Supramolecular systems are held together by non-covalent forces, and include systems involving the interaction of small molecules with biomolecules such as DNA and proteins. The inherent reversibility of supramolecular systems means that dynamic processes are important for many of the functions achieved. The first objective of this work was to develop methodology to study the dynamics and binding mechanism of small molecules with DNA. Though there is a great deal known about the thermodynamics of molecules binding to DNA there is much less known about the binding dynamics. Aminoxanthones were chosen as appropriate guest molecules, and their photophysics were examined in a number of solvents, showing that both the singlet and triplet excited states are strongly affected by solvent polarity, with the excited state energies decreasing in polar solvents. Laser flash photolysis experiments for quenching of the triplet excited state by nitrite anions in the absence and presence of DNA allowed a residence time of microseconds to be estimated for these guests. These experiments also showed that this methodology is not widely applicable when studying the binding dynamics of small molecules with DNA, and that other fast kinetic techniques are necessary. Laser temperature jump experiments allow measurement of dynamics in supramolecular systems, while avoiding the problems encountered in laser flash photolysis experiments. A custom-built system was developed as an adaptation of systems described in the literature, with the main difference being a laser optimized for the excitation of water, and the ability to operate across a wide dynamic range. The laser and the detection systems for absorbance and fluorescence were successfully implemented and a number of artifacts were eliminated. The expected temperature jump was obtained and signals were detected by both fluorescence and absorption; the signal-to-noise ratio still needs improvement before systematic studies can be carried out. The second objective of this work was to study bimolecular reactions in proteins. Using biomolecules to effectively modulate reactivity in bimolecular reactions requires knowledge of the reaction mechanism. When the dimerization of 2-anthracenecarboxylate (AC) takes place in serum albumin proteins enantiomeric excess (ee) is obtained for the chiral products. There are a number of binding sites for AC in these proteins and it has been shown that a balance between strength of binding and mobility of the reactants is essential to achieve high ee's. In human serum albumin remarkable ee's of more than 80% are achieved. It is important to differentiate between reactant molecules bound to different binding sites so that the binding sites where reaction preferentially forms one enantiomer can be identified. Steady-state and time-resolved fluorescence studies identified two types of 2-anthracenecarboxylate bound to HSA: one that has a short lifetime and is very protected from the bulk aqueous solution, and one that has a longer lifetime, but is exposed to the bulk solution. Further work using binding site inhibitors allowed identification of a third type of molecule that has a longer lifetime, but is very protected from the bulk solution, which is likely the species responsible for the majority of the observed ee.

The structure of liquid water and adsorbed leucine at solid surfaces of tunable hydropho¬bicity has been examined by molecular dynamics simulation. The results have been used to extend models of water ordering at superhydrophobic surfaces to create a general model of density-dependent ordering of water and adsorbates at hydrophobic interfaces. In this model, interfacial water structures can be classified according to two hydrophobic regimes, a non-wetting structure and a semi-wetting structure, distinguished by the orientation of interfacial water molecules. We propose that the emergence of the wetting-type order is strongly dependent on the density profile across the interfacial region. Leucine adsorbed at the same surfaces also shows two patterns of adsorption, distinguished by the proportion of time the molecule adopts an orientation parallel to the surface. These patterns correspond to the non-wetting and semi-wetting regimes of water and also arise from the density structure of water in the interfacial region.

Surface-enhanced Raman scattering (SERS) constitutes a spectroscopy of rapidly growing importance. To understand and control the enhancing surface is key for optimizing SERS. In this work, progressively more ordered substrates for SERS are investigated: gold clusters, scratched gold films, nanohole arrays in a copper film and nanoscale gratings in a gold film. Gold clusters constitute the most random SERS substrate: samples were prepared by alternating vapour deposition of gold and plasma-induced polymerization of styrene gas. The relationships between sample preparation parameters, gold-cluster morphology, and SERS intensity were elucidated. Using Wilson’s notation, vibrations were assigned to all bands between 250 and 1750 cm-1 in the ordinary Raman and SERS spectra of polystyrene. The orientation of polystyrene’s phenyl ring, relative to the gold surface, was determined. It has been suggested that reactions involving silver catalyze polystyrene degradation during SERS, but we found that silver is not necessary for the degradation to occur. Of intermediate order are scratched gold films. Polarization-dependent SERS was studied for scratched gold films placed in-situ and under electrochemical control. A quantitative method for evaluating the polarization dependence was developed. In addition, we established that polarization effects may be used to selectively remove solution-phase interference signals from the SERS spectrum of an adsorbed analyte. Nanohole arrays and nanoscale gratings, made by focused ion beam (FIB) milling, constitute the most ordered SERS substrates. SERS was observed for oxazine 720 molecules adsorbed on a copper film pierced by nanohole arrays. Each of the arrays had a different hole-periodicity, and the effect of this periodicity on SERS intensity was examined. Electric fieldstrength perpendicular to the surface of the metal was calculated for each array using the finite-difference time-domain (FDTD) method, and the array with the greatest calculated value matched the array that gave the greatest experimentally observed SERS intensity. Finally, SERS was observed for oxazine 720 molecules adsorbed on a gold film through which nanoscale gratings were milled. We varied the width of the grooves and the width of the metal lines between them, and we examined the resulting effect on SERS intensity.

Asymmetric hydrophosphination, the addition of a P-H bond across a C-C double bond, is an attractive potential route to chiral phosphines, which have important applications in many other types of asymmetric catalysis. However, a highly active and stereoselective catalyst for this reaction has yet to be identified. The ruthenium indenyl complex [RuCl(η5-indenyl)(PPh3)2] (1) was investigated as a potential catalyst for hydrophosphination through an exploration of the steps involved in this process: substrate coordination, P-H bond activation, and P-C bond formation. Substitution of triphenylphosphine ligands at the metal centre of 1 by alkyl- and aryl-substituted secondary phosphines (PR2H: R = Cy (a), Pri (b), Et (c), Ph (d) or Tolp (e)) gave predominantly the monosubstituted secondary phosphine complexes [RuCl(η5-indenyl)(PR2H)(PPh3)] (3a-e). Hydride ([RuH(η5-indenyl)(PR2H)(PPh3)] (6a,d)) and cationic nitrile ([Ru(η5-indenyl)(NCR')(PR2H)(PPh3)][PF6] (7a,d: R' = CH=CH2; 8a-b,d: R = CH3)) derivatives of 3 were prepared and in all cases the potentially reactive P-H bond of the secondary phosphine ligand did not interfere with the chemical transformation. Deprotonation of the P-H bond of the bulky dialkylphosphine-substituted chloro complexes 3a-b with KOBut gave five-coordinate, planar terminal phosphido complexes [Ru(η5-indenyl)(PR2)(PPh3)] (10a-b) that contain a unique Ru-PR2 π-bond. The analogous phosphido complexes 10d-e, containing less bulky aryl substituents at phosphorus, were found to be unstable at room temperature and were observed only by low temperature 31P{1H} NMR spectroscopy. Phosphido complexes 10a-b were found to be highly P-basic, capable of deprotonating the C-H bond of acetonitrile (pKa = 24) to give the metallated acetonitrile complex [Ru(CH2CN)(η5-indenyl)(PR2H)(PPh3)] (9a-b), and to be very P-nucleophilic, reacting with iodomethane (MeI) to give a new P-C bond in [RuI(η5-indenyl)(PCy2Me)(PPh3)] (17a). As might be expected, the addition of donor ligands to low-coordinate 10a-b was found to disrupt the Ru-PR2 π-bond to give six-coordinate terminal phosphido complexes [Ru(η5-indenyl)(L)(PR2H)(PPh3)], with pyramidal, instead of planar, geometry at phosphorus. These additions are irreversible in the case of CO (19a-b) or PCy2H (21a), while pyridine (23a-b) or NCPh (24a-b) adducts were shown by 31P{1H} NMR spectroscopy to be in equilibrium with 10a-b and the uncoordinated ligand. The addition of known substrates for transition metal-mediated hydrophosphination, phenylacetylene and acrylonitrile, to 10a-b resulted in a [2+2] cycloaddition of the unsaturated C-C bond at the Ru-PR2 π-bond to give metallacyclic complexes [Ru(η5-indenyl)(κ2-PhC=CHPR2)(PPh3)] (27a-b) and [Ru(η5-indenyl)(κ2-NCCHCH2PR2)(PPh3)] (32a-b) respectively. Surprisingly the addition of simple non-activated olefins (i.e. ethylene, 1-hexene, or norbornene), which were not previously known to be active substrates for this reaction, also gave [2+2] cycloaddition products. These cycloaddition reactions were found to be 100% regioselective, and are also stereoselective in the case of substituted alkenes (>96%). Experimental evidence suggests that these P-C bond forming reactions proceed via a concerted [2+2] cycloaddition pathway.

The maintenance of dynamic chromatin structures is critical for the proper regulation of cellular activities. The plasticity of chromatin structures can be mediated in several ways, two of which include the incorporation of histone variants and the activities of trans-acting factors. In this dissertation, biochemical methods were used to determine the effects of the histone variant H2A.Z or the methyl-CpG binding protein 2 (MeCP2) on the structural composition of native chromatin. Early, independent biophysical studies of the stability of reconstituted H2A.Z chromatin structures yielded contradictory results. As these studies used H2A.Z expressed as a recombinant protein, it was possible that the absence of any essential folding or post-translational modifications (PTMs) may have been responsible for the diametric findings. To resolve this issue, the stability of various native chromatin structures containing H2A.Z was determined. Using gel filtration chromatography, sucrose gradient sedimentation, and hydroxyapatite chromatography, the partitioning of H2A.Z within dissociated octamers, mononucleosomes, and chromatin fibres were respectively assessed. Within all three structures, H2A.Z associated with stabilized forms. However, the salt-dependent thermal analysis of H2A.Z-H2B dimers by circular dichroism showed that the variant dimer was largely unstructured. The deposition of H2A.Z also occurred independently of linker histones. MeCP2 is a chromatin binding protein best known for its ability to repress transcription. While its roles in neuron development have been well-studied, little is known of its interactions within native chromatin. Shortly after MeCP2 was discovered, it was postulated that MeCP2 would behave as a global repressor. However, recent findings have contested this idea. If MeCP2 does act as a universal silencer, it was hypothesized that changes to global chromatin modifications would affect the distribution of MeCP2 within chromatin. HeLa S3 cultures were chemically treated with 3-aminobenzamide or butyrate to induce either DNA hypermethylation or histone hyperacetylation. Neither treated culture resulted in a redistribution of MeCP2 within chromatin. Moreover, the majority of MeCP2 was present within nuclease-accessible, active chromatin. Interestingly, the butyrate treatment resulted in proportional losses of MeCP2 within fractionated chromatin that were not due to changes in MeCP2 transcription. MeCP2 was also observed to bind to mononucleosomes containing DNA that was >146 bp - ~160 bp. These results suggested that MeCP2 does not act as an indiscriminate silencer, but more likely as a specific transcriptional regulator. Most studies of MeCP2 interactions with chromatin were performed using reconstituted chromatin templates in vitro. However, it is not known if MeCP2 interacts with chromatin in a tissue-specific manner. In addition, as MeCP2 has a broad distribution throughout all chromatin types, it is not known if histone variants or PTMs influence MeCP2 deposition. Therefore, the tissue specificity of MeCP2 binding and the influence of nucleosomal components were investigated. MeCP2 has a differential distribution throughout chromatin extracted from rat brain, liver, and testis. The brain has significantly more MeCP2 than the liver or testis and this was reflected in the MECP2 mRNA amounts. Using native co-immunoprecipitations, MeCP2 was shown to interact with mononucleosomes containing specific histone variants and PTMs: H2AX, H3K27me3, and H3K9me2. These novel interactions may further specialize the MeCP2-bound chromatin regions. Finally, two novel hypotheses regarding the regulation of MeCP2 are proposed. In the first, the regulation of MeCP2 turnover is proposed to occur through the poly-ubiquitination of the two MeCP2 PEST domains, followed by proteolytic degradation. The second hypothesis proposes that the use of histone deacetylase inhibitors could be used to control the levels of MeCP2 expression, in conjunction with gene therapies, for the treatment of Rett syndrome.

The mechanism of the rhodium(I) catalyzed dehydrocoupling of di-n-hexylsilane was investigated by isolating and characterizing products of stoichiometric reactions, by preparing a series of rhodium(I) phosphine precatalysts and silane substrates and measuring catalytic activity, and by observing catalytic reaction mixtures directly using 31P{ 1H} NMR spectroscopy. Catalyst initiation was found to occur via oxidative addition of silane to a rhodium centre, followed by reductive elimination of a chlorosilane generating an unsaturated rhodium hydride complex, the putative active catalyst fragment. The series of precatalysts screened for catalytic activity include [Rh(PPh3)3Cl] (1), [Rh(PPh3)2(µ-Cl)]2 (2). [Rh(dppe)(µ-Cl)]2 (3) [Rh(dppb)(µ-Cl)]2, (4) [Rh(COD)(µ- Cl)]2 (5), [Rh(PPh3)3H] (6), [Rh(PPh3)4H] (7), [Rh(xantphos)(COD)(Cl)]. (8). Of these eight precatalysts the two hydride complexes (6 and 7) displayed the highest catalytic activity. The flexibility of chelating bis(phosphine) ligands was found to be important for catalyst activity. Of the chelating bis(phosphine) rhodium complexes (3, 4, and 8), 4 displayed the highest catalytic activity. The catalyst resting state for all precatalysts containing the monodentate PPh3 ligand was found to be trans-[Rh(PPh3)2LX] when catalytic reactions were observed in situ by 31P{1H} NMR spectroscopy. The substitution and steric bulk of the silane substrate was found to influence reactivity as well. Of the substrates studied, the least bulky primary n-hexylsilane was most reactive. By monitoring the reaction over by 31P{1H} NMR spectroscopy, decomposition of the catalyst was found to involve phosphine dissociation. Decomposition was found to occur more slowly for precatalysts containing chelating bis(phosphine) ligands than for precatalysts containing monodentate phosphine ligands.

The mechanism of the rhodium(I) catalyzed dehydrocoupling of di-n-hexylsilane was investigated by isolating and characterizing products of stoichiometric reactions, by preparing a series of rhodium(I) phosphine precatalysts and silane substrates and measuring catalytic activity, and by observing catalytic reaction mixtures directly using 31P{ 1H} NMR spectroscopy. Catalyst initiation was found to occur via oxidative addition of silane to a rhodium centre, followed by reductive elimination of a chlorosilane generating an unsaturated rhodium hydride complex, the putative active catalyst fragment. The series of precatalysts screened for catalytic activity include [Rh(PPh3)3Cl] (1), [Rh(PPh3)2(µ-Cl)]2 (2). [Rh(dppe)(µ-Cl)]2 (3) [Rh(dppb)(µ-Cl)]2, (4) [Rh(COD)(µ- Cl)]2 (5), [Rh(PPh3)3H] (6), [Rh(PPh3)4H] (7), [Rh(xantphos)(COD)(Cl)]. (8). Of these eight precatalysts the two hydride complexes (6 and 7) displayed the highest catalytic activity. The flexibility of chelating bis(phosphine) ligands was found to be important for catalyst activity. Of the chelating bis(phosphine) rhodium complexes (3, 4, and 8), 4 displayed the highest catalytic activity. The catalyst resting state for all precatalysts containing the monodentate PPh3 ligand was found to be trans-[Rh(PPh3)2LX] when catalytic reactions were observed in situ by 31P{1H} NMR spectroscopy. The substitution and steric bulk of the silane substrate was found to influence reactivity as well. Of the substrates studied, the least bulky primary n-hexylsilane was most reactive. By monitoring the reaction over by 31P{1H} NMR spectroscopy, decomposition of the catalyst was found to involve phosphine dissociation. Decomposition was found to occur more slowly for precatalysts containing chelating bis(phosphine) ligands than for precatalysts containing monodentate phosphine ligands.

This thesis describes the incorporation of lanthanide-doped nanoparticles into sol-gel matrices to improve the optical properties of lanthanide ions and these materials can potentially be used in white light devices, optical amplifiers. lasers. and biolabeling. Bright white light has been generated from sol-gel thin films (SiO2 and ZrO2) made with lanthanide-doped nanoparticles through up-conversion of a single 980 nm light source. The up-conversion mechanisms involved in the generation of light has been discussed. A new and potentially efficient up-conversion process named cross-relaxation-enhanced energy-transfer (CREET) up-conversion process has been described. Preparation of semiconductor sol-gel thin films with lanthanide-doped nanoparticles has been discussed and they show energy transfer from the semiconductor matrix to the lanthanide ions. The preparation and bioconjugation of nearly monodisperse (40 nm) silica-coated LaF3:Ln3 nanoparticles has been described.

The focus of this dissertation is the use of bioinformatics in the identification of highly conserved sequences among a set of poxvirus genomes and the subsequent functional analysis of the conserved functions of these sequences. A novel algorithm, Java Pattern Finder, which identifies sequences of a user-specified length that are conserved with a user-specified number of allowed differences, was used to identify near-perfectly conserved sequences among a set of poxvirus genomes. A scoring method was established to quantify the degree of conservation of these sequences and used to show that the 11 most conserved sequences were significantly more conserved than control sequences. Functional analysis showed that explanations such as low codon degeneracy or the presence of conserved promoter elements partially – but not fully – accounted for the conservation observed in these sequences, suggesting that these highly conserved regions may have novel functions in the poxvirus genome that have yet to be uncovered.

Significant advances in the design, synthesis, and chemistry of verdazyl radicals have been made, including (i) the systematic study of the electrochemistry of verdazyl radicals, (ii) the development of formazans as ancillary ligands en route to inorganic verdazyl radicals, and (iii) magnetostructural studies of verdazyl diradicals and copper (II) verdazyl complexes. The electrochemical properties of a family of verdazyl radicals were explored. Type I and type II verdazyl radicals were reversibly oxidized and reduced, and the potentials of such processes observed to be sensitive to substituent effects. The incorporation of electron-withdrawing substituents made verdazyl radicals harder to oxidize and easier to reduce, while the presence of electron-donating groups had the opposite effect. Type II verdazyls were harder to oxidize and less delocalized (based on relative cell potentials) than type I analogues. The difficulty in oxidation of type II verdazyls relates to the electron-withdrawing nature of the carbonyl functionality, while the decreased delocalization relates to twisting of the N-substituents. Twisting of the N-substituents was confirmed through the use of X-ray crystal structures, and DFT calculations were used to illustrate the decrease in delocalization of the unpaired electron associated with the twisting. The similarities of formazans to -diketiminate ligands prompted the study of their coordination chemistry. Boratatetrazines, the first main group complexes of formazans illustrated their ability to mimick beta-diketiminate ligands. Reduction of boratatetrazines with cobaltocene afforded highly reactive borataverdazyl radical anions isolobal to parent organic systems. The radicals were readily oxidized back to the boratatetrazine precursors limiting their characterization to the solid-state. Synthetic pathways to 3-substituted formazans allowed for the incorporation of bulky N-substituents, a feature of -diketiminates that has influenced their utility as catalysts. 3-Cyanoformazans were shown to exist as either the open or closed structure in solution and the solid-state, while 3-nitroformazans exist exclusively as the closed strcutre due to the presence of the relatively large nitro-substituent. A number of transition metal complexes of 3-substituted formazans were synthesized, and their X-ray crystal structures used to establish a correlation between steric bulk at the ligand and complex structure. When ortho-substituents are incorporated the N-aryl substituents twist relative to the formazan backbone, while relatively smaller N-aryl substituents remain relatively planar. Palladium hexafluoroacetylacetonate complexes of formazans were anticipated to have utility as precursors to palladaverdazyls due to their electron poor nature. However, although the complexes did allow for the structure property relationship of metal-formazan complexes to be further developed, palladaverdazyls were not realized. Comparison with boratatetrazines suggests the nature of the Pd-N bond may play a role in the instability of palladaverdazyls. The synthesis and characterization of verdazyl-based spin dimers was reported. The incorporation of iso-propyl N-substituents allowed for the first truly stable verdazyl diradicals to be isolated. Electrochemical, electronic, and magnetic properties of diradicals bridged by para- and meta-benzene were explored. Diradicals bridged by para-benzene were antiferromagnetically coupled while meta-benzene bridged diradicals were ferromagnetically coupled. Magnetostructural studies of copper (II) complexes of verdazyls were complicated by the coordinative flexibility of copper (II) ions and the presence of Jahn-Tellar distorted ligand fields. However, a correlation between structure and properties was established: axially bound verdazyl radicals were weakly ferromagnetically coupled to copper (II) ions, and equatorially bound verdazyl radicals were strongly antiferromagnetically coupled to copper (II).