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.

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.

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.

Ce travail visait à explorer les interactions supramoléculaires comme un outil dans les domaines de la chimie hôte-invité, les nanomatériaux et les nanotechnologies en général, afin de parvenir à des objectifs différents. D'abord, une interaction classique hôte-invité a été étudiée, au moyen d'une technique innovante telle que l'ITC, puis nous avons exploité les interactions supramoléculaires afin de maitriser la production de graphène exfolié en phase liquide, en mettant un accent particulier sur l'amélioration de la qualité et la quantité du matériau produit. Enfin, nous avons étendu l'utilisation de la chimie supramoléculaire à un dispositif réel par la fonctionnalisation des électrodes d'or avec des molécules photochromiques, ouvrant alors la voie à des dispositifs organiques multifonctionnels, pouvant être contrôlés par la lumière. / This work was aimed at exploring supramolecular interactions as a tool in the fields of host-guest chemistry, nanomaterials and in general nanotechnology, in order to achieve different goals. First, a classical host-guest interaction was studied by means of the ITC technique, then we exploited supramolecular interactions in order to harness the production of liquid-phase exfoliated graphene, with a particular focus on improving the quality and quantity of material produced. Finally, we extended the use of supramolecular chemistry to a real device by functionalization of gold electrodes with photochromic molecules, hence paving the way towards multifunctional organic devices and in prospective to graphene based light-controlled multifunctional devices.

<p>The study and understanding of molecular interactions is fundamentally important in today's field of life sciences and there is a demand for well designed surfaces for biosensor applications. The biosensor has to be able to detect specific molecular interactions, while non-specific binding of other substances to the sensor surface should be kept to a minimum.                                                                                                                                                                                The objective of this master´s thesis was to design sensor surfaces based on self-assembled monolayers (SAMs) and evaluate their structural characteristics as well as their performance in Biacore systems. By mixing different oligo (ethylene glycol) terminated thiol compounds in the SAMs, the density of functional groups for bimolecular attachment could be controlled.  Structural characteristics of the SAMs were studied using Ellipsometry, Contact Angle Goniometry, IRAS and XPS. Surfaces showing promising results were examined further with Surface Plasmon Resonance in Biacore instruments.<p>Mixed SAM surfaces with a tailored degree of functional COOH groups could be prepared. The surfaces showed promising characteristics in terms of stability, immobilization capacity of biomolecules, non-specific binding and kinetic assay performance, while further work needs to be dedicated to the improvement of their storage stability. In conclusion, the SAM based sensor surfaces studied in this thesis are interesting candidates for Biacore applications.</p></p>

<p>The work described in this thesis aims to achieving surface patterning through chemical activation of thiolated silicon oxide surfaces, resulting in a spatially controlled covalent immobilization of biomolecules with high resolution.</p><p>Existing chemical methods to immobilize molecules on surfaces do not reach below the micrometer scale while the ones allowing for spatial control mostly lead to non-covalent adsorption of molecules on surfaces, or require several successive chemical reactions to obtain the final covalent immobilization. Methods with improved chemical processes and novel surface modification techniques had to be developed. </p><p>A basic need for studying interactions of biomolecules on chemically modified surfaces with high resolution is the ability to obtain a simple, inexpensive method resulting in ultraflat densely packed and reproducible organic monolayers. Therefore, a new method for silicon oxide chemical derivatization, fulfilling these requirements, was developed. </p><p>Thiol derivatized silicon oxide surfaces allow for a diversity of activation reactions to occur, resulting in thiol-disulfide exchange. The electrooxidation of surface-bound thiol groups was investigated as a way of generating reactive thiolsulfinates/thiolsulfonates, by application of a positive potential difference to the silicon surfaces. Peptide molecules containing thiol groups were successfully immobilized to the electroactivated surfaces. In addition, this new chemical activation method offers the possibility to release the bound molecules in order to regenerate the surfaces. Subsequently, the thiolated surfaces can be reactivated for further use.</p><p>Since the activated area depends directly on the size of the electrodes used for the oxidation, nanoscale activation of the thiolated surfaces was performed by use of an AFM tip as counter-electrode. Electrooxidized patterns, with a line width ranging from 70 nm to 200 nm, were obtained. A thiol-rich protein, b-galactosidase, was selectively immobilized onto the electroactivated patterns.</p><p>An electrochemical version of microcontact printing was developed in order to activate large surface areas with micrometer scale patterns. Conductive soft polymer stamps were produced using an evaporated aluminum coating. Patterned electroactivation of thiols was achieved, and polystyrene beads were subsequently specifically immobilized onto the patterns.</p><p>As a conclusion, these different projects resulted in a strategy enabling the achievement of nanoscale and microscale positioning and immobilization of biomolecules on silicon surfaces, with potential reversibility and reuse of the surfaces.</p>

The work described in this thesis aims to achieving surface patterning through chemical activation of thiolated silicon oxide surfaces, resulting in a spatially controlled covalent immobilization of biomolecules with high resolution. Existing chemical methods to immobilize molecules on surfaces do not reach below the micrometer scale while the ones allowing for spatial control mostly lead to non-covalent adsorption of molecules on surfaces, or require several successive chemical reactions to obtain the final covalent immobilization. Methods with improved chemical processes and novel surface modification techniques had to be developed. A basic need for studying interactions of biomolecules on chemically modified surfaces with high resolution is the ability to obtain a simple, inexpensive method resulting in ultraflat densely packed and reproducible organic monolayers. Therefore, a new method for silicon oxide chemical derivatization, fulfilling these requirements, was developed. Thiol derivatized silicon oxide surfaces allow for a diversity of activation reactions to occur, resulting in thiol-disulfide exchange. The electrooxidation of surface-bound thiol groups was investigated as a way of generating reactive thiolsulfinates/thiolsulfonates, by application of a positive potential difference to the silicon surfaces. Peptide molecules containing thiol groups were successfully immobilized to the electroactivated surfaces. In addition, this new chemical activation method offers the possibility to release the bound molecules in order to regenerate the surfaces. Subsequently, the thiolated surfaces can be reactivated for further use. Since the activated area depends directly on the size of the electrodes used for the oxidation, nanoscale activation of the thiolated surfaces was performed by use of an AFM tip as counter-electrode. Electrooxidized patterns, with a line width ranging from 70 nm to 200 nm, were obtained. A thiol-rich protein, b-galactosidase, was selectively immobilized onto the electroactivated patterns. An electrochemical version of microcontact printing was developed in order to activate large surface areas with micrometer scale patterns. Conductive soft polymer stamps were produced using an evaporated aluminum coating. Patterned electroactivation of thiols was achieved, and polystyrene beads were subsequently specifically immobilized onto the patterns. As a conclusion, these different projects resulted in a strategy enabling the achievement of nanoscale and microscale positioning and immobilization of biomolecules on silicon surfaces, with potential reversibility and reuse of the surfaces.

The study and understanding of molecular interactions is fundamentally important in today's field of life sciences and there is a demand for well designed surfaces for biosensor applications. The biosensor has to be able to detect specific molecular interactions, while non-specific binding of other substances to the sensor surface should be kept to a minimum.                                                                                                                                                                                The objective of this master´s thesis was to design sensor surfaces based on self-assembled monolayers (SAMs) and evaluate their structural characteristics as well as their performance in Biacore systems. By mixing different oligo (ethylene glycol) terminated thiol compounds in the SAMs, the density of functional groups for bimolecular attachment could be controlled.  Structural characteristics of the SAMs were studied using Ellipsometry, Contact Angle Goniometry, IRAS and XPS. Surfaces showing promising results were examined further with Surface Plasmon Resonance in Biacore instruments.Mixed SAM surfaces with a tailored degree of functional COOH groups could be prepared. The surfaces showed promising characteristics in terms of stability, immobilization capacity of biomolecules, non-specific binding and kinetic assay performance, while further work needs to be dedicated to the improvement of their storage stability. In conclusion, the SAM based sensor surfaces studied in this thesis are interesting candidates for Biacore applications.

This thesis details the development of expertise and tools required for the study of amino acids deposited on Au(111), with a primary focus on the design and testing of a Knudsen cell for controlled deposition of L-cysteine and L-methionine. An ultra-high vacuum preparation chamber designed by Dr. Katie Mitchell and built by Torrovap Industries Inc. was installed. This chamber is connected to the existing scanning tunneling microscopy chamber via a gate valve, and both chambers can operate independently. Various instruments such as a mass spectrometer, quartz crystal microbalance, ion source, and sample manipulator were installed on the preparation chamber. Scanning tunneling microscopy was performed on both homemade and commercial Au(111) thin films. High resolution images of "herringbone" reconstruction and individual atoms were obtained on the commercial thin films, and optimal tunneling conditions were determined. A Knudsen cell was designed to be mounted on the preparation chamber. The Knudsen cell operates over the temperature range 300-400K, with temperatures reproducible to ±0.5K, and stable to ±0.1K over a five minute period. Reproducible deposition rates of less than 0.2Ǻ/s were obtained for both L-cysteine and L-methionine. Electron impact mass spectrometry and heat of sublimation measurements were performed to characterize the effusion of L-cysteine and L-methionine from the Knudsen cell. The mass spectrometry results suggest that L-cysteine was decomposing at 403K while L-methionine was stable during effusion. Heats of sublimation of 168.3±33.2kJ/mol and 156.5±10.1kJ/mol were obtained for L-cysteine and L-methionine respectively.

One the most daunting technical challenges in the realization of biosensors is functionalizing transducing surfaces for the detection of biomolecules. Functionalization is defined as the formation of a bio-compatible interface on the transducing surfaces of bio-chemical sensors for immobilizing and subsequent sensing of biomolecules. The kinetics of functionalization reactions is a particularly important issue, since conventional functionalization protocols are associated with lengthy process times, from hours to days. The objective of this thesis is the improvement of the functionalization protocols and their kinetics for biosensing applications. This objective is realized via modeling and experimental verification of novel functionalization techniques in microfluidic environments. The improved functionalization protocols using microfluidic environments enable in-situ functionalization, which reduces the processing times and the amount of reagents consumed, compared to conventional methods. The functionalization is performed using self-assembled monolayers (SAMs) of thiols. The thiols are organic compounds with a sulphur group that assists in the chemisorption of the thiol to the surface of metals like gold. The two reactions in the functionalization process examined in this thesis are the SAM formation and the SAM/probe molecule conjugation. SAM/probe molecule conjugation is the chemical treatment of the SAM followed by the binding of the probe molecule to the SAM. In general, the probe molecule is selective in binding with a given biomolecule, called the target molecule. Within this thesis, the probe molecule is an antibody and the target molecule is an antigen. The kinetics of the reaction between the probe (antibody) and the target biomolecule (antigen) is also studied. The reaction between an antigen and its antibody is called the immunoreaction. The biosensing technique that utilizes the immunoreaction is immunoassay. A numerical model is constructed using the finite element method (FEM), and is used to study the kinetics of the functionalization reactions. The aim of the kinetic studies is to achieve both minimal process times and reagents consumption. The impact of several important parameters on the kinetics of the reactions is investigated, and the trends observed are explained using kinetic descriptive dimensionless numbers, such as the Damköhler number and the Peclet number. Careful numerical modeling of the reactions contributes to a number of findings. A considerably faster than conventional SAM formation protocol is predicted. This fast-SAM protocol is capable of reducing the process times from the conventional 24-hours to 15 minutes. The numerical simulations also predict that conventional conjugation protocols result in the overexposure of the SAM and the probe molecule to the conjugation reagents. This overexposure consequently lowers conjugation efficiencies. The immunoreaction kinetics of a 70 kilo-Dalton heat shock protein (HSP70) with its antibody in a hypothetical microchannel is also investigated through the FEM simulations. Optimal reaction conditions are determined, including the flow velocity and the surface concentration of the immobilized probes (antibodies). Based on the numerical results and a series of experimental studies, the fast-SAM protocol application is successfully confirmed. Moreover, the optimum reagent concentration for a given one- hour conjugation process time is determined. This functionalization protocol is successfully applied to immobilize the HSP70 antibody on gold surfaces. The use of the fast-SAM protocol and the predicted optimum conjugation conditions result in binding of the HSP70 antibody on gold, with the same or superior immobilization quality, compared to the conventional protocols. Upon implementation of a 70 μm.s^(-1) flow velocity, the reaction is observed to complete in around 30-35 minutes, which is close to the numerically predicted 30 minutes and 16 seconds. This immunoreaction time is considerably less than conventional 4-12 hour processes. The modified in-situ functionalization techniques achieved here are promising for substantially reducing the preparation times and improving the performance of biosensors, in general, and immunoassays, in particular.