Three distinct aspects, disorder, polymorphism and co-crystal formation have been addressed in molecular crystals in terms of intra- and intermolecular interactions involving halogens, weak hydrogen bonds and van der Waals interactions. A basic introductory chapter highlights the importance of these three aspects followed by a foreword to the contents. Chapter 1 employs in situ cryo-crystallization techniques to study the crystal and molecular structures of compounds which are liquids at room temperature. Section 1.1 deals with the crystal structure analyses of low melting chloro- and bromo-substituted anilines which reveal both the importance of hydrogen bonds and weak interactions involving different halogens. The halogen⋅⋅⋅halogen interactions are compared with fluorine and iodine substituted compounds to bring out the relevance of both size and polarizability characteristics. Section 1.2 describes the crystal structures of benzyl derivative compounds utilizing the concept of in situ cryo-crystallization. This analysis brings out the correlation between acidity of benzyl derivative compounds with its preference of either a (sp2)C-H⋅⋅⋅π or (sp3)C-H⋅⋅⋅π interactions in the crystal packing. Chapter 2 consists of two sections dealing with the preference of halogen⋅⋅⋅halogen interactions in supramolecular chemistry. Section 2.1 discusses a statistically large number of crystal structures in halogen substituted benzanilide compounds. It reveals the importance of hetero halogen F⋅⋅⋅X (Cl, Br), homo halogen X⋅⋅⋅X (F, Cl, Br, I), C-X⋅⋅⋅π and C-H⋅⋅⋅F interactions in terms of their directionality and preferences to complement a primary N-H⋅⋅⋅O hydrogen bond in directing the three-dimensional supramolecular assembly. Section 2.2 deals with solvent induced polymorphism which highlights the role of weak interactions in two case studies. The preference and directionality of C-H⋅⋅⋅F and Cl⋅⋅⋅Cl interactions lead to dimorphic modifications in case of 3-chloro-N-(2-fluorophenyl)benzamide whereas in case of 2-iodo-N-(4-bromophenyl)benzamide the interactions are through C-H⋅⋅⋅π and I⋅⋅⋅I contacts. Further, the analysis is supported using morphological evidence, DSC (Differential scanning calorimetry) and Powder X-ray diffraction data. Chapter 3 has three sections, concentrating on disorder and its consequence in crystal structures. Section 3.1 discusses the apparent shortening of the C(sp3)–C(sp3) bond analysed via a variable temperature X-ray diffraction study in racemic 1,1′-binaphthalene-2,2′-diyl diethyl bis(carbonate). Variable temperature single crystal X-ray diffraction studies show that the shortening is entirely due to positional disorder and not due to thermal effects. A supercell formation at T≤150 K depicts the formation of a Z'= 2 structure. Section 3.2 deals with crystal structure analysis of Ethyl-4-(2-fluorophenyl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate which clarifies the discrepancy in the higher value of the residual electron density in the literature in terms of positional disorder of fluorine at ortho sites. The existence of fluorine atom at the para position on the phenyl ring of another isomeric molecule leads to disorder induced conformational polymorphism through the involvement of the ethyl group. The static disorder of ethyl group which is associated with only one molecule (Z′=2) could be resolved at 120 K. This supports the results of the previous section (3.1). Section 3.3 reports crystal structure analysis of disordered fluorine in benzanilide compounds. The preference of interactions involving fluorine in either ortho sites or meta sites could be one of the reasons for the positional disorder of both possible sites. With one of the structure showing high Z′ value due to differences in the occupancy of disordered fluorine atom. CSD (Cambridge Structural Database) analysis indicates that the percentage of disorder in halogenated crystal structures having halogen atom at either ortho site or meta site decreases from fluorine to iodine. Further, the analysis points out that the disorder in fluorine containing compounds is mostly localized at the fluorine position whereas for other halogenated disordered structures, the disorder appears at other parts of the molecule. Chapter 4 discusses co-crystal formation and analysis of intermolecular interactions. It consists of two sections. Section 4.1 discusses co-crystal formation of nicotinamide with benzoic acid and seven other derivatives by changing the functional group at different positions of benzoic acid. Hydroxyl (-OH) group at 4/3-postion of benzoic acid prefers phenol⋅⋅⋅pyridine synthon when at 2-position it prefers acid⋅⋅⋅pyridine synthon. The preference of amide anticatemer over dimer synthon is supported by additional C-H⋅⋅⋅O hydrogen bonds. In case of 3,5-dinitro-2-hydroxy benzoic acid, the disorder in hydroxyl (-OH) group at ortho site leads to salt formation. Section 4.2 describes co-crystal study of adenine and thymine (AT) as free nucleobases. This result reveals the formation of AT (2:1) complex with both Hoogsteen and “quasi-Watson-Crick” hydrogen bonds. The hydrogen bonded bases using the Hoogsteen and the “quasi-Watson-Crick” interactions generate a hexagonal supramolecular motif. Four water molecules are located inside the hexagonal void of this complex. A high temperature study on the same crystal shows that at 313K, one of the water molecules escapes from the lattice resulting in the small change in unit cell parameters. However, the space group remains the same and the hexagonal void remains unaltered. With further increase in temperature, the crystal deteriorates irreversibly which clearly brings out the importance of water molecule in the molecular recognition of adenine-thymine complex. Chapter 5 discusses crystal structure analysis of trans-atovaquone (antimalarial drug), its new polymorph form including one stereoisomer (cis) and five other derivatives with different functional groups. Based on the conformational features of these compounds and the characteristics of the nature of hydrogen bonding and other weak intra and intermolecular interactions, docking studies with cytochrome bc1 complex provide valuable insight into the atomistic details of protein-inhibitor interactions. The docking results reveal that atovaquone and its derivatives, owing to their nature of hydrogen bond and the propensity towards the formation of weaker hydrogen bonds involving the chlorine atom as well appear as good candidates for drug evaluation.

Les travaux décrits dans ce manuscrit utilisent les principes de la tectonique moléculaire pour générer des polymères de coordination hautement fluorés et /ou chiraux pour une application potentielle en séparation chirale. La synthèse de 13 porphyrines de type A2B2 substituées en position méso par deux pyridines et par deux chaines fluorées et/ou alkyles a été mise au point. Des réseaux de coordination ont été obtenus en présence de Zn(II) et de Cd(II) et caractérisés par diffraction des RX sur monocristal (DRX). Une analyse systématique des interactions supramoléculaires et notamment de interactions F---F présentes à l’état solide a été conduite. Des réseaux à base de liaisons halogènes ont également été obtenus en présence de di- et tri-iodoarènes et caractérisés par DRX.Le premier chapitre est une introduction générale sur la tectonique moléculaire, le deuxième chapitre décrit les voies des synthèses utilisées pour générer les ligands chiraux et fluorés et leur caractérisation à l’état solide. Le troisième chapitre présente la structure des réseaux mono, bi, et tridimensionnels formés en présence de Zn(II) ou de Cd(II), l’analyse structurale met en évidence un nombre croissant d’interaction F---F en fonction du nombre de fluors présents à la périphérie du macrocycle porphyrinique. Le dernier chapitre se concentre sur l’utilisation des liaisons halogènes de type N---I impliquant des porphyrines ou des tectons de type bipyridine et une série d’ iodofluoroarenes. / This manuscript focuses on the use of molecular tectonics to generate chiral and / or fluorinated coordination polymers based on porphyrin building blocks for potential application in chiral separation. Synthesis of novel A2B2 fluorinated porphyrin tectons is described and their combinations with metal ions and haloarenes molecules are characterized by X-Ray diffraction.The first chapter gives a general introduction on molecular tectonics; the second chapter focuses on the synthetic routes used for the synthesis of highly fluorinated and/or chiral porphyrins and their solid state characterization by X-Ray diffraction analysis, highlighting the importance of the number of fluorine atoms present at the periphery of the tecton on the crystal packing. The third chapter presents the mono-, bi- and three dimensional networks formed by a combination of the porphyrins with Zn(II) or Cd(II). In the solid state, short F---F contacts were observed depending on the number of fluorine atoms present on the porphyrin backbone. The last chapter focuses on the use of halogen bonds, by merging the neutral porphyrin or bipyridine tectons with a series of iodofluoroarenes. The crystalline materials described in this work can be used as potential candidates for the separation of chiral and fluorinated molecules.

Conselho Nacional de Desenvolvimento Científico e Tecnológico / This study shows the triazenes ligands and complexes Pd(II), K+ and Au(I) obtained from reactions of the ligands with fragments para-sulfonamidephenyl, comprising triazene ligand 1,3-bis (4 - sulfonamidephenyl) (1) and the complex {trans-Bis[1,3-bis(4-sulfonamidephenyl)triazenide-κN1]bis(pyridine-κN)palladium(II)}{tetra(pyridine-κN)palladium(II)}bis(potssium)·water (2) and for compounds containing orto-halophenyl fragments represented by [1,3-bis(2-fluorophenyl)triazenide-κN1](triphenylphosphine- κP)gold(I) (3), [1,3-bis(2-chlorinephenyl)triazenide-κN1](triphenylphosphine-κP)gold(I) (4), [1,3-bis(2-bromidephenyl)triazenide-κN1](triphenylphosphine-κP)gold(I) (5) and [1,3-bis(2-iodinephenyl)triazenide-κN1](triphenylphosphine - κP)gold(I) (6) complexes. The compounds reported were characterized by X-ray diffraction on single crystal, and their structures in solid state are formed through supramolecular arrangements via classical and non-classical hydrogen bonding, as in the case of the compounds with the sulfonamide grouping, one can observe the formation of supramolecular synthons. In complexes 4, 5 and 6 it is observed to occur interactions halogen···halogen characterized by the formation of dimeric units associated by a center of inversion, besides having geometries classified by the angle of the links formed between the halogen and carbon atoms. Compounds 1, 2, 3, 4, 5 and 6 were subjected to evaluation front of biological activity, such as plasmidial DNA cleavage studies, evaluation of cytotoxicity and antibacterial activity, showing promising results. / Este trabalho apresenta o estudo de ligantes triazenos e complexos de Pd(II), K+ e Au(I) obtidos a partir de reações com os ligantes com fragmentos para-sulfonamidafenila compreendendo o ligante 1,3-bis-(4-sulfonamidafenil)triazeno (1) e o complexo {trans-Bis[1,3-bis(4-sulfonamidafenil)triazenido-κN1]bis(piridina-κN)paládio(II)}{tetra(piridina-κN)paládio(II)}bis(potássio)·água (2) e para compostos contendo fragmentos orto-halofenila representados pelos complexos [1,3-bis(2-fluorofenil)triazenido-κN1](trifenilfosfina- κP)ouro(I) (3), [1,3-bis(2-clorofenil)triazenido-κN1](trifenilfosfina- κP)ouro(I) (4), [1,3-bis(2-bromofenil)triazenido-κN1](trifenilfosfina- κP)ouro(I) (5) e [1,3-bis(2-iodofenil)triazenido-κ-N1](trifenilfosfina- κP)ouro(I) (6). Os compostos relatados foram caracterizados por difração de raios X em monocristal, e suas estruturas no estado sólido são formadas através de arranjos supramoleculares via ligações de hidrogênio clássicas e não clássicas, como no caso dos compostos com o grupamento sulfonamida, pode-se observar a formação de synthons supramoleculares. Nos complexos 4, 5 e 6 é observada a ocorrência de interações halogênio···halogênio caracterizadas pela formação de unidades díméricas associadas por um centro de inversão, além de apresentarem geometrias classificadas pelo ângulo de ligações formado entre os átomos de halogênio e carbono. Os compostos 1, 2, 3, 4, 5 e 6 foram submetidos a avaliação frente a atividade biológica, como estudos na clivagem do DNA plasmidial, avaliação da citotoxicidade e atividade antibacteriana, mostrando resultados promissores.