Les polydiacétylènes sont des polymères π-conjugués, obtenus par polymérisation topochimique à l'état solide de motifs diacétyléniques, sous l'effet d'un stimulus thermique ou photochimique. Depuis leur découverte en 1969 par Wegner, les polydiacétylènes ont fait l'objet de nombreux travaux de recherche. Ces travaux ont consisté tout d'abord à élucider le mécanisme de polymérisation, puis à étudier les diverses propriétés photophysiques, optiques, et électroniques des polymères. Néanmoins, la plupart des diacétylènes étudiés ne possédaient pas de substituants susceptibles d'être modifiés chimiquement. Le premier chapitre de cette thèse décrit la synthèse de nouvelles molécules diacétyléniques symétriques comportant des groupements azoles, et l'étude de leur polymérisation à l'état solide. La modification de l'organisation des motifs diacétyléniques.par interaction avec des molécules capables de former des liaisons hydrogène, et l'incorporation de ces motifs dans des matériaux hybrides organiques-inorganiques de type,. MOF ont également été examinées.Dans le deuxième chapitre, nous nous sommes intéressés aux composés diacétyléniques dicationiques fonctionnalisés par des groupements triéthylammoniums, imidazoliums et benzimidazoliums. La synthèse de ces composés, leur caractérisation spectroscopique, et cristallographique, ainsi que l'étude de leur réactivité thermique et photochimique ont été réalisées.Dans le troisième chapitre, nous proposons une méthode directe de préparation de carbone dopé à l'azote par pyrolyse des molécules diacétyléniques neutres, ainsi que la synthèse de carbone mésoporeux en présence d'un sel métallique. Un autre aspect de ce chapitre est l'optimisation des teneurs en azote en utilisant comme précurseurs les composés diacétyléniques dicationiques, associés à des anions riches en azote, notamment l'anion dicyanamide [dca] et tricyanométhide [tcm]. / Diacetylenes (DA) are unusual molecules owing to their ability to polymerize in the solid state. Such a polymerization is triggered off thermally or photochemicaly, and leads to the formation of enyne structures. Since their discovery in 1969 by Wegner, polydiacetylenes (PDA) have been the focus of much attention. Initially, many studies were devoted to elucidating the mechanism of polymerization, then assessment of the diverse photophysical, optical, and electronic properties of the polymers became the main goal. Yet, the vast majority of the DA that were studied did not possess substituents that could be modified chemicallyThe first chapter describes the synthesis of new symmetrical diacetylenic molecules functionalized with azole substituents and the study of the polymerization of these compounds in the solid state. Then, we present the modification of the organization of these diacetylenes by the interaction with molecules capable of forming hydrogen bonds, and the use of these molecules as ligands for the synthesis of Metal Organic Frameworks (MOF).The second chapter is devoted to the synthesis, characterization and crystallographic study of ionic diacetylenic compounds bearing triethylammonium, imidazolium and benzimidazolium groups. The photochemical and thermal behaviors of these DA have been tested.In the third chapter, we propose a straightforward route to N-doped graphitic carbon by direct pyrolysis of neutral diacetylenic precursors, and investigate the possibility of forming porous materials by adding a metal salt as a catalyst. Furthermore, another aspect of this chapter was to optimize the nitrogen content of these materials by using dicationic DA with N-rich anions, e.g. dicyanamide [dca] and tricyanomethide [tcm].

As propriedades no estado sólido de um insumo farmacêutico ativo (IFA) estão diretamente relacionadas com a eficácia terapêutica de um medicamento. Entre todas as propriedades físicas e químicas, que são dependentes doarranjo cristalinodo IFA, destaca-se a solubilidade e a estabilidade, que são as características mais importantes de um fármaco, na medida em que podem alterar a biodisponibilidade. Dentro dessa perspectiva, a engenharia de cristaistem cada vez mais se consolidado como uma estratégia para aperfeiçoar as propriedades no estado sólido de um IFA. Neste trabalho, oito novas formas sólidas cristalinas, entre sais e cocristais, dos fármacos com ação anti-tuberculose etionamida (ETH), etambutol (ETB) e isoniazida (INH), foram preparadas e tiveram suas estruturas cristalinas determinadas por difração de raios X por monocristal. Além disso, todas as modificações cristalinas obtidas foram caracterizadas por difração de raios X por policristais, espectroscopia vibracional no infravermelho e Raman, calorimetria exploratória diferencial, termogravimetria e microscopia ótica térmica. Por fim, estudos de solubilidade em equilíbrio e de estabilidade em atmosfera úmida também foram realizados. A nova modificação cristalina da ETH, o sal nitrato de ETH, foi planejada visando melhorar a solubilidade aquosa deste IFA (∼0,4 mg mL-1). Este é o primeiro relato de uma estrutura de ETH que cristalizou com quatro independentes pares iônicos (ETH+/NO3-) na unidade assimétrica. A análise do empacotamento cristalino e das interações intermoleculares permitiu estabelecer os atributos estruturais que explicam a menor estabilidade térmica e a elevada solubilidade (cerca de 300 vezes maior) deste sal, em comparação com a forma neutra da ETH. A preparação dos novos sais de ETB foi feito considerando o cárater básico da molécula, o que permitiu a obtenção de três novos sais a partir da reação do ETB com os ácidos oxalico, maleico e tereftálico. O desenho dessas formas sólidas teve como principal objetivo minimizar os efeitos da elevada higroscopicidade do ETB, que é tão prejudicial para formulações farmacêuticas. Este objetivo foi alcançado, uma vez que o sal oxalato de ETB, reportado neste trabalho, mostrou ser não-higroscópico. Por fim, quatro novos cocristais da INH, sendo dois cocristais polimórficos, foram preparados por meio de reações estequiométricas deste IFA com ácidos carboxílicos aromáticos derivados do ácido benzóico. O desenho dessas novas modificações cristalinas teve como intuito principal explorar a diversidade de síntons supramoleculares formados entre a INH e moléculas contendo o grupo COOH. A análise dos empacotamentos cristalinos das formas I e II do cocristal INH-PABA, mostrou que este é um típico caso de polimorfismo orientacional. Portanto, os resultados desta dissertação trazem importantes contribuições científicas para a diversidade de formas sólidas, apresentando revelância para o setor farmacêutico no que se refere ao desenvolvimento de novas formulações contendo fármacos anti-tuberculose. / Solid state properties of an active pharmaceutical ingredients (API) are directly related to drug performance. Among all physical and chemical properties dependent on the crystal arrangement of a drug, stability and solubility are the main ones that alter its bioavailability. In this sense, crystal engineering is a strategy to improve solid state properties of drugs. In this work, eigth new multicomponent solid forms (salts and cocrystals) of the tuberculostatic drugs ethionamide (ETH), ethambutol (ETB) and isoniazid (INH) were prepared and their crystal structures were elucidated by single crystal X-ray diffraction. In addition, the crystal modifications were also characterized by powder X-ray diffraction, infrared and Raman vibrational spectroscopy, differential scanning calorimetry, thermogravimetry and Hot-stage microscopy. Finally, equilibrium solubility studies and stability experiments in humid atmosphere were also performed. The new supramolecular modification of ETH, ethionamide nitrate salt, was designed in order to improve the aqueous solubility of the API (∼0.4 mg ml-1). This salt is the first ETH structure that has been crystallized with four independent ionic pairs (ETH+/NO3-) in the asymmetric unit. The analysis of crystal packing and intermolecular interactions allowed to establish the structural attributes that explain the lower thermal stability and high solubility (about 300 times higher) of this salt compared to the neutral ETH form. Due its high hygroscopicity, ETB is known for catalyzing the degradation of isoniazid and rifampicinin pharmaceutical formulations. In order to avoid or even minimize these mutual drug-drug interactions, in this work we have focused on the development of less hygroscopic multicomponent solid forms of ETB. The preparation of the new ETB crystal modifications was carried out considering the pKa values of the molecule, which allowed the design of three new salts (namely oxalate, maleate and terephthalate). These salts were obtained from the reaction of ETB with the carboxylic acids: oxalic, maleic and terephthalic. The hygroscopic nature of these salts was evaluated and all of them were found to be hygroscopic, with exception of ETB oxalate. Finally, four novel INH cocrystals, being two polymorphic forms, with aromatic carboxylic acids derivatives were rationally prepared. The design of these crystal forms aimed to explore the diversity of supramolecular synthons formed between INH and molecules containing COOH. The crystal packing analysis of the INH-PABA cocrystals (polymorphs I and II), showed that this is a typical case of orientational polymorphism. Therefore, the scientific contributions of this work show the diversity of the solid forms and define candidates to new anti-tuberculosis API\'s solid formulations.

Este documento de Tese é o resultado de um trabalho de pesquisa voltado à análise cristalográfica de novas formas sólidas cristalinas derivadas de fármacos antirretrovirais, diante do contexto da engenharia de cristais para o desenho das novas formas sólidas, e principalmente diante da ótica da análise das densidades de carga, o que permitiu um entendimento mais acurado da estrutura eletrônica molecular desta classe de compostos. Compostos farmacêuticos antirretrovirais do tipo inibidores nucleosídeos da transcriptase reversa (INTRs), são de grande importância, uma vez que são amplamente usados na terapêutica antirretroviral, principalmente contra o vírus HIV. Nesse contexto, são conhecidos alguns problemas associados na manufatura destes fármacos, principalmente aos processos de extração e purificação dos fármacos Lamivudina (3TC) e Emtricitabina (FTC). Diante desta problemática, a engenharia de cristais fornece uma solução, mediante o planejamento racional de formas sólidas (sais, cocristais, solvatos, polimorfos, etc.) que apresentam maior estabilidade e facilitem principalmente o processo de purificação em grande escala. Daí surge a importância de estudar a estrutura molecular das diferentes formas sólidas derivadas destes fármacos, sendo uma das principais técnicas para este estudo a difração de raios X em monocristais (DRXM). Neste trabalho um total de nove novas formas sólidas foram avaliadas e reportadas, com uma discussão detalhada das conformações moleculares e supramoleculares. Entretanto, é realizada uma análise das densidades de carga mediante métodos experimentais, uma vez que foram conduzidos experimentos de DRXM em alta resolução, em virtude da boa qualidade dos cristais que algumas das formas sólidas apresentaram. Desta maneira foi possível propor modelos de densidade de carga experimentais construídos mediante o formalismo de Hansen & Coppens, utilizando refinamento por mínimos quadrados baseados nos dados de difração em alta resolução. Por último, com o intuito de ter um estudo mais completo e detalhado da estrutura eletrônica, foram realizados cálculos teóricos de primeiros princípios em condições gasosas e periódicas de contorno. Desta forma, é apresentada uma sinergia entre os resultados obtidos pelas análises das distribuições de densidade de cargas de algumas formas sólidas, com os resultados gerais da engenharia de cristais e, portanto, concluir e extrapolar alguns aspectos importantes, principalmente no que se refere às energias associadas com as interações intermoleculares. A sinergia dos estudos de engenharia de cristais e de densidade de carga, é um tipo de pesquisa pouco publicada dentro da área da cristalografia de pequenas moléculas. / This Thesis is the result of the research proposal aimed to the crystallographic analysis of new crystalline solid forms derived from antiretroviral drugs, in the context of the crystal engineering for the design of the new solid forms, mainly since the viewpoint of the charge density analysis, which allowed an accurate comprehension of the molecular electronic structure of this kind of compounds. Antiretroviral drug compounds of nucleoside analog reverse-transcriptase inhibitors (NRTI) type, are of great importance once they are large used in the antiretroviral therapy, mainly against the HIV. In this context, some problems are known regard to the manufacture process of these drugs, mainly in the extraction and purification procedures of the lamivudine (3TC) and emtricitabine (FTC) drugs. On this issue, the crystal engineering provides an answer, through the rational planning of solid forms (salts, cocrystals, solvates, polymorphs, etc.) that exhibit an increased stability and facilitate mainly the large-scale purification process. Hence is important to study the molecular structure of the diverse solid forms derived from these drugs, mainly through the single-crystal X-ray diffraction (SCXD) experiments. In this research a total of nine new solid forms were assessed and reported, along with a detailed discussion of the molecular and supramolecular conformations. Meantime, it was carried out an analysis of the experimental charge density, once it was performed high-resolution SCXD experiments, since some of the solid forms showed good quality single crystals. In this way, it was possible to propose models of experimental charge density through the Hansen & Coppens formalism, using least-square refinement against high-resolution X-ray diffraction data. Finally, with the aim to have a more complete and detailed study of the electronic structure, it was also carried out first principles theoretical calculations in gas-phase and periodic boundary conditions. Thus, it is shown a synergy between the results obtained by the analysis of the charge density distributions of some solid forms and the crystal engineering results and, therefore, to conclude and to extrapolate some important aspects, mainly involved with the intermolecular interaction energies. The synergy of the crystal engineering and charge density studies is a kind of research little published, within the small molecule crystallography area.

Βασικός στόχος της παρούσης Διπλωματικής Εργασίας ήταν η μελέτη της κρυσταλλικής μηχανικής συμπλόκων ενώσεων του CuII με το 2-φαινυλοϊμιδαζόλιο ως υποκαταστάτη. Η κρυσταλλική μηχανική μπορεί να θεωρηθεί ως ο κλάδος της υπερμοριακής χημείας στη στερεά κατάσταση. Η υπερμοριακή χημεία (supramolecular chemistry) είναι μια από τις πλέον δημοφιλείς και γρήγορα αναπτυσσόμενες περιοχές της πειραματικής χημείας. Χαρακτηρίζεται ως η χημεία των ασθενών διαμοριακών δυνάμεων και εστιάζει στη δομή και λειτουργία χημικών συστημάτων με υψηλή πολυπλοκότητα (υπερμόρια) που προκύπτουν από το συνδυασμό δύο ή περισσοτέρων διακριτών χημικών ειδών (μορίων, ιόντων) και συγκρατούνται με ασθενείς (και αντιστρεπτές) διαμοριακές δυνάμεις (π.χ. αλληλεπιδράσεις π-π, δεσμούς υδρογόνου, υδρόφοβες αλληλεπιδράσεις, δυνάμεις van der Waals, αλληλεπιδράσεις διπόλου-διπόλου, δεσμούς ένταξης μετάλλου-υποκαταστάτη κλπ). Ένα σημαντικό πεδίο της υπερμοριακής χημείας είναι αυτό της κρυσταλλικής μηχανικής (crystal engineering) που αναφέρεται στη στρατηγική σχεδιασμού ενός κρυσταλλικού υλικού με επιθυμητές ιδιότητες και βασίζεται στην κατανόηση και τον έλεγχο των διαμοριακών αλληλεπιδράσεων των μορίων στην κρυσταλλική κατάσταση. Καταρχήν, πραγματοποιήθηκε η σύνθεση συμπλόκων ενώσεων με γενικό τύπο ΜΙΙ/Χ-/L, όπου ΜΙΙ = CuII, X- = Cl-, NO3-, ClO4-, SiF62-, SO42- και L = 2-φαινυλοϊμιδαζόλιο. Από τις συνθετικές παραμέτρους που μεταβάλλαμε -γραμμομοριακή αναλογία μετάλλου:υποκαταστάτη, πολικότητα του διαλύτη (MeOH, EtOH, MeCN, DMF, CH2Cl2), συνθήκες θερμοκρασίας και μέθοδο κρυστάλλωσης– απομονώσαμε και χαρακτηρίσαμε τα σύμπλοκα: (LH)+(NO3)- (1), [CuCl2L2] (2), [Cu2(OMe)2(L)4(NO3)2]∙2MeOH (3∙2MeOH), [Cu(L)4](NO3)2 (4), [Cu2(OMe)2(L)4](ClO4)2 (5), [Cu(L)4](ClO4)2 (6), [Cu2(OMe)2(L)4]SiF6 (7) και [Cu2(SO4)2(L)4] (8). Με τη βοήθεια της κρυσταλλογραφικής ανάλυσης με ακτίνες Χ των ανωτέρων συμπλόκων, διαπιστώθηκε ότι οι διαμοριακές αλληλεπιδράσεις που είναι υπεύθυνες για την υπερμοριακή οργάνωση των δομών τους είναι ισχυροί και ασθενείς δεσμοί υδρογόνου και αλληλεπιδράσεις τύπου π-π. Αναλυτικότερα: • Σταθερά μοτίβα διαμοριακών αλληλεπιδράσεων (συνθόνια) σχηματίζονται μεταξύ των τεκτονίων N-H των ιμιδαζολικών δακτυλίων και των ανόργανων ανιόντων X- (Cl-, NO3-, ClO4-, SiF62-, SO42-) ή/και πλεγματικών μορίων διαλύτη, οδηγώντας σε 1D, 2D και 3D υπερμοριακές δομές. • Οι δομές σταθεροποιούνται περαιτέρω μέσω ενδομοριακών (σύμπλοκα 4, 5 και 6) και διαμοριακών (σύμπλοκο 2) αλληλεπιδράσεων τύπου π-π. • Το μέγεθος και το φορτίο των ανιόντων δεν επηρεάζουν τους δομικούς πυρήνες των μορίων, σε αντίθεση με την υπερμοριακή οργάνωση που επηρεάζεται καθοριστικά και οδηγεί σε 2D και 3D αρχιτεκτονικές. / The main target of this diploma thesis was the crystal engineering studies of coordination compounds of CuII using 2-phenylimidazole as ligand. Crystal engineering may be regarded as the solid-state branch of supramolecular chemistry. Supramolecular chemistry is one of the most popular and rapidly developing areas of experimental chemistry. It may be defined as the chemistry of weak intermolecular forces and focuses on the structure and function of chemical systems of high complexity (supermolecules), resulting from the association of two or more discrete chemical species (molecules, ions) held together by weak (and reversible) intermolecular forces (e.g. π-π interactions, hydrogen bonds, hydrophobic interactions, van der Waals forces, dipole-dipole interactions, metal-ligand coordination bonds etc). Crystal engineering is an important field of supramolecular chemistry that refers to the design and synthesis of a crystalline material with desired properties, based on the understanding and exploitation of intermolecular interactions in the crystalline state. Initially the synthesis of coordination complexes with general formula ΜΙΙ/Χ-/L [ΜΙΙ = CuII, X- = Cl-, NO3-, ClO4-, SiF62-, SO42- and L =2-phenylimidazole] took place. By altering the parameters of synthesis –metal:ligand molar ratio, solvent polarity (MeOH, EtOH, MeCN, DMF, CH2Cl2), temperature, as well as crystallization method– we were able to isolate and study the following complexes: (LH)+(NO3)- (1), [CuCl2L2] (2), [Cu2(OMe)2(L)4(NO3)2]∙2MeOH (3∙2MeOH), [Cu(L)4](NO3)2 (4), [Cu2(OMe)2(L)4](ClO4)2 (5), [Cu(L)4](ClO4)2 (6), [Cu2(OMe)2(L)4]SiF6 (7) και [Cu2(SO4)2(L)4] (8). Based on the X-ray crystal structure determination of the above complexes, it was established that the intermolecular interactions responsible for the supramolecular organization of the structures are strong and weak hydrogen bonds, as well as π-π interactions. Specifically: • Supramolecular synthons between the N-H tectons of imidazole rings and the inorganic anions X- (Cl-, NO3-, ClO4-, SiF62-, SO42-) or/and lattice solvent molecules are formed, leading to 1D, 2D and 3D supramolecular structures. • The structures are further stabilized by intramolecular (complexes 4, 5 and 6) and intermolecular (complex 2) π-π interactions. • The size and charge of the anions X- used does not affect the structural core of the complexes, in contrast to their supramolecular organization which is decisively affected, leading to 2- and 3D architectures.

Βασικός στόχος της παρούσης Διπλωματικής Εργασίας ήταν η μελέτη της κρυσταλλικής μηχανικής μίας σειράς συμπλόκων ενώσεων του CoII με ιμιδαζολικά παράγωγα ως υποκαταστάτες και ειδικότερα με το 2-φαινυλοϊμιδαζόλιο και το 4-φαινυλοϊμιδαζόλιο. Η κρυσταλλική μηχανική μπορεί να θεωρηθεί ως ο κλάδος της υπερμοριακής χημείας στη στερεά κατάσταση. Η υπερμοριακή χημεία (supramolecular chemistry) είναι μία από τις πλέον δημοφιλείς και γρήγορα αναπτυσσόμενες περιοχές της πειραματικής χημείας. Χαρακτηρίζεται ως η χημεία των ασθενών διαμοριακών δυνάμεων και εστιάζει στη δομή και λειτουργία των χημικών συστημάτων με υψηλή πολυπλοκότητα (υπερμόρια) που προκύπτουν από το συνδυασμό δύο ή περισσοτέρων διακριτών χημικών ειδών (μορίων, ιόντων) και συγκρατούνται με ασθενείς (και αντιστρεπτές) διαμοριακές δυνάμεις (π.χ. αλληλεπιδράσεις π-π, δεσμούς υδρογόνου, υδρόφοβες αλληλεπιδράσεις, δυνάμεις van der Waals, αλληλεπιδράσεις διπόλου-διπόλου κλπ). Ένα σημαντικό πεδίο της υπερμοριακής χημείας είναι αυτό της κρυσταλλικής μηχανικής (crystal engineering) που αναφέρεται στη στρατηγική σχεδιασμού ενός κρυσταλλικού υλικού με επιθυμητές ιδιότητες και βασίζεται στην κατανόηση και τον έλεγχο των διαμοριακών αλληλεπιδράσεων των μορίων στην κρυσταλλική κατάσταση. Στην παρούσα Διπλωματική Εργασία πραγματοποιήθηκε η σύνθεση συμπλόκων ενώσεων με γενικό τύπο ΜΙΙ/Χ-/L ή L', όπου ΜΙΙ = CoII, X- = Cl-, I-, SCN-, NO3-, L = 2-φαινυλοϊμιδαζόλιο και L' = 4-φαινυλοϊμιδαζόλιο. Με μεταβολή των σημαντικότερων συνθετικών παραμέτρων –γραμμομοριακή αναλογία μετάλλου:υποκαταστάτη, πολικότητα του διαλύτη (MeOH, MeCN, Me2CO, CH2Cl2, CHCl3), συνθήκες θερμοκρασίας και μέθοδο κρυστάλλωσης– απομονώσαμε και χαρακτηρίσαμε τα εξής σύμπλοκα: [CoCl2L2] (1), [CoI2L2] (2), [Co(NCS)2L2] (3), [Co(NO3)2L2] (4), [CoL'4(MeCN)(H2O)](NO3)2 (5), [CoL'4(MeCN)(H2O)]I2 (6), [Co(NCS)2L'2] (7), [Co(NCS)2L'4]•MeOH (8•MeOH). Όπως διαπιστώθηκε με την βοήθεια της κρυσταλλογραφικής ανάλυσης ακτίνων Χ επί μονοκρυστάλλων των ανωτέρω συμπλόκων, οι διαμοριακές αλληλεπιδράσεις που είναι υπεύθυνες για την υπερμοριακή οργάνωση των δομών τους είναι ισχυροί και ασθενείς δεσμοί υδρογόνου και αλληλεπιδράσεις τύπου π-π. Ειδικότερα, τα δεδομένα για τα σύμπλοκα με τον L διαπιστώθηκε ότι: • Σταθερά μοτίβα διαμοριακών αλληλεπιδράσεων (συνθόνια) σχηματίζονται μεταξύ των τεκτονίων N-H των ιμιδαζολικών δακτυλίων και των ενταγμένων ιόντων X (X = Cl, I, NO3, SCN) όλων των συμπλόκων οδηγώντας σε μονο- ή δισδιάστατες δομές. Οι δομές αυτές ενισχύονται περαιτέρω από ασθενείς αλληλεπιδράσεις C-H∙∙∙X (X= Cl, I, O, S) προς 3D υπερμοριακές δομές. • Εκτός του συμπλόκου 2 στο οποίο παρατηρούνται ενδομοριακές π-π αλληλεπιδράσεις σε καμία άλλη δομή δεν παρατηρούνται τέτοιες ενδο- ή διαμοριακές αλληλεπιδράσεις. Για τα σύμπλοκα με τον υποκαταστάτη L' διαπιστώθηκε παρόμοια ότι: • Σταθερά μοτίβα διαμοριακών αλληλεπιδράσεων (συνθόνια) σχηματίζονται μεταξύ των τεκτονίων N-H των ιμιδαζολικών δακτυλίων και των ανόργανων ανιόντων X- (X- = NO3-, I-) στα σύμπλοκα 5 και 6 ή του ενταγμένου SCN στα σύμπλοκα 7 και 8•MeOH ή/και πλεγματικών μορίων διαλύτη (σύμπλοκο 8•MeOH), οδηγώντας σε μονο- ή δισδιάστατες δομές. Παρόμοια με τις δομές 1-4, ασθενείς C-H∙∙∙X (X= O, S) αλληλεπιδράσεις οδηγούν τελικά σε συγκρότηση 3D δομών. • Στα σύμπλοκα 7 και 8•MeOH η οργάνωση της δομής ευνοεί παράλληλα το σχηματισμό διαμοριακών π-π αλληλεπιδράσεων. • Στα σύμπλοκα 5 και 6 είναι απαραίτητη η παρουσία αντισταθμιστικών ιόντων στο πλέγμα τους καθώς πρόκειται για κατιοντικά σύμπλοκα του τύπου [CoL'4(MeCN)(H2O)]2+. • Μόνο το σύμπλοκο 8•MeOH περιέχει πλεγματικά μόρια διαλύτη (MeOH) χωρίς να είναι απαραίτητη η παρουσία αντισταθμιστικών ιόντων στο πλέγμα του. Συμπερασματικά, ο κυρίαρχος παράγοντας που καθορίζει την υπερμοριακή οργάνωση των συμπλόκων και των δύο κατηγοριών (δηλ. με υποκαταστάτες τα ισομερή, 2- και 4-φαινυλοϊμιδαζόλιο) είναι τα ισχυρά συνθόνια N-H∙∙∙X (X = Cl, I, NO3, SCN). / The main target of this diploma thesis was the crystal engineering studies of a series of coordination compounds of CoII with substituted imidazoles as ligands and specifically, with 2-phenylimidazole and 4-phenylimidazole. Crystal engineering may be regarded as the solid-state branch of supramolecular chemistry. Supramolecular chemistry is one of the most popular and rapidly developing areas of experimental chemistry. It may be defined as the chemistry of weak intermolecular forces and focuses on the structure and function of chemical systems of high complexity (supermolecules), resulting from the association of two or more discrete chemical species (molecules, ions) held together by weak (and reversible) intermolecular forces (e.g. π-π interactions, hydrogen bonds, hydrophobic interactions, van der Waals forces, dipole-dipole interactions etc). Crystal engineering is an important field of supramolecular chemistry that refers to the design and synthesis of a crystalline material with desired properties, based on the understanding and control of intermolecular interactions in the crystalline state. In this diploma thesis the synthesis of a series of coordination complexes with general formula ΜΙΙ/Χ-/L or L' [ΜΙΙ = CoII, X- = Cl-, I-, SCN-, NO3- and L = 2-phenylimidazole, L' = 4-phenylimidazole] took place. By altering the parameters of synthesis –metal:ligand molar ratio, solvent polarity (MeOH, MeCN, Me2CO, CH2Cl2, CHCl3), temperature, as well as crystallization method– we were able to isolate and study the following complexes: [CoCl2L2] (1), [CoI2L2] (2), [Co(NCS)2L2] (3), [Co(NO3)2L2] (4), [CoL'4(MeCN)(H2O)](NO3)2 (5), [CoL'4(MeCN)(H2O)]I2 (6), [Co(NCS)2L'2] (7), [Co(NCS)2L'4]•MeOH (8•MeOH). As established by the single-crystal X-ray structure determination of the above complexes, the intermolecular interactions responsible for the supramolecular organization of the structures are strong and weak hydrogen bonds, as well as π-π interactions. A detailed study of the complexes with ligand L reveals that: • Supramolecular synthons between the N-H tectons of imidazole rings and the coordinated X ion (X = Cl, I, NO3, SCN) are formed, leading to 1- or 2D structures, which are further enhanced by weak C-H∙∙∙X (X= Cl, I, O, S) interactions, leading to 3D supramolecular architectures. • There are no intra- or intermolecular π-π interactions observed in complexes 1-4, with the exception of one such intramolecular interaction in complex 2. A detailed study of the complexes with ligand L' reveals that: • Supramolecular synthons between the N-H tectons of imidazole rings and the inorganic anions X- (X- = NO3-, I-) of complexes 5 and 6 or the coordinated SCN of complexes 7and 8 or/and lattice solvent molecules (complex 8•MeOH) are formed, leading to 1- or 2D structures, further organized in 3D architectures by means of weak C-H∙∙∙X (X= O, S) interactions. • In certain complexes (7 and 8•MeOH) the disposition of the complexes favors the formation of intermolecular π-π interactions. • In complexes 5 and 6 the presence of counter ions in their crystal structures is necessary since they are cationic complexes with the [CoL'4(MeCN)(H2O)]2+ unit as their structural core. • Only complex 8•MeOH contains lattice solvent molecules (MeOH) without the presence of counter ions in its crystal lattice. In conclusion, the determining factor of the supramolecular organization of the two series of complexes, that is with the isomers 2- and 4-phenylimidazole as ligands, is the presence of the strong synthons N-H∙∙∙X (X = Cl, I, NO3, SCN).

Crystal engineering is widely applied in the design of new solids with desired physical and chemical properties based on an understanding of intermolecular interactions in terms of crystal packing. The understanding of such structure-property correlations increased my interest in the modulation of macroscopic properties of solid compounds. Establishing connections between structure and macroscopic properties is a classical aspect of materials science and engineering. With the advent of the nanoindentation technique, it is now possible to make such a link between micro-level structures with mechanical properties of molecular solids - in other words, between chemistry and engineering. Nanoindentation is a quantitative probe for the assessment of mechanical behavior of small volume materials. In this technique, applied load and indenter depth penetration are measured simultaneously for a molecular crystal specimen, with high precision and resolution. From this data, one can obtain the elastic modulus and hardness of molecular crystals. Being able to accordingly assess the relative strengths of intermolecular interactions, such a technique has become relevant to the subject of crystal engineering. We have used nanoindentation to study the packing anisotropy of molecular crystals and to establish structure-property relationships. This thesis demonstrates that nanoindentation is a state-of-the-art technique to probe the mechanical properties of molecular crystals and assists the development of the subject of crystal engineering towards property design. Chapter 1 gives an overview of the development of crystal engineering from solid state organic chemistry and a brief introduction of the nanoindentation technique which has become relevant to the subject of crystal engineering to establish structure-property relationships. The study of the mechanical properties of molecular solids as a function of their crystal structures is a very active branch of crystal engineering. Chapter 2 explores the insights of well-known odd-even alternative mechanical, physical and thermal properties of α,ω-alkanedicarboxylic acids such as elastic modulus, hardness and melting temperature through nanoindentation technique. These properties are well correlated with their crystal structure packing. The odd acids were found to be softer and lower melting temperature as compared to the even ones, possibly due to the strained molecular conformations in the odd acids in easier plastic deformation. Shear sliding of molecular layers past each other during indentation is a key to the mechanism for plastic deformation in the molecular crystals. Relationships between structural features such as interplanar spacing, interlayer separation distance, molecular chain length and signatures of the nanoindentation responses, discrete displacement bursts have also been discussed in this chapter. Chapter 3 explores the use of the nanoindentation measurement as a signature response to study the microstructure that exists in a single crystal of organic solids. The analysis of microstructure through X-ray crystallography can be misleading. This is because crystal structures as determined from the single-crystal diffractometer data represent only space- and time-averaged structures. Thus, due to higher spatial resolution of the nanoindentation technique compared to X-ray diffraction (XRD) it become a local probe, which allows for discrimination between different microstructure or domains in the single crystal. Chapter 4 attempts to explore an understanding of the underlying relationship between crystal structure and the mechanical properties of molecular crystals which are relevant for the systematic design of organic solids with a desired combination of mechanical properties such as elasticity and hardness through crystal engineering. Elastic properties in molecular solids are largely determined by the isotropy of crystal packing. By using the techniques of crystal engineering, seven halogenated N-benzylideneanilines (Schiff bases) crystals have been systematically designed and observed common underlying structural features which lead to high flexibility and elasticity. Elasticity in those crystals arises from a criss-cross packing of molecular tapes in isotropic structures with energetically comparable halogen bonds (Cl···Cl or Cl···Br). The chapter also demonstrates that the solid solution strengthening can be effectively employed to engineer hardness of organic solids. High hardness can be attained by increasing lattice resistance to shear sliding of molecular layers during plastic deformation. Chapter 5 demonstrates the broad applications of mechanical properties of molecular solids in the context of the pharmaceutical industry, which can be understood through nanoindentation. Crystal engineering is applied in designing active pharmaceutical ingredients (APIs) so as to obtain materials that exhibit optimum combinations of important physicochemical properties such as solubility, dissolution rate, and bioavailability. In the context of industrial-scale pharmaceutical manufacturing, it can also be used to tune mechanical properties such as grindability and tabletability, which often determine the processing steps that are adopted. Hence, there is always interest in the crystal structure−mechanical property correlations of APIs. The study of the mechanical properties of polymorphic drugs is an important for developing an understanding of their stability in the solid state. Overall, the main aim of this thesis is to explore an understanding for establishing structure-mechanical properties correlations of molecular crystals with recent advances in the nanoindentation technique and to gain knowledge for the design and synthesis of new materials using the crystal engineering approach. Nanoindentation of molecular crystals provides insights related to crystal packing, interaction characteristics, polymorphism and topochemistry.

Doctor of Philosophy / Chemistry / Christer B. Aakeroy / A series of co-crystallizations between four biimidazole based compounds with nine symmetric aliphatic di-acids and fifteen perfluorinated halogen-bond donors were carried out to determine if a MEPS based ranking can be used to effectively assign selectivity in hydrogen- and halogen-bond interactions. The results suggested that a simple electrostatic view provides a reliable tool for successfully implementing the practical co-crystal synthesis with desired connectivity. MEPS based selectivity guidelines for halogen-bond interactions were explored in co-crystallizations between twelve asymmetric ditopic acceptors and nine halogen-bond donors. If the difference between the two acceptor sites is below 35 kJ/mol, no selectivity was observed; above 65 kJ/mol halogen bond selectivity dominates and mid ΔE range was recognized as the grey area where predictions cannot be made. To examine competition between hydrogen and halogen bonds, five heteroaryl-2-imidazoles were co-crystallized with fifteen halogen-bond donors. It was found that halogen bonds prefer best the acceptor site, demonstrating that a suitably activated halogen-bond donor can compete with a strong hydrogen-bond donor. The benefits of ‘double activation’ for promoting halogen bond effectiveness was explored with nine haloethynylnitrobenzenes. The positive potential on halogen atoms was enhanced through a combination of an sp-hybridized carbon and electron-withdrawing nitro group(s). Iodoethynylnitrobenzenes were identified as the most effective halogen-bond donors reported to date and the compounds were exploited for the interaction preferences of nitro group and nitro⋯X-Csp interactions were identified as synthetic tools for energetic co-crystal assembly. A synthetic strategy for the deliberate assembly of molecular polygons was developed utilizing bifurcated halogen bonds constructed from N-oxides and complementary halogen-bond donors via co-crystallization. A convenient, effective, and scalable protocol for stabilizing volatile liquid chemicals with co-crystallization was achieved. Through the use of halogen-bonding, liquid iodoperfluoroalkanes were transformed into crystalline materials with low-vapor pressure, considerable thermal stability and moisture resistance. To stabilize the energetic compound ethylenedinitramine, a co-crystallization approach targeting the acidic protons was employed. Eight co-crystals were obtained and the acceptors were identified as supramolecular protecting groups leading to diminished reactivity and enhanced stability while retaining the desirable energetic properties.

Crystal engineering offers a rational way of analyzing crystal structures and designing new structures with properties. The supramolecular synthon concept was introduced in 1995 and has shown versatility and utility in the design of molecular solids. Chapter 1 gives a general introduction about the development of the concept of supramolecular synthons over the years which has seen a transition from synthesis to structures and dynamics. This thesis focuses on the later phase of the development of the concept of supramolecular synthons. Chapter 2 introduces the idea of structural landscape and describes a structural landscape of a conformationally flexible molecule, orcinol, and explores the synthon preferences of this particular molecule towards cocrystal formation. Chapter 3 explores a combinatorial matrix to show both global and local features of a structural landscape. Chapter 4 takes a component of this landscape namely 4,4'-bipyridine and 4-hydroxybenzoic acid and shows the occurrence of synthon polymorphism in cocrystals which originates from the interplay of geometrical and chemical factors. Chapter 5 introduces a four step method for the identification of multiple synthons by FTIR spectroscopy. Along with, it shows that the rarity of synthon polymorphism is not a case of overlooking of crystals in the process of selecting good looking crystals. Chapter 6 takes a series of dihalogenated phenols and indicates that the Br prefers type II. This chapter also explains elastic bending on the basis of halogen bonds. Chapter 7 attempts to explore the Cl/Br isostructurality in the light of type I and type II contacts and concludes that Cl/Br isostructurality arises from a geometrical model and therefore it is quite similar to Cl/Me isostructurality. Chapter 8 attempts to analyze the class of trichlorophenols and reveals structural modularity in this class of compounds. The modularity of 3,4,5-trichlorophenol is explored in crystal design in chapter 9 in terms of LSAM (Long Range Synthon Aufbau Module) A subsequent study in solution by NMR reveals the presence of LSAM in solution and establishes a hierarchy of the dissociation of its components. The concept of supramolecular synthon has come a long way from being a tool in a crystal engineer’s toolbox to a structural unit responsible for crystallization and therefore offer multiple possibilities both in terms of structures and dynamics. This thesis attempts to explore some of these possibilities based mainly on the concepts of structural landscape and halogen bonds which are blended with the concept of supramolecular synthons.

As propriedades no estado sólido de um insumo farmacêutico ativo (IFA) estão diretamente relacionadas com a eficácia terapêutica de um medicamento. Entre todas as propriedades físicas e químicas, que são dependentes doarranjo cristalinodo IFA, destaca-se a solubilidade e a estabilidade, que são as características mais importantes de um fármaco, na medida em que podem alterar a biodisponibilidade. Dentro dessa perspectiva, a engenharia de cristaistem cada vez mais se consolidado como uma estratégia para aperfeiçoar as propriedades no estado sólido de um IFA. Neste trabalho, oito novas formas sólidas cristalinas, entre sais e cocristais, dos fármacos com ação anti-tuberculose etionamida (ETH), etambutol (ETB) e isoniazida (INH), foram preparadas e tiveram suas estruturas cristalinas determinadas por difração de raios X por monocristal. Além disso, todas as modificações cristalinas obtidas foram caracterizadas por difração de raios X por policristais, espectroscopia vibracional no infravermelho e Raman, calorimetria exploratória diferencial, termogravimetria e microscopia ótica térmica. Por fim, estudos de solubilidade em equilíbrio e de estabilidade em atmosfera úmida também foram realizados. A nova modificação cristalina da ETH, o sal nitrato de ETH, foi planejada visando melhorar a solubilidade aquosa deste IFA (∼0,4 mg mL-1). Este é o primeiro relato de uma estrutura de ETH que cristalizou com quatro independentes pares iônicos (ETH+/NO3-) na unidade assimétrica. A análise do empacotamento cristalino e das interações intermoleculares permitiu estabelecer os atributos estruturais que explicam a menor estabilidade térmica e a elevada solubilidade (cerca de 300 vezes maior) deste sal, em comparação com a forma neutra da ETH. A preparação dos novos sais de ETB foi feito considerando o cárater básico da molécula, o que permitiu a obtenção de três novos sais a partir da reação do ETB com os ácidos oxalico, maleico e tereftálico. O desenho dessas formas sólidas teve como principal objetivo minimizar os efeitos da elevada higroscopicidade do ETB, que é tão prejudicial para formulações farmacêuticas. Este objetivo foi alcançado, uma vez que o sal oxalato de ETB, reportado neste trabalho, mostrou ser não-higroscópico. Por fim, quatro novos cocristais da INH, sendo dois cocristais polimórficos, foram preparados por meio de reações estequiométricas deste IFA com ácidos carboxílicos aromáticos derivados do ácido benzóico. O desenho dessas novas modificações cristalinas teve como intuito principal explorar a diversidade de síntons supramoleculares formados entre a INH e moléculas contendo o grupo COOH. A análise dos empacotamentos cristalinos das formas I e II do cocristal INH-PABA, mostrou que este é um típico caso de polimorfismo orientacional. Portanto, os resultados desta dissertação trazem importantes contribuições científicas para a diversidade de formas sólidas, apresentando revelância para o setor farmacêutico no que se refere ao desenvolvimento de novas formulações contendo fármacos anti-tuberculose. / Solid state properties of an active pharmaceutical ingredients (API) are directly related to drug performance. Among all physical and chemical properties dependent on the crystal arrangement of a drug, stability and solubility are the main ones that alter its bioavailability. In this sense, crystal engineering is a strategy to improve solid state properties of drugs. In this work, eigth new multicomponent solid forms (salts and cocrystals) of the tuberculostatic drugs ethionamide (ETH), ethambutol (ETB) and isoniazid (INH) were prepared and their crystal structures were elucidated by single crystal X-ray diffraction. In addition, the crystal modifications were also characterized by powder X-ray diffraction, infrared and Raman vibrational spectroscopy, differential scanning calorimetry, thermogravimetry and Hot-stage microscopy. Finally, equilibrium solubility studies and stability experiments in humid atmosphere were also performed. The new supramolecular modification of ETH, ethionamide nitrate salt, was designed in order to improve the aqueous solubility of the API (∼0.4 mg ml-1). This salt is the first ETH structure that has been crystallized with four independent ionic pairs (ETH+/NO3-) in the asymmetric unit. The analysis of crystal packing and intermolecular interactions allowed to establish the structural attributes that explain the lower thermal stability and high solubility (about 300 times higher) of this salt compared to the neutral ETH form. Due its high hygroscopicity, ETB is known for catalyzing the degradation of isoniazid and rifampicinin pharmaceutical formulations. In order to avoid or even minimize these mutual drug-drug interactions, in this work we have focused on the development of less hygroscopic multicomponent solid forms of ETB. The preparation of the new ETB crystal modifications was carried out considering the pKa values of the molecule, which allowed the design of three new salts (namely oxalate, maleate and terephthalate). These salts were obtained from the reaction of ETB with the carboxylic acids: oxalic, maleic and terephthalic. The hygroscopic nature of these salts was evaluated and all of them were found to be hygroscopic, with exception of ETB oxalate. Finally, four novel INH cocrystals, being two polymorphic forms, with aromatic carboxylic acids derivatives were rationally prepared. The design of these crystal forms aimed to explore the diversity of supramolecular synthons formed between INH and molecules containing COOH. The crystal packing analysis of the INH-PABA cocrystals (polymorphs I and II), showed that this is a typical case of orientational polymorphism. Therefore, the scientific contributions of this work show the diversity of the solid forms and define candidates to new anti-tuberculosis API\'s solid formulations.

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.