This thesis describes three investigations, ranging in subject matters, all of which relating to systems capable of photoinduced reactions involving energy or electron transfer. The phenomenon and the effects of environment in the various systems are explored using different methodologies of optical spectroscopy. As the chapters progress, different investigations introduce and build on fundamental concepts encountered and in complexity of the methodologies used to explore the systems. The first chapter introduces the preparation of water-soluble CdSe nanocrystal clusters. The clusters, created using a protein, are 3-D close-packed self-assemblies of nanocrystals. Due to this close-packed nature, electronic interactions between the nanocrystals allow for energy migration within the cluster. The structural and optical properties of the clusters were described. Then using steady-state spectroscopy, properties of the original nanocrystals were compared to that of the cluster to determine the consequence of nanocrystal coupling interactions and their potential use toward the development of artificial light-harvesting systems. In the second chapter, CdSe nanocrystals are functionalized with a unique electro-active polymer, and the electron transfer between the nanocrystal and the electro-active polymer adsorbate is investigated. Using fluorescence decay measurements, the electron transfer reaction inherent to the system with respect to a comprehensive range of dielectric solvents was explored. The study illustrates the high complexity of seemingly typical nanocrystal-based systems and provides general awareness of what factors need to be considered when dealing with such systems. The final chapter starts with an informal review of ultrafast nonlinear spectroscopy, focusing on two methods, three-pulse photon echo peak shift (3PEPS) and two-dimensional photon echo (2DPE) electronic spectroscopy, and how they are related. A straightforward approach for extracting 3PEPS data from 2DPE results is presented in a preliminary case study of a dye in two different solvents, one of which is electron-donating.

Protein folding pathways can be extraordinarily complex. In this study, circular dichroism (CD) and 19F NMR are used to investigate the folding network of calmodulin, a calcium-binding protein, which is biosynthetically enriched with 3-fluorophenylalanine. In calmodulin’s calcium-loaded state, CD experiments identify the existence of a folding intermediate along a heat-denaturation pathway. In comparison to the native state, 19F NMR solvent isotope shifts reveal decreased accessibility of water to hydrophobic core, whereas O2 paramagnetic shifts show increased hydrophobicity of this folding intermediate. 15N-1H and methyl 13C-1H HSQC NMR spectra demonstrate that this folding intermediate retains a near-native tertiary structure, whose hydrophobic interior is highly dynamic. 19F NMR CPMG relaxation dispersion measurements suggest that this near-native intermediate state is transiently adopted below the temperature associated with its onset. The folding network also involves an unproductive off-pathway intermediate. In contrast, calmodulin’s calcium-free state exhibits a simpler folding process which lacks discernible intermediates.

Lateral diffusion of phospholipids is a process essential to membrane function, and can be measured by nuclear magnetic resonance (NMR). This project will use CODEX (Centerband-Only Detection of Exchange), the most highly-evolved NMR experiment combining magic angle spinning with exchange sensitivity, to measure lateral diffusion. 31P CODEX NMR measurements were performed on phospholipids in small unilamellar vesicles (SUV) in a high viscosity solution to slow the rotational tumbling of the SUV and minimize its influence on the CODEX decay. For SUV composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), alone or mixed with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) or cholesterol (CHOL), 31P CODEX spectra showed well-resolved resonances for POPC and POPG, with monoexponential decays for both, from which the correlation time for molecular motion could be extracted. The lateral diffusion coefficients were determined, and fell in the range of 1.0 - 3.3 x 10-12 m2s-1 at 10°C, which agree with established literature values for POPC and POPG.

Lateral diffusion of phospholipids is a process essential to membrane function, and can be measured by nuclear magnetic resonance (NMR). This project will use CODEX (Centerband-Only Detection of Exchange), the most highly-evolved NMR experiment combining magic angle spinning with exchange sensitivity, to measure lateral diffusion. 31P CODEX NMR measurements were performed on phospholipids in small unilamellar vesicles (SUV) in a high viscosity solution to slow the rotational tumbling of the SUV and minimize its influence on the CODEX decay. For SUV composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), alone or mixed with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) or cholesterol (CHOL), 31P CODEX spectra showed well-resolved resonances for POPC and POPG, with monoexponential decays for both, from which the correlation time for molecular motion could be extracted. The lateral diffusion coefficients were determined, and fell in the range of 1.0 - 3.3 x 10-12 m2s-1 at 10°C, which agree with established literature values for POPC and POPG.

Master of Science / Department of Chemistry / Paul E. Smith / The increasing importance of ion-water interactions in the field of chemistry and biology is leading us to examine the structure and dynamic properties of molecules of interest, based on the application of computer-aided models using molecular dynamics simulations. To enable this type of MD study, a molecular mechanics force field was developed and implemented. Kirkwood-Buff theory has been proved to be a powerful tool to provide a link between molecular quantities and corresponding thermodynamic properties. Parameters are the vital basis of a force field. KB integrals and densities were used to guide the development of parameters which could describe the activity of aqueous solutions of interest accurately. In this work, a Kirkwood-Buff Force Field (KBFF) for MD simulation of ammonium sulfate, sodium sulfate, sodium perchlorate and sodium nitrate are presented. Comparison between the KBFF models and existing force fields for ammonium sulfate was also performed and proved that KBFF is very promising. Not only were the experimentally observed KB integrals and density reproduced by KBFF, but other properties like self diffusion constant and relative permittivity are also well produced.

The emerging field of nanotechnology, which spans diverse areas such as nanoelectronics, medicine, chemical and pharmaceutical industries, biotechnology and computation, focuses on the development of devices whose improved performance is based on the utilization of self-assembled nanoscale components exhibiting unique properties owing to their miniaturized dimensions. The first phase in the conception of such multifunctional devices based on integrated technologies requires the study of basic principles behind the functional mechanism of nanoscale components, which could originate from individual nanoobjects or result as a collective behaviour of miniaturized unit structures. The comprehensive studies presented in this thesis encompass the mechanical, dynamical and photophysical aspects of three nanoscale systems. A newly developed europium sulfide nanocrystalline material is introduced. Advances in synthetic methods allowed for shape control of surface-functionalized EuS nanocrystals and the fabrication of multifunctional EuS-CdSe hybrid particles, whose unique structural and optical properties hold promise as useful attributes of integrated materials in developing technologies. A comprehensive study based on a new class of multifunctional nanomaterials, derived from the basic unit of barcoded metal nanorods is presented. Their chemical composition affords them the ability to undergo autonomous motion in the presence of a suitable fuel. The nature of their chemically powered self-propulsion locomotion was investigated, and plausible mechanisms for various motility modes were presented. Furthermore functionalization of striped metallic nanorods has been realized through the incorporation of chemically controlled flexible hinges displaying bendable properties. The structural aspect of the light harvesting machinery of a photosynthetic cryptophyte alga, Rhodomonas CS24, and the mobility of the antenna protein, PE545, in vivo were investigated. Information obtained through a combination of steady-state and time-resolved spectroscopy in conjunction with quantum chemical calculations aided in the elucidation of the dynamics and the mechanism of light harvesting in the multichromophoric phycobiliprotein phycocyanin PC645 in vitro. Investigation of the light-harvesting efficiency and optimization of energy transfer with respect to the structural organization of light-harvesting chromophores on the nanoscale, can provide us with fundamental information necessary for the development of synthetic light-harvesting devices capable of mimicking the efficiency of the natural system.

In this thesis several classes of directed paths are considered as models of linear polymers in a dilute solution. We obtain the generating functions for each model by considering factorization arguments. Information about the polymer behaviour can be extracted from the singularity structure of the associated generating functions. By using modified versions of these models we study the adsorption and localization of polymer molecules, the behaviour of polymers subject to a tensile force, the effects of stiffness, as well as the behaviour of polymers in confined geometries. In each of these situations the resulting generating functions contain at least two physical singularities. We identify the phase transitions in these systems by a changeover in the dominant singularity of the generating function. In the study of localization and polymers subject to a force, we utilize both homopolymer and random copolymer models. For copolymers, the physically relevant properties are obtained by considering a quenched average of the free energy over all possible monomer sequences. This procedure is intractable even for the simplest models. By considering the Morita approximation for several walk models we obtain results which give a bound on the corresponding features of the quenched system. We use a mapping between a simple model of duplex DNA and an adsorbing Motzkin path in order to study the mechanical unzipping of duplex DNA. From this model, we obtain force-temperature diagrams which show re-entrant behaviour of the force. We also develop a simple low temperature theory to describe the behaviour of the force close to T=0 and find that the shape of the force-temperature curve is associated with entropy in the ground state of the system. We consider the effect of stiffness on polymer adsorption and find that the phase transition is second order for all finite stiffness parameters. For systems of polymers in confined geometries, we find that the behaviour of the polymer depends on the distance between the confining surfaces and the associated interactions with each surface. In this problem, there exist regimes where the polymer exerts a force on the surfaces which can be attractive, repulsive or zero.

Apertureless near-field scanning infrared microscopy is a technique in which an impinging infrared beam is scattered by a sharp atomic force microscopy (AFM) tip oscillating at the resonant frequency of the cantilever in close proximity to a sample. Several advantages offered by near-field imaging include nanoscale imaging with high spatial resolution (near-field imaging is not restricted by the diffraction limit of light) and the ability to differentiate between chemical properties of distinct compounds present in the sample under study due to differences in the scattered field. An overview of the assembly, tuning, and implementation of the near-field instrumentation is provided, as well as detailed descriptions about the samples probed and other instrumentation used. A description of the near-field phenomena, a comparison between aperture and apertureless-type near-field microscopy, and the coupled dipoles model explaining the origin of the chemical contrast present in near-field infrared imaging was discussed. Simultaneous topographic and chemical contrast images were collected at different wavelengths for the block copolymer thin film, polystyrene-b-poly(methyl ethacrylate) (PS-b-PMMA) and for amyloid fibrils synthesized from the #21-31 peptide of β2-microglobulin. In both cases it was observed that the experimental scattered field spectrum correlates strongly with that calculated using the far-field absorption spectrum, and using near-field microscopy, nanoscale structural and/or compositional variations were observed, which would not have been possible using ensemble FTIR measurements. Lastly, tip-enhanced Raman spectra of the #21-31 and #16-22 peptide fragments from the β2-microglobulin and Aβ(1-40) peptide were collected, examined, and an outline of the optimization conditions described.

Several nanomaterials systems, both inorganic and organic in nature, have been extensively investigated by a number of characterization techniques including atomic force microscopy (AFM), electron microscopy, Fourier transform infrared spectroscopy (FTIR), and energy dispersive x-ray spectroscopy (EDX). The first system consists of boron nitride nanotubes (BNNTs) synthesized via two different methods. The first method, silica-assisted catalytic chemical vapour deposition (SA-CVD), produced boron nitride nanotubes with different morphologies depending on the synthesis temperature. The second method, growth vapour trapping chemical vapour deposition (GVT-CVD), produced multiwall boron nitride nanotubes (MWBNNTs). The bending modulus of individual MWBNNTs was determined using an AFM three-point bending technique, and was found to be diameter-dependent due to the presence of shear effects. The second type of nanomaterial investigated is the biomineralized calcareous shell of the serpulid Hydroides dianthus. This material was found to be an inorganic-organic composite material composed of two different morphologies of CaCO3, collagen, and carboxylated and sulphated polysaccharides. The organic components were demonstrated to mediate the mineralization of CaCO3 in vitro. The final system studied is the proteinaceous cement of the barnacle Amphibalanus amphitrite. The secondary structure of the protein components was investigated via FTIR, revealing the presence of β-sheet conformation, and nanoscale rod-shaped structures within the cement were identified as β-sheet containing amyloid fibrils via chemical staining. These rod-shaped structures exhibited a stiffer nature compared with other structures in the adhesive, as measured by AFM nanoindentation.

Understanding the assembly of monomeric components into specific molecular motifs is a central theme in materials and surface engineering. Motif designs, specifically using a controllable template, can yield materials with desired optical or electronic properties. The objective of this thesis is to understand the aggregate size, packing, and monomer orientation for the cationic dye, pseudoisocyanine. These organic molecules assemble into crystals in solution, on planar bilayer templates, and on the membranes of living cells. Pseudoisocyanine J-aggregates were found to form on top of the heterogeneous lipid domains in a phospholipid bilayer. This behaviour is limited to a few headgroup chemistries and lateral packing motifs, allowing one to control aggregation via a combination of these two factors. These aggregates are low-dimensional and display polymorphism. Using atomic force microscopy and visible-light spectroscopy, distinct optical characteristics can be correlated to different bilayer templated J-aggregate morphologies. The molecular packing of a similar J-aggregate crystal was resolved using both atomic force microscopy and selected area electron diffraction. The infrared absorption spectra of different polymorphs also displayed distinct differences. These separate examinations enabled a perspective that clarifies the geometry, packing, orientation, and size of templated J-aggregates. Insights into the templating of J-aggregates on the molecular scale reveals that they are sensitive reporters of membrane phase in adherent cells, and are compatible with established cell biology techniques. Lipid domains in live mammalian cells were visualized using fluorescent J-aggregates in combination with endogenous marker proteins of the endocytic process. Analysis of live cell images and additional biophysical work revealed that pseudoisocyanine J-aggregates formed on domains of the anionic lipid bis(monoacylglycerol)phosphate. Only by using J-aggregates can this lipid be shown to form well-ordered domains during endosomal maturation, leading to multivesicular body formation. These data demonstrate that a correlated optical and topographical approach is necessary to understand the structure of fluorescent molecular assemblies, and form the basis for utilizing such aggregates in a biological context.