The first thermal cycling experiments of ionic self-assembled multilayer (ISAM) films have been reported examining their survivability through repeated thermal cycles from -20° C to 120° C in ambient atmospheric conditions. The films were constructed from alternating layers of Nile Blue A and gold nanoparticles which provided a strong absorbance in the optical wavelength range. No degradation of the optical characteristics of the ISAM films was observed [1]. Techniques for measuring the capacitance and resistivity of various ISAM films have also been developed allowing for a more complete electrical characterization of ISAM films. Capacitance measurements enabled a calculation of the dielectric function and breakdown field strength of the ISAM films. The capacitance measurement technique was verified by measuring the dielectric function of a spin-coated thin film PMMA, which has a well characterized dielectric function [2]. Surface-enhanced Raman spectroscopy (SERS) has been studied as a possible detection method for malignant melanoma revealing spectral differences in blood sera from healthy horses and horses with malignant melanoma. A SERS microscope system was constructed with the capability of resolving the Raman signal from biologically important molecules such as beta-carotene and blood sera. The resulting Raman signals from sera collected from horses with malignant melanoma were found to have additional peaks not found in the Raman signals obtained from sera collected from healthy horses. A systematic analysis of the combination of absorbance and fluorescence signals of blood sera collected from populations of healthy dogs and dogs with cancer has resulted in a rapid and cost-effective method for monitoring protein concentrations that could possibly be used as part of a cancer screening process. This method was developed using the absorbance and fluorescence signals from known serum proteins, the combinations of which were used to match the absorbance and fluorescence signals of blood sera allowing for an accurate determination of protein concentrations in blood sera [3]. Finally, a novel method for measuring the melting point of DNA in solution using capacitance measurements is presented. This method allows for the determination of the melting temperature as well as the melting entropy and melting enthalpy of DNA strands. Two different short strands of DNA, 5'-CAAAATAGACGCTTACGCAACGAAAAC-3' along with its complement and 5'-GGAAGAGACGGAGGA-3' along with its complement were used to validate the technique as the characteristics of these strands could be modeled using theoretical methods. This experimental technique allows for the precise determination of the melting characteristics of DNA strands and can be used to evaluate the usefulness of theoretical models in calculating the melting point for particular strands of DNA. Additionally, a micro-fluidic device has been proposed that will allow for a rapid and cost-effective determination of the melting characteristics of DNA [4]. / Ph. D.

Biosensors have a multitude of important applications in basic research, environmental monitoring, biodefense, and medicine. This research aims to show that Ionic Self-Assembled Multilayers (ISAMs) adsorbed on Long Period Gratings (LPGs) can serve as a highly sensitive, robust, inexpensive optical-based biosensor platform. The ISAM technique is a layer-by-layer deposition method that builds nanometer-thick films based on the principle of Coulomb attraction between oppositely charged polyelectrolyte solutions while LPGs cause strong attenuation bands that enable an optical fiber to be extremely sensitive to changes in the surrounding environment. LPGs have been shown to be highly sensitive to the adsorption of nanoscale self-assembled films on the optical fiber cladding surface. In this work, we utilize Turnaround Point (TAP) LPGs, which possess even greater sensitivity than standard LPGs. This thesis focuses on evaluation of approaches to increasing the sensitivity of the sensor platfom, implementation of a biosensor for detection of several biomolecules, and preliminary evaluation of the potential for pH sensing. For a thin-film coated TAP LPG, we have demonstrated that shifts in the transmitted light intensity at the resonant wavelength of the LPG can result from the variation in film thickness and/or refractive index. We have observed decreases in intensity as large a 7 dB for one bilayer of ISAM film (~1 nm), which corresponds to an 80% decrease in the transmitted light intensity at the resonant wavelength. We have also shown that the sensitivity of the TAP LPG sensor can be increased by implementing nm-thick ISAM films that have a refractive index greater than silica. Furthermore, it is shown that incorporation of silica nanoparticles into the ISAM films significantly increases sensitivity through increased surface area and thickness. The biotin-streptavidin system was used as a model for implementaion and optimization of the ISAM-coated TAP LPG biosensor platform. Through evaluation of various biotin derivatives to maximize the amount functionalized onto the ISAM film, optimization of the ISAM film properties, and use of LPGs designed for higher sensitivity, the minimum detectable concentration of streptavidin was decreased from 0.0125 mg/ml to 12.0 ng/ml. The biosensor platform was then tested on prostate specific antigen (PSA), which is used as a clinical marker for early diagnosis of potential prostate cancer. Using a direct crosslinking approach of the monoclonal antibody to PSA into the ISAM film, a sensitivity level of 11.64 ng/ml PSA was obtained through combined optimization of the ISAM film and antibody surface coverage. Finally, the potential of ISAM TAP LPGs as pH sensors was examined based on the pH dependent swelling of ISAM films. / Ph. D.

A full understanding of chemical reaction dynamics at the gas/organic-surface interface requires knowledge of energy-transfer processes that happen during the initial gas/surface collision. We have examined the influence of mass and rovibrational motion on the energy-transfer dynamics of gas-phase species scattering from model organic surfaces using theory and experiment. Molecular-beam scattering techniques were used to investigate the rare gases, Ne, Ar, Kr, and Xe, and the diatomics, N₂ and CO, in collisions with CH₃- and CF₃-terminated self-assembled monolayer (SAM) surfaces. Complementary molecular-dynamics simulations were employed to gain an atomistic view of the collisions and elucidate mechanistic details not observable with our current experimental apparatus. We developed a systematic approach for obtaining highly accurate analytic intermolecular potential-energy surfaces, derived from high-quality ab initio data, for use in our classical-trajectory simulations. Results of rare gas scattering experiments and simulations indicate mass to be the determining factor in the energy-transfer dynamics, while other aspects of the potential-energy surface play only a minor role. Additionally, electronic-structure calculations were used to correlate features of the potential-energy surface with the energy-transfer behavior of atoms and small molecules scattering from polar and non-polar SAM surfaces. Collisions of diatomic molecules with SAMs are seen to be vibrationally adiabatic, however translational energy transfer to and from rotational modes of the gas species, while relatively weak, is readily apparent. Examination of the alignment and orientation of the final rotational angular momentum of the gas species reveals that the collisions induce a stereodynamic preference for the expected "cartwheel" motion, as well as a surprising propensity for "corkscrew" or "propeller" motion. The calculated stereodynamic trends suggest that the CH₃-SAM is effectively more corrugated than the CF₃-SAM. Finally, the feasibility for collisional-energy promoted, direct gas/organic-surface reactions was interrogated using the 1,3-dipolar azide-alkyne cycloaddition reaction. We found that geometrical constraints prevented the reaction from proceeding at the probed conditions. / Ph. D.

Biosensors have widespread applications in many areas. Currently the Surface Plasmon Resonance (SPR) biosensor is one of the most prevalent types of biosensor. However, it has several disadvantages such as being delicate, expensive, and non-portable. Ionic Self-Assembled Multilayers (ISAMs) adsorbed on Long Period Fiber Gratings (LPGs) provides an attractive platform for building optical sensors, which could potentially overcome the disadvantages of SPR biosensors. The ISAM technique is a type of layer-by-layer deposition technique for building nanoscale thin films. An LPG is a type of fiber device that is sensitive to physical property changes of the ambient environment. LPGs have been extensively investigated for use as optical sensors. We have carried out a study on combining these two techniques to build efficient biosensors. In this thesis, we demonstrate ultra-sensitive LPGs whose attenuation can be changed by 25 dB (~99.7%) over a 48-nm spectral band, with ambient-index changes of only 2.7E-4. The device schematic allows arbitrarily high index sensitivities to be achieved, which makes it an attractive platform for realizing sensors and modulators that respond to small index changes. For a thin-film coated LPG, we find theoretically that the resonant wavelength shift of the LPG can result from either the variation of the thickness of the film and/or the variation of its refractive index. Furthermore, results illustrate that the sensitivity of the sensor could be enhanced using a nm-thick thin-film (e.g. ISAM films) whose refractive index is greater than silica. Experimentally, we demonstrate the fabrication of nm-thick ISAM films deposited on LPGs, which induces dramatic shifts in the resonant wavelength. The refractive index and the thickness of the ISAM film was precisely controlled by altering the relative fraction of the anionic and cationic materials combined with layer-by-layer deposition. Finally, we demonstrate that ISAM-coated LPGs can function effectively as biosensors by using the biotin-streptavidin system. These demonstrations confirm that the ISAM-LPG scheme provides a thermally-stable, reusable, and robust platform for building efficient optical sensors. / Ph. D.

Comprehension of reactive chemical dynamics in the gas phase and at the gas/organic-surface interface and non-reactive dynamics at the interface between hydrophobic surfaces and water requires an understanding of the fundamental atomic and molecular interactions that undergird these important phenomena. In an effort to study these regimes of chemical interaction, we have performed computational simulations that probe the dynamics of chemical systems that exemplify each of these domains. To study gas-phase chemical dynamics, we reparametrized semiempirical Hamiltonians so that they can accurately describe the potential energy surfaces for two distinct atom+alkane reactions. In addition to their demonstrated accuracy, these methods possess the attractive quality of being computationally inexpensive enough to afford extensive direct-dynamics trajectory studies. Our results on the dynamics of atom+alkane hydrogen-abstraction reactions have shown good agreement with experimental metrics that are as diverse as product velocity distributions, excitation functions, angular distributions and rovibrational state distributions for diatomic products of the abstraction. We have demonstrated that our reparametrized Hamiltonians are suitable for investigating gas-phase reactions with up to 15 (5 heavy) atoms and that they are appropriate for studying reactions beyond the gas phase, especially gas/surface reactions. By employing our semiempirical methods within a quantum-mechanics/molecular-mechanics hybrid scheme we are able to examine hydrogen-abstraction reactions of fluorine atoms with alkanethiolate self-assembled monolayers. Our simulations reproduce the general trends of experimental results for the cousin F+squalane reaction. Our simulations also probe the role that secondary collisions play in determining the final internal and translational energy of the product HF molecules. For instance, we determined that very few interactions with the SAM surface were required to cool rotational and translational modes of the HF product, while its vibrational energy remains unchanged on the time scale that HF molecules trap on the SAM surface. Moving beyond the gas/organic surface interface, we have also performed molecular-dynamics simulations of thin water films confined between hydrophobic SAM surfaces. These simulations illuminated the structural and dynamics behavior induced in the water films by confinement in hydrophobic environments. While most effects of the surface do not penetrate deep into the water layers we have noted that enhanced lateral diffusion of water molecules can persist in these films with > 1 nm length scales. We have elucidated a possible mechanistic precursor for the attractive forces seen in experimental measurement of the hydrophobic effect. / Ph. D.

Various technologies depend on interfacial events that are influenced by various molecular interactions at a solid-liquid interface. The functionality of a surface plays an important role in many applications such as catalysis, sensing, and bio-compatibility, which can benefit from distinctive chemical and physical surface properties. To create tailor-made functional surfaces, surface host-guest assemblies based on Langmuir-Blodgett and self-assembly technique have been employed as a model system as they may offer the potential ability to regenerate surface properties via intercalation of various functional guest molecules. This thesis ranges over the development and characterization of host-guest assemblies and their feasibilities for the regeneration of surface properties via intercalation of functional guests. In our work, 3-dimensional host structures with cavities are constructed on a targeted solid substrate using Langmuir-Blodgett and self-assembly techniques. In particular, by adopting the fundamental concept of host-guest interaction in supramolecular chemistry, we expect that structurally homologous guest molecules where functional groups are anchored can be intercalated into the cavities between hydrophobe arrays at the liquid-solid interface from solution under well-controlled conditions. This approach offers the potential of separating the functional of the monolayer from the inherent structure of the host. The first part of this thesis details two-dimensional host-guest assemblies consisting of guanidinium (G), octadecylsulfonate (S) and various functional alkane guests at the air-aqueous interface and following deposition onto solid substrates via the Langmuir-Blodgett technique. In particular, we evaluated the stability of the host-guest assemblies and the feasibility of exchanging molecular guests under exposure to various organic solvent environments. Analysis of X-ray reflectivity measurements of the thin films showed that good stability of the host-guest assembly could not be achieved due to weak interactions between the host monoalyer and the solid surface. In addition, no evidence of intercalation of guest molecules into guest-free host-cavities was observed. The second part of this thesis discusses the effective methodologies to prepare low-density self-assembled monolayers (LDSAMs) with cavities on silicon substrates. We employed a step-wise reaction based on hydrolytic or silane chemistry: integral spacer molecules such as anthracene-derivatives were anchored to the Si substrate and then long alkane chains were appended to the spacer molecules. The results showed that LDSAMs using an anthryl spacer are attached at the SAM/Si interface via a Si-O-C linkage, and the films do not exhibit a densely packed monolayer quality as would be expected for a non-sterically hindered alkyltrichlorosilane on Si. Thus, the resulting LDSAMs (with cavities) may be capable of accommodating other guest molecules with hydrocarbon chains through intercalation in order to form host-guest assemblies. The third part of this thesis demonstrates the ability of LDSAMs to produce functional surfaces via the intercalation of various functional guest molecules. Self-assembled monolayers of (10-octadecyl)-9-anthracenethiol (host-SAMs) on Au substrates were prepared. Quartz crystal microbalance with dissipation (QCM-D) measurements was used to demonstrate the capacity of LDSAMs to confine guest molecules in the cavities and to probe the structural changes of the host-guest assembly during guest intercalation from ethanol solution. X-ray photoelectron spectroscopy (XPS) measurements were then used to probe host-guest monolayers formed by immersing the host monolayer in solutions in a variety of other solvents. A combined study of QCM-D and XPS showed that guest molecules were intercalated into host-cavities. The reversibility of the intercalation process allows a guest already situated in a host-cavity to be replaced with second guest under well-regulated solvent conditions. / Ph. D.

Fabrication of surfaces with versatile functional groups is an important research area. Hence, it is essential to control and tune the surface properties in a reliable manner. Vinyl-terminated self-assembled monolayers (SAMs) offer significant flexibility for further chemical modification and can serve as a versatile starting point for tailoring of surface properties. Here a synthetic route for the preparation of vinyl-terminated trichlorosilane self-assembling molecules: 9-decenyltrichlorosilane (CH₂=CH-(CH₂)₈-SiCl₃), 10-undecenyltrichlorosilane (CH₂=CH-(CH₂)₉-SiCl₃), and 14-pentadecenyltrichlorosilane (CH₂=CH-(CH₂)₁₃-SiCl₃) is presented. These molecules were used for the preparation of SAMs in either liquid or vapour phase processes. Commercially available methyl-terminated self-assembling molecules: decyltrichlorosilane (CH₃-(CH₂)₉-SiCl₃) and octadecanetrichlorosilane (CH₃-(CH₂)₁₇-SiCl₃) were used as controls. The resultant films were characterised by X-ray photoelectron spectroscopy (XPS), contact angle analysis, ellipsometry, and atomic force microscopy (AFM). Well defined, vinyl-terminated SAMs were further chemically modified with carbenes (:CCl₂, :CBr₂, :CF₂) and hexafluoroacetone azine (HFAA). The reactions were performed in the liquid or the vapour phase. The resulting SAMs were characterised using the same methods as for the vinyl-terminated monolayers. Successful modification was confirmed by the appearance of new signals in the XPS spectrum, with simultaneous changes in water contact angle values and unchanged thickness values. Methyl-terminated SAMs were also exposed to carbenes and HFAA as a control system. These are the first examples of C-C bond formation on SAMs in the vapour phase.

L’oxydoréduction de monocouches auto-assemblées (SAMs) de ferrocénylalcanethiolates à la surface d’or (FcRSAu) a été étudiée en temps réel par la spectroscopie de résonance de plasmons de surface couplée avec l’électrochimie (E-SPR). La sensibilité de cette technique permet de déterminer des changements d’épaisseur de couche l’ordre de quelques angström résultant d’un changement de structure de la SAM. Plusieurs études antérieures ont proposé que l’oxydation électrochimique d’une SAM de FcRSAu induit une réorientation moléculaire. L’E-SPR est utilisé pour identifier l’origine de ce changement structurel. D’abord, une calibration du réfractomètre SPR utilisé a été effectuée afin de trouver une équation de conversion du signal SPR obtenu en pixel en angle d’incidence pour que l’on puisse calculer le changement d’épaisseur de monocouche à partir du changement d’angle de résonance avec le modèle de Fresnel. Par la suite, une caractérisation approfondie des SAMs de FcCnSAu (où n = 6, 8, 12, 14) en contact avec du NaClO4 acidifié a été réalisée par électrochimie, éllipsométrie, spectroscopie infrarouge et microscopie à force atomique. Les résultats obtenus montrent que l’augmentation de la longueur des chaînes alkyles donne des SAMs de ferrocènes plus épaisses et moins désordonnées. L’analyse par l’E-SPR de ces SAMs pures montre que le changement d’épaisseur induit par l’électro-oxydation dépend linéairement du nombre de méthylènes sur la chaîne alkyle. En appliquant la déconvolution mathématique aux voltampérogrammes cycliques enregistrés pour les SAM mixtes (FcC12SAu/C11SAu) de différentes compositions, on arrive à la conclusion qu’il y a un redressement des chaînes alkyles dans les domaines des ferrocènes agrégés mais la réorientation des têtes de ferrocène dans les domaines de ferrocènes agrégés ou dispersés ne peut pas être exclue. Enfin, l’effet de l’anion électrolytique sur le changement d’épaisseur de la SAM mesuré par l’E-SPR a été étudié. L’analyse électrochimique montre que la capacité de pairage d’anions avec les ferrocéniums décroit comme suit : PF6- > ClO4- > BF4- > NO3-. Tandis que l’épaisseur de la SAM donnée par le changement d’angle de résonance suit la tendance suivante : NO3- ≥ ClO4- > PF6- ≈ BF4-. Des études plus approfondies seront nécessaire pour clarifier cette tendance observée par E-SPR. / The oxidation and reduction of self-assembled ferrocenylalkanethiolate monolayers formed on gold surfaces (FcRSAu) have been followed in real-time by electrochemical surface plasmon resonance (E-SPR) spectroscopy. Film thickness changes on the order of angstroms resulting from SAM structural changes can be detected by SPR. The electrochemically-induced reorientation of the ferrocenylalkanethiolates has been proposed by several spectroelectrochemistry studies. We have used E-SPR to elucidate the nature of the molecular reorientations. The SPR refractometer was first calibrated to find a pixel to angle equation so that Fresnel modeling could be used to calculate SAM thickness changes from the measured resonance angle changes (Δθmin). SAMs of FcCnSAu (where n = 6, 8, 12, 14) were characterized by electrochemistry, infrared spectroscopy and atomic force microscopy. The results obtained show that an increase in the alkyl chain length gives a thicker and less disordered SAM. Oxidation of the surface-bound ferrocenes to ferroceniums and pairing with ClO4- anions produces a similar change in Δθmin for these SAMs, but the variation in the SAM thickness is linearly dependent on the chain length. Mathematical deconvolution of the cyclic voltammograms of binary SAMs (FcC12SAu/C11SAu) of different compositions was used to separate the contributions of the different ferrocene domains (aggregated vs. isolated ferrocenes). We conclude that the aggregated-ferrocenes undergo a change in the orientation of the alkyl chain orientation. We cannot however exclude that the cyclopentadiene rings also reorient themselves. Anion pairing effect was studied by E-SPR. Our electrochemistry results indicate that the ability of the electrolyte anion to pair with the electrogenereted ferrocenium decreases in the following order: PF6- > ClO4- > BF4- > NO3-. On the other hand, the change in Δθmin does not follow the associated trend observed for the anion pairing capacity but rather NO3- ≥ ClO4- > PF6- ≈ BF4-. We hypothesize that the difference in the uptake water molecules by the oxidized SAM may be the reason for this observation. This hypothesis still needs to be verified.

Ce travail concerne l'étude de monocouches auto-assemblées (SAMs) sur l'or par simulation moléculaire. Des SAMs électroactives formées de chaines ferrocenylalcanethiols et alcanethiols et des SAMs constituées de β-cyclodextrines immobilisées sur des surfaces pouvant donner lieu à la formation de complexes d'inclusion à l'interface ont été étudiées. L'objectif était d'obtenir des grandeurs macroscopiques qui soient directement comparables aux grandeurs expérimentales. Pour cela, des simulations de dynamique moléculaire ont été couplées à des calculs de perturbation thermodynamique afin d'obtenir des grandeurs rédox et des propriétés thermodynamiques d'association. La reproduction de grandeurs expérimentales a dans un premier temps permis de valider les méthodologies de simulation et les champs de forces utilisés. Ceci a ensuite conduit à envisager la simulation moléculaire comme une technique prédictive pour l'étude de nouveaux systèmes. Les grandeurs macroscopiques obtenues ont pu être interprétées grâce à une caractérisation structurale et énergétique des processus mis en jeu. / This work concerns the study of self-assembled monolayers (SAMs) on gold surfaces by molecular simulation. Electroactive SAMs formed by both ferrocenylalkanethiol and alkanethiol chains and SAMs of immobilized β-cyclodextrins that can form inclusion complexes at the interface were investigated. The objective of this study was to use molecular simulation to reproduce macroscopic properties that can be directly compared with experimental results. Molecular dynamics simulations are coupled to perturbation methods in order to calculate redox properties and thermodynamic properties of association. The comparison with experimental data allows us to validate simulation methodologies and forcefields and to consider simulation as a predictive tool for the study of new systems. Molecular dynamic also provides a rationalization of the macroscopic properties at the atomic level by a structural and energetic analysis of the processes involved in the reactions.

Pour mimer le repliement des structures tridimensionnelles des biomolécules, les chimistes ont développé des oligomères artificiels capables d’adopter des formes repliées et bien définie en solution : les foldamères. Néanmoins, la variété des structures secondaires isolées que l’on rencontre au sein des foldamères n’atteint pas encore celle des biomolécules. La combinaison de différentes séquences d’oligoamides aromatiques ayant des structures secondaires distinctes a permis le développement d’architectures de type « hélice-feuillet-hélice » définie dans lesquelles chaque sous-composant secondaire conserve son intégrité respective. Ces objets uniques en forme de panier possèdent une fenêtre ouverte modulable inscrite dans le squelette du foldamère par laquelle une molécule invitée peut être accueillie. Comme preuve de concept, la liaison et le relargage d’une molécule invitée à l’une de ces structures se sont révélées rapides à l’échelle de la RMN 1H. Ensuite, le développement de brins oligomériques composés de monomères codant pour de faibles rayons de courbure a permis l’obtention d’hélices doubles. Ces structures auto-assemblées de haut-poids moléculaires possèdent un diamètre de l’ordre du nanomètre. Enfin, des segments hélicoïdaux codant pour des diamètres larges ont été couplés à des pseudo-coudes artificiels dans le but d’obtenir des architectures possédant une large cavité polaire inspirés de la structure des tonneaux β. Ces approches ouvrent la voie vers la conception d’objets moléculaires toujours plus complexes au-delà la chimie des biomolécules. / To mimic the particular folding of the biomolecules’ three-dimensional structures, chemists have developed artificial oligomers that fold into a compact and well-defined structures in solution: foldamers. Nevertheless, the variety of isolated secondary structures of foldamers is not equal to those of biomolecules. The association of different sequences of aromatic oligoamide having distinct secondary structures allowed the development of well-defined helix-sheet-helix architectures in which subcomponents conserve their respective integrity. These unique basket-like objects possess an open-window within the foldamer backbone in which a molecular guest can be accommodate. As a proof of concept, guest binding to one of these structures was found to be fast on the NMR time scale. Then, the development of oligoamide aromatic strands made of monomer encoding for low curvature has allowed to obtain double helices structures. These self-assembled structures showing high molecular weights present a nanometer scale diameter. Eventually, these oligomeric strands were coupled to artificial turn units to obtain β-barrels-like architectures having a large polar cavity. These approaches open the access to the design of ever more complex molecular objects beyond the chemistry of biomolecules.