPr)2] ([iPrNO′N]2−) and [O((CH2)2N−iPr)2] ([iPrNN′N]2−) were synthesized, characterized and compared with similar diamido complexes.

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

An examination of the mixing of low-lying excited 0+ states in 116sn

Date created: 
2013-08-15
Abstract: 

The even-even tin isotopes are known to exhibit shape coexistence, the phenomenon where multiple shapes coexist in a narrow energy region at relatively low-lying levels of the nucleus. These nuclei have a 0+ spherical ground state and multipleexcited 0+ states, one of which is a band head for a deformed rotational band, caused by the promotion of two protons across the Z=50 shell gap. Experimental and theoretical investigations have been performed on 116Sn to describe the nature of the mixing that occurs between the vibrational phonon levels and the deformed rotational band by probing the character of the excited 0+ states. At the time it was thought that the 0+ states showed almost equal mixing of rotational and vibrational character, but this result was based on an indirect observation and fit of the intensity of a weak 85 keV transition. The current work, a high-statistics 116Sn measurement, demonstrates unequal mixing of character between the two excited 0+ states based on a direct measurement of the intensity of the 85 keV transition. These new results might prompt a new interpretation of the structure of 116Sn. The experiment to investigate the low-lying structure of 116Sn was conducted at TRIUMF, Canada’s National Laboratory for Nuclear and Particle Physics. A high-intensity and high-purity beam of 116In was used to populate states in 116Sn via beta decay. The resulting gamma rays were observed with the 8π detector array, which consists of twenty high-purity Compton-suppressed germanium detectors coupled to a suite of ancillary detectors for β particle detection and conversion electron spectroscopy. From this high-statistics measurement 57 gamma-ray transitions were observed,with 4 new transitions that depopulate the 3096 keV level observed for the first time with energies of 101 keV, 296 keV, 447 keV, and 871 keV. Branching ratios were determined for all of the observed transitions. For the 57 transitions observed, a relative intensity had not been reported for 17 of them, and a branching ratio had not been reported for 12 of them. Transition rates were determined for 25 transitions that depopulate levels with previously reported lifetimes, and 2 of these transition rates had not been previously observed.

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

Modelling cathode catalyst degradation in polymer electrolyte fuel cells

Date created: 
2013-08-23
Abstract: 

Nano-sized Pt particles in the cathode catalyst layer of a polymer electrolyte fuel cell afford a high initial electrochemically active surface-area. However, the gain in active surface area for desired surface reactions is offset in part by enhanced rates of degradation processes that cause losses in catalyst mass, catalyst surface-area, and electrocatalytic activity. The loss of electrochemically active surface-area of the catalyst causes severe performance degradation over relevant lifetimes of polymer electrolyte fuel cells yet a consistent theoretical approach, linking experimental observations of surface-area loss related phenomena to purported mechanisms of degradation was missing. Accordingly, a dynamic model of surface-area loss and Pt mass balance phenomena based on the theories of Lifshitz, Slyozov and Wagner, and Smoluchowski is developed. It relates kinetic rates of degradation processes to the evolution of the particle-size distribution and its moments. We pursue model validation and evaluation by analyzing an extensive set of electrochemical surface-area loss experiments probing the impact of accelerated stress test control levers. Our Pt mass balance model unifies degradation characterization approaches and accordingly discriminates the predominant degradation mechanisms. The evaluation and validation approaches established a firm link between surface-area loss, Pt dissolution and Pt oxidation. As a consequence of our evaluation results, a kinetic model for Pt(111) oxide formation and reduction is developed and validated against a wide range of electrochemical, spectroscopic and theoretical work found in the relevant literature. The model provides a comprehensive picture of surface electrochemical processes that occur at Pt(111). In closing we discuss future routes of research. Foremost is the extension of cyclic voltammetry work to polycrystalline Pt and Pt nanoparticle electrodes, we suggest that these are the logical steps towards linking dynamic Pt oxidation with surface tension, Pt dissolution, surface-area loss and the oxygen reduction reaction.

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

Monitoring rainwater and seaweed reveals the presence of 131I in southwest and central British Columbia, Canada following the Fukushima nuclear accident in Japan

Date created: 
2013-08-26
Abstract: 

Detailed analysis of 131I levels in rainwater and in three species of seaweed (Fucus distichus Linnaeus, Macrocystis pyrifera, and Pyropia fallax) collected in southwest British Columbia and Bella Bella, B.C., Canada was performed using gamma-ray spectroscopy following the Fukushima nuclear power plant accident on March 11, 2011. The maximum 131I activity was found to be 5.8(7) Bq/L in rainwater collected at the campus of Simon Fraser University in Burnaby, B.C. nine days after the accident. Concomitantly, the maximum observed activity in the brown seaweed Fucus distichus Linnaeus was observed to be 130(7) Bq/kg dry weight in samples collected in North Vancouver 11 days following the accident and 67(6) Bq/kg dry weight in samples collected from the Bamfield Marine Sciences Centre on Vancouver Island 17 days following the accident. The 131I activity in seaweed samples collected in southwest B.C. following the Fukushima accident was an order of magnitude less than what was observed in similar measurements performed in British Columbia following the Chernobyl accident. Iodine-131 activity in Fucus distichus Linnaeus remained detectable for 60 days following the accident and was detectable in each seaweed species collected. The Germanium Detector for Elemental Analysis and Radioactivity Studies (GEARS) was modeled using the GEANT4 software package and developed as an analytical tool by the Nuclear Science group in the Simon Fraser University Department of Chemistry for the purpose of these measurements.

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