No description available.

The PIXEL method has been used for several years to analyse intermolecular interactions in organic crystals. The simplicity and speed of the calculations, along with the breakdown of intermolecular energies into physical contributing terms, mean that it has had a massive influence on the way organic crystal structures are interpreted. In the work done to date, the parameters required to perform a PIXEL calculation have been established for 1st, 2nd and 3rd row transition metals. Using these parameters, lattice energies of several transition metal complexes containing various chemical environments have been calculated and compared to experimental sublimation enthalpies. Straight line parameters for these results have been comparable to work by Gavezzotti, the author of the program, in testing the method for organic crystal structures. In addition to lattice energies, PIXEL gives dimer interaction energies of molecules in a crystal structure. The values of these interactions have been compared to single point DFT energy calculations. PIXEL has shown good agreement with a range of different intermolecular interactions, along with a significant saving in computer time over the higher level calculations. Aside from four empirical parameters, PIXEL requires only fundamental atomic properties such as ionisation potentials, electronegativities and van der Waals radii. For the most part, these values are obtained from standard reference tables and texts with the exception of atomic polarizabilities. This parameter is of great importance as it is used during the calculation of the dispersion term, an interaction which has a major influence on crystal packing. In previous work, atomic polarizabilities have been calculated using either the Slater-Kirkwood approximation or the Clausius-Mossotti relation. Both of these methods are rather simple, and do not account for possible changes in atomic polarizability resulting from differences in chemical environment. The Atoms in Molecules (AIM) approach has been used to attempt to obtain a range of polarizability values for atoms common to organic chemistry. It is observed that in the series of straight chained primary monoamines, Cn-H2n+3N, an alternation in melting points occurs between odd and even values of n. This alternation could be traced to differences in hydrogen-bonding and chain-packing that occur between odd and even-membered amines. Molecular interaction energy calculations were carried out using the PIXEL method, enabling quantitative energetic analysis of the packing differences. In this work, the crystal structures of the primary amines from ethylamine to decylamine were solved for the first time. All of these compounds are liquids at room temperature, so crystals were grown in situ by laser-assisted zone refinement at 10 K below their melting points. Diffraction data were then collected at 150 K. From propylamine to decylamine, all crystal structures are orthorhombic (or pseudo-orthorhomic) with the unit cell dimensions ~5 Ǻ x ~7 Ǻ x c Ǻ, where c increases with chain length. In the case of ethylamine, a phase characterised by single crystal diffraction at 180 K underwent a transition to a different phase on cooling to 150 K. The low-temperature phase was investigated using powder methods.

Noncovalent intermolecular interactions, widely found in molecular clusters and bio-molecules, play a key role in many important processes, such as phase changes, folding of proteins and molecular recognition. However, accurate calculation of interaction energies is a very difficult task because the interactions are normally very weak. Rigorous expressions for the electrostatic and polarization interaction energies between two molecules A and B, in term of the electronic densities, have been programmed: (see formula in document). Z is atomic charge, ρ0 is the electron density of the isolated molecule and Δρind is the electron density change of the molecule caused by polarization. With some approximations, procedures for electrostatic and polarization energy calculations were developed that involve numerical integration. Electrostatic and polarization energies for several bimolecular systems, some of which are hydrogen bonded, were calculated and the results were compared to other theoretical and experimental data. A second method for the computing of intermolecular interaction energies has also been developed. It involves a “supermolecule” calculation for the entire system, followed by a partitioning of the overall electric density into the two interacting components and then application of eq. (1) to find the interaction energy. In this approach, according to Feynman’s explanation to intermolecular interactions, all contributions are treated in a unified manner. The advantages of this method are that it avoids treating the supersystem and subsystems separately and no basis set superposition error (BSSE) correction is needed. Interaction energies for several hydrogen-bonded systems are calculated by this method. Compared with the result from experiment and high level ab initio calculation, the results are quite reliable.

The majority of pharmaceutical products are formulated as solids in the crystalline state. With the potential to exist in different crystalline modifications or polymorphs, each solid form bears its own physical and chemical properties, influencing directly bioavailability and manufacturability of the final dosage form. In view of the importance of crystalline form selection in the drug development process, it is imperative for pharmaceutical scientists to work arduously on various aspects of polymorphism, ranging from fundamental understanding of the phenomenon at the molecular level to practical utilization of a specific crystalline form. One common feature of organic crystals is the existence of distinct molecular conformations in different polymorphic structures, known as conformational polymorphism. Conformational polymorphs are routinely observed in drug development, produced when crystal growth conditions vary. Crystallization from solution involves nucleation and crystal growth, the mechanisms that influence the polymorphic outcome. The embryonic solute aggregate has been recognized to play a critical role in dictating the final crystal structure, and solution conditions are also known to drastically influence the self-association behavior of solute molecules during crystallization, affecting crystal packing of organic molecules. For the crystal growth of conformational polymorphs, changes in molecular conformation not only determine the growth kinetics, but also influence the nature and strength of interactions present in the crystal structures. How conformation and intermolecular interaction affect each other underlines the intricacy and the wonder of crystal growth of the organic. Thus, the overall goal of this research is to provide the fundamental understanding of the extent to which solution conditions influence the molecular conformation in the solid-state of a model drug, tolfenamic acid. By combining experimental studies with advanced computational tools, this dissertation offers novel insights into solution species during pre-nucleation and molecular packing of conformational polymorphs of tolfenamic acid. In-depth understanding of the underlying connection between molecular conformation and crystal packing will help advance the knowledge required for rational control of crystal growth.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第19197号 / 農博第2136号 / 新制||農||1034(附属図書館) / 学位論文||H27||N4943(農学部図書室) / 32189 / 京都大学大学院農学研究科森林科学専攻 / (主査)教授 西尾 嘉之, 教授 木村 恒久, 教授 髙野 俊幸 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

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No / We investigated five different methods for evaluating the electrostatic interaction between atoms in force field calculations on organic solids. Atomic charges and multipoles were obtained by fitting them to the molecular electrostatic potential, calculated in vacuum with an ab initio quantum mechanical method. Multipole moments were derived using three schemes, differing in the order in which the monopoles, dipoles and quadrupoles were fitted. For comparison, Gasteiger charges were also calculated. Using these electrostatic models, the lattice parameters and the molecular geometry of 48 organic crystals were optimised with the DREIDING force field. During the optimisation, the atomic multipoles were rotated with their local environment to account for molecular flexibility. For comparative reasons, rigid-body optimisations were performed on a subset of structures. The results were analysed in terms of structural parameters of the lattice and the molecules, and, for the ten polymorphic systems present in the test set, in terms of relative stability. On average, the multipole methods were not superior to the point charge methods for the full optimisation. For rigid molecules, however, the multipole models gave a substantial improvement in lattice parameters. No evidence was found that parameters for van der Waals energies need to be refitted for a specific electrostatic model. Energy differences between polymorphs were less than 5 kcal mol¿1 in eight out of ten cases, independent of the electrostatic model used. The results show that our use of distributed multipoles to describe the intra-molecular as well as inter-molecular electrostatic interactions does lead to an improvement in accuracy for rigid molecules, but not for flexible molecules. The investigation shows that accurate descriptions of the intra-molecular as well as the inter-molecular energies are crucial for the successful optimisation of crystal structures of organic solids.

No presente trabalho utilizamos as espectroscopias eletrônica e vibracional, com o apoio de simulação computacional de líquidos para estudar o comportamento solvatocrômico e ionocrômico de diaminoantraquinonas. Adicionalmente estudamos a potencialidade da 1,2-diaminoantraquinona (1,2-DAAQ) no reconhecimento de ânions em superfícies de prata. Utilizando espectroscopia de absorção obtivemos espectros da 1,2-DAAQ e alguns isômeros em diversos solventes. Estes resultados foram analisados por métodos empíricos de solvatocromismo, principalmente, pela escala solvatocrômica de Kamlet-Taft. Esta análise nos propiciou um conhecimento preciso sobre o comportamento da 1,2-DAAQ em meio solvente e serviu de suporte para o estudo do ionocromismo, e da interação com as superfícies. Através da simulação computacional geramos estruturas de soluções da 1,2-DAAQ em três solventes e analisamos a estrutura destas soluções via análise das Funções de Distribuição Radial de pares, o que nos possibilitou uma visão no nível microscópico do efeito das interações com o solvente. As estruturas geradas serviram de base para o cálculo do espectro de absorção para comparação com os valores experimentais. Baseado nesta comparação foi possível especular que a estrutura da 1,2-DAAQ é afetada pelo solvente no estado excitado. Utilizando espectroscopia no infravermelho e eletrônica foi possível caracterizar o tipo de interação entre a 1,2-DAAQ e o ânion fluoreto, como sendo por ligação de hidrogênio de força moderada. A atribuição vibracional da 1,2-DAAQ foi realizada com base nos espectros Raman, auxiliada por cálculos de freqüência. A atribuição foi utilizada para a determinação da orientação da 1,2-DAAQ nas superfícies de prata e principalmente para estudar a natureza desta interação. A análise destes resultados nos permitiu traçar um panorama bastante claro sobre esta interação além de auxiliar no entendimento do uso da 1,2-DAAQ como sonda aniônica de superfícies. Finalmente, através da espectroscopia Raman ressonante foi possível confirmar e detalhar a atribuição da transição eletrônica observada na região do visível, característica das diaminoantraquinonas. / In the present work, the ionochromic and solvatochromic behavior of several diaminoantraquinones were investigated by means of optical and vibrational spectroscopies, alongside computational simulation. The UV-Vis spectra of 1,2- diaminoantraquinone (1,2-DAAQ) were analyzed using empirical solvatochromic scales, like the Kamlet-Taft. Such analysis enabled an accurate description of its solvatochromic behavior that was instrumental to understand its interaction with anions and metallic surfaces. Computational simulation provided the structures of 1,2-DAAQ solutions in three different solvents, and the analyses of the radial distribution functions revealed a microscopic view of its interactions with the solvents. The obtained structures were the departing points for the calculation of the electronic spectrum, then compared with the experimental one. The results suggest that the structure of 1,2-DAAQ is substantially affected by the solvent in the excited state. Infrared spectroscopy clearly indicates that the interaction of the 1,2-DAAQ and fluoride involves a hydrogen bonding of moderate strength. Raman spectroscopy and quantum chemical calculations provided the means for the vibrational assignment that was instrumental to understand the orientation of the molecule in its interaction with silver surface.

Ce travail a pour objet de synthétiser de nouveaux matériaux hybrides organiques-inorganiques, de types silsesquioxanes pontants. La structure locale et les propriétés de luminescence sont caractérisées en vue d’applications potentielles dans le domaine de la photonique durable comme les concentrateurs solaires.Dans ce contexte, trois familles distinctes de matériaux sont synthétisées, basées sur six précurseurs pouvant s’auto-assembler à travers des liaisons hydrogènes et dont les parties sililées peuvent être poly-condensées lors de la réaction sol-gel. Ces précurseurs diffèrent par leur sous structure organique i.e. 1) structure linéaire où la partie organique est basée sur le groupement malonamide (P2-m et P4-m); 2) structure linéaire dans laquelle un aromatique sépare deux groupements amide et/ou thioamide (P(UU), P(UT) and P(TT)) et 3) une structure à trois embranchements dont la partie organique est basée sur des groupements amides (t-UPTES (5000)).Les deux hybrides organiques inorganiques (M2-m et M4-m) résultant de l’hydrolyse condensation des précurseurs P2-m et P4-m sont synthétisés en présence de lanthanides. On étudie l’impact de la présence d’un ou deux groupes malonamides sur la structure locale et les propriétés de photoluminescence.Les hybrides organiques-inorganiques (H(UU), H(UT) and H(TT)) sont obtenus par hydrolyse condensation des précurseurs des précurseurs (P(UU), P(UT) and P(TT)). Des composés organiques modèles des trois sous structurels organiques sont également synthétisés. L’impact de la substitution du groupement urée par le groupement thio-urée sur la structure locale des modèles et des hybrides est étudié par spectroscopie vibrationnelle. Les mécanismes de compressions et les propriétés optiques des matériaux sont ensuite analysés à la lumière des différents types de liaisons hydrogènes (urée-urée, urée-thio-urée et thio-urée--thio-urée) mises en évidence dans ces composés.es hybrides basés sur les précurseurs t-UPTES(5000) sont synthétisés selon différentes stratégies. En changeant la concentration de HCl et d’eau ou en effectuant la synthèse dans un environnement contrôlé, on montre une amélioration des propriétés optiques de ce système, en particulier, le rendement quantique absolu et le coefficient d’absorption. De plus, les mécanismes de recombinaison responsables de l’émission sont étudiés à travers la comparaison entre les propriétés de luminescence des modèles organiques et inorganiques.Finalement, de par leur affinité pour les ions lanthanides les précurseurs P2-m and P4-m ont été dopés par des ions Eu3+. La structure locale des hybrides correspondants montre une coordination entre l’hybride et l’hôte. Grâce à un rendement quantique de luminescence très élevé pour ces matériaux, des concentrateurs solaires luminescents peuvent être développés présentant un maximum de rendement quantique absolu de 0.60+/-0.06 et un rendement de conversion optique de 12.3% dans la région spectrale (300-380 nm). / The present work aims to synthesize new organic-inorganic hybrid materials, bridge silsesquioxanes type, and characterize the local structure and photoluminescence properties overlooking potential applications in the area of sustainable photonics, namely, in solid-state lighting as luminescent solar concentrators.In this context, three distinct families of materials based on six precursors which differ in their structural organization are synthesized, i.e. precursors with structure: 1) linear where the organic component is based on malonamide group (P2-m and P4-m); 2) linear which is added an aromatic ring whose organic part is based on amide and/or thioamide (P(UU), P(UT) and P(TT)) and 3) tri-branched which the organic component is based on amide group (t-UPTES (5000)).Two organic-inorganic hybrids (M2-m and M4-m) which results from hydrolysis and condensation of the precursors P2-m and P4-m are synthetized. The role of the presence of one or two malonamide groups is studied in terms of local structure and photoluminescence properties.Three organic-inorganic hybrids (H(UU), H(UT) and H(TT)) based on (P(UU), P(UT) and P(TT)) aresynthesized and structurally characterized aiming to study the role of the hydrogen bond in the self-assembling of these materials. The presence of different types of hydrogen bonds (bifurcated, linear and cyclic) induces different conformations which affect the physical properties (mechanical and optical) of the materials.Hybrids based on t-UPTES(5000) precursor are synthesized based on different synthesis strategies. Changing the concentration of HCl and water content as well as the synthesis in a controlled environment allow the improvement of the optical properties of this system, in particular, the absolute quantum yield and the absorption coefficient. In addition, it is studied the recombination mechanisms responsible for the emission through the comparison between the corresponding photoluminescence properties of the organic and inorganic models.Finally, due to the structural simplicity of the precursors and affinity with lanthanide ions, P2-m and P4-m precursors are doped with Eu3+. The local structure of the corresponding hybrids shows local coordination between the ion and host. Efficient materials concerning the quantum yield values lead to the development of luminescent solar concentrators with a maximum absolute quantum yield of 0.600.06 and optical conversion efficiency in the absorption spectral region (300-380 nm) of 12.3%.

No presente trabalho utilizamos as espectroscopias eletrônica e vibracional, com o apoio de simulação computacional de líquidos para estudar o comportamento solvatocrômico e ionocrômico de diaminoantraquinonas. Adicionalmente estudamos a potencialidade da 1,2-diaminoantraquinona (1,2-DAAQ) no reconhecimento de ânions em superfícies de prata. Utilizando espectroscopia de absorção obtivemos espectros da 1,2-DAAQ e alguns isômeros em diversos solventes. Estes resultados foram analisados por métodos empíricos de solvatocromismo, principalmente, pela escala solvatocrômica de Kamlet-Taft. Esta análise nos propiciou um conhecimento preciso sobre o comportamento da 1,2-DAAQ em meio solvente e serviu de suporte para o estudo do ionocromismo, e da interação com as superfícies. Através da simulação computacional geramos estruturas de soluções da 1,2-DAAQ em três solventes e analisamos a estrutura destas soluções via análise das Funções de Distribuição Radial de pares, o que nos possibilitou uma visão no nível microscópico do efeito das interações com o solvente. As estruturas geradas serviram de base para o cálculo do espectro de absorção para comparação com os valores experimentais. Baseado nesta comparação foi possível especular que a estrutura da 1,2-DAAQ é afetada pelo solvente no estado excitado. Utilizando espectroscopia no infravermelho e eletrônica foi possível caracterizar o tipo de interação entre a 1,2-DAAQ e o ânion fluoreto, como sendo por ligação de hidrogênio de força moderada. A atribuição vibracional da 1,2-DAAQ foi realizada com base nos espectros Raman, auxiliada por cálculos de freqüência. A atribuição foi utilizada para a determinação da orientação da 1,2-DAAQ nas superfícies de prata e principalmente para estudar a natureza desta interação. A análise destes resultados nos permitiu traçar um panorama bastante claro sobre esta interação além de auxiliar no entendimento do uso da 1,2-DAAQ como sonda aniônica de superfícies. Finalmente, através da espectroscopia Raman ressonante foi possível confirmar e detalhar a atribuição da transição eletrônica observada na região do visível, característica das diaminoantraquinonas. / In the present work, the ionochromic and solvatochromic behavior of several diaminoantraquinones were investigated by means of optical and vibrational spectroscopies, alongside computational simulation. The UV-Vis spectra of 1,2- diaminoantraquinone (1,2-DAAQ) were analyzed using empirical solvatochromic scales, like the Kamlet-Taft. Such analysis enabled an accurate description of its solvatochromic behavior that was instrumental to understand its interaction with anions and metallic surfaces. Computational simulation provided the structures of 1,2-DAAQ solutions in three different solvents, and the analyses of the radial distribution functions revealed a microscopic view of its interactions with the solvents. The obtained structures were the departing points for the calculation of the electronic spectrum, then compared with the experimental one. The results suggest that the structure of 1,2-DAAQ is substantially affected by the solvent in the excited state. Infrared spectroscopy clearly indicates that the interaction of the 1,2-DAAQ and fluoride involves a hydrogen bonding of moderate strength. Raman spectroscopy and quantum chemical calculations provided the means for the vibrational assignment that was instrumental to understand the orientation of the molecule in its interaction with silver surface.