This dissertation focused on the applications of self-assembled monolayers (SAMs) technique for the investigation of molecule based electronics, plasmon coupling between CdSe quantum dots and metal nanoparticles (MNPs), and copper ion detection using enhanced emission of CdSe quantum dots (QDs). The SAMs technique provides an approach to establish a robust, two-dimensional and densely packed structure which can be formed on metal or semiconductor surfaces. This allows for the design of molecular assemblies that can be used to understand the details of molecular conduction by employing various electrical testbeds. In this work, the strategy of molecular assemblies was used to pattern metal nanoparticles on GaAs surfaces, thereby furnishing a platform to explore the interactions between QDs and MNPs. The enhanced emission of CdSe QDs by MNPs was then used as a probe for ultrasensitive, cheap, and rapid copper(II) detection. The study is divided into three main facets. The first one aimed at controlling electron transport behavior through porphyrins on surfaces with an eye toward optoelectronic and light harvesting applications. The binding of the porphyrin molecules to Au surfaces, pre-covered with a dodecanethiol matrix, was characterized by FTIR, XPS, AFM, STM, of. This study has shown that the perfluoro coupling group between the porphyrin macrocycle and the thiol tether may provide a means of controlling the tunneling behavior. The second area of this study focused on the design of a simple platform to examine the coupling between metal nanostructures and quantum dot assemblies. Here we demonstrate that by using a patterned array of Au or Ag nanoparticles on GaAs, plasmon enhanced photoluminescence (PL) can be directly measured and quantified by direct scaling of regions with and without metal nanostructures. The third field presented a simple manner for using the enhanced PL of CdSe QDs as a probe for ultrasensitive Cu2+ ion detection and quantitative analysis. The PL of QDs was enhanced by two processes: first, photobrightening of the material, and second, plasmonic enhancement by coupling with Ag nanoprisms. This strong PL leads to a high sensitivity of the QDs over a wide dynamic range for Cu2+ detection, as Cu2+ efficiently quenches the QD emission.

Two-dimensional materials such as self-assembled monolayers (SAMs), graphene, etc. are candidate materials for improving the performance of microelectronics components and MEMS/NEMS devices. In view of their relatively large in-plane dimensions, surface forces are likely to dominate their behavior. The purpose of the current work was to extract not only the adhesion energy (or steady state fracture toughness) but also the traction-separation relation associated with interactions between various two-dimensional materials and substrates. In particular, interactions between SAMs terminated by carboxyl and diamine (COOH/NMe2) groups, hydroxylated silicon surfaces, graphene and silicon, graphene and its seed copper and graphene and epoxy over large areas was considered. Traction-separation relations, which are a continuum description of such molecular interactions, were determined by a direct method, which makes use of measurements of crack tip opening displacements; an inverse approach where the key parameters are extracted by comparing measured global parameters with finite element solutions and a hybrid approach in which the direct method was supplemented by finite element analysis. Furthermore, the surface free energy of graphene was measured by contact angle measurements. The most striking observation across all the interactions that were considered is that the interaction ranges were much larger than those attributed to van der Waals forces. While van der Waals models might have been at play between graphene and its seed copper foil and graphene and epoxy, the adhesion energies were surprisingly high. This coupled with the long interaction range suggests that roughness effects modulated the basic force field. Interactions between graphene and silicon and hydroxylated silicon surfaces may have been due to capillary and/or electrostatic again possibly modulated by roughness. The interactions between COOH and NMe2 SAMs became stronger under vacuum, which may have induced chemical bonding, and tougher under mixed-mode loading. / text

Self-assembled monolayers (SAMs) of organosulfur precursors on gold have been extensively used since they offer a wide range of technological applications such as corrosion inhibition, lubrication, adhesion promotion/inhibition, nanofabrication, chemical and biosensors, catalysis, and molecular electronics. Furthermore, the electronic and optical properties of aromatic SAMs make them a potential candidate for molecular electronics. However, these practical applications are limited by the short-range ordering, low packing density, irreproducibility, and inferior quality of SAMs, which are more critical for aromatic SAMs. Therefore, the discovery of alternative precursors is essential. This thesis reports for the first time, the use of organic sulfenyl chlorides as precursors for the modification of gold surfaces. These precursors may help to overcome some practical limitations of the traditional organosulfur precursors. The modification is done in a non-aqueous medium. Characterization of the modified surfaces is performed by X-ray photoelectron spectroscopy (XPS), cyclic voltammetry (CV), polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS), and scanning tunnelling microscopy (STM). Through the use of 4-nitrophenyl sulfenyl chloride, evidence for the formation of well-ordered aromatic SAMs formation on gold is provided. XPS data shows that the modification involves the scission of the S-Cl bond. PM-IRRAS studies further indicate that the adsorbed molecules are nearly vertically oriented on the surface. Both short and long-range well-ordered aromatic SAMs (a 4 x √3 rectangular and √3 x √3 hexagonal unit cells) are obtained from the STM images using two different modification conditions. This molecular density is usually only observed for aliphatic SAMs using the traditional precursors. Along with the main hexagonal lattice, the reversible distinct superstructures including hexagons, partial hexagons, parallelograms, and zigzags resulting from specific arrangements of adsorbed molecules provide submolecular details. This is the first direct experimental example, where the STM has shown its effectiveness to provide physical structure information of standing-up aromatic SAMs at room temperature. This work also provides some insight into a heavily debated issue regarding the origin of the various features and contrasts obtained in STM images of SAMs. The use of 2-nitrophenyl sulfenyl chloride and 2,4-dinitrophenyl sulfenyl chloride for the formation of aromatic SAMs on Au provides some insight regarding the modification extent and the effect of a nitro substituent (at ortho position ) on the quality of nitrophenyl thiolate SAMs on gold. XPS, PM-IRRAS, electrochemistry and STM provide evidence for the formation of less ordered, low density and less stable SAMs that may decompose to sulfur at longer modification times. The efficient deposition of sulfur on gold is observed using a series of substituted methane sulfenyl chlorides (triphenylmethane sulfenyl chloride, trichloromethane sulfenyl chloride and chlorocarbonyl sulfenyl chloride). The XPS, STM and electrochemical data show the formation of high density sulfur phases. These include rhombus, rectangular, and zig-zag sulfur structures. A mechanism is suggested involving the cleavage of the S-Cl bond and the ejection of the molecular backbone. This study also suggests that substituted methane sulfenyl chlorides do not form long-range ordered SAMs.

This thesis outlines a study of the physical changes that hybridisation imposes on single-stranded DNA (ssDNA) immobilised by one end to a substrate, and of how such physical changes can be exploited to detect specific sequences of DNA in a target solution. The system studied was composed of a mixed monolayer of 20mer ssDNA with C6 alkanethiolate modifications on their 3??? ends and short-chain hydroxyterminated alkanethiolates, on a gold substrate. It was prepared using the self-assembly properties of alkanethiols on gold. Atomic force microscopy images showed that the end-immobilised ssDNA is flexible enough to lie over the diluent hydroxy-terminated self-assembled monolayer (SAM). Hybridisation was shown to cause the DNA to become more rigid and stand up off the substrate due to an increase in persistence length. Such physical changes of the DNA upon hybridisation were significant enough to be exploited in the development of a DNA recognition interface. The recognition interface was designed with the view of keeping it both simple to make and simple to use, and was coupled with electrochemical transduction. A label-free recognition interface was developed that relied on the oxidation of the sulfur head group of the alkanethiolate SAM to detect hybridisation (firstly air oxidation and then electrochemical oxidation). It produced a positive signal upon hybridisation with complementary target DNA. Improvements in the reliability and robustness of the recognition interface were made using a labelled approach. The labelled version employed electroactive molecules as labels on the 5??? ends of the probe DNA strands. Two labels were investigated ??? anthraquinone and ferrocene. The flexibility of the ssDNA ensured that the redox labels were able to directly access the underlying gold electrode. Hybridisation was expected to remove the labels from the electrode due to an increase in the DNA???s persistence length, and thus perturb the electrochemical signal. The use of ferrocene as a label provided a ???proof-of-concept??? for the system. The labelled recognition interface provides a foundation for the future development of a simple, reliable, and selective DNA hybridisation biosensor.

Absorption of octadecanethiol and p-nitrobenzenethiol onto gold surfaces from ethanol solutions has been studied by means of contact angle, optical ellipsometry, angle-resolved XPS (ARXPS), and with grazing angle total reflection FTIR. Growth of the monolayers from dilute solutions has been monitored and Langmuir isotherm adsorption curves were fitted to experimental data. A saturated film is formed within approximately 5h after immersion in solutions of concentrations ranging from 0.0005mM to 0.01mM. We found, that the final density of monolayer depends on the concentration of the solution.

Interactions of gas-phase molecules with surfaces are important in many ordinary events, such as ozone depletion, corrosion of metals, and heterogeneous catalysis. These processes are controlled by the bonding, diffusion, and reactivity of the impinging gas species. Our research employs molecular beam techniques and well-characterized surfaces to study these processes. The goal of this study is to better understand how the physical and chemical nature of the surface interface influences energy transfer dynamics in gas-surface collisions. An atomic beam is used to probe the energy transfer dynamics in collisions of Argon with model surfaces of functionalized self-assembled monolayers (SAMs) (1-dodecanethiol and 11-mercapto-1-undecanol) on gold. The beam is directed towards the surface at an incident angle of 30 degrees and the scattered Ar atoms are detected at the specular angle of 30 degrees. Time-of-flight scans measure the velocity distributions of atoms leaving the surface, which correlate with the energy transfer dynamics of the impinging gas atoms. Gas-surface energy transfer experiments are accomplished by directing an 80 kJ/mol Ar atomic beam at a clean Au(111) surface and surfaces composed of hydroxyl-terminated or methyl-terminated SAMs on Au(111). The fractional energy transferred to the bare gold surface is 69 %, while it is grater than 77 % for the monolayer-covered surfaces. The extent of thermalization on the surface during the collision is significantly greater for the methyl-terminated surface than for the hydroxyl-terminated surface. Since the two monolayers are similar in structure, packing density, and mass, the differences in scattering dynamics are likely due to a combination of factors that may include differences in the available energy modes between the two terminal groups and the hydrogen-bonding nature of the hydroxyl-terminated SAM. / Master of Science

4-(12-mercaptododecyloxy)phenol (1), 3-(12-mercaptododecyloxy)phenol (2), 4-(12-mercaptododecyl)phenol (3), 4-(12-mercapto-dodecyl)phenol (4), 12-phenyldodecyl-mercaptan (5), 12-phenylundecyoxymercaptan (6), 4-(6-mercapto-hexyl)phenol (7), and 4-(12-mercaptododecyloxy)phenol (8) were synthesized. The thiol products were characterized by NMR, HRMS, and elemental analysis. Self-assembled monolayers (SAMs) on gold substrates were prepared from thiols 1-8, and the resulting monolayer surfaces were analyzed using Reflectance Absorbance Infrared Spectroscopy (RAIRS), contact angle goniometry, ellipsometry, reductive desorption cyclic voltametry, and impedance spectroscopy. Several aromatic C-C vibrational frequencies in the RAIRS spectra, for SAMs of 1-8, reveal a dependence of peak intensity on substitution regiochemistry of the aromatic ring. This result suggests that the orientation of the aromatic ring changes with substitution. Peak intensity, and peak widths of alkyl C-H vibrational features in the RAIRS spectra also reveal a dependence of the environment of the alkyl chain on structure of thiols 1-8. Meta-substitution seems to significantly alter the projection of the terminal -OH group relative to para-substitution. Contact angles were obtained for each SAM surface using water, glycerol, and ethylene glycol. From the contact angle data, Zisman and Fowkes analyses were performed in order to determine surface free energy values and also to determine the dispersive contribution to the surface energy. The energy values obtained from the Zisman plots as well as the dispersive contributions obtained from the Fowkes plots suggest a dependence of surface energy on substitution regiochemistry of the aromatic ring. The results are consistent with the interpretation of the RAIRS spectra as they relate to the effect substitution regiochemistry has on SAM structure and interfacial properties. The results of the reductive desorption measurements performed on each monolayer surface, indicate that changes in substitution regiochemistry do not seem to affect the surface coverage of SAMs 1-8. Desorption potentials however, are affected by the structure of the thiols composing the SAM, which suggests that the lateral stability resulting from interactions of the terminal groups and alkyl chains, is different for each monolayer surface. Specifically SAMs of 12-phenyldodecylmercaptan (5) and SAMs of 4-(12-mercaptododecyloxy)phenol (1) seem to be more stable due to interactions of the terminal aromatic ring in SAMs of (5) and due to an increase in van der Waals interactions in SAMs of (1). Film thicknesses, as determined by ellipsometry, also suggest that meta-substitution of the aromatic ring results in lower thicknesses for SAMs of (4), which is consistent with the interpretation of the structural changes resulting from meta-substitution, suggested by the interpretation of the RAIRS spectrum of SAMs of (4). Thickness measurements also indicate that most of the functionalized SAMs (1-4, 7, 8) react with OTS, which suggests the terminal -OH group is not shielded at the interface and is available for reaction. Following reaction with OTS the RAIRS spectra of the reacted surfaces reveal structural changes to the underlying SAM. Impedance spectroscopic measurements performed on SAMs of 1-8 reveal what seems to be a correlation between the orientation of the aromatic ring and the resistance properties of the SAM. It appears meta-substitution of the ring lowers the monolayers ability to resist electron transfer. These data suggest that meta-substitution of the aromatic ring has a significant impact upon the structure of the resulting monolayer relative to monolayers composed of para-substituted molecules. The data also suggests that there is a correlation between molecular structure and interfacial properties particularly as it relates to surface energy and reactivity. Small atomic changes in the molecules composing the SAM result in measurable differences in macroscopic properties of the interface. It is important to recognize the need for understanding structure-property relationships in self-assembled monolayers particularly if logical design of surfaces is to be achieved and applied towards solving problems associated with corrosion and adhesion of metal surfaces. / Ph. D.

Lors de la mise au point de biocapteurs, le contrôle de l'état de surface sur laquelle sontimmobilisées les biomolécules est un paramètre crucial pour la fiabilité et la reproductibilité desmesures. Pour ce travail de Thèse, deux objectifs principaux ont été fixés :- obtenir de façon reproductible des films organiques fonctionnels capables de rendre lessurfaces inorganiques biocompatibles afin d'immobiliser des biomolécules sans les dénaturer.- se doter d'outils innovants afin d'analyser la distribution de biomolécules sur la surface etd'évaluer leur activité biologique à l'échelle de la molécule unique.L'immobilisation a été réalisée sur des SAMs terminées par une fonction acide carboxylique.Pour imager les surfaces nous avons choisi la Microscopie Atomique de Force (AFM) qui permetd'obtenir des informations à l'échelle nanométrique et de mesurer des interactions moléculaires del'ordre du piconewton (10-12 N).Des CNTs, générés par dépôt chimique en phase vapeur, sont fixés sur une pointe AFM. Puis Ilssont biofonctionnalisés selon un protocole de trempage original afin d'obtenir une modificationchimique sélective de leur apex. Les interactions entre un récepteur, immobilisé sur la surface, et sonligand, lié de façon covalente au CNT, sont mesurées à l'échelle de la molécule unique. / During the development of biosensors, control of the surface on which the biomolecules areimmobilized is a crucial parameter for the reliability and reproducibility of the measurements. For thisPhD work, two main objectives were set:- obtain in a reproducible way functional organic films able to make inorganic surfacebiocompatible for the immobilization of biomolecules without any denaturation.- develop innovative tools in order to analyze the distribution of biomolecules on the surface etevaluate their biological activity at single molecule scaleThe immobilization step was done on SAMs terminated by a carboxylic acid function.In order to image surfaces, Atomic Force Microscopy (AFM) was chosen. This technique permits toobtain information at nanometric scale and to measure molecular interactions in the range ofpiconewton forces (10-12 N).MWCNTs were linked to a commercial AFM tip by micro-welding under optical microscopy. CNTswere biofunctionalized at the nanotube apex by an original dipping procedure.The interactions between a ligand, immobilized on the surface, and a receptor covalently linked to aCNT have been characterized.

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.

Les cryptophanes sont des molécules sphériques pouvant encapsuler dans leur cavité lipophile des molécules neutres (halogénométhanes, xénon) mais aussi des espèces ioniques comme les cations césium et thallium. Notre objectif a été d’immobiliser ces cages moléculaires de manière covalente sur un support solide dans le but de créer un matériau capable d’extraire des cations toxiques comme le thallium en milieu aqueux. Différentes stratégies ont été envisagées pour optimiser l’immobilisation de dérivés du cryptophane-A sur des surfaces de silice et d’or (surfaces planes et nanoparticules magnétiques de type coeur-écorce). Les cryptophanes-A mono-acide (1) et hexa-acide(2) ont été immobilisés sur des surfaces de silice préalablement fonctionnalisées par des groupements amines. Le cryptophane-A alcanethiol (3), ainsi que les cryptophanes 1 et 2 modifiés par lacystéamine (respectivement 4 et 5) ont été immobilisés sur des surfaces d’or. La caractérisation des surfaces planes par spectroscopie infrarouge de réflexion-absorption par modulation de polarisation(PM-IRRAS) a permis d’estimer le taux de recouvrement des différentes monocouches de cryptophanes et, ainsi, d’évaluer la méthode d’immobilisation la plus efficace. Un taux de recouvrement proche de 100% a été obtenu pour le cryptophanes 3 immobilisé sur les surfaces d’or.Ce composé a également été immobilisé de façon très efficace sur des nanoparticules magnétiques(γ-Fe2O3/SiO2) enrobées d’une nano-écorce d’or. Ces résultats permettent d’envisager la synthèse d’un cryptophane portant cinq fonctions hydroxyles et une fonction thiol afin de créer des matériaux capables d’extraire des cations toxiques. / Cryptophanes are spherical molecules that can encapsulate neutral molecules(halogenomethanes, xenon), and ionic species like cesium and thallium cations in their lipophiliccavity. Our objective was to covalently immobilize these molecular cages onto solid substrates tocreate a material able to extract toxic cations such as thallium in aqueous media. Different strategieswere considered to optimize the immobilization of cryptophane-A derivatives onto silica and goldsurfaces (flat surfaces and core-shell magnetic nanoparticles). Mono-acid cryptophane-A (1) andhexa-acid cryptophane-A (2) were immobilized onto silica surfaces that were functionalized by aminogroups beforehand. Alcanethiols cryptophane-A (3), 1 and 2 modified by cysteamine (cryptophanes 4and 5 ,respectively) were immobilized onto gold surfaces. Flat surfaces were characterized bypolarization modulation infrared reflection-absorption spectroscopy (PM-IRRAS) to estimate thesurface coverage of different cryptophane monolayers and to evaluate the most effective method. Asurface coverage close to 100% was obtained for the cryptophane 3 immobilized onto gold surfaces.This compound has been also immobilized efficiently onto magnetic nanoparticles (γ-Fe2O3/SiO2)coated with gold nano-shell. These results allow to consider the synthesis of cryptophane bearing fivehydroxyl and one thiol functions to create materials able to extract toxic cations