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O estudo das reações de agregação em sistemas automontados é de grande interesse científico pela grande variedade de aplicações que tais colunas podem desempenhar. O presente trabalho teve como objetivo investigar as propriedades gerais de colunas supramoleculares formadas por complexos de coordenação que contêm platina, paládio e zinco. Esta investigação foi feita através do método semiempírico PM7. Os agregados supramoleculares investigados tiveram suas geometrias otimizadas e foram submetidos a cálculos termoquímicos. Pôde-se investigar as influências do metal e dos ligantes nos mecanismos gerais e propriedades das colunas, uma vez que utilizaram-se dois ligantes distintos. Estudou-se compostos de coordenação cujos ligantes foram o 2,6-bis(1H-1,2,4-triazol-5-il)piridina e oligofenilenoetinilenos (OPE) piridínicos. Realizou-se cálculos utilizando o modelo de solvatação contínua COSMO com água e metilciclohexano (MCH), o que permitiu avaliar os efeitos dos solventes nas energias de dimerização dos sistemas estudados. Os resultados obtidos para os derivados de OPE indicaram que as colunas supramoleculares desta classe que contêm Zn(II) apresentam anticooperatividade, exibindo energias de Gibbs de formação para o vácuo a 298 K positivas do dímero ao decâmero. Os resultados de solvatação contínua indicaram que a formação de um dímero deste composto é termodinamicamente favorável de 278 K para água e 267 K para o MCH, enquanto que para o vácuo a temperatura na qual a energia de Gibbs de dimerização é negativa ocorre em 246 K. Tal resultado aponta que o principal efeito de formação de colunas baseadas neste composto em altas temperaturas é primariamente um efeito solvofóbico que depende da polaridade do solvente. Observou-se a cooperatividade em vácuo e em ambos os solventes das colunas de derivados de OPE que contêm Pd(II) e Pt(II). Além destes fatos, as distâncias entre os centros metálicos diminuíram conforme monômeros eram adicionados à coluna, o que indica a existência de interações metalofílicas no sistema. Este resultado é corroborado experimentalmente por um artigo de Albuquerque el al. no caso do sistema de derivado de OPE que contém Pd(II). Para os sistemas cujos ligantes eram a 2,6-bis(1H-1,2,4-triazol-5-il)piridina, houve cooperatividade para ambas as colunas baseadas em Pd(II) e Pt(II), e houve para o sistema cujos centros metálicos são o Pt(II) uma transição não observada para todos os outros sistemas estudados; houve comportamento distinto das mudanças de distâncias entre monômeros no sistema triazol pridínico baseado em Pd(II) em relação àquele baseado em Pd(II) derivado de OPE. Este resultado indica a soma de dois efeitos no sistema OPE baseado em Pd(II): o de interações metalofílicas e de empilhamentos π-π. Como um todo, os resultados indicam que as principais interações envolvidas nas formações das colunas supramoleculares são interações de empilhamento π-π e metalofílicas para quatros compostos em graus diversos, exceto para o derivado de OPE baseado em Zn(II), que tem como principal força-motriz de agregação interações solvofóbicas. Perspectivas para este projeto: continuação da modelagem dos sistemas estudados por dinâmica molecular, com a simulação das interações de várias colunas formadas pelos monômeros estudados através do CP2K e publicação de um artigo com os resultados obtidos. / The study of aggregation reactions in self-assembled systems is of great scientific interest due to the wide range of applications which such resulting columns can play. Herein, we had the objective of investigating the general properties of supramolecular columns formed coordination complexes which contain platinum, palladium and zinc. This investigation was carried through the semiempirical method PM7. The investigated supramolecular aggregates were optimized, and their optimized geometries were subjected to thermochemical calculations. In this sense we could probe the influences of metals and ligands onto the general mechanisms and columnar properties, once were herein used two different ligands. The two ligands were 2,6-bis(1H-1,2,4-triazol-5-il)pyridine and oligophenyleneethynediyl (OPE) pyridine derivatives. COSMO solvation model -based calculations in water and methylcyclohexane (MCH) were performed in order to evaluate solvents effects on dimerization Gibbs energies of the studied systems. The results obtained for the OPE derivative based on Zn(II) pointed an anticooperative process in vacuum at 298K, exhibiting positive Gibbs energies of formation from the dimer to the decamer. The results from continuum solvation calculations indicate the formation of a dimer based on this Zn(II) molecule to be thermodynamically favorable at 278 K for water and at 267 K for MCH, while in vaccum this point lies at 246 K. This results indicates the formation of supramolecular columns based on this compound are formed in higher temperatures primarily due to solvophobic effects, and the intensity of this effect depends on the solvent polarity. The columns of OPE derviatives which contained Pd(II) and Pt(II) both showed cooperativity in the aggregation process. Besides these thermodynamic results, both of those columns showed monotonic distance shortening due to columns increasing process. This is an indicative of metallophilic interactions taking place in these aggregates. This result for Pd(II) is experimentally supported by a paper od Albuquerque et al. for the columns containing 2,6-bis(1H-1,2,4-triazol-5-il)pyridine cooperativity was observed for both the columns--those which contain Pd(II) and Pt(II)--, and for the Pt(II)-based columns of this class it was observed a transition not of most eneregetically favoured mechanisms not observed for all the other systems studied. A difference on the behavior of average monomer distances took place in the triazol pyridine Pd(II) compound when compared to its metal-related OPE derivative. This result indicates the summation of effects in the OPE-based Pd(II) system: the one of metallophilic interactions and π-π stacking interactions. As a whole, the results indicate π-π stacking and metallophilic interactions to be responsible for aggregation processes in diverse intensities for four of the compounds, except for that in the Zn(II)-based OPE derivative, which has the main aggregation effect as solvophobic interactions. The main perspectives for this project are the continuation of the modelling of the herein studied systems by molecular dynamics, simulating the interactions of many columns by the CP2K program, and the publication of a paper which contains the results obtained and presented in this dissertation.

Recentemente, nanopartículas (NP) de FePt de fase tetragonal de face centrada (fct) em sistemas auto-organizados tem sido sintetizados como potenciais candidatos para gravação magnética de ultra-alta densidade (UHMR), devido a sua elevada anisotropia magnetocristalina. Entretanto, o alinhamento magnético de NP esféricas tem sido constantemente um problema, pois os eixos de fácil magnetização das NP permanecem randomicamente orientados nas três direções. Na tentativa de superar os problemas decorrentes da falta de alinhamento magnético, trabalhos recentes sugerem que NP alongadas em sistemas auto-organizados orientados perpendicularmente a superfície do substrato como possível solução para a textura e alinhamento magnético. Até o presente momento, as sínteses de nanobastões (NB) e de nanofios (NF) de FePt reportadas na literatura levam a obtenção de NP na fase cúbica de face centrada (fcc), a qual possui baixa anisotropia magnetocristalina e se mostrou termicamente instável, resultando em NP esferoidais após o processo de recozimento para a transformação da fase fcc para fct. Neste trabalho, NP de Fe55Pt55 com tamanho e composição química controlada e morfologia de nanofios e nanobastões foram sintetizadas através da adequação do método do poliol modificado. Além disso, as condições de sínteses foram ajustadas para a obtenção direta das NP na fase fct. Sistemas auto-organizados de NB orientados longitudinalmente ou perpendicularmente em arranjos hexagonais compactos foram obtidos utilizando, respectivamente, ácido oléico (AO) e oleilamina (Oam) ou hexadecilamina (HDA) como agentes espaçadores. Sistemas de NB orientados perpendicularmente com alinhamento magnético devido à anisotropia de forma combinado com as propriedades magnéticas resultantes da fase parcialmente tetragonal obtida sugerem um forte candidato a aplicação em UHMR com densidade de gravação magnética na ordem de terabits/pol2. / Recently, self-assembled FePt nanoparticles (NP) in face-centered tetragonal phase (fct) has been synthesizes as potential candidates for Ultra-High Magnetic Recording Systems (UHMR) due to high magnetocrystalline anisotropy. However, the magnetic alignment of these self-assembled fct-FePt nanoparticles also has been a constant limiting factor, since the axes of easy magnetization of spherical nanoparticles are presented randomly oriented in three directions. Concerning to avoid these restrictions arising from magnetic alignment, one-dimensional NP perpendicularly oriented on the magnetic medium surface has been reported as a possible solution for texture and magnetic alignment. To date, the reported nanorods (NR) and nanowires (NW) synthesized in the literature showed face centered cubic phase (fcc) which present poor magnetocrystalline anisotropy, instead the fct desirable phase, and were found to be thermally unstable resulting in spheroidal NP after annealing required to phase transformation from fcc to fct. In this work, Fe55Pt45 NP with morphologies varying from nanospheres, NR with different lengths up to NW were synthesized by a modified polyol process. Furthermore, the synthesis conditions were adjusted to obtain FePt NP directly in fct phase. Either longitudinal or perpendicular self-assembled NR systems in a hexagonal compact array were obtained using oleic acid (OA) and oleylamine (Oam) or hexadecylamine (HAD), respectively, as molecular organic spacers. Perpendicularly oriented NR system led to magnetic alignment due to shape anisotropy and combined with the magnetic properties due to partial tetragonal phase suggest a strong future candidate to ultra-high magnetic density recording applications capable to achieve density of Terabits/in2.

Made available in DSpace on 2017-07-24T19:37:59Z (GMT). No. of bitstreams: 1 ClicianeGuadalupeJesus.pdf: 2429700 bytes, checksum: c3ac935bcc2b97480f80dc8cf9ff472d (MD5) Previous issue date: 2009-02-27 / Nanostructured films composed by a 3-n-propylpyridinum silsesquioxane polymer (designated as SiPy+Cl-) and copper (II) tetrasulphophthalocyanine (CuTsPc) were produced using the Layer-by-Layer technique (LbL). The deposition of the bilayers was monitored by UV-Vis spectroscopy accompanying the absorbance of Q-band at 617 nm. It was observed that the absorbance linearly increased with the number of SiPy+Cl-/CuTsPc or CuTsPc/SiPy+Cl- bilayers, indicating that the same amount of material was deposited at each step of film formation. FTIR spectra showed that there is a specific interaction by the SO3 - groups of CuTsPc and the pyridinium groups of the polycation, SiPy+Cl-. Morphological studies of films surfaces showed that their roughness and thickness increase with the number of bilayers. The films were employed to detect dopamine (DA) and ascorbic acid (AA) using cyclic voltammetry. It was observed that the number and the sequence of bilayers deposition directly influenced on the electrochemical response in presence of the analytes. LbL films with lower number of bilayers (1 to 5 bilayers) presented higher current values in presence of the analytes, which is attributed to the higher facility of diffusion of target species to the electrode surface and enhancement of the efficiency of the electron transfer process. Considering the sequence of bilayers deposition, it was observed that the CuTsPc/SiPy+Cl- film did not show any redox peaks in the potential range -0.2 V to 1.6 V vs Ag/AgCl in presence of DA and AA. In contrast, the SiPy+Cl-/CuTsPc LbL film, presented a defined oxidation redox peak at approximately 1.2 V for DA and 0.8 V for AA, which linearly increased with DA concentration in HCl 1.0x10-3 molL-1 electrolyte solution (pH 3). Studies in different scan rates for the SiPy+Cl-/CuTsPc LbL film in presence of these analytes showed that the anodic peak current (Ipa) linearly increased with the square root of the scan rate (n1/2 ) which is a typical behavior for systems governed by a diffusion controlled mechanism. The relationship Ipa/ n1/2 vs n resulted in an exponential profile, confirming the existence of an electrocatalytical process for both AA and DA provided by CuTsPc in the LbL film. Using differential pulse technique, films comprising SiPy+/CuTsPc were able to distinguish between DA and ascorbic acid (AA), with a potential difference of approximately with 400 mV, in the concentration range of 9.0x10-5 to 2.0x10-4 molL- 1(in pH 3.0) and detection limits in the order of 10-5 molL-1. / Filmes nanoestruturados formados entre o polímero 3-n-propilpiridínio silsesquioxano (designado como SiPy+Cl-) e ftalocianina tetrasulfonada de cobre (II) (CuTsPc) foram produzidos usando a técnica Layer-by-Layer (LbL). A formação dos filmes foi monitorada por espectroscopia na região do UV-Vis, acompanhando-se a absorbância da banda Q da ftalocianina em 617 nm. Observou-se que a absorbância aumentou linearmente com o número de bicamadas para os filmes SiPy+Cl-/CuTsPc ou CuTsPc/SiPy+Cl-, indicando que a mesma quantidade de material foi depositado a cada bicamada depositada. Espectros FTIR mostraram que há interação específica entre os grupos SO3 - da CuTsPc e o anel piridínio do policátion, SiPy+Cl-. Estudos da morfologia da superfície dos filmes mostraram que a rugosidade média e espessura dos filmes aumentam de acordo com o número de bicamadas. Os filmes foram empregados para detectar DA e AA, utilizando-se a técnica de voltametria cíclica. Observou-se que o número de bicamadas e a seqüência de deposição das mesmas influenciam diretamente sobre a resposta eletroquímica na presença dos analitos. Filmes LbL com menor número de bicamadas (1 a 5 bicamadas) apresentaram maiores valores de corrente, fato este atribuído a maior facilidade de difusão das espécies à superfície do eletrodo, aumentando a eficiência do processo de transferência de elétrons. Com relação à sequência de deposição das bicamadas constatou-se que o filme CuTsPc/SiPy+Cl- não mostrou picos redox na faixa de potencial de -0,2 V a 1,6 V vs Ag/AgCl na presença de DA e AA. Enquanto que o filme SiPy+Cl-/CuTsPc, apresentou um pico de oxidação bem definido em aproximadamente 1,2 V, para DA e em 0,8 V para AA, o qual aumentou linearmente com a concentração dos analitos utilizando HCl como eletrólito suporte. Estudos em diferentes velocidades de varredura do eletrodo SiPy+Cl-/CuTsPc na presença dos analitos mostraram que a corrente de pico anódica (Ipa) aumenta linearmente com a raiz quadrada da velocidade de varredura (n1/2), indicando que o processo de transferência de elétrons é controlado pela difusão das espécies à superfície do eletrodo. A relação entre Ipa/n1/2 vs n, resultou numa curva exponencial, confirmando a existência do processo eletrocatalítico resultante da oxidação da DA e AA proporcionada pela CuTsPc. Utilizando-se a técnica de voltametria de pulso diferencial, o eletrodo SiPy+Cl-/CuTsPc foi capaz de distinguir AA e DA quando presentes numa mesma solução, com um diferença de potencial de aproximadamente 400 mV, no intervalo de concentração de 9,0x10-5 a 2,0x10-4 molL-1(em pH 3) e limites de detecção (LOD) da ordem de 10-5 molL-1.

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>