A Ciprofloxacina é um antibiótico muito relevante, porém com efeitos colaterais indesejáveis, como convulsões, rompimento de tendão entre outros. Com o intuito de reduzir estes efeitos colaterais e para a liberação do fármaco em locais específicos, o uso de materiais lamelares, como cápsulas de armazenamento e transportador com alvo específico para biomoléculas ou células, tem sido sugerido pela literatura. A combinação de estudos teóricos e experimentais pode fornecer uma melhor compreensão da estrutura de agregados lamelares com o antibiótico Ciprofloxacina. Neste trabalho estudamos os diferentes estados iônicos da Ciprofloxacina (Cipro), obtendo os espectros de vibração (Infravermelho, Raman), Ressonância magnética nuclear de carbono e ótico (Ultravioleta-Visual). Estes resultados teóricos são comparados a resultados experimentais para investigar e caracterizar o estado molecular após intercalação. Utilizamos cálculos de estrutura eletrônica desenvolvidos no âmbito Teoria do Funcional da Densidade (DFT). Nossos resultados de análise dos espectros teóricos de Uv-Vis e de deslocamento químico obtido por RMN de Carbono revelaram que os espectros dos quatro estados iônicos da Cipro aqui estudados são muito semelhantes, o que não permite a diferenciação destes estados através destas técnicas. Por outro lado, nossos resultados de análise vibracional demonstraram frequências características de cada um dos estados iônicos. Este fato é importante, uma vez que permite identificar, através do espectro vibracional, cada um dos compostos presentes em uma dada amostra como, por exemplo, um agregado lamelar, utilizado para fins de liberação controlada de fármacos. / Ciprofloxacin is an important antibiotic, but with undesirable side effects. The use of layered materials as drug storage capsules and drug carriers can enable the development of target-specific drugs with high specificity for biomolecules or cells, which allow the release of drugs in chosen locations, thus reducing side effects .The combination of theoretical and experimental studies can provide a better understanding of the structure of lamellar aggregates with Ciprofloxacin antibiotic. In this context, to assist in the complete characterization of Ciprofloxacin, we perform theoretical calculations in the framework of the Density Functional Theory (DFT). We study different ionic states, obtaining the vibrational (IR, Raman), C-NMR and optical (UV/Vis) spectra. These theoretical results are compared with experimental results in order to unravel the molecular state upon encapsulation. Our results have shown that the Uv-Vis and NMR chemical shifts are not able to clearly differentiate the ionic states studied here. On the other hand, our calculation for the vibrational spectra reveals characteristic fingerprints of the Ciprofloxacin ionic states. This may permit, the identification of the ionic state of Ciprofloxacin in a certain sample, as layered materials, when used as drug carriers.

Neste trabalho, várias reações de Heck foram investigadas utilizando principalmente métodos baseados na Teoria do Funcional de Densidade (DFT). Na primeira parte foi proposto um novo ciclo catalítico de Heck, com etapas aniônicas e neutras combinadas desencadeado por um complexo de paládio (Pd) suportado por um ligante carbeno N-heterocíclico (NHC) inédito. Posteriormente, a influência estérica do ligante NHC foi investigada na seletividade da reação de Heck inicialmente estudada. Para o NHC pouco volumoso, a componente eletrônica era majoritária comparada às contribuições de caráter não-covalente. Entretanto, quando o NHC com maior impedimento estérico foi analisado, somente alguns funcionais de densidade (TPSS-D3, ωB97x-D, BP86-D3, e M06-L), juntamente com o método de função de onda DLPNO-MP2, foram capazes de predizer a tendência de seletividade experimental. Por fim, a natureza do metal foi analisada por meio de uma comparação entre catalisadores NHC de níquel (Ni) e Pd nas reações de Heck. Os resultados teóricos forneceram indícios mecanísticos para o entendimento da menor atividade catalítica usualmente encontrada nos processos envolvendo complexos NHC de Ni e da necessidade experimental da formação de complexos de Ni catiônicos para atingir uma maior eficiência catalítica nessas reações. Na segunda parte deste estudo, dois exemplos marcantes da literatura sobre as reações de Heck-Matsuda enantiosseletivas foram teoricamente investigadas. Os cálculos DFT mostraram a influência crucial do substrato (olefina) na seletividade destas reações. Em um dos casos a seletividade da reação foi aprimorada através dos dados mecanísticos fornecidos pelos cálculos DFT. / In this work, several examples of Heck reactions were investigated using mostly Density Functional Theory (DFT) methods. At the first part, a new Heck catalytic cycle was proposed with combined anionic and neutral steps initiated by a newly N-heterocyclic carbene (NHC) based palladium (Pd) complex. Posteriorly, the influence of steric demanding of NHC ligand was investigated on selectivity of Heck reaction initially studied. In the case of small NHC ligand, the electronic component is more important than the noncovalent contributions. However, when the crowded NHC ligands were studied only selected density functionals (TPSS-D3, ωB97x-D, BP86-D3, e M06-L), and the wavefunction based method DLPNO-MP2, were capable to predict the experimental selectivity trends reported. Finally, the metal nature was analyzed by a comparison of the nickel (Ni) and Pd catalyzed Heck reactions. The theoretical results provided mechanistic insights that help to understand the low catalytic activity usually reported when Ni catalysts were used and the experimental requirement of cationic intermediates to achieve some efficiency for NHC-Ni-catalyzed Heck coupling. At second part, two representative examples from literature about the enantioselective Heck-Matsuda reactions were theoretically investigated. DFT calculations shown the crucial influence of substrate (olefin) on the selectivity of these reactions. One of cases studied, the selectivity of reaction was improved by the DFT results

A molécula de ácido orto-aminobenzóico tem sido intensamente empregada como sonda fluorescente no estudo de peptídeos e membranas e o entendimento dos efeitos de solvente sobre suas propriedades espectroscópicas apresenta grande interesse científico. Neste trabalho realizamos um estudo experimental e cálculos DFT sobre alterações nos espectros de absorção e emissão da sonda em solução aquosa, em função do pH do meio. Examinamos também o seu derivado 2-amino-N-metil benzamida (o-Abz-NHCH3) e as mudanças espectrais na interação com micelas de SDS. Resultados de experimentos de titulação mostraram-se coerentes com a existência de três estados de protonação para o-Abz à medida em que o pH torna-se ácido, resultantes da protonação dos grupos amino e carboxila, de modo semelhante ao que ocorre com aminoácidos. Para cada estado de protonação, realizamos cálculos de otimização de geometria e verificação de mínima energia com a teoria DFT utilizando diferentes funcionais e conjuntos de bases para orbitais atômicos. Partindo das geometrias de menor energia, com a teoria TD-DFT (B3LYP/311++G(d,p)) fizemos cálculos das transições eletrônicas. A melhor concordância com os resultados experimentais foi obtida com a molécula na forma aniônica. Na comparação dos resultados da posição espectral da transição de mais baixa energia, no processo de absorção ótica, observamos uma diferença relativa de 0,6%. Para a fluorescência otimizamos e verificamos a geometria do estado excitado e obtivemos as energias de transição vertical com o método TD-DFT (B3LYP/Def2-TZVP) com o qual tivemos um resultado de lambda = 407nm considerado satisfatório quando comparado com o valor experimental lambda= 394nm. Nas formas neutra e catiônica, as diferenças relativas entre os cálculos e os experimentos foram maiores, chegando a 11% na posição da banda de fluorescência da molécula neutra. Usando simulações de Dinâmica Molecular conseguimos estimar quantas moléculas de água se distribuem em torno do o-Abz. Os resultados mostram que, embora exista um número parecido de moléculas de água solvatando a molécula nas formas aniônica e catiônica, há uma redução na quantidade de ligações de hidrogênio realizadas pela protonação catiônica em relação à aniônica. O modelo utilizado para simular o o-Abz-NH(CH3) em micelas de SDS apresentou resultados satisfatórios com erro relativo entre 0,7\\% e 0,9%, no entanto são necessárias outras abordagens computacionais e experimentais para indicar em qual região a molécula se encontra na micela, dando assim mais confiabilidade e uma melhor interpretação aos resultados. / The ortho-aminobenzoic acid is a molecule largely employed as a fluorescent probe in peptide and membrane studies. The solvent dependence of its spectroscopic properties deserves great interest and we describe here results of experimental measurements and computational calculations by \\textit and Molecular Dynamics methods about spectroscopic and solvation properties of the molecule in aqueous medium at different pH values. We also examined the derivative 2-amino-N-methyl-benzamide (o-Abz-NHCH3), investigating the spectral modifications in its interaction with SDS micelles. The results of titration experiments could be interpreted as originated from three protonation states for o-Abz: in neutral pH and above, both carboxy and amine groups are deprotonated, and the molecule is in the anionic form. Decreasing the pH, protonation of amino group or carboxy renders the molecule neutral (pK = 5.0) and at low pH both groups are protonated and the molecule is in the cationic form (pK = 2.3). Geometry optimization and determination of energy minima were performed with the molecule in each protonation state using Density Functional Theory (DFT) with different functionals and basis set for atomic orbitals. Eletronic transitions were calculated from lowest energy geometry using TD-DFT (B3LYP/311++G(d,p)). The best agreement with experimental results were obtained for the anionic molecule: we observed a relative difference of 0.6\\% for the lowest energy optical transition. From the optimized geometry of the excited state the vertical transition was calculated with TD-DFT (B3LYP/Def2-TZVP), and the emission was predicted to occur at 407nm, a reasonable result compared with the experimental value or 394nm. For the molecule in neutral or cationic state, the relative differences between experimental and calculation results were greater, amounting to 11\\% for the fluorescence band in the neutral species. From Molecular Dynamics simulation we estimated the number of water molecules distributed aroud the o-Abz molecule. The results show that, although there is similar number of water molecules solvating the o-Abz in anionic and cationic state, there is a decrease in the amount of hydrogen bond in the cationic molecule. The simulation of the derivative o-Abz-NHCH3 in SDS micelles by implicit solvent methods gave results comparable to the experimental ones, with relative deviations lower than 1\\%. It should be noted that further study should be carried out in order to have a better knowledge about the location of the probe in the micelle, and to afford a beter interpretation of the results.

Dans une société qui peine à renoncer à l'utilisation des énergies fossiles, la production d'hydrogène à partir d'eau par photocatalyse solaire est une alternative que les chimistes se doivent d'explorer. La mise en place de cette solution est conditionnée à la résolution de deux problèmes majeurs : augmenter l'efficacité de la conversion solaire par le développement de nouveaux semi-conducteurs, et améliorer la réactivité en surface par le développement de co-catalyseurs efficaces. Dans un premier temps, nous avons contribué à l'étude d'une nouvelle famille de semi-conducteurs par des calculs ab initio DFT. Différentes propriétés clés ont été calculées et comparées aux valeurs expérimentales. Nous avons montré que pour une même famille de matériaux, l'absorption peut être contrôlée par modification de la composition.Ensuite, nous nous sommes focalisés sur la réaction d'oxydation de l'eau (OER). Pour cette réaction les catalyseurs de type oxyhydroxydes et leurs dérivés sont très prometteurs car à la fois efficaces et contenant des éléments abondants sur Terre, mais la compréhension de son mécanisme reste limitée. Sur le composé modèle CoOOH, nous en avons réalisé une analyse approfondie par une étude exhaustive des intermédiaires ainsi que par modélisation explicite du potentiel électrochimique. Nos études ont montré la nécessite de prendre en compte plusieurs sites réactionnels dans la détermination des mécanismes d'oxydation de l'eau sur la surface de ces catalyseurs. Enfin, une étude préliminaire de l'utilisation de la biomasse a été menée, dans le but de combiner valorisation de la biomasse et production d'hydrogène. Le cas de l'oxydation du glycérol est envisagé. / In a society struggling to waive the use of fossil fuels, hydrogen production from water by solar photocatalysis is a alternative chemists have to consider. Setting up of this solutions asks to tackle two major issues : increase solar energy conversion by developing new semiconductors, and enhance the surface reactivity by developing efficient cocatalysts.First, DFT \emph{ab initio} calculations were carried out on a new family of semiconductor materials. Different key properties were computed and compared to experimental values. We showed that for a same material family, absorption can be controlled by changing the composition.Then, we focused on Oxygen Evolution Reaction (OER). For this reaction oxyhydroxides catalysts and their derivatives seem promising as both efficient and containing earth-abundant elements, but the understanding of its mechanism still remains unclear. On CoOOH model compound, we realised an extended analysis by a comprehensive study of intermediates and by explicit modelling of electrochemical potential. Our studies showed that taking into account several reactive sites is necessary to determine the OER mechanism on these catalysts' surface.Last, a preliminary study of biomass use was carried, in order to combine its valorization along with hydrogen production. The case of glycerol photoreforming is considered.

Les facteurs de réponse UV-visible sont des éléments clés utilisés en chimie analytique afin d'évaluer les proportions des différents constituants d'un mélange. Particulièrement prisés par le monde de l'industrie, ces facteurs sont le plus souvent difficiles à obtenir, surtout lorsque les composés mis en jeu sont des impuretés difficiles à isoler ou à synthétiser. Dans ce contexte, la chimie théorique, et plus particulièrement la Théorie de la Fonctionnelle de la Densité Dépendant du Temps peut devenir un atout non négligeable, capable d'apporter des réponses en un minimum de temps. Afin de parvenir à ce type d'informations, une étude approfondie de la spectroscopie UV-visible est nécessaire. Cette étude met en lumière les capacités de la TD-DFT à simuler, non seulement la position des bandes d'absorption d'un spectre, mais également à être utilisée pour faire de la quantification de composés. À ce titre, plusieurs nouvelles fonctionnelles de la densité ont ici été développées afin de tenter d'améliorer la précision de la méthode, à la fois d'un point de vue structural, et d'un point de vue de la simulation de propriétés comme les énergies d'excitations. En somme, plusieurs modèles ont été éprouvés, dont certains développés, tous visant principalement à reproduire au mieux la structure parfois complexe des bandes d'absorption d'un spectre UV-visible. Non seulement centrée sur le processus d'absorption, cette étude s'étend également au processus de fluorescence, montrant et démontrant l'utilité de la chimie théorique en science et dans l'industrie.

Theoretical methods can be used to describe surface chemical reactions in detail and with sufficient accuracy. Advances, especially in density functional theory (DFT) method, enable to compare computational results with experiments. Quantum chemical calculations employing ONIOM DFT/B3LYP/6-31G**-MM/UFF cluster method provided in Gaussian 03 are conducted to investigate water adsorption on rutile (110), and water and ammonia adsorption on anatase (001) surfaces of titanium dioxide. Water and ammonia adsorption on anatase (001) surface is studied by also performing PW:DFT-GGA-PW91 periodic DFT method by using VASP code and the results are compared with the results of ONIOM method. The results obtained by means of ONIOM method indicate that dissociative water adsorption on rutile (110) surface is not favorable due to high activation barrier, whereas on anatase (001) surface, it is favorable since molecular and dissociative water adsorption energies are calculated to be -23.9 kcal/mol and -58.12 kcal/mol. Moreover, on anatase (001) surface, dissociative ammonia adsorption is found energetically more favorable than molecular one (-37.17 kcal/mol vs. -23.28 kcal/mol). Thermodynamic functions at specific experimental temperatures for water and ammonia adsorption reactions on anatase (001) surface are also evaluated. The results obtained using periodic DFT method concerning water adsorption on anatase (001) surface indicate that dissociative adsorption is more favorable than molecular one (-32.28 kcal/mol vs. -14.62 kcal/mol) as in ONIOM method. On the same surface molecular ammonia adsorption energy is computed as -25.44 kcal/mol. The vibration frequencies are also computed for optimized geometries of adsorbed molecules. Finally, computed adsorption energy and vibration frequency values are found comparable with the values reported in literature.

The nature and role of defects is of primary importance to understand the physical properties of C and BN single walled nanotubes. Transmission electron microscopy (TEM) is a well known powerful tool to study the structure of defects in materials. However, in the case of SWNTs, the electron irradiation of the TEM may knock out atoms. This effect may alter the native structure of the tube, and has also been proposed as a potential tool for nanoengineering of nanotubular structures. Here we develop a theoretical description of the irradiation mechanism. First, the anisotropy of the emission energy threshold is obtained via density functional based calculations. Then, we numerically derive the total Mott cross section for different emission sites of carbon and boron nitride nanotubes with different chiralities. Using a dedicated STEM microscope with experimental conditions optimised on the basis of derived cross-sections, we are able to control the generation of defects in nanotubular systems. Either point or line defects can be obtained with a spatial resolution of a few nanometers. The structure, energetics and electronics of point and line defects in BN systems have been investigated. Stability of mono- and di- vacancy defects in hexagonal boron nitride layers is investigated, and their activation energies and reaction paths for diffusion have been derived using the nudged elastic band method (NEB) combined with density functional based techniques. We demonstrate that the appearance of extended linear defects under electron irradiation is more favorable than a random distribution of point defects and this is due to the existence of preferential sites for atom emission in the presence of pre-existing defects, rather than thermal vacancy nucleation and migration.

The goal of solid state physics and chemistry is to gain deeper understanding of the basic principles of condensed matter. This ongoing process is achieved by the combination of experimental methods and theoretical models. One theoretical approach are the so-called first-principles calculations, which are based on the concept of density functional theory (DFT). In order to test the reliability of a band structure calculation, its results have to be compared with experiments. Since the electron density, the main constituent of DFT codes, cannot be directly determined experimentally with sufficient accuracy (e.g., by X-ray diffraction), other experimentally available properties are needed for the comparison with the calculation. A quantity that can be measured with high accuracy and that provides indirect information about the electron density is the electric field gradient (EFG). The EFG reflects local structural symmetry properties of the charge distribution surrounding a nucleus: the EFG is nonzero if the density deviates from cubic symmetry and therefore generates an inhomogeneous electric field at the nucleus. Since the EFG is highly sensitive to structural parameters and to disorder, it is a valuable tool to extract structural information. Furthermore, the evaluation of the EFG can provide valuable insight into the chemical bonding. Whereas the experimental determination of the quadrupole frequency and the closely related EFG has been possible for more than 70 years, reliable values for calculated EFGs could not be obtained before 1985, when an EFG module was implemented in the full-potential, linearised-augmented-plane-wave code WIEN. Since the full-potential local-orbital minimum-basis scheme FPLO is numerically very efficient and its local-orbital scheme allows an easy analysis of the different contributions to the EFG, one goal of this work was the implementation of an EFG module within the FPLO code. The newly implemented EFG module was applied to different systems: starting from simple metals, then approaching more complex systems and finally tackling strongly correlated oxides. Simultaneously, the EFGs for the studied compounds were determined experimentally by NMR spectroscopists. This close collaboration enables the comparison of the calculated EFGs with the experimental observations, which makes it possible to extract more physical and chemical information from the measured values regarding structural relaxation, distortion, the chemical bond or the relevance of electron correlation. In the last part of this work, the importance of corrections that go beyond the EFG are discussed. Such corrections arise for any multipole order of the hyperfine interactions, and are due to electron penetration into the nucleus. A correction similar to the isomer shift, coined here the "quadrupole shift" is examined in detail.

Supramolekulinė chemija – tyrimų kryptis, nagrinėjanti struktūras, sudarytas iš riboto ir neriboto skaičiaus molekulių (tektonų), sąveikaujančių tarpusavyje silpnosiomis nekovalentinėmis sąveikomis. Žinoma, kad medžiagų savybės užkoduotos ne tik molekulių struktūroje, bet ir jų tarpusavio išsidėstyme. Savo ruožtu, chirališkumas yra vienas iš faktorių, leidžiančių vienoms molekulėms atpažinti kitas. Pagrindiniai disertacijos tikslai: nustatyti 1) chiralinių, konformaciškai suvaržytų bei labilių junginių, turinčių biciklo[3.3.1]nonano fragmentą, chromoforų prigimties, tarpusavio orientacijos ir atstumo įtaką chiroptinėms savybėms, 2) chiralinių tripakeistų aromatinių, turinčių biciklo[3.3.1]nonano pakaitus, ir kompleksinių paladžiociklinių junginių chirališkumo ir struktūros įtaką formuojant įvairaus lygio tvarkias supramolekulines struktūras. Naudojantis apskritiminio dichroizmo spektroskopijair teoriškai atliktais ab initio skaičiavimais charakterizuotos molekulės, turinčios įvairios elektroninės prigimties chromoforus, bei jose vykstantys elektroniniai šuoliai. Susintetinti tripakeisti aromatiniai junginiai, turintys išorinius biciklo[3.3.1]nonano ir įvairių dydžių aromatinius fragmentus. Ištirta tokių save atpažįstančių chiralinių tripakeistų aromatinių junginių struktūros įtaka supramolekulinei asociacijai tirpale ir ant paviršiaus. Nustatyta, kad susintetinti V formos chiralinis ir raceminis dialkinbiciklo[3.3.1]nonenil- ligandai, turintys koordinuojantį piridino pakaitą... [toliau žr. visą tekstą] / The supramolecular chemistry of assemblies composed of a limited or infinite number of the molecular tectons interacting with each other via noncovalent interactions was investigated with a special emphasize on the chirality of the building blocks. The following objectives were pursued in this work: 1) to determine the electronic structure of both conformationally rigid and labile chiral bicyclo[3.3.1]nonane compounds, the mutual orientation and distance of the chromophores and its impact on chiroptical properties, 2) to study the influence of chirality and structure of palladacycle and trisubstituted compounds, containing external bicyclo[3.3.1]nonanyl- and aromatic fragments of different size on the formation of various supramolecular structures. The chiral bicyclo[3.3.1]nonane compounds with chromophores of different electronic nature were synthesized. The possibilities of exciton interaction and charge transfer phenomena were studied in the obtained molecules. The influence of chirality and structure of trisubstituted compounds containing external bicyclo[3.3.1]nonanyl- and aromatic fragments of different size on supramolecular association in solution and on the surface was investigated. In solution, the trisubstituted compounds exist in the form of nanoparticles with regular supramolecular structure. It was shown that the V-shaped chiral and racemic dialkynbicyclo[3.3.1]nonenyl- ligands having coordinating pyridine moiety, form rhomb-shaped palladacycle. The racemic and... [to full text]

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