Doctor of Philosophy / Department of Chemistry / Paul E. Smith / In the past several decades, molecular dynamics (MD) simulations have played an important role in providing atomic details for phenomena of interest. The force field used in MD simulations is a critical factor determining the quality of the simulations. Kirkwood-Buff (KB) theory has been applied to study preferential interactions and to develop a new force field. KB theory provides a path from quantities determined from simulation data to the corresponding thermodynamic data. Here we combine KB theory and molecular simulations to study a variety of intermolecular interactions in solution. First, a force field for the computer simulation of aqueous solutions of alcohols is presented. The force field is designed to reproduce the experimentally observed density and KB integrals for a series of alcohols, allowing for an accurate description of alcohols’ activity. Other properties such as the translational diffusion constant and heat of mixing are also well reproduced. Second, the newly developed force field is then extended to more complicated systems, such as peptide or mini-proteins, to determine backbone dihedral potentials energetics. The models developed here provide a basis for an accurate force field for peptides and proteins. Third, we have then studied the surface tension of a variety water models. Results showed that different simulation conditions can affect the final values of surface tension. Finally, by using the Kirkwood-Buff theory of solution and surface probability distributions, we attempted to characterize the properties of the Gas/Liquid interface region. The same approach is then used to understand the relationship between changes in surface tension, the degree of surface adsorption or depletion, and the bulk solution properties.

Master of Science / Department of Biology / Peter P. Wong / Abstract Water purification methods that remove pathogens and harmful or distasting molecules make water potable. Recently, silver loaded ion-exchange resins have demonstrated a strong role in removing microbes. The goal is to make an effective silver ion-based water purifier that is portable, environmentally stable, and cost efficient. The project was conducted as a collaborative effort with Safewater A/S, an up and coming entrepreneurial business located in Denmark that is interested in developing novel water purifiers for developing nations, adventurers and military personnel. Purolite, a prominent business in ion-exchange resins located in Whales, designed and provided Safewater A/S and our research team with experimental resins for water purification, which will be discussed in the body of this thesis. The data reveals critical issues that may render this tool unavailable for commercial production in some countries due to the mode of action for killing the bacteria and the amount of silver leaching. Tests were conducted using Escherichia coli K12 and Enterococcus faecalis OG1SSp as model fecal organisms using different silver ion-exchange resins. Surveillance of leached silver ions, pH changes, and total dissolved solids (TDS) were also monitored to find correlations with capacity (liters of purified water produced) and effectiveness of microbicidal action. Overall, one resin was found to contain properties consistent with the stated objectives; however its use in some countries as a water purifier for human consumption will be nullified due to extensive silver leaching. Although this resin could be used in the United States of America since it passes the Environmental Protection Agency (EPA) standards, Safewater A/S is interested in further developing it for countries with stricter regulatory constraints before mass production. The goal of the present thesis report is to address the stated objectives in the development of a water purifier.

Doctor of Philosophy / Department of Chemistry / Viktor Chikan / The research work in this thesis aims at investigating the basic physic-chemical properties of magnetic and metal nanoparticles (NPs) for biomedical applications such as magnetic hyperthermia and controlled drug release. Magneto-plasmonic properties of magnetic NPs are important to evaluate potential applications of these materials. Magnetic property can be used to control, monitor and deliver the particles using a magnetic field while plasmonic property allows the tracking of the position of the particles, but aggregation of NPs could pose a problem. Here, the aggregation of NPs is investigated via the Faraday rotation of gold coated Fe[subscript]2O[subscript]3 NPs in alternating magnetic fields. In addition, the Faraday rotation of the particles is measured in pulsed magnetic fields, which can generate stronger magnetic fields than traditional inductive heaters used in the previous experiments. In the second project, the formation of protein-NPs complexes is investigated for hyperthermia treatment. The interactions between gold and iron-platinum NPs with octameric mycobacterial porin A from Mycobacterium smegmatis (MspA) and MspA[superscript])cys protein molecules are examined to assemble a stable, geometrically suitable and amphiphilic proteins-NPs complex. Magnetic NPs show promising heating effects in magnetic hyperthermia to eliminate cancer cells selectively in the presence of alternating magnetic field. As a part of investigation, the heating capacity of a variety of magnetic NPs and the effects of solvent viscosity are investigated to obtain insight into the heating mechanism of these particles. Finally, the controlled drug release of magnetic NPs loaded liposomes by pulsed magnetic field is investigated. The preliminary data indicate about 5-10% release of drug after the application of 2 Tesla magnetic pulses. The preliminary experiments will serve as the initial stage of investigation for more effective magnetic hyperthermia treatment with the help of short magnetic pulses.

Thèse réalisée en cotutelle avec l'Université catholique de Louvain, Belgique / Les nanotubes de carbone possèdent des propriétés uniques qui en font des matériaux prometteurs dans de nombreux domaines. En particulier, leur structure quasi-unidimensionnelle et leur rapport surface/volume élevé font de ces matériaux des candidats de choix pour leur utilisation comme senseurs. A ce jour, les études concernant l'utilisation des nanotubes de carbone pour la conception de senseurs se concentrent principalement sur la détection de gaz, de molécules biologiques ou chimiques. Dans le cadre de cette thèse, nous nous intéressons à l'utilisation des nanotubes de carbone comme senseurs pour détecter en temps réel une transformation chimique, au travers d'une réaction catalytique. Pour ce faire, des catalyseurs supportés sur nanotubes de carbone sont préparés grâce à des méthodes de fonctionnalisation appropriées de ces matériaux. En pratique, nous développons dans ce travail deux approches distinctes pour la préparation de catalyseurs supportés sur nanotubes de carbone. D'une part, nous mettons au point une méthode de fonctionnalisation monovalente des nanotubes de carbone, permettant de déposer des nanoparticules métalliques à la surface des nanotubes en vue de la préparation de catalyseurs hétérogènes supportés. A cette fin, les nanotubes sont dans un premier temps fonctionnalisés par des sels de diazonium. Cette première étape permet d'établir un point d'accroche sur les nanotubes permettant une post-fonctionnalisation ultérieure, en vue de l'ancrage de clusters métalliques. Une étape d'activation thermique permet ensuite de former des nanoparticules métalliques, au départ de ces précurseurs moléculaires. D'autre part, un catalyseur homogène supporté est préparé via l'ancrage de complexes à base de Pd(0) sur des nanotubes de carbone fonctionnalisés de manière à présenter des liaisons triples. Pour ce faire, les nanotubes de carbone sont fonctionnalisés de façon divalente, par la réaction de Bingel-Hirsch. Cette approche divalente assure l'ancrage covalent des sites actifs, tout en préservant la conductivité électrique des nanotubes de carbone. Quelle que soit l'approche envisagée, la préparation de ces catalyseurs est attentivement suivie par des méthodes classiques de caractérisation telles que la spectroscopie Raman, la spectroscopie des photoélectrons X et l'analyse thermogravimétrique. En outre, une caractérisation électrique est également effectuée à chaque étape de la préparation des catalyseurs, afin d'étudier l'influence des différentes étapes de fonctionnalisation sur les propriétés électriques du nanotube. Ces matériaux sont ensuite testés en catalyse, pour la transformation hydrolytique du diméthylphénylsilane en diméthylphénylsilanol ou pour la réaction de couplage croisée de Suzuki-Miyaura, respectivement pour les catalyseurs hétérogènes et homogènes supportés. L'activité de ces catalyseurs, ainsi que leur recyclabilité, est étudiée grâce à un suivi réactionnel par chromatographie gazeuse. Enfin, nous démontrons dans cette thèse la possibilité d'utiliser les nanotubes de carbone comme senseurs pour détecter in situ l'activité catalytique. A cette fin, des mesures électriques en temps réel sont enregistrées au cours de la réaction de catalyse. L'activité catalytique se traduit par des changements de la conductivité des nanotubes au cours du temps. / Due to their outstanding properties, carbon nanotubes are being considered as promising materials in various fields. Namely, their quasi-one-dimensionality and their high surface/volume ratio make them ideal candidates for sensing applications. To date, studies dealing with the use of carbon nanotubes in sensing mainly focus on gas, biological and chemical molecules detection. In this thesis, we aim to use carbon nanotubes as sensors for the real-time detection of a chemical transformation through a catalytic reaction. In order to do this, carbon nanotube supported catalysts are prepared thanks to appropriate functionalization methods. In practice, we develop in this work two distinct approaches for the preparation of carbon nanotube supported catalysts. On one hand, we develop a monovalent functionalization pathway for the deposition of metallic nanoparticles on carbon nanotube surface. For this purpose, carbon nanotubes are first functionalized by diazonium salts. This first step allows to bind a tethering point for a subsequent post-functionalization. Metallic clusters are then coordinated on these functionalized moieties. A thermal activation step ensures the formation of metallic nanoparticles from these nanoparticle molecular precursors. On the second hand, a homogeneous supported catalyst is prepared by anchoring Pd(0) complexes on carbon nanotube surface. In order to do this, carbon nanotubes are divalently functionalized by Bingel-Hirsch reaction to present dangling triple bonds at their surfaces. This divalent approach ensures a covalent anchoring of the active sites on the nanotube surface, while preserving their electrical conductivity. Whichever the considered approach, the catalyst preparation is carefully analyzed by common characterization techniques, such as Raman spectroscopy, X-ray photoelectron spectroscopy and thermogravimetric analysis. Moreover, the materials are also electrically characterized at each step of the catalyst preparation process. This electrical characterization allows to study the influence of the different steps of the functionalization strategy on the nanotube electrical properties. These materials are then tested in catalysis, for the hydrolytic transformation of dimethylphenylsilane in dimethylphenylsilanol or for the Suzuki-Miyaura cross-coupling reaction, respectively for heterogeneous and homogeneous supported catalysts. The activity and recyclability of these catalysts is monitored by gas chromatography. Finally, we demonstrate in this thesis the possibility of using carbon nanotubes as sensors for the in situ detection of catalytic activity. For this purpose, real-time electrical measurements are recorded during the catalytic reaction. The catalytic activity is revealed by fluctuations of the nanotube conductivity over time.

Hydrophobic interactions guide important molecular self-assembly processes such as protein folding. On the macroscale, hydrophobic interactions consist of the aggregation of "oil-like" objects in water by minimizing the interfacial energy. However, the hydration mechanism of small hydrophobic molecules on the nanoscale (~1 nm) differs fundamentally from its macroscopic counterpart. Theoretical studies over the last two decades have pointed to an intricate dependence of molecular hydration mechanisms on the length scale. The microscopic-to-macroscopic cross-over length scale is critically important to hydrophobic interactions in polymers, proteins and other macromolecules. Accurate experimental determination of hydration mechanisms and their interaction strengths are needed to understand protein folding. This thesis reports the development of experimental and analytical techniques that allow for direct measurements of hydrophobic interactions in a single molecule. Using single molecule force spectroscopy, the mechanical unfolding of a single hydrophobic homopolymer was identified and modeled. Two experiments examined how hydrophobicity at the molecular scale differ from the macroscopic scale. The first experiment identifies macroscopic interfacial tension as a critical parameter governing the molecular hydrophobic hydration strength. This experiment shows that the solvent conditions affect the microscopic and macroscopic hydrophobic strengths in similar ways, consistent with theoretical predictions. The second experiment probes the hydrophobic size effect by studying how the size of a non-polar side-chain affects the thermal signatures of hydration. Our experimental results reveal a cross-over length scale of approximately 1 nm that bridges the transition from entropically driven microscopic hydration mechanism to enthalpically driven macroscopic hydration mechanism. These results indicate that hydrophobic interactions at the molecular scale differ from macroscopic scale, pointing to potential ways to improve our understanding and predictions of molecular interactions. The system established in this thesis forms the foundation for further investigation of polymer hydrophobicity.

Segmental long spacing (SLS) collagen self-assembly was studied by analyzing aggregates formed from different nucleoside triphosphates at various protonation stages. Triple-negatively charged triphosphate groups were determined to be critical for SLS assembly, electrostatically bridging basic residues between collagen monomers. In the second part of this thesis, the nominal elastic modulus for each of the three forms of Type I collagen aggregate was measured and compared. Fibrous long spacing collagen, often associated with diseased tissues, exhibited lower stiffness in comparison to the other forms, native and SLS, suggesting decreased structural stability in diseased tissues. In the last section, a unidirectional pattern of native fibrils was assembled using mica as a template; the ability to customize and change the surface morphology was also demonstrated. For the first time, collagen monomers deposited on the mica were demonstrated to gain lateral mobility.

Segmental long spacing (SLS) collagen self-assembly was studied by analyzing aggregates formed from different nucleoside triphosphates at various protonation stages. Triple-negatively charged triphosphate groups were determined to be critical for SLS assembly, electrostatically bridging basic residues between collagen monomers. In the second part of this thesis, the nominal elastic modulus for each of the three forms of Type I collagen aggregate was measured and compared. Fibrous long spacing collagen, often associated with diseased tissues, exhibited lower stiffness in comparison to the other forms, native and SLS, suggesting decreased structural stability in diseased tissues. In the last section, a unidirectional pattern of native fibrils was assembled using mica as a template; the ability to customize and change the surface morphology was also demonstrated. For the first time, collagen monomers deposited on the mica were demonstrated to gain lateral mobility.

The air-water interface is abundant in the environment, thus it is an important proxy for atmospheric processes such as the uptake and transfer of molecules, heterogeneous reactions, photochemistry, and cloud condensation. This thesis aims to elucidate the role of semi-soluble and insoluble organic coatings on atmospheric processes at the air-water interface. Using glancing-angle LIF it was found that monolayer coatings of 1-octanol and of octanoic acid have opposing effects on the ozonation rate of pyrene at the air-water interface. LIF was also coupled with a Profile Analysis Tensiometer (PAT-1) to measure the effect of stearic acid coating compression on the uptake of HCl to a water droplet. Due to preliminary issues with this novel technique, no significant uptake suppression was observed. The oxidation of benzene by OH radical was also explored briefly, as were the photophysics of photosensitizers and the angle dependence of Raman signal from a D2O pendent droplet.

This work presents a new implementation of the QP algorithm, a computer method to diagonalize the extremely large matrices arising in multimode vibronic problems. Benchmark calculations are included, showing the accuracy of the program. The QP algorithm is extended to treat multiple electronic surfaces for competitive control and this is demonstrated with an Hamiltonian including three electronic states, a model of the benzene radical cation. Finally, the evolution of zeroth-order states in a simple two electronic states, two dimensional model with a conical intersection is explored, towards building a time-dependent view of overlapping resonances coherent control.

The air-water interface is abundant in the environment, thus it is an important proxy for atmospheric processes such as the uptake and transfer of molecules, heterogeneous reactions, photochemistry, and cloud condensation. This thesis aims to elucidate the role of semi-soluble and insoluble organic coatings on atmospheric processes at the air-water interface. Using glancing-angle LIF it was found that monolayer coatings of 1-octanol and of octanoic acid have opposing effects on the ozonation rate of pyrene at the air-water interface. LIF was also coupled with a Profile Analysis Tensiometer (PAT-1) to measure the effect of stearic acid coating compression on the uptake of HCl to a water droplet. Due to preliminary issues with this novel technique, no significant uptake suppression was observed. The oxidation of benzene by OH radical was also explored briefly, as were the photophysics of photosensitizers and the angle dependence of Raman signal from a D2O pendent droplet.