The research presented herein focus upon crystal engineering of co-crystals with an emphasis upon the exploration of co-crystals in the context of delineation of the reliability of hydrogen bonded supramolecular synthons and their hierarchies. The approach involves a combination of systematic Cambridge Structural Database analysis and a series of model co-crystal experiments. In addition, the viability of solid state methodologies toward supramolecular synthesis of co-crystals and the effect on polymorphism is also addressed. The application of the acquired knowledge is towards the crystal engineering of pharmaceutical co-crystals. The rational design and synthesis of pharmaceutical co-crystals accomplished by the selection of appropriate co-crystal formers facilitated by analysis of existing crystals structures in the CSD will be demonstrated. The processing of pharmaceutical co-crystals will also be addressed in terms of slurry conversion, solvent drop grinding and solution crystallization.

Neutral or charge-assisted hydrogen bonds occurring between organic molecules represent strong and directional forces that mediate the molecular self-assembly into well defined supramolecular architectures. A proper understanding of hydrogen bonding interactions, their types, geometries, and occurrence in supramolecular motifs, is a prerequisite to crystal engineering, i.e. to the rational design of functional solid materials.Multiple-component organic crystals represent ideal systems to study the intermolecular interactions between the constituent molecules that can be pre-selected for their hydrogen bonding sites and geometrical capabilities. In particular, the systematic structural analysis of supramolecular systems that are comprised of simple molecules facilitates the development of strategies for the rational design of new multiple-component compounds involving more complex components such as drug molecules.The work presented herein shows a combination of systematic database and experimental studies in the context of reliability and hierarchy of several hydrogen bonded supramolecular synthons that exist in a series of model co-crystals and organic salts. The acquired paradigms are ultimately utilized in crystal engineering of pharmaceuticals. In addition, the viability of a mechanichemical approach toward supramolecular synthesis in the context of its efficacy and the effect on polymorphism in multiple-component compounds is also addressed.

Submitted by Jaqueline Silva (jtas29@gmail.com) on 2014-09-19T19:05:02Z No. of bitstreams: 2 Silva, Cameron-2014-dissertação.pdf: 4685861 bytes, checksum: 35a25c14813b0206d3d9c8fa6c8bfdaf (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Jaqueline Silva (jtas29@gmail.com) on 2014-09-19T19:05:31Z (GMT) No. of bitstreams: 2 Silva, Cameron-2014-dissertação.pdf: 4685861 bytes, checksum: 35a25c14813b0206d3d9c8fa6c8bfdaf (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2014-09-19T19:05:31Z (GMT). No. of bitstreams: 2 Silva, Cameron-2014-dissertação.pdf: 4685861 bytes, checksum: 35a25c14813b0206d3d9c8fa6c8bfdaf (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2014-03-06 / Fundação de Amparo à Pesquisa do Estado de Goiás - FAPEG / Co-crystallization of active pharmaceutical ingredients has been widely studied lately in order to improve the solid state features of such compounds, for example solubility, and also to protect the intellectual property of such compounds. Multicomponent molecular crystals can be prepared from both supramolecular synthon and screening approaches, which involve the variation of crystallization conditions. In this way, molecular crystal engineering is a strategy to improve solid state properties of drugs related to their efficacies. One branch of the lamivudine crystal engineering deals with its protonable pyrimidine-based nitrogen being a recipe of crystallization with carboxylic acids. Such strategy has yielded several pharmaceutical co-crystals and salts of APIs that have lamivudine-like heterocyclic nitrogens by choosing suitable carboxylic acids as a salt/co-crystal former. In this context and in relation to the drug antiretroviral nucleoside reverse transcriptase inhibitor lamivudine, four new crystalline phases thereof were prepared, their crystal structures were determined by X-ray diffraction by single crystal, and their solubility in water were measured. For the first time it was observed an in-plane pairing of lamivudine with the carboxylate and carboxyl functionalities of a same salt former unit giving rise to a trimer and a tetramer in the structures of lamivudine hydrogen phthalate hemihydrate and lamivudine hydrogen 4,5-dichlorophthalate, respectively. Besides, a new synthon have been found in the first salt. All lamivudine salts were less soluble than the lamivudine form II (free base). The unexpected heterosynthon can be related to the slightly higher solubility of lamivudine hydrogen 4,5-dichlorophthalate when compared to the other salts prepared in this study. / Co-cristalização de insumos farmacêuticos ativos tem sido largamente estudada ultimamente a fim de melhorar as propriedades do estado sólido, como, por exemplo, a solubilidade, e também manter a propriedade intelectual de tais compostos. Cristais moleculares multicomponentes podem ser preparados a partir da abordagem de sínton supramolecular e também através de métodos sistemáticos de investigação laboratorial, o que envolve a variação de condições de cristalização dos fármacos. Neste sentido, a engenharia de cristais moleculares é uma estratégia para aperfeiçoar as propriedades de estado sólido relacionadas às eficácias dos fármacos. Um ramo da engenharia de cristais de lamivudina lida com sua base nitrogenada pirimidina, a qual pode ser protonada, sendo assim um alvo de co-cristalização com ácidos carboxílicos. Tal estratégia tem rendido vários co-cristais e sais de insumos farmacêuticos ativos que possuem nitrogênio heterocíclico como a lamivudina pela escolha adequada de ácidos carboxílicos como um formador de sal/co-cristal. Nesse contexto, e com relação ao fármaco antirretroviral inibidor nucleosídeo de transcriptase reversa, a saber, lamivudina, quatro novas fases cristalinas foram preparadas, suas estruturas cristalinas foram elucidadas por difração de raios X por monocristal, e suas solubilidades em água foram aferidas. Nesse estudo, pela primeira vez foi observado um duplo pareamento da droga com ambas as funcionalidades ácidas do contra-íon originando uma tríade e um tetrâmero planar nas estruturas de biftalato de lamivudina hemidratado e 4,5-diclorohidrogenoftalado de lamivudina, respectivamente. Além disso, um novo sínton foi encontrado no primeiro sal. Todos eles foram menos solúvel do que a forma II da lamivudina (base livre). O inesperado heterosínton pôde ser correlacionado com a solubilidade ligeiramente maior do 4,5-diclorobiftalato de lamivudina quando comparado com os demais sais preparados.

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.

Crystal engineering underlies the essence of natural affiliation between the molecule on the one side and the crystal as a supramolecular assembly on the other. Molecular recognition is the fundamental cause for this efficient transformation and if we consider the crystal as a supramolecular entity then it is not at all difficult to conceive crystallization as an outstanding example of molecular recognition. In general, organic compounds often facilitate closed packed crystal structures as described by A. I. Kitaigorodskii in the form of the close packing principle but based on chemical features, there is still a small window to understand, to rationalize and to fashion new crystal structures. Extending the chemical viewpoint as first proposed by J. M. Robertson, the supramolecular synthon model as a descriptor of collective crystal structures has been invoked that enables one to trail the molecular behaviour from an entropy dominated situation in solution to an enthalpy driven progression in the solid state. After 20 years, the concept of the supramolecular synthon has stood the test of time because of its simplicity and effectiveness towards the implementation in complex crystal structures and has led the scientific community to further handle complex and interesting ideas in structural chemistry and supramolecular synthesis. The complexity of dynamic and progressive behavior of molecules during crystallization may be understood by the analogous argument of protein folding; both these complex phenomena decode the emergence of multiple metastable forms before the final structures are attained. These intermediate kinetically driven species may be high energy polymorphs and pseudopolymorphs of the compound in question or semicompact random globules for proteins. Understanding the role of these species in their respective processes is of critical importance in elucidating mechanisms. As an alternative approach, crystal structure prediction (CSP) is also of fundamental importance in the context of understanding the crystallization process. All energy based computational methods of CSP address this problem by scanning the multi-dimensional energy hypersurface. This is performed by computing lattice energy changes with respect to parameters like unit cell dimensions, space group symmetry and the positional coordinates of atoms in the asymmetric unit. Further, the computational prediction of the crystal structure of an organic compound results in several choices, and it is possible that a collection of some of these when taken together forms a pattern that mimics the course of the crystallization process very much in the manner that structure correlation mimics covalent bond breaking and making. With all these developments, one is truly at the stage today when any experimental or computed crystal structure is just that, a crystal structure of the molecule in question and it is part of a complex and dynamic structural space which may include a part of the supramolecular reaction trajectory for crystallization itself. Accordingly, this thesis emphasizes the importance of kinetic events during crystallization and proposes some strategies to access the inaccessible domains of this structural space of a given compound. I have exploited the supramolecular synthon model to understand the kinetics of the crystallization process and have further extended this understanding towards the isolation of stoichiometric ternary solids. The synthon model also helps one to provide a logical step to explore these remote domains of the complex hyperenergy surface that have collectively been termed as the crystal structure landscape of the compound in question. The precise descriptions of the chapters are mentioned below. Chapter 2 describes fluorosubstitution as a unique chemical probe to explore the high energy crystal structures of benzoic acid in ambient conditions. This landscape exploration of benzoic acid is based on the robust (kinetically favoured) supramolecular homosynthon as well as consistent fluorosubstitution in native compound. This analysis is also supported by synthon based crystal structure prediction which is one of the best ways of monitoring high energy virtual crystal structures. Chapter 3 extends the idea of landscape exploration towards multicomponent systems. The incorporation of an additional compound during crystallization facilitates even complex kinetic environments but using fluorosubstitution as a chemical probe, it again helps to analyse the high energy virtual domains of the given multicomponent system. Similar to chapter 2, the landscape exploration of multicomponent system is also based on the robust (kinetically favoured) supramolecular heterosynthon as well as consistent fluorosubstitution in the native multicomponent system. Chapter 4 emphasizes the importance of synthon modularity as a chemical probe to traverse in the crystal structure landscape of the given multicomponent system. Here, I have quantified the role of the definitive synthon, by using the supramolecular synthon based fragment approach (SBFA), in the emergence of polymorphism in cocrystals. In latter part of this chapter, I utilized this collective kinetic information in order to realize the combinatorial nature of the crystallization process and showed the complex combinatorial synthesis of ternary solids which itself is considered to be an arduous exercise. Chapter 5 discusses the importance of kinetic information which were fetched from the corresponding multicomponent landscapes and were further utilized for combinatorial synthesis of ternary solids. Although the combinatorial idea is well established in solution, this chapter highlights the first experimental evidence of this idea in the solid state and shows preferred amplification of certain supramolecular synthons from corresponding libraries in the supersaturated crystallizing medium. Chapter 6 extends the combinatorial idea of crystallization even further by using highly flexible organic compounds that collectively provide larger structural space during crystallization. Using the delicate kinetic information about the molecular and supramolecular features, this chapter describes the preferential selection of molecular conformation and supramolecular synthons from the supersaturated solution during the molecule→crystal pathway. In summary, the idea of the crystal structure landscape provides an extended interpretation about some of the complex ideas namely, crystal energy landscape and polymorphism in modern crystal engineering. The crystallization of an organic compound often depends upon intrinsic chemical features and accordingly one selects optimized crystallization routes in the corresponding landscape through decisive experimental conditions. As a final note, the idea of the crystal structure landscape enables one to (at least qualitatively) understand the importance of crystallization kinetics which is understandably a difficult task.