Ce travail de thèse porte sur l’élaboration de microgels biocompatibles et multi-stimulables à base de méthacrylate d’oligo(éthylène glycol) et de nanoparticules d’oxyde de fer. Des microgels sensibles au pH, à la température et au champ magnétique ont été élaborés au cours de cette étude via une stratégie multi-étape partant de : 1. la synthèse et la caractérisation de microgels pH- et thermosensibles à base d’oligo(éthylène glycol), 2. l'élaboration de microgels hybrides par imprégnation de nanoparticules magnétiques au sein des microgels d’oligo(éthylène glycol). L’étude de la synthèse des microgels et de leurs propriétés physico-chimiques a permis de mettre en avant l’effet important de la structure interne des microgels sur leurs propriétés de gonflement/contraction. La caractérisation des microgels hybrides a mis en évidence l’importance des fonctions acide carboxylique réparties de manière homogène au sein des microgels, le tout permettant d’encapsuler efficacement et de manière homogène des nanoparticules magnétiques tout en préservant les propriétés colloïdales et thermo-stimulables des microgels hybrides. Enfin des films structurés constitués de multicouches de microgels ont ainsi pu être élaborés via un procédé simple de séchage de dispersion aqueuse de microgels. Une étude prospective des propriétés optique et mécanoélectrique de films auto-assemblés de microgels d’oligo(éthylène glycol) hybride et non hybride par évaporation de solvant a permis de mettre en évidence le rôle positif des groupements ioniques issus des fonctions carboxylates sur le potentiel électrique induit lors de la compression des films. / Smart polymer materials can provide wide range of options to induce advanced functional features and relevant surface properties in one material. This all-in-one concept is of great interest for applications that require several simultaneous treatments such as cosmetic application. Herein, we aim to develop oligo(ethylene glycol)-based biocompatible multiresponsive microgels that could both interact on the skin as smart drug delivery system (DDS) while fulfilling advanced properties such as surface protection, mechanical and optical properties. Specifically, aqueous dispersed microgels responsive to pH, temperature and magnetic field were synthesized via multi-step strategy: 1. The synthesis and characterization of pH- and thermo-responsive oligo(ethylene glycol)-based microgels by precipitation polymerization, 2. The encapsulation of pre-formed magnetic nanoparticles via adsorption of the nanoparticles into the multiresponsive microgels. The effect of the microgel microstructure on their pH- and thermo-responsive properties were highlighted thanks to a rational investigation of the crosslink density and acid-functional units distribution within the microgels. Oligo(ethylene glycol)-based microgels with homogeneous distribution of both acid-functional unit and crosslinker allowed the synthesis of highly pH-and thermo-responsive microgels. The hybrid microgels prepared by straightforward encapsulation of pre-formed magnetic nanoparticles were characterized. The homogeneous microstructure of the initial stimuli-responsive biocompatible microgels plays a crucial role for the design of unique well-defined ethylene glycol-based thermoresponsive hybrid microgels. Thus, robust monodisperse thermoresponsive magnetic microgels were produced, exhibiting both a constant value of the swelling-to-collapse transition temperature and good colloidal stability whatever the NPs content. These smart microgels can spontaneously form a transparent film with perfect arrangement of the microgels by simple solvent evaporation process. The characterization of the optical and mechanoelectrical properties of the self-assembled microgel films were performed. We highlighted that the presence of anionic charges inside the microgels emphasizes the mechanoelectrical effect of the films.

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.

La formation de biofilms bactériens pathogènes est un problème important, particulièrement dans les secteurs médicaux et agro-alimentaires. La formation contrôlée de biofilms de la bactérie probiotique Lactobacillus rhamnosus GG (LGG) est sélectionnée ici comme méthode potentielle pour prévenir la contamination de surfaces par des bactéries pathogènes. Nous avons étudié le développement de biofilms de LGG ainsi que leur possible contrôle en combinant des approches physico-chimiques et de fonctionnalisation de surface. L’impact des conditions environnementales sur la cinétique de croissance des biofilms et sur leur composition biochimique a été analysé par des mesures in situ et en temps réel par spectroscopie infrarouge à transformée de Fourier en réflexion totale atténuée (ATR-FTIR) sous conditions de flux. Ces données ont été complétées par des images de microscopie en épifluorescence permettant d’obtenir des informations sur la distribution et la forme des cellules bactériennes sur la surface à des étapes clé du développement du biofilm. Compatible avec les mesures ATR-FTIR, un cristal de séléniure de zinc a été choisi comme substrat, nu ou fonctionnalisé avec des monocouches auto-assemblées d’alcane-thiols (SAMs). Différents groupes fonctionnels ont été étudiés : méthyl (-CH3), hydroxyle (-OH) ou amine (-NH2) pour obtenir respectivement des substrats hydrophobe, hydrophile ou chargé positivement. La cinétique d’auto-assemblage des SAMs, leur organisation et l’énergie de surface ont été étudiées en combinant ATR-FTIR, spectroscopie de rétrodiffusion de Rutherford à hautes énergies et mesures d’angles de contact. L’analyse des spectres ATR-FTIR des biofilms de LGG enregistrés in situ et en temps réel pendant 24 heures a montré un rôle important du milieu nutritif sur la composition biochimique et le métabolisme bactériens. Les propriétés du substrat ont un impact faible sur la composition biochimique des biofilms, mais ont un rôle crucial sur leur force d’attachement à la surface. Ce travail pluridisciplinaire a fourni des informations sur l’influence de l’environnement, et particulièrement des caractéristiques du support, sur les propriétés des biofilms aux échelles moléculaire et cellulaire. La méthodologie développée dans ce travail peut notamment être utilisée dans la recherche des conditions les plus favorables à la croissance des biofilms de bactéries probiotiques. / Biofilm formation by pathogenic bacteria brings concerns, particularly in food and medical sectors, and is associated with high sanitary risks and economic losses. Biofilms of probiotic bacteria can potentially be used to prevent the surface contamination by pathogenic species. This work was focused on the investigation of the development of biofilms of probiotic Lactobacillus rhamnosus GG (LGG) and the possible control of their formation by combining surface functionalisation and physico-chemical approaches. The effect of different environmental conditions on the kinetics of the biofilm growth and on its biochemical composition was analysed by in situ and real time measurements with infrared spectroscopy in attenuated total reflection mode (ATR-FTIR) under flow conditions. These data were complemented by epifluorescence images providing information on the surface distribution and the shape of the bacterial cells at specific stages of the biofilm development. Compatible with ATR-FTIR measurements, a zinc selenide (ZnSe) crystal was chosen as a substrate, bare or functionalised with self-assembled monolayers (SAMs). SAMs were formed from alkanethiols terminated by methyl (-CH3), hydroxyl (-OH) or amine (-NH2) groups to obtain hydrophobic, hydrophilic and positively charged substrates, respectively. The kinetics of self-assembly of the alkanethiols onto ZnSe, the organisation of the molecules, their areal density and the surface energy of thus obtained surfaces were studied preliminarily to the biofilm cultivation by means of ATR-FTIR spectroscopy, high energy Rutherford backscattering spectrometry, and contact angle measurements. The analysis of the ATR-FTIR spectra of LGG biofilms recorded in situ and in real time during 24 hours revealed an important role of the nutritive medium in the biosynthesis of nucleic acids, phospholipids, polysaccharides and lactic acid. Substrate properties had low impact on the biochemical composition of LGG biofilms, but had a critical role in the strength of attachment of cultivated biofilms. The findings of this multidisciplinary work provide a fundamental understanding of how the direct environment, including a support surface, influences the properties of bacterial biofilms at the molecular and cellular scales, based on which favourable conditions for the enhancement of probiotic biofilm growth and its mechanical stability can be chosen.

PhD / SYNOPSIS OF THIS THESIS The aim of this thesis is to more fully understand and explain the binding mechanism of organic molecules to the Au(111) surface and to explore the conduction of such molecules. It consists of five discreet chapters connected to each other by the central theme of “The Single Molecule Device: Conductance and Binding”. There is a deliberate concentration on azine linkers, in particular those with a 1,10-phenanthroline-type bidentate configuration at each end. This linker unit is called a “molecular alligator clip” and is investigated as an alternative to the thiol linker unit more commonly used. Chapter 1 places the work in the broad context of Molecular Electronics and establishes the need for this research. In Chapter 2 the multiple break-junction technique (using a Scanning Tunnelling Microscope or similar device) was used to investigate the conductance of various molecules with azine linkers. A major finding of those experiments is that solvent interactions are a key factor in the conductance signal of particular molecules. Some solvents interfere with the molecule’s interaction with and attachment to the gold electrodes. One indicator of the degree of this interference is the extent of the enhancement or otherwise of the gold quantized conduction peak at 1.0 G0. Below 1.0 G0 a broad range for which the molecule enhances conduction indicates that solvent interactions contribute to a variety of structures which could bridge the electrodes, each with their own specific conductance value. The use of histograms with a Log10 scale for conductance proved useful for observing broad range features. vi Another factor which affects the conductance signal is the geometric alignment of the molecule (or the molecule-solvent structure) to the gold electrode, and the molecular alignment is explored in Chapters 3 for 1,10-phenanthroline (PHEN) and Chapter 4 for thiols. In Chapter 3 STM images, electrochemistry, and Density Functional Theory (DFT) are used to determine 1,10-phenanthroline (PHEN) structures on the Au(111) surface. It is established that PHEN binds in two modes, a physisorbed state and a chemisorbed state. The chemisorbed state is more stable and involves the extraction of gold from the bulk to form adatom-PHEN entities which are highly mobile on the gold surface. Surface pitting is viewed as evidential of the formation of the adatom-molecule entities. DFT calculations in this chapter were performed by Ante Bilic and Jeffery Reimers. The conclusions to Chapter 3 implicate the adatom as a binding mode of thiols to gold and this is explored in Chapter 4 by a timely review of nascent research in the field. The adatom motif is identified as the major binding structure for thiol terminated molecules to gold, using the explanation of surface pitting in Chapter 3 as major evidence and substantiated by emergent literature, both experimental and theoretical. Furthermore, the effect of this binding mode on conductance is explored and structures relevant to the break-junction experiment of Chapter 2 are identified and their conductance values compared. Finally, as a result of researching extensive reports of molecular conductance values, and having attempted the same, a simple method for predicting the conductance of single molecules is presented based upon the tunneling conductance formula.

<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>

Nanofabrication techniques were used to manufacture nanometer scale protein templates. The fabrication approach employs electron beam lithography (EBL) patterning on poly(ethylene glycol) (PEG) thiol (CH3O(CH2CH2O)17NHCO(CH2)2SH) self-assembled monolayers (SAM) on Au. The PEG SAM prevented protein surface adhesion and binding sites for protein were created in the SAM by EBL. Subsequent to EBL, the patterns in the PEG SAM were backfilled with 40-nm NeutrAvidin-coated fluorescent spheres (FluoSpheres). The spontaneous and directed immobilization of the spheres from a solution to the patterns resulted in high resolution protein patterns. The FluoSpheres could be arranged in any arbitrary pattern with ultimately only one or a few FluoSpheres at each binding site. Growth dynamics and SAM morphology of PEG on Au were studied by atomic force microscopy (AFM). PEG SAMs on three types of Au with different microstructure were examined: thermally evaporated granular Au and two types of Au films produced by hydrogen flame annealing of granular Au, Au(111) and "terraced" Au (crystal orientation unknown). The different Au surfaces' substructure affected the morphology and mechanical properties of the PEG SAM. On Au(111), AFM imaging revealed monolayer formation through three distinct steps: island nucleation, island growth, and coalescence. The fine-structure of the SAM revealed dendritic island formation - an observation which can be explained by attractive intermolecular interactions and diffusion-limited aggregation. Island growth was not observed on the "terraced" Au. AFM studies of EBL patterned PEG SAMs on Au(111) revealed two different patterning mechanisms. At low doses, the pattern formation occurs by SAM ablation in a self-developing process where the feature depth is directly dose dependent. At higher doses electron beam induced deposition of material, so-called contamination writing, is seen in the ablated areas of the SAM. The balance between these two mechanisms is shown to depend on the geometry of the pattern. In addition to PEG SAMs, fibronectin monolayers on SiO2 surfaces were patterned by EBL. The areas exposed with EBL lose their functionality and do not bind anti-fibronectin. With this approach we constructed fibronectin templates and used them for cell studies demonstrating pattern dependent cell geometries and cell adhesion. / QC 20101008

A novel cyclopentadienylruthenium(II) thiolato Schiff base, [Ru(SC6H4NC(H)C6H4OCH2CH2SMe)(&eta / 5-C2H5]2 was synthesized and deposited as a selfassembled monolayer (SAM) on a gold electrode. Effective electronic communication between the Ru(II) centers and the gold electrode was established by electrostatically cycling the Shiff base-doped gold electrode in 0.1 M NaOH from -200 mV to +600 mV. The SAMmodified gold electrode (Au/SAM) exhibited quasi-reversible electrochemistry. The integrity of this electro-catalytic SAM, with respect to its ability to block and electro-catalyze certain Faradaic processes, was interrogated using Cyclic and Osteryoung Square Wave voltammetric experiments. The formal potential, E0', varied with pH to give a slope of about - 34 mV pH-1. The surface concentration, &Gamma / , of the ruthenium redox centers was found to be 1.591 x 10-11 mol cm-2. By electrostatically doping the Au/SAM/Horseradish peroxidase at an applied potential of +700 mV vs Ag/AgCl, a biosensor was produced for the amperometric analysis of hydrogen peroxide, cumene hydroperoxide and tert-butylhydroperoxide. The electrocatalytic-type biosensors displayed typical Michaelis-Menten kinetics with their limits of detection of 6.45 &mu / M, 6.92 &mu / M and 7.01 &mu / M for hydrogen peroxide, cumene hydroperoxide and tert-butylhydroperoxide respectively.

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.