Atualmente a fabricação de sensores poliméricos tem sido de grande interesse tecnológico e científico, devido à grande demanda por sensores de diversos tipos em inúmeras aplicações. Nesse contexto, a Embrapa Instrumentação Agropecuária tem buscado o desenvolvimento de novas tecnologias, instrumentação, e sensores; visando a preservação do meio ambiente, tema de grande importância mundial. Muitos produtos comercializados nos países em desenvolvimento não atendem ao padrão de qualidade FAO, e o seu mau uso leva a riscos de contaminação de solos, águas de rios, mananciais, e lençóis freáticos; prejudicando a vida aquática, e consequentemente a vida humana. Este trabalho teve um caráter exploratório, e os objetivos foram a preparação, caracterização e desenvolvimento de unidades sensoriais à base de polímeros, com o intuito de avaliar a qualidade da água através da detecção de vários pesticidas. Utilizou-se uma \"língua eletrônica\" constituída por diferentes unidades sensoriais, nas quais foram depositados filmes de polímeros condutores com composições selecionadas e otimizadas a fim de se obter respostas elétricas características para cada tipo de pesticida. Para tanto: i) sintetizou-se quimicamente os polímeros polianilina e poli(oetoxianilina) e caracterizou-se os mesmos; ii) depositou-se (através de automontagem) filmes ultrafinos dos polímeros condutores poli(o-etoxianilina), polianilina e poli(3,4-etilenodioxitiofeno) sobre microeletrodos interdigitados. Estes filmes foram investigados quanto à sensibilidade frente aos pesticidas; iii) Caracterizou-se espectroscopicamente por técnicas de ultra-violeta visível (UVVIS), e microscopicamente (MEV) os filmes e as interações entre os pesticidas e os polímeros; iv) Caracterizou-se o conjunto de unidades sensoriais através de medidas elétricas de capacitância em corrente alternada através de espectroscopia de impedância e análise estatística de Componentes Principais (PCA). Resultados bastante interessantes foram obtidos, e a \"língua eletrônica\" foi capaz de distinguir águas contaminadas com 1 µ mL-1 de pesticidas, de águas não contaminadas / Nowadays the manufacturing of polimeric sensors has been attractingv technological and cientific interests, due to the demand for different sensors in a large number of applications. In this context. Embrapa Agriculturial Instrumentation rias been looking for the development of new technologies, instrumentation and sensor, envisaging environment monitoring, theme of huge global importance. Many products that are in the market in developing countries do not follow the FAO quality standards and their use can cause risks of contamination to soil and water, damaging the acquatic life and consequently the human life. The aim of this project was the preparation. characterization and development of sensing units made by thin layers of conducting polymers, in order to evaluate the water quality mainly due to contamination of pesticides. To achieve these aims, we made use of an \"electronic tongue\" designed with different sensing units in which conductor polymeric films with specific compositions were deposited, in order to have electric responses for each type of pesticide. For that, the following studies were carried out: i) The polymers PANI and POEA were synthesized and characterized ii) these films (PANI, POEA and PEDOT/PSS) were deposited by self-assembly on gold interdigited microelectrodes. The sensibility of these films to different pesticides was evaluated; iii) the interactions between pesticides and polymers were monitored by visible ultraviolet spectroscopic (UV-VIS) and microscopy techiques (SEM); iv) the sensing units were characterized by impedance measurements and by Principal Component Analysis (PCA). Using eight sensing units with PANI, POEA and PEDOT/PSS films it was demonstrated the possibility to detect some pesticides in concentration of 1 µ mL-1 and to distinguish contaminated samples from non contaminated

Dans cette thèse, les caractéristiques de l’adsorption de dithiols sur des métaux sont étudiées en utilisant principalement l’XPS à haute résolution sur synchrotron, TOF DRS at LEED. L’objectif est de caractérisé les couches auto-assemblées de dithiols formées par évaporation sous vide, comprendre la transition de dithiols d’une phase couchée vers une phase debout, et des processus de réarrangement et de dissociation. Nous avons constaté que sur Au (111) une phase couchée de butanedithiol (C4DT) pouvait être remplacé par un octanethiol pour former une phase debout mixte, et aussi que la phase C4DT debout pouvait être formée lors d’exposition rapide à des grandes doses de vapeurs de C4DT.Cela montre que la phase couchée ne doit pas empêcher la formation d'une phase debout. L'adsorption de 1,4-benzenedimethanethiol (BDMT) sur Au (111), Ag (111), Au (110), Cu (111), Cu (100) et de Pd (111) ont été étudiés dans cette thèse. La phase debout peut être formée dans certains cas, lorsque la surface n'est pas très réactive. Dans le cas de Cu et Pd, la dissociation de BDMT a été observée et un sulfure de surface a été formé sur Pd. On a étudié également l'interaction entre les atomes de chalcogène (S et Se) et certains métaux en rapport avec le travail de l'auto assemblage. Les informations détaillées sur leurs caractéristiques d'adsorption devraient aider à résoudre des ambiguïtés dans la caractérisation des assemblages de thiols et sulfures. Lors de l’adsorption de Se atomes sur Au surface on observe la chemisorption de Se et la formation de structures de Se₈, tandis que pour l'Ag le séléniure d'argent est formé. L’adsorption de soufre sur des (111), Cu (100) et de Pd (111) résulte en la sulfuration et des structures ordonnées intéressantes ont été observées. / In this thesis, the characteristics of SAMs of dithiol molecules adsorption on metals are investigated mainly by HRXPS based on synchrotron radiation, TOF-DRS and LEED. The aim is to characterize self-assembled dithiol monolayers formed by evaporative assembly, to understand the transition of dithiols from a lying down phase to standing up phase, and eventually existence of rearrangement and dissociation processes. We found that on Au(111) a lying down phase of butanedithiol (C4DT) could be substituted by octanethiols to form a mixed standing up phase, and also that standing-up C4DT phase could be formed upon rapid very large exposure to C4DT vapors. This shows that the lying down phase should not impede formation of the standing up one. The adsorption of 1,4-benzenedimethanethiol (BDMT) on Au(111), Ag(111), Au(110), Cu(111), Cu(100) and Pd(111) were investigated in this thesis. The standing up phase could be formed in some cases, when the surface is not very reactive. In case of Cu and Pd dissociation of BDMT was observed and surface sulphide was formed on Pd. Also the interaction between chalcogen atoms (S and Se) and some metals was investigated in relation to the self assembly work. The detailed information about their adsorption characteristics should help in resolving ambiguities in characterization of thiol and sulphide assemblies. The result of Se atoms adsorption on Au surface shows chemisorbed Se and Se₈ features, while for Ag the silver selenide is formed. S atoms adsorption on Cu(111), Cu(100) and Pd(111) surfaces result in metal sulfidation and some interesting structures were observed.

There is an important need to immobilise enzymes for use in industry, to do this I have the promising idea that by conjugating the enzyme to a hydrogel network, thus fabricating a stable biocatalytic network would be a potential method for immobilising enzymes for the manufacture of fine chemicals, this has not been done before for octapeptide systems. Hydrogels have been previously shown as a viable way of immobilising and stabilising enzymes. In this thesis the octapeptide VKVKVEVK (V is valine, K is lysine and E is glutamic acid) is used to immobilise enzymes tagged with VKVKVEVK. This peptide sequence is chosen as it forms stable hydrogels at enzyme appropriate conditions (pH 7). The enzymes chosen are; PETNR as it is well understood and is therefore a good starting point, CDH and CHMO were also chosen as they could combine with PETNR to form a cascade reaction. PETNR was both chemically conjugated to VKVKVEVK (SpepPETNR) and also genetically modified to express the peptide tag (CpepPETNR), whilst CDH and CHMO were genetically modified to express the tag (NpepCDH and CpepCHMO respectively). For S/CpepPETNR retention within the hydrogels was superior to retention for untagged PETNR. NpepCDH was found to not precipitate within the hydrogel whilst untagged was found to do so. CpepCHMO functionalised hydrogels were found to be heterogeneous. Characterisation of CpepPETNR functionalised hydrogels was undertaken using micro differential scanning calorimetry (µDSC), rheology, small angle neutron scattering (SANS) and atomic force microscopy (AFM). From the µDSC evidence of 'protective immobilisation' was observed by the increase in denaturation energy (+253 kJ mol-1) in the hydrogel in comparison to in solution (+18 kJ mol-1). The ability of S/CpepPETNR functionalised hydrogels to perform the ketoisophorone to levodione biotransformation reaction was explored with yields of 86%. S/CpepPETNR within VKVKVEVK hydrogels was found to retain ~90% conversion for at least 9 months at room temperature. Incubation overnight at 90°C resulted in a yield of 84% of levodione. These two results added more evidence for 'protective immobilisation'. Hydrogels functionalised with NpepCDH or CpepCHMO were characterised using rheology and atomic force microscopy. The biotransformation ability of NpepCDH was elucidated; the overall yield of carvone was a maximum of 54% from the hydrogel phase. NpepCDH was used alongside CpepPETNR for the cascade reaction producing dihydrocarvone in low yields; however, an improvement from 2% to 13% in yield is presented. The yield of lactone products from CpepCHMO functionalised hydrogel was low at 15%. The CpepPETNR/ CpepPETNR cascade reaction proceeded with a yield of 36%. The initial activities of CpepPETNR, NpepCDH and CpepCHMO were assayed in both solution and in gel phase using a modified method. The activities were assessed with varying conditions; temperature, pH, quantity of ethanol and incubation at high and low temperatures. Generally, it was found that immobilisation within the hydrogel phase resulted in 'protective immobilisation' against non-optimal conditions. This work will be of benefit to those who are interesting immobilising enzymes within hydrogels in the future.

Self-assembly of colloidal particles into ordered structures is hailed as the preferred route to production of functional devices on the nanometre and micron length scales. The shape of a colloidal particle is one of the most influential factors determining the type of ordered structure that is assembled. Thus this thesis is devoted to understanding the role of particle shape on phase behaviour of colloidal systems. The effect of particle shape is isolated by using computer simulations to model particles as hard, anisotropic bodies which interact via purely repulsive interactions. Two particle models are studied which are representative of real colloids: non-convex wireframe polyhedra, and convex spherical caps. This thesis investigates the densest packings of several wireframe polyhedra. By comparing packings of six distinct polyhedra some general conclusions are drawn regarding the effects of rounded polyhedra edges, and a new shape descriptor is given which can suggest whether a wireframe polyhedron is likely to form new interpenetrating crystal structures. Wireframe cubes were studied in more detail, where the full phase behaviour was mapped out. A curious phenomenon was found whereby crystals formed by cubic wireframes exhibit plastic fluctuations. This unusual behaviour, if reproduced experimentally, may lead to useful optical properties. A systematic study of spherical caps demonstrates the effect of shape on collective behaviour as the particle model interpolates between a sphere and a thin platelet. Purely repulsive interactions are responsible for a range of different crystal structures, but the nucleation of these structures is challenging due to slow dynamics. Furthermore, there are often many ways for a spherical cap to pack in a given volume, which leads to multiple metastable states. The self-assembly of spherical caps was directed by sedimentation on a solid template which resulted in increased nucleation rates and more stable crystals. However, there is still a lack of control over the exact crystal structure due to the degeneracy in ways to pack.

Inspired by biological membrane shaping in the cell through means of curvature-inducing proteins, we investigate the interplay between membrane curvature and the distribution and movement of shape-inducing objects which are free to move as a consequence of the underlying shape. We initially study the self-assembly of a filament, taken as a proxy for the cross-section of a biomembrane, which is primarily driven by the chemical kinetics of attaching proteins and find that, under certain mechanical stiffness regimes of the attaching proteins, pattern formation occurs. Regions of high and low protein concentration form before spatially uniform filament shapes are obtained by means of protein adhesion and movement governed by diffusion and local curvature-seeking. However, noting that the curvature-mediated protein movement on membranes has been biologically observed to be long-range, we next study the self-assembly of embedded inclusions on a membrane as a result of the underlying geometry. We first derive an interaction law for the shape-mediated interaction of inclusions which break symmetry and find that there is a finite equilibrium distance to which the inclusions will aggregate. We derive corresponding equations of motion which describe this curvature-mediated aggregation mechanism and, using this framework, we investigate some of the properties of these self-assembled configurations, including their energy, stability, and their collective elastic behavior. Lastly, we consider the interaction energies of embedded inclusions on a periodic domain and determine that this mechanism may explain computational results of how proteins form rings to promote tubulation on cylindrical membranes.

Amostras de titânia foram sintetizadas por seis rotas diferentes: quatro pelo método sol-gel, utilizando condições e precursores distintos, por combustão de solução líquida e pelo método Pechini. Após tratamento térmico que variou de 100°C a 900°C, as amostras foram analisadas por difratometria de raios X, termogravimetria e pelo método BET de obtenção de áreas superficiais específicas. As amostras obtidas por sol-gel utilizando como precursores o isopropóxido de titânio (Pro) e o n-butóxido de titânio (But) geraram materiais de elevada área superficial, com alta fração molar de anatase e sem resíduos a 500°C. As amostras obtidas por sol-gel com excesso de íon peptizante (Nan) possuiam também altas áreas superficiais, além de estabilizarem a fase anatase a até 500°C, com resquícios de bruquita. As amostras obtidas por sol-gel utilizando um surfactante não iônico (Sur) demonstraram as maiores áreas superficiais, os menores tamanhos de cristais e estabilidade de anatase pura a 500°C. Esses materiais têm, pois, potencial para aplicação em fotocatálise, em células solares sensibilizadas por corantes e em células a combustível, entre outras. Os métodos da combustão (Com) e de Pechini (Pec) geraram produtos de baixa área superficial e com baixa ou com nenhuma fração de anatase. Porém, são métodos simples e eficientes de obtenção de titânia para aplicações que não necessitem da anatase como fase única. / Titania samples were prepared by six different routes, four of them by the sol-gel method using different precursors and reaction conditions, a solution combustion route and a Pechini method route. After thermal treatment ranging from 100 C to 900 C, the resulting materials were analyzed by X-ray diffraction, thermogravimetric analysis and surface area determination (BET method). The materials obtained by the sol-gel method using titanium isopropoxide (Pro) and titanium n-butoxide (But) as precursors yielded ceramics with high surface area, a high anatase molar fraction, without residues when heated at 500 C. Samples obtained by the sol-gel route using excess peptization agent (Nan) also showed high surface areas and yielded anatase with traces of brookite which was stable up to 500 C. Samples obtained using the sol-gel route with non-ionic surfactant (Sur) exhibit the highest surface area, smallest crystallite sizes and stable anatase with traces of brookite up to 500 C. These materials have, therefore, potential application in the areas of photocatalysis, dye- sensitized solar cells and fuel cells, among others. The combustion (Com) and Pechini (Pec) methods yielded materials with low surface area, with little or no presence of anatase. They are, however, simple and efficient methods for obtaining pure titania when the pure form of anatase is not a necessity.

Amostras de titânia foram sintetizadas por seis rotas diferentes: quatro pelo método sol-gel, utilizando condições e precursores distintos, por combustão de solução líquida e pelo método Pechini. Após tratamento térmico que variou de 100°C a 900°C, as amostras foram analisadas por difratometria de raios X, termogravimetria e pelo método BET de obtenção de áreas superficiais específicas. As amostras obtidas por sol-gel utilizando como precursores o isopropóxido de titânio (Pro) e o n-butóxido de titânio (But) geraram materiais de elevada área superficial, com alta fração molar de anatase e sem resíduos a 500°C. As amostras obtidas por sol-gel com excesso de íon peptizante (Nan) possuiam também altas áreas superficiais, além de estabilizarem a fase anatase a até 500°C, com resquícios de bruquita. As amostras obtidas por sol-gel utilizando um surfactante não iônico (Sur) demonstraram as maiores áreas superficiais, os menores tamanhos de cristais e estabilidade de anatase pura a 500°C. Esses materiais têm, pois, potencial para aplicação em fotocatálise, em células solares sensibilizadas por corantes e em células a combustível, entre outras. Os métodos da combustão (Com) e de Pechini (Pec) geraram produtos de baixa área superficial e com baixa ou com nenhuma fração de anatase. Porém, são métodos simples e eficientes de obtenção de titânia para aplicações que não necessitem da anatase como fase única. / Titania samples were prepared by six different routes, four of them by the sol-gel method using different precursors and reaction conditions, a solution combustion route and a Pechini method route. After thermal treatment ranging from 100 C to 900 C, the resulting materials were analyzed by X-ray diffraction, thermogravimetric analysis and surface area determination (BET method). The materials obtained by the sol-gel method using titanium isopropoxide (Pro) and titanium n-butoxide (But) as precursors yielded ceramics with high surface area, a high anatase molar fraction, without residues when heated at 500 C. Samples obtained by the sol-gel route using excess peptization agent (Nan) also showed high surface areas and yielded anatase with traces of brookite which was stable up to 500 C. Samples obtained using the sol-gel route with non-ionic surfactant (Sur) exhibit the highest surface area, smallest crystallite sizes and stable anatase with traces of brookite up to 500 C. These materials have, therefore, potential application in the areas of photocatalysis, dye- sensitized solar cells and fuel cells, among others. The combustion (Com) and Pechini (Pec) methods yielded materials with low surface area, with little or no presence of anatase. They are, however, simple and efficient methods for obtaining pure titania when the pure form of anatase is not a necessity.

abstract: DNA and RNA are generally regarded as one of the central molecules in molecular biology. Recent advancements in the field of DNA/RNA nanotechnology witnessed the success of usage of DNA/RNA as programmable molecules to construct nano-objects with predefined shapes and dynamic molecular machines for various functions. From the perspective of structural design with nucleic acid, there are basically two types of assembly method, DNA tile based assembly and DNA origami based assembly, used to construct infinite-sized crystal structures and finite-sized molecular structures. The assembled structure can be used for arrangement of other molecules or nanoparticles with the resolution of nanometers to create new type of materials. The dynamic nucleic acid machine is based on the DNA strand displacement, which allows two nucleic acid strands to hybridize with each other to displace one or more prehybridized strands in the process. Strand displacement reaction has been implemented to construct a variety of dynamic molecular systems, such as molecular computer, oscillators, in vivo devices for gene expression control. This thesis will focus on the computational design of structural and dynamic nucleic acid systems, particularly for new type of DNA structure design and high precision control of gene expression in vivo. Firstly, a new type of fundamental DNA structural motif, the layered-crossover motif, will be introduced. The layered-crossover allow non-parallel alignment of DNA helices with precisely controlled angle. By using the layered-crossover motif, the scaffold can go through the 3D framework DNA origami structures. The properties of precise angle control of the layered-crossover tiles can also be used to assemble 2D and 3D crystals. One the dynamic control part, a de-novo-designed riboregulator is developed that can recognize single nucleotide variation. The riboregulators can also be used to develop paper-based diagnostic devices. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2019

Crystal engineering has recently emerged as a method of choice for the design and the construction of functional materials. Solid-state synthesis, of the most commonly studied aspects of crystal engineering, has been shown to provide access to molecular targets that are hardly obtainable using principles of conventional (i.e. solution-based) organic synthesis. Reactions in the solid state are, however, not routinely used in organic synthetic chemistry. The scarce use of solid-state reactions can be attributed to the difficulty of predicting molecular arrangements in the solid state, as well as to the lack of methodologies to control crystal packing. Template-directed solid-state synthesis is a recently developed modus operandi that enables control over reactivity within multi-component crystals. The thesis is focused on the application of template-directed solid-state approach to [2+2] photocycloaddition reactions in the solid state, as well as on the understanding of intermolecular interactions in crystals. Synthetic templates have been utilized to construct cocrystals that enable a class of hitherto underdeveloped organic solid-state reactions, namely [2+2] cross-photoaddition reactions. In addition, products derived form templated solid state reactions, namely tetrapyridylcyclobutanes, have been utilized to generate exceptional materials, such as thixothropic hydrogels based on nano-dimensional metal-organic particles. The utility of crystal engineering has also been expanded to the nanoscience and the development of nanomaterials. A crystallization method for the preparation of nano-dimensional cocrystals has been developed. The method has been shown to enable single-crystal-to-single-crystal [2+2] photodimerizations of olefins. In addition, nano-dimensional cocrystals have been shown to exhibit distinctive mechanical properties upon single-crystal-to-single-crystal transformations. In addition to solid-state reactions and materials derived therefrom, we systematically studied hierarchies of supramolecular synthons in pharmaceutical cocrystals comprised of multi-functional molecules. Pharmaceutical cocrystals have been recently shown to exhibit physical properties superior to those of parent drugs. Our studies involved xanthine alkaloids as pharmaceutical agents and a series of hydroxylated benzoic acids as cocrystal formers. Synthon hierarchies have been established for three xanthine alkaloids. We also discovered pharmaceutical salts that formed where cocrystallization was expected to occur. Reasons contributing to such unexpected salt formation were investigated using X-ray crystallography and computational methods. The established synthon hierarchies are expected to contribute to a better understanding of self-assembly processes in cocrystals that is crucial for the development of state-of-art drugs, and the design of organic reactions in the solid state.

L’auto-assemblage moléculaire au niveau des surfaces est un exemple majeur de l'auto-organisation de la matière avec des applications technologiques d’intérêt. La capacité́ de prédire la structure de la monocouche auto-assemblée (SAM) formée à l'équilibre est d'une importance fondamentale. Dans cette thèse, je présente une théorie aux premiers principes pour l’interprétation de l’auto-assemblage 2D basée sur la modélisation et la thermodynamique statistique. La méthode mise au point permet d'accéder à la stabilité́ thermodynamique de la SAM et à sa dépendance à l'égard de la concentration. Cela permet d'étudier les équilibres concurrentiels au niveau des surfaces et de rationaliser le polymorphisme en 2D. De plus, cette théorie prédit l'existence d'une concentration critique de monomères au-dessus de laquelle l’auto-assemblage 2D est favorisé. Celle-ci est utilisée pour définir une échelle absolue définissant la propension à l’auto-assemblage en 2D. Enfin, quatre applications technologiques sont discutées, exposant les possibilités de la méthode développée. / Molecular self-assembly at surfaces is a prominent example of self-organization of matter with outstanding technological applications. The ability to predict the structure of the self-assembled monolayer (SAM) formed at equilibrium is of great fundamental and technological importance. In this dissertation I present a self-consistent theory for a first-principle interpretation of 2D self-assembly based on modeling and statistical thermodynamics. The developed framework provides access to the thermodynamic stability of the SAM and to its concentration dependence. This allows to study competitive equilibria at surfaces and to rationalize the 2D polymorphism evidenced by scanning probe techniques. The theory predicts the existence of a critical concentration of monomers, which is used to set an absolute scale for the 2D self-assembly propensity. Last, four technological applications are discussed, showing the potentials of the developed framework.