<p>The first part of this study details the formation and characterization of octadecanethiol (ODT) self-assembled monolayers (SAMs) on GaAs (100) substrates from solution and vapor phases. The liquid-phase-deposited monolayers were prepared by immersing the substrate in an ethanolic solution, while vapor-deposited monolayers were prepared by the vapor phase transport of ODT in an ultrahigh vacuum (UHV) environment. The structural and optical properties of the resulting SAMs were examined with contact angle (CA) analysis, photoluminescence (PL) spectroscopy, atomic force microscopy (AFM), high-resolution x-ray photoelectron spectroscopy (HRXPS), and spectroscopic ellipsometry. Although well-ordered films were formed by both preparation routes, PL, AFM, CA analysis, HRXPS, and ellipsometry measurements revealed that the overall quality, structure, and durability of the mono layers depend on the deposition technique. Collectively, the results suggested that more robust monolayers exhibiting greater surface coverage and therefore, increased passivation and stability characteristics are assembled from vapor phase. </P> <P> The second part of this work describes the development of a hybrid GaAsaptamer biosensor for the label-free detection of analytes. The implemented sensmg strategy relies on the use of functional alkanethiol SAMs as biorecognition elements as well as the sensitivity of the GaAs PL emission to the local environment at its surface. Specifically, GaAs substrates were modified with thiol-derivatized aptamers and exposed to the target biomolecules. The resulting modification in the PL intensity is attributed to a specific aptamer-target biorecognition interaction and the accompanying ligand-induced structural change in the aptamer conformation. Modeling the performance data by means of Poisson-Boltzmann statistics in combination with the dead layer model indicates a good correlation between the structural conformation of the aptamers and the GaAs PL yield. The results demonstrate the potential of the prospective luminescence-based GaAs-SAM biosensor in real-time sensing assays requiring a simple and effective means of direct analytical detection. </p> / Thesis / Doctor of Philosophy (PhD)

The preparation and spectroscopic characterizations of size-controlled Pyridine-functionalized gold clusters formed self-assembled 2D superlattices with hexagonal packing were studied. The characterizations of pyridine-modified Au clusters using TEM, UV-vis, NMR and ESCA techniques are also reported. Pyridine-functionalized monolayer-protected Au clusters (MPCs) were prepared as illustrated in Scheme 1. The gold nanoparticles prepared by the reduction with NaBH4 have 3.2 ¡Ó 0.88 nm average core diameters established by TEM. The ~3 nm particles were used to induce size and shap evolution with heating treatment in toluene or in TOABr (tetraoctylammonium bromide). The pyridine-functionalized MPCs exhibit an identifiable plasmon resonance band at ~515 nm. The confirmation of the functionalization of pyridyl octanethiol in Au MPCs came from the downfield NMR resonances in the region of 120-150 ppm, which were established the resonances of the Py moiety.

We examine the electrochemical properties of SAM of alkanethiols terminated with biferrocenyl group (complex 7) to understand the interactions between metal surface and molecules. The cyclic voltammogram of complex 8 shows two successive reversible one-electron redox waves corresponding to the oxidation of the biferrocenyl moiety and all peak-to-peak separations are smaller than 59 mV (ideal value of one electron transfer with diffusing controlling). In addition, the peak currents are linear to scan rate, i.e., i£\V. This observation is corresponding to the electrochemical property of SAM, and we would like to suggest that the electron transfer process in the electrochemical measurements is direct controlling. Furthermore, we synthesized a nano-material by using of redox stable biferrocenylalkanethiol attached to gold cluster (complex 10). The clusters are stable in air, soluble in nonpolar organic solvents and the characters could be examining by traditional chemical instruments such as NMR, IR, UV/Vis, TEM. The cyclic voltammogram shows that the electron transfer process in the electrochemical measurements is also direct controlling. Finally, the well-known mechanism of intramolecular electron transfer in mixed-valence biferroceniums and the stable biferrocene on Au (111) surface and on gold clusters let to the more advanced concept. We believe that the microstructure of biferrocene assembled on an electrode surface or on gold clusters might enable to carry out a particular function extraordinarily well, for example, optical switch.

Molecules that contain linear alkane chains self-assemble on a variety of surfaces changing the degree of wetting, lubricity, and reactivity. We report on the reoxidation of GaAs(100) in air after adsorbing five alkanethiols (C$_n$H$_{2n+1}$-SH where $n=$ 3, 6, 12, 18, 20) and one alkanedithiol (HS-(CH$_2$)$_8$-SH) deposited from the liquid phase. The alignment of the alkane chains forms a self-assembled layer, however, air diffuses readily through the carbon layer and reaches the surface. The impact of alignment is to improve the bonding of sulfur with the surface atoms which reduces the oxidation rate based on fitting the data to a reaction-diffusion model. The layer thickness and molecular density scale linearly with the number of carbon atoms in the alkane chain. The thickness of the alkanethiolate (RS$^{-}$) layer grows by $0.87 \pm 0.06$ {\AA} for each C atom in the chain and the surface density by $0.13 \pm 0.03$ molecule per nm$^2$ per C atom up to a coverage of 5.0 molecules/nm$^2$ for $n=20$ or 0.8 monolayer. The surface coverage increases with length because interactions between methylene (CH$_2$) groups in neighboring chains reduce the tilt angle of the molecules with the surface normal. The tight packing yields areas per alkanethiolate as low as 20 \AA$^2$ for $n=20$. The amount of C in the layer divided by the chain length is approximately constant up to $n=12$ but increases sharply by a factor of 2-4$\times$ for $n=18$ and 20 based on the C 1s x-ray photoelectron spectroscopy (XPS) peak. Fourier transform infrared (FTIR) spectroscopy shows that the asymmetric methylene stretch shifts continuously to lower wavenumber and the relative peak area increases sharply with the length of the alkane chain. Fitting the data to a reaction-diffusion model shows that for times less than 30 min the surface oxide coverage does not depend on the thickness of the self-assembled layer nor the diffusivity of oxygen through the layer. Instead increasing the layer thickness makes more S available for bonding with the predominately As termination and reduces the rate coefficient for reaction of oxygen with the GaAs surface.

Alkanethiols spontaneously assembles from solution or vapour on oxide free metal surfaces resulting in a close-packed molecular stuctures with a high degree of orientation and molecular order. In this study, inkjet printing technique is used to immobilize monolayers of alkanethiols on gold electrodes. The quality of the inkjetted monolayers are analyzed by electrochemical methods, i.e. cyclic voltammetry and electrochemical impedance spectroscopy, and by Polarization Modulation Infrared Reflection-Absorption Spectroscopy (PM-IRRAS) which show a similar molecular quality to those produced by immersion technique, the standard technique. The kinetic and mass transfer behaviours of micro-scale structures of inkjetted monolayers, e.g. bands and dots array electrodes, are explored by electrochemical methods. The microscale inkjetted structures of monolayers are of interest in the fields of microelectronic devices (e.g. chemical and biosensors) and optoelectronic devices. Taking benefits from multichannel existing in the printhead, mixtures of SAMs are demonstrated. Mixing of monolayers differing in functional groups provides a model surface to study interface phenomena at molecular level such as ion permeation, selective chemical binding, and electron transfer kinetic.

A series of novel metallic nanoparticle and suspension were developed and synthesized for ink-jet printing and spin coating applications. Organic components, such as alkanethiols and amines, were used as new capping agent design. The suspension was characterized by NMR, ESCA, TEM, SEM, EDS, TGA, DTG, DSC, TA-MS for chemical composition and three-dimension SAMs desorption.

No description available.

This thesis is an investigation of surface morphology and electronic structure of self-assembled monolayers (SAMs) and solid water films deposited on these SAMs using metastable impact electron spectroscopy (MIES) and infrared reflection-absorption spectroscopy (IRRAS). MIES uses electronically excited slow helium atoms which interact exclusively with the outermost surface layer. The results suggested that in the SAMs containing an odd number of carbon atoms the molecular orbitals localized on the terminal methyl groups are more exposed at the surface compared to those with an even number of carbon atoms. It was also established that solid water films are more uniform on a SAM substrate containing an odd number of carbon atoms. Thermal transformation of amorphous solid water to polycrystalline ice was also observed. MIES suggested that the molecular orbital of water attributed to the lone pair on the oxygen atom became less accessible at the surface upon the transformation.

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.

Estudos de interface têm presenciado um recente crescimento devido as novas propriedades físico-químicas, que puderam ser explorados com o advento de técnicas com resolução ao nível molecular/atômico. Dessas técnicas, dois ramos que merecem destaque são as Microscopias de Varredura por Ponta de Prova e Espectroscopias Óticas. Neste trabalho fazemos uso de algumas destas técnicas (o Microscópio de Tunelamento de Elétrons e Espectroscopia Vibracional por Geração de Soma de Freqüências) para estudar a adsorção de moléculas alifáticas e aromáticas em Au. Dois casos são abordados: como a rugosidade do substrato influencia no mecanismo de automontagem de monocamadas de alcanotióis e a automontagem de derivados de uracil em interfaces eletroquímicas. No primeiro caso, mostra-se que a quantidade de defeitos moleculares na monocamada adsorvida e extremamente sensível a rugosidade do substrato utilizado. Unem-se os resultados das técnicas acima aos resultados de sondas eletroquímica para se chegar a um modelo. Também e estudado a dependência das etapas de fisisorção e quimisorção em função da concentração da solução de alcanotiól. Para o segundo caso, um derivado halogenado do uracil (5-fluorouracil), mostra-se como a substituição química na base nitrogenada leva a diferentes mecanismos de formação de monocamadas na interface eletroquímica. Imagens de Microscopia de Tunelamento de Elétrons com resolução atômica e molecular mostram que em densidade de cargas negativas as moléculas estão fisisorvidas, porém não formam estruturas periódicas em contraste com uracil e timina, entretanto em densidades de cargas positivas formam estruturas periódicas quimisorvidas, assim como uracil e timina. E discutido como são diferentes os mecanismos de interação intermolecular: no caso dos alcanotiois preponderando às interações de van der Waals e no caso dos derivados de uracil pelas ligações via pontes de hidrogênio são dominantes. / Interface science has experienced a new rebirth since the development of new probes with atomic/molecular resolution, giving new insights about the physical-chemical properties, which differ substantially from the bulk. Among these techniques, two branches deserve special attention: the Scanning Probe Microscopies and Optical Spectroscopy. In this work, two derivatives of theses techniques (the Scanning Tunnelling Microscopy and Vibrational Spectroscopy by Sum-Frequency Generation) are combined giving new insights about the molecular adsorption onto Au. Two examples are focused: how roughness plays a key role in the structure of self-assembled alkanethiol monolayer and the uracil derivatives self-assembling at electrochemical interfaces. For the former, it has been shown that the amount of defects on the adsorbed monolayer is highly sensitive to substrate roughness. Combining the results of each technique with a well-known electrochemical probe, a physical model is proposed. The physisorbed and chemisorbed states are studied as a function of alkanethiol solution concentration as well. For the later case, the chemical substitution of uracil leads to drastically different results for the physisorbed phase (negative charge densities), compared to uracil and thymine. In the chemisorbed phase (positive charge densities) imaging with molecular resolution is achieved showing a quasi-hexagonal structure, similar to the structure of thymine and uracil. It is discussed what are the main driving forces for the self-assembling mechanism: van der Waal interactions for the alkanethiols and hydrogen bonding for uracil derivatives.