Os métodos computacionais da química quântica foram empregados para estudar as estruturas moleculares e as energias de interação de cátions e ânions que são componentes de alguns líquidos iônicos funcionalizados, derivados do imidazólio. O estudo teve como objetivo comparar e relacionar os efeitos da presença de funcionalização nos substituintes das posições 1 e 3 do cátion imidazólio, nas propriedades desses líquidos iônicos. Essa funcionalização pode ocorrer pela presença de insaturações, grupos aromáticos, éteres, álcoois, tióis, aminas, nitrilas entre outros grupos nas cadeias dos substituintes. Nesta tese são reportados os estudos dos complexos formados por ânions tetrafluorborato e cátions imidazólio substituídos por grupos metila, etila, propila, butila, isobutila, vinila, propargila, alila, crotila e metalila, observando assim o efeito da presença de substituintes contendo cadeias insaturadas em comparação com os de cadeias saturadas nas estruturas, distribuições de carga, energias de interação e propriedades físico-químicas desses sistemas. Nesses sistemas foram observados intensos efeitos de polarização e transferência de carga ânion-cátion. Foram encontradas diversas relações entre volumes iônicos, energias de interação dos íons e as propriedades de transporte dos respectivos líquidos iônicos. / The methods of computational quantum chemistry have been used to study the molecular structures and the interaction energies of cations and anions which are components of some functionalized ionic liquids derived from imidazolium. The objective of this study is comparing and relating the effects of the presence of functionalization of the side chains of the imidazolium with the properties of these ionic liquids. This functionalization can occur by the presence of unsaturated side chains, aromatic groups, ether, alcohols, thiols, amines, nitriles among other groups in the side chains. In this thesis are reported the studies of the complexes formed of tetrafluorborate anions and imidazolium cations with side chains methyl, ethyl, propyl, butyl, isobutyl, vinyl, propargyl, allyl, crotyl and methallyl, thus observing the effects of the presence of unsaturated side chains compared to saturated ones on the structures, charge distributions, interaction energies and physicochemical properties of these systems. It was observed in these systems strong effects of polarization and anion-cation charge transfer. It was found several relations between ionic volumes, interation energies of the ions and the transport properties of the respective ionic liquids.

Made available in DSpace on 2014-07-29T15:30:35Z (GMT). No. of bitstreams: 1 dissertacao maria regilda araujo fernandes.pdf: 889828 bytes, checksum: eeac21e7e2102f6042640b9c030c3870 (MD5) Previous issue date: 2009-02-27 / The pathogenic fungus Paracoccidioides brasiliensis is the etiologic agent of Paracoccidioidomycosis (PCM). The main route of contamination is the inhalation of fungal propagules that convert to yeast in the host tissues. The urease is among the factors of virulence described for dimorphic fungus. It hydrolyzes the urea producing molecules of ammonia and carbamate. Pbure has 3,012 bp, corresponding to a predicted protein of 837 amino acids, predicted molecular mass of 90 kDa and pI 6.0. PbURE has signature to nickel-dependent enzyme for its activity. The phylogenetic relationship between PbURE and urease from other fungi was evaluated. The cDNA that encodes PbURE was inserted into the expression vector pET-32a and recombinant protein of 103 kDa was expressed. Polyclonal antibody were produced against PbUREr and used on Western blot, Far-Western blot and ELISA. The results showed that PbUREr interferes on interaction between P. brasiliensis and pulmonary epithelial cells A549. PbUREr was able to bind to proteins fibronectin and type IV collagen, components of the extracellular matrix (ECM). The interaction between PbURE and calnexin protein was identified by the technique of two-hybrid. / O fungo patogênico humano Paracoccidioides brasiliensis é o agente etiológico da Paracoccidioidomicose (PCM). A principal via de contaminação é a inalação de micélios ou conídios do fungo que se convertem em leveduras no hospedeiro. Dentre os fatores de virulência descritos para fungos dimórficos está a urease, a qual hidrolisa uréia produzindo amônia e carbamato. Pbure possui 3.012 pb, correspondendo a uma proteína predita de 837 aminoácidos, massa molecular predita de 90 kDa e pI 6.0. PbURE possui assinatura de uma enzima dependente de níquel para sua atividade. A relação filogenética entre PbURE e ureases de outros fungos foi avaliada. O cDNA que codifica PbURE foi inserido no vetor de expressão pET-32a e a proteína recombinante de 103 kDa foi expressa. Anticorpo policlonal foi produzido contra PbUREr e utilizados nos ensaios de Western blot, Far-Western blot e ELISA. Os resultados mostram que PbUREr interfere na interação entre P. brasiliensis e células epiteliais pulmonares A549. PbUREr foi capaz de se ligar às proteínas fibronectina e colágeno tipo IV, componentes da matriz extracelular (MEC). A interação entre PbURE e a proteína calnexina foi identificada através da técnica de duplo-híbrido.

Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2017-04-24T13:45:43Z No. of bitstreams: 2 Dissertação - Andrea Leite Camargo Santana - 2017.pdf: 3114758 bytes, checksum: 4fa4c3e9a2e7062f2940b053f1250619 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2017-04-24T13:46:06Z (GMT) No. of bitstreams: 2 Dissertação - Andrea Leite Camargo Santana - 2017.pdf: 3114758 bytes, checksum: 4fa4c3e9a2e7062f2940b053f1250619 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2017-04-24T13:46:06Z (GMT). No. of bitstreams: 2 Dissertação - Andrea Leite Camargo Santana - 2017.pdf: 3114758 bytes, checksum: 4fa4c3e9a2e7062f2940b053f1250619 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-03-29 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / Paracoccidioides fungi are the causative agents of paracoccidioidomycosis, an endemic disease in Latin America with great socioeconomic importance. Inhalation of spores, the infectious particles of the fungus, is a common way to get the infection. Its treatment is slow and generates long-term side effects making it necessary to study new metabolic pathways that can be potential targets for antifungal development. In this context, stands out the chiquimate pathway in Paracoccidioides spp., related to the production of chorismate and production of aromatic amino acids, and the chorismate synthase involved in the last stage of this pathway. The chorismate synthase from Pb18 was cloned into pGEX-4T3 vector, expressed in pLysS cells and purified on a glutathione-sepharose column. Antibodies were produced from the immunization of mice with the recombinant protein obtained and used in Western blot assay to confirm protein expression. For characterization of the enzyme, its modeling was carried out. Pull-down-GST assay was performed to identify interactions between the chorismate synthase and soluble proteins present in total protein extract of Pb18. The interactions found included proteins of different functional categories related to protein synthesis, related with metabolism of common intermediates such as folate and quinolinate or related with the availability of ATP, phosphoenolpyruvate and erythrose-4-phosphate required in the chiquimate pathway. Unexpected interactions with proteins of the cell cycle and also with regulating proteins of the cell division process were observed. / Fungos do gênero Paracoccidioides são os agentes causadores da paracoccidioidomicose, uma doença endêmica na América Latina de grande importância socioeconômica. A inalação de esporos, partículas infecciosas do fungo, é uma forma comum de adquirir a infecção. O seu tratamento é lento e gera efeitos colaterais tornando necessário o estudo de novas vias metabólicas que sejam potenciais alvos para o desenvolvimento de antifúngicos. Nesse contexto, destaca-se a via do chiquimato em Paracoccidioides spp., relacionada à obtenção de corismato e produção de aminoácidos aromáticos, sendo corismato sintase a enzima envolvida na última etapa dessa via. A corismato sintase proveniente de Pb18 foi clonada em vetor pGEX-4T3, expressa em células pLysS e purificada em coluna de glutationa-sefarose. Anticorpos foram produzidos a partir da imunização de camundongos com a proteína recombinante obtida e utilizados em ensaio de Western blot a fim de confirmar a expressão proteica. A modelagem da corismato sintase foi realizada e os aminoácidos envolvidos no sítio ativo foram identificados. Ensaios de pull-down-GST foram realizados a fim de identificar os complexos de interações entre a corismato sintase e proteínas solúveis presentes em extrato proteico total de Pb18. As interações encontradas incluíram proteínas de diferentes categorias funcionais relacionadas à síntese proteica, ao metabolismo de intermediários comuns como folato e quinolinato ou ainda com a disponibilidade de ATP, fosfoenolpiruvato e eritrose-4-fosfato necessários na via do chiquimato. Interações inesperadas com proteínas do ciclo celular e também com proteínas reguladoras do processo de divisão celular foram observadas.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-05-08T17:51:58Z No. of bitstreams: 1 charlaneciminicorrea.pdf: 11668631 bytes, checksum: a7ab701003fdf688b49377e542ceb430 (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-05-17T14:03:22Z (GMT) No. of bitstreams: 1 charlaneciminicorrea.pdf: 11668631 bytes, checksum: a7ab701003fdf688b49377e542ceb430 (MD5) / Made available in DSpace on 2017-05-17T14:03:22Z (GMT). No. of bitstreams: 1 charlaneciminicorrea.pdf: 11668631 bytes, checksum: a7ab701003fdf688b49377e542ceb430 (MD5) Previous issue date: 2011-03-04 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Este trabalho de tese de doutorado consistiu na síntese e caracterização de arranjos supramoleculares com os metais Mn2+, Co2+, Cu2+ e Zn2+ da primeira série de transição contendo ligantes nitrogenados 1,3-bis(4-piridil)propano (BPP), sulfeto de di(4-piridila) (DPS) e dissulfeto de di(4-piridila) (DPSS) e policarboxilatos 1,2,4,5-benzenotetracarboxilato (BT), p-sulfobenzoato (SF) e 1,3,5-benzenotricarboxilato (BTC). Foram obtidos vinte e seis compostos que foram caracterizados por técnicas analíticas e espectroscópicas, tais como, análise elementar (CHN), análise térmica (TG/DTA) e espectroscopia vibracional (infravermelho e Raman). Dentre esses, vinte e dois compostos foram obtidos na forma de monocristais e tiveram suas estruturas determinadas por difração de raios X de monocristal. A análise térmica mostrou que todos os compostos apresentam-se hidratados, com moléculas de água de coordenação e/ou de cristalização. A espectroscopia vibracional foi importante para inferir sobre os modos de coordenação dos grupos carboxilatos através do cálculo do ∆ν (νassimCOO-νsimCOO). Nos compostos contendo o ligante BT, o grupo carboxilato atuou sempre de modo monodentado. Para os compostos com o ligante SF foram observados os modos monodentado e quelato e para o ligante BTC os modos monodentado, quelato e em ponte syn-syn e syn-anti. Foram descritas a síntese e caracterização dos compostos envolvendo o carboxilato BT e os ligantes nitrogenados BPP, DPS e DPSS que originaram onze complexos inéditos nomeados como: MnBTBPP, CoBTBPP, CuBTBPP, ZnBTBPP, MnBTDPS, CoBTDPS, CuBTDPS, ZnBTDPS, MnBTDPSS, CoBTDPSS e ZnBTDPSS. O ligante BT está presente em todos estes compostos e, com exceção do CoBTDPSS, apresentaram o ligante nitrogenado coordenado em ponte. Todos os compostos exceto o ZnBTBPP tiveram suas estruturas determinadas por difração de raios X de monocristal. Em especial, MnBTDPS e CoBTDPS são isoestruturais e os compostos ZnBTDPS e ZnBTDPSS apresentam estruturas semelhantes inclusive com a mesma topologia de rede. Realizou-se o estudo da síntese e caracterização de nove compostos utilizando o carboxilato SF e os ligantes nitrogenados BPP, DPS e DPSS nomeados, MnSFBPP, CoSFBPP, CuSFBPP, ZnSFBPP, CoSFDPS, CuSFDPS, ZnSFDPS, CoSFDPSS e ZnSFDPSS. Todos os compostos com exceção do CoSFDPSS tiveram suas estruturas determinadas por difração de raios X de monocristal. Em todas as estruturas analisadas os ligantes nitrogenados se coordenaram aos centros metálicos em ponte. No composto MnSFBPP o ligante SF não estava presente. Nos compostos CoSFBPP e CoSFDPS este ligante permaneceu na rede agindo como ânion estabilizando estas estruturas. Os arranjos bidimensional e tridimensional dos compostos foram observados pela presença de ligações de hidrogênio clássicas e não-clássicas, mostrando a importância das interações não covalentes na formação do arranjo supramolecular, bem como da estabilização das estruturas. Por fim, através das sínteses envolvendo o carboxilato BTC com os ligantes nitrogenados BPP, DPS e DPSS, seis complexos foram descritos como MnBTCBPP, CoBTCBPP, ZnBTCBPP, MnBTCDPS, ZnBTCDPS e ZnBTCDPSS. Os complexos CoBTCBPP, MnBTCDPS e ZnBTCDPS não apresentaram o ligante nitrogenado na estrutura, sendo que em todos eles pôde-se observar a presença do ligante BTC. Os complexos MnBTCBPP, CoBTCBPP, ZnBTCBPP e ZnBTCDPSS foram obtidos na forma de monocristais e tiveram suas estruturas cristalinas determinadas por difração de raios X de monocristal. Confirmaram-se então diversos modos de coordenação do ligante BTC nestes complexos tais como monodentado, quelato e em ponte syn-syn e syn-anti. / This work presents the synthesis and characterization of supramolecular arrays with Mn2+, Co2+, Cu2+ and Zn2+ first row transition metal ions, polydentate nitrogen ligands 1,3-bis(4-pyridyl) propane (BPP); di(4-pyridyl)sulfide (DPS) and di(4-pyridyl)disulfide (DPSS) and polycarboxylates 1,2,4,5-benzenotetracarboxylate (BT), p-sulfobenzoate (SF) and 1,3,5-benzenotricarboxylate (BTC). Twenty six compounds were synthesized and characterized of elemental analysis (CHN), thermal analysis (TG/DTA) and vibrational spectroscopy (infrared and Raman). Among these, twenty two compounds were isolated as single crystals and had their structures determined by single crystal X-ray diffraction analysis. Thermal analysis showed that all compounds are hydrated with coordination and/or lattice water molecules. Vibrational spectroscopy was very important to inform about the carboxylate groups coordination mode through ∆ν (νasymCOO - νsymCOO) value. In compounds containing BT ligand, the carboxylate group always acted in monodentate mode. For compounds containing SF ligands, monodentate and bidentatechelate modes were observed and for BTC ligand, monodentate, bidentate-chelate and syn-syn and syn-anti bridging modes were noted. The synthesis and characterization of compounds involving the BT carboxylate ligand and BPP, DPS and DPSS nitrogen ligands gives rise to eleven complexes described as MnBTBPP, CoBTBPP, CuBTBPP, ZnBTBPP, MnBTDPS, CoBTDPS, CuBTDPS, ZnBTDPS, MnBTDPSS, CoBTDPSS and ZnBTDPSS. BT ligand is present in all compounds and, except CoBTDPSS, they showed the nitrogen ligand in bridging coordination mode. All compounds, except ZnBTBPP, had their structures determined by single crystal X-ray diffraction analysis. In particular, MnBTDPS and CoBTDPS are isostructural and ZnBTDPS and ZnBTDPSS present similar structures with the same network topology. Studies of the synthesis and characterization of nine compounds using SF carboxylate and BPP, DPS and DPSS nitrogen ligands were realized, appointed as MnSFBPP, CoSFBPP, CuSFBPP, ZnSFBPP, CoSFDPS, CuSFDPS, ZnSFDPS, CoSFDPSS and ZnSFDPSS. All compounds, except CoSFDPSS, had their structures determined by single crystal X-ray diffraction analysis. In all structures the nitrogenated ligands coordinate to the metal centers in the bridging mode. For MnSFBPP the absence of ligand SF was noted. In CoSFBPP and CoSFDPS, this ligand remained uncoordinated, acting as a counter anion stabilizing these structures. The two- and three-dimensional arrays of the compounds were observed by the presence of classic and non-classic hydrogen bondings showing the importance of non-covalent interactions in the supramolecular arrangement, as well as in the structure stabilization. Finally, through the syntheses involving the BTC carboxylate with nitrogenated ligands BPP, DPS and DPSS, six complexes are described as MnBTCBPP, CoBTCBPP, ZnBTCBPP, MnBTCDPS, ZnBTCDPS and ZnBTCDPSS. CoBTCBPP, MnBTCDPS and ZnBTCDPS do not present nitrogen ligands in their structures and in all of them the presence of BTC ligand is observed. MnBTCBPP, CoBTCBPP, ZnBTCBPP and ZnBTCDPSS were obtained as single crystals and had their crystal structures determined by X-ray diffraction analysis. Great diversity of BTC ligand coordination modes as monodentate, chelate and syn-syn, syn-anti bridging modes were confirmed.

Les huit ARN viraux (ARNv) génomiques des influenzavirus de type A sont sélectivement empaquetés dans les virions, vraisemblablement sous la forme d’un complexe supramoléculaire maintenu par des appariements ARN/ARN entre signaux d’empaquetage. Afin d’améliorer la compréhension des règles qui gouvernent ce mécanisme, nous avons déterminé le réseau d’interactions formé entre les ARNv de la souche modèle de laboratoire A/Puerto Rico/8/34 (H1N1). Nous avons ensuite défini, au nucléotide près et par deux approches in vitro, les séquences des ARNv impliquées dans la formation de certaines interactions. Le rôle fonctionnel de deux d’entre elles a été testé en contexte infectieux. Nous avons également poursuivi l’étude d’une interaction identifiée au laboratoire entre deux ARNv de la souche A/Moscou/10/99 (H3N2) circulante. Enfin, nous avons collaboré avec le Dr L. Brown (Australie) sur l’étude du rôle d’une interaction entre deux ARNv de la souche A/Udorn/307/72 (H3N2). / The genome of influenza A viruses comprises eight viral RNAs (vRNAs) likely to be selectively packaged into progeny virions as organized supramolecular complexes where vRNAs are held together by base pairing within the packaging signals. To better understand the rules governing this mechanism, we investigated the vRNA/vRNA interaction network of the A/Puerto Rico/8/34 (H1N1) strain. We then identified, at the nucleotide level, using two in vitro approaches, the vRNA sequences involved in several of the interactions. Two of them were functionally tested in an infectious context. We also studied an interaction previously identified in the laboratory between two vRNAs belonging to the circulating A/Moscow/10/99 (H3N2) strain. Finally, we collaborated with Dr L. Brown (Australia) in order to assess the role of an interaction between two vRNAs of the A/Udorn/307/72 (H3N2) strain.

Le travail présenté dans ce mémoire de thèse est consacré aux études théorique et expérimentale du profil spectral des raies d'absorption de la vapeur d'eau, une espèce clé dans l'atmosphère de la Terre. Le but de ce travail est de proposer une approche générale permettant de modéliser précisément la forme des raies d'absorption de H2O.La première partie de cette thèse porte sur la mesure des paramètres spectroscopiques de H2O pur et de H2O dans l'air dans l'infrarouge proche en utilisant un système de diode laser à cavité externe et la technique de spectroscopie d'absorption directe. Différents modèles de profil spectral existants sont utilisés pour ajuster les spectres mesurés. Les résultats montrent que le profil de Voigt habituel mène à de larges différences avec les spectres mesurés et qu'il est nécessaire de prendre en compte à la fois les changements de vitesse et les dépendances en vitesse des paramètres collisionnels pour décrire correctement le profil spectral. Dans la deuxième partie, une nouvelle modélisation du profil spectral de H2O est proposée. Le modèle développé est basé sur des résultats obtenus à partir de simulations de dynamique moléculaire et de calculs semi-classiques. Ce modèle tient compte à la fois des effets de changements de vitesse dus aux collisions et des dépendances en vitesse des paramètres collisionnels. En particulier, nous avons montré qu'il est important, pour H2O, de prendre en compte la corrélation entre les changements de la vitesse et ceux de l'état interne. Le modèle proposé est en très bon accord avec des spectres de H2O (H2O/H2O, H2O/N2 et H2O/Air) mesurés par différentes techniques et pour de larges gammes de pression et domaine spectral. En raison de sa complexité et de son temps de calcul élevé, l'utilisation du nouveau modèle est difficile dans des applications pratiques telles que les calculs de transfert radiatif. Dans la troisième partie, ce nouveau modèle est donc utilisé comme une référence afin de tester les différentes approches simplifiées existantes. Les résultats montrent que le modèle pCqSDHC (partially-Correlated quadratique-Speed-Dependent Hard-Collision) est le plus adapté pour modéliser le profil spectral des raies isolées de H2O, mais aussi d'autres systèmes moléculaire. Il permet en effet un très bon compromis entre la précision et l'efficacité demandée dans des applications pratiques / This work is devoted to a theoretical and experimental study of the spectral shape of isolated transitions of water vapor, a key species of the Earth atmosphere. The purpose of these studies is to develop an accurate line-shape model taking into account different velocity effects affecting the spectral shape of H2O lines. In the first part of this thesis, spectroscopic line parameters of pure H2O and H2O diluted in air have been measured using an external cavity diode laser and a long-path absorption cell. Different existing line-shape models have been used to adjust the measurements. The results show that the widely-used Voigt profile leads to large differences with measured spectra and that it is necessary to take into account both the velocity changes and speed dependence effects to correctly model H2O line shapes. The second part of this work is devoted to the development of a new line-shape model, based on the results obtained from classical molecular dynamics simulations and semi-classical calculations. Both collision-induced velocity changes and speed dependence effects are taken into account by this model. Furthermore, we also show that the correlation between velocity changes and internal-state changes has to be accounted for to correctly describe H2O line shapes. Spectra of pure H2O, H2O in N2 and in air, calculated with the new model are in excellent agreement with those measured by different techniques and for large ranges of pressure and spectral domain. Its complexity and its large computational cost make the new model difficult to use for practical applications such as atmospheric radiative transfer. It is thus used, in the third part, as a “benchmark” in order to test different simplified line profiles and then to choose the proper one to fit measured spectra and to be used for atmospheric spectra prediction. The results show that the pCqSDHC (partially-Correlated quadratic-Speed-Dependent Hard-Collision) model is the most adapted to represent the line shape of H2O, but also of other molecules. This model offers a very good compromise between accuracy and computation efficiency and can be easily used in different practical applications

Le kétoprofène est un anti-inflammatoire non stéroïdien connu par ses propriétés analgésiques et antipyrétiques. Cependant, il présente une très faible solubilité dans l'eau, ce qui limite sa biodisponibilité. Afin de résoudre ce problème, le principe actif est administré sous forme de sels solubles dans l’eau avec le sodium, la lysine, l’arginine, la N-méthylglucamine et le trométamol. L’objectif de cette thèse était d’apporter pour la première fois la caractérisation structurale des sels de kétoprofène racémique et du S-kétoprofène avec la L-lysine et le trométamol, et de chercher à obtenir la structure cristalline de nouveaux co-cristaux ou sels de kétoprofène, pour analyser la relation structure-propriétés de ces formes solides. Nous avons réussi à faire la croissance cristalline des sels de kétoprofène racémique et de S-kétoprofène avec le trométamol et la L-lysine, ainsi qu’avec l’amine 2-amino-2-méthylpropanol. L’analyse des structures de ces sels a montré qu’ils sont tous formés par des couches anioniques de kétoprofènates entre les quelles s’insèrent les cations grâces aux liaisons hydrogène fortes de type N-H…O et O-H…O. Les cations forment des couches dans les sels avec le trométamol et la L-lysine. Cependant, ils ne sont connectés que par des interactions de Van der Waals dans les sels de 2-amino-2-méthylpropanol. La cohésion des couches anioniques est assurée par des interactions faibles de type C-H…O, C-H…π ou C-H…N. L’étude de l’épaisseur des couches anionique, ainsi que la surface et le volume occupé par un anion kétoprofènate dans une couche montre des variations significatives dans les différents sels. Ces variations peuvent être expliquées par des différences des conformations des anions kétoprofènates. L’étude des paramètres géométriques des anions kétoprofènates dans les sels et ceux des molécules de kétoprofène dans les principes actifs montre que les variations les plus importantes touchent les angles de torsions engageant le groupement carboxylate/acide carboxylique qui interagit avec les molécules/anions voisines par des liaisons hydrogène intermoléculaires courtes et fortement directionnelles. Les interactions dans lesquelles les cycles aromatiques sont engagés sont plutôt faibles, par conséquent les angles de torsions mettant en jeu ces cycles varient peu dans les différentes structures cristallines. Différentes techniques ont été également utilisées pour caractériser les sels : diffraction des rayons X sur poudre, calorimétrie différentielle à balayage (DSC), spectroscopie infrarouge (IR), analyse thermogravimétrique (ATG) et résonance magnétique nucléaire à l’état solide (RMN). Les résultats obtenus ont été corrélés aux structures cristallines. Les mesures de solubilité du sel de kétoprofène racémique-trométamol et des deux polymorphes des sels de S-kétoprofène avec le trométamol confirment que ces derniers ont des solubilités très améliorées par rapport aux principes actifs purs / Ketoprofen is a non-steroidal anti-inflammatory drug known by its analgesic and antipyretic properties. However, it has a very low water solubility, which limits its bioavailability. To solve this problem, the active pharmaceutical ingredient is administered as a water soluble salt with sodium, lysine, arginine, N-methylglucamine or trometamol. The scope of this thesis is to study, for the first time, the crystal structures of salts of both racemic and S-ketoprofen with L-lysine and trometamol, and to obtain the crystal structure of new ketoprofen co-crystals or salts, in order to analyze the relationship between the structure and the properties of these solid forms. We succeeded to control the crystal growth of the salts of racemic and S-ketoprofen with trometamol and L-lysine, and with 2-amino-2-methyl propanol. The analysis of these salt structures has shown that they are formed by anionic layers of ketoprofenates which are inserted between the cations thanks to strong N-H...O and O-H...O hydrogen bonds. The cations form layers in trometamol and L-lysine salts. However, they are only connected by van der Waals interactions in the salts of 2-amino-2-methylpropanol. The cohesion of the anionic layers is ensured by weak C-H...O, C-H...π or C-H...N interactions. The study of the thickness of anionic layers, as well as that of the surface and the volume occupied by a ketoprofenate anion in each anionic layer, shows significant differences in the salts. These variations may be explained by differences in the conformations of ketoprofenates anions. The study of geometrical parameters of ketoprofenate anions in the salts and those of the ketoprofen molecules in the pure active ingredients shows that the most important changes affect the twisting angles engaging the carboxylate/carboxylic acid that interacts with neighboring molecules/anions by short and highly directional intermolecular hydrogen bonds. The interactions in which the aromatic rings are incurred are rather weak, therefore the twisting angles involving these cycles slightly vary in the different crystal structures. Various techniques have also been used to characterize the salt, such as powder X-ray diffraction, differential scanning calorimetry (DSC), infrared (IR) spectroscopy, thermogravimetric analysis (TGA) and solid state nuclear magnetic resonance (NMR). The results were correlated with the crystal structures. The solubility measurements of the racemic ketoprofen-trometamol salt and the two polymorphs of S-ketoprofen-trometamol salts confirm that they have greatly improved solubility compared to the pure active ingredients

The thesis entitled “Intermolecular Interactions in Molecular Crystals: Quantitative Estimates from Experimental and Theoretical Charge Densities” consists of four chapters and an Appendix. Chapter 1 highlights the principles of crystal engineering from charge density point of view. Chapter 2 (Section I - III) deals with the evaluation of weak intermolecular interactions and in particular related to the features of concomitant polymorphism. Chapter 3 describes the co-operative role of weak interactions in the presence of strong hydrogen bonds in small bioactive molecules in terms of topological properties. Chapter 4 unravels the inter-ion interactions in terms of charge density features in an ionic salt. The general conclusions of the works presented in this thesis are provided at the end of the chapters. Appendix A explores the varieties of hydrogen bonds in a simple molecule. Identification of intermolecular interactions based purely on distance-angle criteria is inadequate and in the context of ‘quantitative crystal engineering’, recognition of critical points in terms of charge density distribution becomes extremely relevant to justify the occurrence of any interaction in the intermolecular space. The results from single crystal X-ray diffraction data at 90K (compound in chapter 4 at 113K) have been compared with those from periodic theoretical calculations via DFT method at high-level basis set (B3LYP/6-31G**) in order to establish a common platform between theory and experiment. Chapter 1 gives a brief review on crystal engineering to analyze intermolecular interactions along with the description of both experimental and theoretical approaches used in the analysis of charge densities in molecular crystals. The eight of Koch and Popelier’s criteria, defined using the theory of “Atoms in Molecules”, to characterize hydrogen bonds have also been discussed in detail. Chapter 2 (I) presents the charge density analysis in coumarin, 1-thiocoumarin, and 3-acetylcoumarin. Coumarin has been extensively studied as it finds applications in several areas of synthetic chemistry, medicinal chemistry, and photochemistry. The packing of molecules in the crystal lattice is governed by weak C−HLO and C−HLπ interactions only. The variations in charge density properties and derived local energy densities have been investigated in these regions of intermolecular interactions. The lacuna of the identification of a lower limit for the hydrogen bond formation has been addressed in terms of all eight of Koch and Popelier’s criteria, to bring out the distinguishing features between a hydrogen bond (C−HLO) and a van der Waals interaction (C−HLπ) for the first time. Chapter 2 (II) highlights the nature of intermolecular interactions involving sulfur in 1-thiocoumarin, 2-thiocoumarin, and dithiocoumarin. These compounds pack in the crystal lattice mainly via weak C−HLS and SLS interactions. The analysis of experimental and theoretical charge densities clearly categorizes these interactions as pure van der Waals in nature. The distribution of charge densities in the vicinity of the S atom has been analyzed to get better insights into the nature of sulfur in different environments. Chapter 2 (III) provides a detailed investigation of the charge density distribution in concomitant polymorphs of 3-acetylcoumarin. The electron density maps in the two forms demonstrate the differences in the nature of the charge density distribution particularly in the features associated with C−HLO and C−HLπ interactions. The net charges derived based on the population analysis via multipole refinement and also the charges evaluated via integration over the atomic basins and the molecular dipole moments show significant differences. The lattice energies calculated from experimental charge density approach clearly suggest that form A is thermodynamically stable compared to form B. Mapping of electrostatic potential over the molecular surfaces also bring out the differences between the two forms. Chapter 3 describes the analysis of charge density distribution in three small bioactive molecules, 2-thiouracil, cytosine monohydrate, and salicylic acid. These molecules pack in the crystal lattice via strong hydrogen bonds, such as N−HLO, N−HLS, and O−HLO. In spite of the presence of such strong hydrogen bonds, the weak interactions like C−HLO and C−HLS also contribute in tandem to the packing features. The distribution of charge densities in intermolecular space provides a quantitative comparison on the strength of both strong and weak interactions. The variations in electronegativity associated with the S, O, and N atoms are clearly seen in the electrostatic potential maps over the molecular surfaces. Chapter 4 deals with study of intermolecular interactions in N,N,N´N´-tetramethylethlenediammonium dithiocyanate, analyzed based on experimental charge densities from X-ray diffraction data at 113 K and compared with theoretical charge densities. The packing in the crystal lattice is governed mainly by a strong N+−H…N− hydrogen bond along with several weak interactions such as C−HLS, C−HLN, and C−HLπ. The charge density distribution in the region of inter-ionic interaction is also highlighted and the electrostatic potential map clearly provides the insights in to its interacting feature. Appendix A describes the experimental and theoretical charge density studies in 1-formyl-3-thiosemicarbazide and the assessment of five varieties of hydrogen bonds.

Solvent effects play diverse roles in myriads of chemical, physical and biological processes. The solvent interacts with the solute by: i) non-specific (Coulombic, van der Waals interactions) and ii) specific interactions (hydrogen bonding, etc.). These interactions are responsible for solvation of the solute and are collectively termed as “solvent polarity”. Differential solvation of ground and excited electronic states is manifested in the absorption spectrum as a change in the band position, intensity or shape, which is termed as “solvatochromism”. Intermolecular hydrogen bonding (IHB) is a kind of specific solute-solvent interaction, which plays a key role in molecular or supramolecular photochemistry, as well as in photobiology. Solvation and its influence on various physico-chemical and biological processes can be understood by i) top-down; and ii) bottom-up approaches. In the top-down approach, the macroscopic properties like dielectric constant, refractive index are used to understand the microscopic solvation. This approach fails when specific interactions like hydrogen bonding interactions come into play, and furthermore it can reproduce only the macroscopic polarization of the solvent but fails miserably at the cybotactic region of solvation. With the recent advancements in the computational field, the molecular level description of solvation has been within reach for chemical physicists and experimentalists to corroborate their experimental results and in turn to visualize processes of fundamental or technologically relevant problems. The energy levels of the nπ* and ππ* singlet and triplet excited states of aromatic ketones are close-lying and therefore their energy levels can be altered by the substituents. The solvent polarity can be used as a surrogate to tune their energy levels. In certain cases, the lowest triplet or singlet excited states can switch their electronic character with increasing solvent polarity known as “electronic state switching” and thus modulate their photochemical or photophysical properties. Therefore, aromatic ketones were used as solvatochromic probes in this work. Comprehensive analyses of the solvent effects on xanthone (XT), 9,10-phenanthrenequinone (PQ) and benzophenone (Bzp) were carried out using steady-state and nanosecond time-resolved absorption, and resonance Raman spectroscopy in conjunction with ad hoc and classical-molecular dynamics and simulations generated supermolecule-continuum solvent model quantum mechanical calculations to corroborate the experimental outcomes and in turn to visualize the solvation process at the molecular level. The present thesis is divided into eight chapters and the summary of each chapter is described below: Chapter 1 provides a brief literature review of solvation effects and their influence on various physico-chemical and biological processes. Furthermore, the importance of understanding solvation at the molecular level and key concepts are discussed, which forms the heart of this thesis. Chapter 2 discusses the experimental and computational approaches used to study the solvation processes at the molecular level. A detailed explanation of spectroscopic techniques like resonance Raman (RR) and nanosecond-time resolved resonance Raman (ns-TR3) spectroscopy and their experimental and theoretical aspects are discussed, followed by a discussion on the fundamental concepts of computational methods like ab initio calculations density functional theory (DFT), and classical molecular dynamics and simulations (c-MDS) utilized in this study. Chapter 3 focuses on microscopic understanding of solvatochromic shifts observed for 9,10-phenanthrenequinone in protic solvents using UV-Vis and RR spectroscopy in conjunction with an ad hoc explicit solvation model and time-dependent density functional theory (TDDFT) calculations. The hypsochromic shift and bathochromic shift of the singlet nπ* and ππ* electronic transitions in protic solvents are due to hydrogen bond weakening and strengthening in the excited state for the corresponding electronic transitions, respectively as indicated by TD-DFT calculations and Kamlet-Taft linear solvation energy relationships. The hydrogen bond strengthening in the singlet ππ* excited state is further confirmed by Raman excitation profile (REP) analysis of PQ in different solvents. Furthermore, with increasing solvent polarity the two lowest singlet excited states undergo different hydrogen bonding mechanisms, leading to a decreasing energy gap between them. Therefore, hyperchromism of the nπ* transition has been hypothesized to be due to an increasing vibronic coupling between the lowest singlet nπ* and ππ* excited states. In Chapter 4, a real time observation of the thermal equilibrium between the lowest triplet excited states of PQ in acetonitrile solvent was carried out using ns-TR3 spectroscopy and this can explain its high reactivity towards H-atom abstraction, despite the fact that the lowest triplet excited state has ππ* character. Furthermore, extending the concept of hydrogen bonding mechanisms of the lowest singlet to the triplet excited states, the different hydrogen bonding mechanisms exhibited by them can lead to alteration of the intersystem crossing mechanisms in PQ. Chapter 5 highlights the very different role of intermolecular hydrogen bonding in the reduced reactivity of the xanthone (XT) triplet towards H-atom abstraction in protic solvents. The different hydrogen bonding mechanisms exhibited by the two lowest triplet excited states in protic solvents are derived from an ad hoc explicit solvation model, TD-DFT calculations and ns-time resolved absorption (ns-TRA): they separate them further in energy and thereby the nearest T2(nπ*) triplet state to the T1(ππ*) excited state plays an insignificant role in the reactivity towards H-atom abstraction, in contrast to the PQ triplet discussed in Chapter 4. Chapter 6 discusses the structure of XT triplet states using TR3 spectroscopy in combination with TD-DFT studies. The TR3 spectrum of the XT in acetonitrile identified a vibronic coupling mode responsible for the reactivity of XT towards H-atom abstraction, despite the fact that the lowest triplet excited state (T1) has ππ* character. This vibronic active mode is absent in the TR3 spectra of XT in protic solvents (methanol and ethanol). Furthermore, the REP analysis suggests that the nanosecond triplet-triplet absorption spectrum of XT in acetonitrile involves two different species, while in methanol it involves only one species. This observation is in agreement with the previous chapter (Chapter 5) which proposes a different hydrogen bonding mechanisms for the two lowest triplet excited states and their influence on the reduced reactivity towards H-atom abstraction. Chapters 3-6 emphasize the need for a proper solvation model at the molecular level to describe the various photophysical and photochemical processes of aromatic ketones. Therefore, Chapter 7 includes discussions on the bottom-up solvation methodology applied to benzophenone (Bzp) to understand its vibrational and electronic solvatochromic behaviour at the molecular level. Raman and UV-Vis spectroscopic techniques were used in conjunction with a c-MDS-generated supermolecule continuum solvation model DFT calculation to corroborate and to visualize the experimental outcome. The carbonyl stretching frequency of Bzp in protic solvents has two bands, corresponding to free carbonyl and hydrogen bonded carbonyl. Despite the fact that the macroscopic polarity of acetonitrile and methanol solvents are similar, the free carbonyl stretching of Bzp in methanol solvent was blue-shifted by 4 cm-1 with respect to the carbonyl stretching in acetonitrile solvent. The Gutmann’s acceptor number plot for carbonyl stretching frequencies indicates that the free carbonyl group is neighboured by a hydrophobic environment. The c-MDS-generated supermolecule-continuum solvation model DFT calculations suggest that the extended hydrogen bonding network of methanol solvent is responsible for the hydrophobic solvation around the free carbonyl. Furthermore, a linear correlation was obtained for the vibrational and electronic solvatochromism of the carbonyl frequency and energy of the singlet nπ* transition, respectively, which indicates that a variation in excitation wavelength for the singlet nπ* transition can arise from different solvation states. This can have implications for ultrafast processes associated with electron transfer, charge-transfer and also the photophysical aspects of excited states.Finally, Chapter 8 contains overall conclusions of the thesis and future directions for the present research area.

We have investigated the noncovalent interactions in carbohydrate-aromatic interactions which are pivotal to the recognition of carbohydrates in proteins. We have employed quantum mechanical methods to study carbohydrate-aromatic complexes. Due to the importance of dispersion contribution to the interaction energy, we mainly use density functional theory augmented with an empirical correction for the dispersion interactions (DFT-D). We have validated this method with a limited number of high level ab initio calculations. We have also analysed the vibrational and NMR chemical shift characteristics using the DFT-D method. We have mainly studied the complexes involving β-glucose with 3-methylindole and p-hydroxytoluene, which are analogues of tryptophan and tyrosine, respectively. We find that the contribution for interaction energy mainly comes from CH/π and OH/π interactions. We find that the interaction energy of complexes involving CH/π and OH/π interactions is reflected in the associated blue and red shifts of vibrational spectrum. We also find that the interactions involving 3-methylindole are somewhat greater than those for p-hydroxytoluene. The C-H blueshifts are also in parallel with the predicted NMR proton shift. We have also tested different density functionals including both standard density functionals and newly developed M0x functionals and MP2 method for studying carbohydrate-aromatic complexes. The DFT-D method and M06 functionals of the M0x family are found to perform better, while B3LYP and BLYP functionals perform poorly. We find that the inclusion of a dispersion term to BLYP is found to perform better. The dispersion energy dominates over the interaction energy of carbohydrate-aromatic complexes. From the DFT-D calculations, we found that the complexes would be unstable without the contribution from dispersive energy. We have also studied the importance of noncovalent interactions in functionalization of nanotubes by nucleic acid bases and aromatic amino acids by using semi-empirical methods with dispersion term such asPM3-D and PM3-D*. We find that the both semi-empirical schemes give reasonable interaction energies with respect to DFT-D interaction energies. We have also used PM3-D method to study the adsorption of organic pollutants on graphene sheet and on nanotubes. We found that the semi-empirical schemes, which are faster and cheaper, are suitable to study these larger molecules involving noncovalent interactions and can be used as an alternative to DFT-D method. We have also studied the importance of dispersion interaction and the effect of steric hindrance in aggregation of functionalized anthracenes and pentacenes. We have also employed molecular dynamics simulation methods to study the aggregation of anthracene molecules in toluene solution.