The present thesis describes a novel photonic crystal platform dubbed the photonic nose, a color-based analogue of the human olfactory system. The platform is founded on a one dimensional photonic crystal architecture known as Bragg stacks, which are fabricated using bottom-up self-assembly approaches. Structural and compositional aspects of this novel class of photonic crystals are established that provide them with functionality and utility. Silicon dioxide, titanium dioxide, tin oxide, clays and zeolites are among the materials incorporated into one-dimensional photonic structures. Retention of materials functionality is demonstrated by vapor and liquid sensing experiments. This class of Bragg stacks displays well defined optical properties that have been thoroughly investigated by use of spectroscopic ellipsometry, as we demonstrate in a chapter dedicated to the technique. Utilizing conventional building blocks comprised of nanostructured silicon and titanium dioxide we discuss various aspects of technique pertaining single layered as well as multilayered films. In terms of practical applications these kinds of Bragg stacks show significant potential in areas such as display and sensors that exploit their vibrant and tunable colors. These colors are an important attribute of photonic crystals with bandgaps in the visible range and in this thesis work we present new approaches for characterizing photonic crystal color using well established methods from the field of color imagery. With this knowhow we have been able to assemble a pixilated array of chemically functionalized Bragg stacks in which each pixel responds differently to vapor phase analytes. The combinatorial response of the entire array enables a unique diagnostic fingerprint of a given analyte vapor as determined from color imagery and multivariate statistical methods of analysis. It was possible to discriminate between ethanol, butanol, hexanol, hexane, octane and decane. We also demonstrate the power of the photonic nose platform by distinguishing different bacteria from a photonic nose color analysis of the complex mixture of vapors in the bacteria culture headspace. Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis, and Pseudomonas aeruginosa could be discriminated based on this technique.

The present thesis describes a novel photonic crystal platform dubbed the photonic nose, a color-based analogue of the human olfactory system. The platform is founded on a one dimensional photonic crystal architecture known as Bragg stacks, which are fabricated using bottom-up self-assembly approaches. Structural and compositional aspects of this novel class of photonic crystals are established that provide them with functionality and utility. Silicon dioxide, titanium dioxide, tin oxide, clays and zeolites are among the materials incorporated into one-dimensional photonic structures. Retention of materials functionality is demonstrated by vapor and liquid sensing experiments. This class of Bragg stacks displays well defined optical properties that have been thoroughly investigated by use of spectroscopic ellipsometry, as we demonstrate in a chapter dedicated to the technique. Utilizing conventional building blocks comprised of nanostructured silicon and titanium dioxide we discuss various aspects of technique pertaining single layered as well as multilayered films. In terms of practical applications these kinds of Bragg stacks show significant potential in areas such as display and sensors that exploit their vibrant and tunable colors. These colors are an important attribute of photonic crystals with bandgaps in the visible range and in this thesis work we present new approaches for characterizing photonic crystal color using well established methods from the field of color imagery. With this knowhow we have been able to assemble a pixilated array of chemically functionalized Bragg stacks in which each pixel responds differently to vapor phase analytes. The combinatorial response of the entire array enables a unique diagnostic fingerprint of a given analyte vapor as determined from color imagery and multivariate statistical methods of analysis. It was possible to discriminate between ethanol, butanol, hexanol, hexane, octane and decane. We also demonstrate the power of the photonic nose platform by distinguishing different bacteria from a photonic nose color analysis of the complex mixture of vapors in the bacteria culture headspace. Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis, and Pseudomonas aeruginosa could be discriminated based on this technique.

Doctor of Philosophy / Department of Chemistry / Christopher J. Levy / This work examines the synthesis of novel chiral Schiff-base complexes derived from (1R,2R)-cyclohexanediamine and (R)-[1,1’-binaphthalene]-2-2’-diamine structural backbones with quinoline, isopropyl-quinoline, and benzoquinoline structural side-arms. We incorporated some degree of flexibility in the ligands and complexes so they can accommodate the sterics of different substrates during a catalytic reaction. We successfully achieved this by reducing the imine bond in the ligands to the corresponding amine bond. Therefore, the successful reduction and metallation of some of these ligands to give structures of different symmetries is reported. We had difficulty reducing ligands with the binaphthalene backbone but were able to partially reduce the ligand through a one-pot reaction with a zinc(II) salt and NaBH4. The complete 1H NMR assignments of the complexes reported in this thesis serve as a valuable tool for use in the characterization of future complexes. The complete NMR characterization of compounds reported is a complex process because they are polycyclic aromatic systems and the coupling network similarity in different parts of the molecule usually results in severe overlap of their 1H resonances. To overcome this impediment, we took advantage of various 2D-NMR techniques (COSY, NOESY, ROSEY, HSQC, and HMBC) along with other 1D-NMR experiments (1H HOMODEC, 1H, and 13C) to completely assign the desired complexes. Subsequently we also studied the coordination chemistry of several meal cations with our ligand system with the goal of obtaining single stranded monhelices. The potential use of some of the complexes in the area of NMR discrimination and kinetic resolution of racemic mixtures was examined and shown to be promising. Several NMR experiments were conducted using the racemic olefins 3-buten-2-ol and 1-penten-3-ol to demonstrate the discriminating power of our silver(I) complexes. We discovered that sterics play an important role in this resolution experiment and the bulky nature of our complexes affect the overall efficiency of the NMR discriminatory process as it diminishes the contact between the reactive metal center and the olefins involved. Temperature also plays a vital role in the chiral recognition of racemic olefins as we examined the ideal temperature needed to reduce the various dynamic processes that take place in solution at room temperature.

Doctor of Philosophy / Department of Chemistry / Duy H. Hua / The first chapter in this thesis includes the design, synthesis, and evaluation of anti-Alzheimer and anti-norovirus activities of tricyclic pyrones (TPs). Alzheimer’s disease is a major cause of dementia and sixth leading cause of death; it is a growing problem all over the world. On the other hand, norovirus, a highly contagious agent is responsible for more than 90% of non-bacterial gastroenteritis causing severity mainly in the closed environments. No drugs exist to eradicate the symptoms developed by both of these disorders. Studies have shown that the development of Alzheimer’s disease and the infection of norovirus are dependent on cholesterol metabolism. More specifically, the inhibition of acyl-CoA: cholesterol acyltrasferase (ACAT) led to the reduction of plaques in Alzheimer’s disease as well as reduced the infection of norovirus. Mimicking the structure of CP2, a TP with promising anti-Alzheimer activities, a library of tricyclic pyrones containing phenyl, naphthyl, heterocyclic, and dipeptidyl moieties were synthesized and evaluated for their anti-Alzheimer and anti-norovirus efficacies. Several TPs containing phenyl and naphthyl groups showed sub-micromolar to nanomolar potencies for the protection of neuronal MC65 cells from Aβ-oligomers induced death. Similarly, the TPs containing pyrrolyl, imidazolyl, and quinolinyl moieties were effective to inhibit the norovirus replication in low micromolar range. The most effective TPs from MC65 cells protection assay were also effective in the inhibition ACAT and up-regulation ABCA1 gene. The second chapter in this thesis includes the design, synthesis, and anti-norovirus activity of thiouridine nucleosides. Many nucleosides have demonstrated effective inhibition of viral RNA polymerase, and some are progressing at different level of clinical trials for the treatment of hepatitis C virus. Some of the nucleosides, including 2’-C-methyl and 2’-amino substituted analogs, were found to effectively inhibit the norovirus replication. In the search of more potent anti-noroviral compounds, two thiouridine nucleosides were synthesized and evaluated as anti-norovirus agents. Both of these analogs were ineffective up to 50 μM for the inhibition of norovirus replication in cell based assay. Proposed work of converting these nucleosides to their phosphoramidate derivatives is also described.

Master of Science / Department of Chemistry / Daniel A. Higgins / The potential-dependent reorientation dynamics of double stranded DNA (ds-DNA) covalently attached to planar glassy carbon electrode (GCE) surfaces were studied in this thesis. The orientation of ds-DNA was investigated via the distance-dependent quenching of fluorescence from a 6–carboxyfluorescein (FAM6) flurophore to the electrode surface. The fluorophore was covalently bound to the distal end of the DNA. Fluorescence microscopy was employed for optical detection of FAM6 fluorescence and hence the DNA dynamics. The variation of the fluorescence from the dye with electrode potential is attributed to distance-dependent dipole-electrode energy transfer. Application of positive potentials (i.e., +0.2 V vs. open circuit potential, OCP) to the GCE caused the ds-DNA to align approximately parallel to the surface, yielding strong FAM6-electrode energy transfer and low fluorescence intensity. With the switching of the potential towards negative values (i.e., -0.4 V vs. OCP) the ds-DNA realigned perpendicular to the GCE surface leading to a reduction in energy transfer and high fluorescence intensity. Initial DNA reorientation upon a change in electrode potential is very fast. These fast dynamics have been observed and characterized in a number of previous publications. We have observed subsequent slow dynamics that we attribute to slow orientational relaxation of the DNA. Our observations were first reported by Q. Li, et al., J. Am. Chem. Soc. 2012, 134, 14467. In this thesis, this prior work is extended to verify the reproducibility of these new dynamics and to eliminate the possibility of certain artifacts as their source. Specifically, the experiments are repeated using a new cell design and a different buffer. In the primary experiments performed in this thesis, the dependence of the DNA reorientation dynamics on surface coverage was investigated by observing the fluorescence modulation as a function of probe concentration in the functionalization bath. Concentrations of 0.25, 1.0 and 1.5 µM 35-mer ds-DNA were employed. Electrodes functionalized at these concentrations have ds-DNA surface coverages of 1.18 x 10[superscript]12, 3.24 x 10[superscript]12 and 4.26 x 10[superscript]12 cm[superscript]-2, respectively. With increasing concentration of the DNA probe, the reorientation time constant at positive applied bias (vs. OCP) increased, indicting reorientation was slowed. In contrast, the time constant decreased with the negative applied bias (vs. OCP) indicating faster orientational relaxation. The possible origins for the observed trends in the reorientation time constant are discussed.

Doctor of Philosophy / Department of Chemistry / Eric A. Maatta / The thesis focuses on the design and synthesis of novel organoimido delivery reagents capable of forming bimetallic polyoxometalate (POM) hybrids, and their use in the assembly of bimetallic hexamolybdate derivatives. These delivery reagents have been designed thoughtfully and separate organic moieties have been selected for coordinating to both the POM cluster and the second metal atom. A series of three ligands [4-aminopiperidine, 4-(4-aminophenyl) piperazine, and 4-(4-aminophenyl) piperidine] were selected and used to synthesize the dithiocarbamate metal-coordinating ligands, which in turn were used for preparing the corresponding metal (M = Cr, Mn, Fe, Co, Ni, Cu, Zn, Ag) complexes. All the complexes were characterized by infrared spectroscopy (IR). Reported routes were followed for the covalent grafting of these metal complexes onto hexamolybdate. But, the poor solubility of these metal complexes was found to be a major stumbling block in our endeavors to synthesize the dithiocarbamate based polyoxometalate hybrids. The observed poor solubility of metal dithiocarbamate complexes was overcome by synthesizing [potassium(I) tris(3,5-diphenylpyrazole)borate] and [potassium(I) tris(3,5-dimethylpyrazole)borate] via thermal dehydrogenative condensation between tetrahydroborate and the respective pyrazole molecule. A series of corresponding transition metal (M = Co, Ni, Cu, Mn) complexes of tris(3,5-diphenylpyrazole)borate and tris(3,5-dimethylpyrazole)borate were synthesized, and characterized by IR and UV-visible spectroscopy, and single crystal X-ray diffraction. The single crystal structure of [manganese(II) (tris(3,5-dimethylpyrazole)borate)2] turned out to an outlier as it displayed the formation of a bis-complex, thus having no substitutable anion for further reaction with dithiocarbamates. Thereafter, a series of metal dithiocarbamate complexes of these [hydrotris(pyrazolyl)borates] (M = Co, Ni, Cu ) were prepared using [sodium 4-aminopiperidyldithiocarbamate] and were characterized by IR and UV-visible spectroscopy. A remarkable improvement in the solubility of these metal dithiocarbamates in organic solvents was observed. Furthermore, attempts to covalently graft these complexes onto hexamolybdate cluster were undertaken, and found to be unsuccessful possibly due to the strong oxidizing nature of PPh[subscript]3Br[subscript]2 and hexamolybdate. Although, we were able to successfully tailor the solubility of the dithiocarbamate complexes to suit our needs, our efforts to achieve the primary goal of synthesizing dithiocarbamate based polyoxometalate hybrids have so far been unsuccessful. A series of three pyridyl based ligands i.e., 3,5-di(pyridin-2-yl)-4H-1,2,4-triazol-4-amine, 4-(pyridin-4-ylethynyl)aniline and 4-(pyridin-3-ylethynyl)aniline were synthesized and characterized. Covalent attachment of these ligands to hexamolybdate were attempted following various well-known routes. Although, no evidence of covalent attachment of 3,5-di(pyridin-2-yl)-4H-1,2,4-triazol-4-amine to hexamolybdate was observed, the covalent grafting of 4-(pyridin-4-ylethynyl)aniline and 4-(pyridin-3-ylethynyl)aniline to hexamolybdate cluster was successfully achieved. Characterization of these novel organic-inorganic hybrids was done using IR and NMR spectroscopy as analytical tools. Attempts have been undertaken to obtain single crystals of these hybrids. Also, a novel route involving halogen bonding as a purification and separation technique for pyridyl functionalized hexamolybdate hybrids is also being explored. The novel acetylacetonate moiety has been explored as an imidodelivery reagent for synthesizing hexamolybdate covalent hybrids, wherein [3-(4-((4-aminophenyl)ethynyl)phenyl)-4-hydroxypent-3-en-2-one] ligand has been successfully synthesized and characterized. Traditional methods along with unconventional methods such as heating at elevated temperatures and microwave reaction conditions, have so far proved to be unsuccessful in the synthesis of the hybrids. A series of the corresponding metal complexes have been synthesized and characterized, where the ligand and its corresponding copper(II) complex have been characterized by single crystal XRD. In the crystal structure of the copper complex, the metal ion sits in a slightly distorted square-planar pocket, where no coordination to the -NH[subscript]2 group is observed, which highlights the potential of using it as an imidodelivery reagent.

As of 2010, cancer remains the leading cause of death in Canada, and second in the United States of America. This is despite decades of research into development of chemotherapeutics and diagnostics. A number of major challenges have prevented new discoveries from translating into a reduction in mortality rates. One challenge is the poor efficiency with which anti-cancer agents (diagnostic contrast agents and therapeutics) reach deregulated cells in the body. Therefore, development of new methods and technologies for improving efficiency of delivery has been a focus of research. Nanoparticles are leading candidates for improving the efficiency of delivery because they can act as payload vehicles for anti-cancer agents, because it is possible to mediate their interaction with biological systems and thus their pharmaockinetics, and because they can exploit inherent vulnerabilities of tumours. This thesis describes the results from a series of research projects designed to progress our understanding of how nanoparticles behave in vivo, and how their design can be optimized to improve tumour targeting.

Doctor of Philosophy / Department of Chemistry / Paul E. Smith / Computer simulations have provided a wealth of information concerning a wide range of systems. The precision of computer simulation results depends on the degree of sampling (time scales) achieved, while the accuracy of the results (given sufficient sampling) depends on the quality of force field used. A force field provides a description of the energy for a system of interest. Recently, we have been developing a Kirkwood Buff (KB) force field for molecular dynamics simulations of biological systems. This force field is based on the KB Theory of solutions, emphasizing the accurate description of intermolecular interactions, and reasonably reproducing a range of other physical properties from experiment. In this approach simulation results in terms of KB integrals can be directly compared with experimental data through a KB analysis of the solution properties. The approach therefore provides a simple and clear method to test the capability of a force field. Here we firstly studied a series of alcohol-water mixtures in an attempt to validate the transferability and additivity of the force field. A general fluctuation theory was applied to investigate the properties of these systems, and to compare with computer simulation results. The possible effects of cosolvents on peptides and proteins were then investigated using N-methylacetamide as model for the peptide backbone and urea as cosolvent. A possible explanation for the urea denaturation of protein structure was provided using a thermodynamics point of view involving transfer free energies and preferential interactions obtained from the KB integrals. Finally, potentials for protein backbone and sidechain torsions were developed by fitting to quantum mechanical calculations and NMR data. Simulations of a variety of peptides and proteins in aqueous solutions were then performed to demonstrate the overall reliability of the force field.

Doctor of Philosophy / Department of Chemistry / Takashi Ito / Polymer thin films have played an important role in our everyday lives ranging from industrial to biomedical applications. In this thesis, two major topics based on polymer thin films including photopolymerized self-assembled monolayer and nanoporous thin films derived from diblock copolymer are discussed. In the first part of this thesis, a well-packed self-assembled monolayer with phosphonic acid as head group and diacetylenic functional group in the tail formed on AlGaN/GaN surface. According to water contact angle and UV/Vis absorption spectroscopy data, the stability of this self assembled monolayer on oxidized AlGaN/ GaN surface can be improved by photopolymerization of SAMs. The photopolymerization efficiency of the SAMs is effected by the position of polymerization functional group in the alkyl chain. In the second part of this thesis, PS-b-PMMA diblock copolymer thin films were prepared, characterized and applied as a template for electron transfer efficiency determination. The surface COOH group in nanoporous thin films derived from PS-b-PMMA were modified with ferrocene redox moieties having different linker lengths in the organic phase. The surface functionalization efficiency was quantitatively assessed by measuring the monovalent probe cations released from the surface COOH groups via cation-exchange processes using highly- sensitive analytical techniques including spectrofluorometry and inductively coupled plasma mass spectrometry (ICP-MS). The surface coverage of the redox moieties is an important parameter to determine the electron hopping efficiency. The electron propagation resulted from electron hopping across relatively large spacing that was controlled by the motion of anchored redox sites. The longer linker led to the larger physical displacement range of anchored ferrocene moieties, facilitating the approach of the adjacent ferrocene moieties within a distance required for electron self-exchange reaction. Faradic currents originating from redox-involved electron hopping through the ferrocene moieties anchored onto the insulator surface decreased with increasing the concentration of beta-cyclodextrin ([beta]-CD) in aqueous solution. The current could be recovered by adding redox-inactive guest molecules of [beta]-CD to the solution.

Doctor of Philosophy / Department of Chemistry / Kenneth J. Klabunde / New photocatalystic materials Ti-In oxy(nitride) and nanosized Ru-loaded strontium titanate doped with Rh (Ru/SrTiO3:Rh) have been synthesized. The textural and surface characteristic properties were studied by nitrogen BET analysis, diffuse reflectance UV-vis spectroscopy, X-ray photoelectron spectroscopy, transmission electron microscopy, scanning electron microscopy and powder XRD. The photocatalytic properties were enhanced by the binary metal oxides of titanium dioxide and indium oxide. The XRD patterns confirmed the oxygen exchange between two metal oxides during the synthesis. Moreover, the presence of titanium dioxide can help the stabilization of InN during hot NH3(g) treatment. On the other hand, the particle sizes of aerogel prepared Ru/SrTiO3:Rh varied from 12 to 25 nm depended on different Rh doping. A mixture of ethanol and toluene was found to be the best binary solvent for supercritical drying, which yielded a SrTiO3 sample with a surface area of 130 m2 Enhanced photocatalytic hydrogen production under UV-vis light irradiation was achieved by ammonolysis of intimately mixed titanium dioxide and indium oxide at high temperatures. Gas chromatography monitored steadily the formation of hydrogen when sacrificial (methanol or ethanol) were present. XRD patterns confirmed that the photocatalysts maintain crystalline integrity before and after water splitting experiments. Moreover, the presence of InN may be crucial for the increase of hydrogen production activities. /g and an average crystallite size of 6 nm. These Ru/SrTiO3:Rh photocatalysts have been studied for photocatalytic hydrogen production under visible light. The band gap of the bulk SrTiO3 (3.2 eV) does not allow response to visible light. However, after doping with rhodium and loaded with ruthenium, the modified strontium titanates can utilize light above 400 nm due to the formation of valence band or electron donor levels inside of the band gap. Moreover, the surface areas of these photocatalysts are much larger than conventional solid-state synthesized samples (1-2 m 2/g), which yielded more Ru loading and reaction sites. The areogel and hydrothermal synthesized samples required basic (alkaline) conditions for hydrogen generation facilitation compared with acidic conditions for conventional solid-state samples.