Thesis (MTech (Chemistry))--Cape Peninsula University of Technology, 2017. / Crystal engineering principles were used to cocrystallize sulfa drugs, sulfapyridine (SFP) and sulfadiazine (SFD) with aromatic acids and an amine via solution crystallization. Sulfapyridine formed cocrystals with 3-nitrobenzoic acid (SFP∙3NBA), 5-bromosalicylic acid (SFP∙5BSA), 4-dimethylaminopyridine (SFP∙4DMAP) and salts with 4-nitrobenzoic acid [SFP+][4NBA-], 3,5-dinitrosalicylic acid [SFP+][DNSA-] and 3,5-dibromosalicylic acid [SFP+][DBSA-], while sulfadiazine formed a salt with 3,5-dinitrosalicylic acid [SFD+][DNSA-]. The newly formed complexes were analyzed by differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), fourier transform infrared spectroscopy (FTIR), single crystal X-ray diffraction (SCXRD), powder X-ray diffraction (PXRD) and nuclear magnetic resonance spectroscopy (1H and 13C NMR). The hydrogen bonding and crystal packing of the new solid forms were analyzed with the aid of Mercury and CrystalExplorer. The SFP and SFD compounds exhibit tautomerism. In this work it was investigated how the introduction of coformers with varying acidity provides the possibility to form a variety of synthons, and therefore disrupt the common preferred interactions within the sulfonamides. Using selected acids as coformers, the effect on crystal packing of the coformer’s substituent position was examined by using the isomers 3NBA and 4NBA. 5BSA and DBSA were employed to analyse the effect of the number of substituents on hydrogen bond formation and crystal packing. In addition, it was investigated how small structural changes in the pharmaceutical compound influences the crystal packing by cocrystallising structurally similar SFP and SFD with the same coformer. Evaluation of the change in coformer acidity was studied by using a pyridine coformer, 4DMAP, and its crystal packing was analyzed and compared to structures formed with carboxylic acid coformers. Finally, we examined how inter-conversion of tautomers promotes crystal formation by conforming to the geometric demands of the different coformers. / National Research Foundation(NRF)

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Cette thèse porte sur le développement d’une plateforme microfluidique polyvalente pour la cristallisation des protéines alliant études statistiques, économie de matière, rapidité d’exécution et facilité d’utilisation. L’objectif est de développer un outil unique pour répondre aux différentes problématiques de la cristallisation des protéines : identification d’une condition de cristallisation robuste via le criblage et l’optimisation et co-cristallisation d’une protéine et de ligands pour le structure-based drug design. Une méthode microfluidique versatile à base de gouttes sans tensioactif est utilisée. Elle permet la génération de centaines voire milliers de gouttes de quelques nL dans lesquelles la cristallisation peut avoir lieu indépendamment. La composition des gouttes est contrôlée par les débits des différentes solutions et vérifiée en ligne par spectrométrie UV-vis. De nombreuses conditions de cristallisation différentes peuvent ainsi être testées rapidement : nature et concentration de(s) agent(s) de cristallisation, ajout d’un ligand... Les cristaux obtenus à l’aide de cette plateforme sont caractérisés in situ et ex situ par DRX.Cette plateforme est appliquée à la cristallisation de deux protéines, une protéine modèle, le lysozyme, et une protéine d’intérêt pharmaceutique, la quinone réductase 2. Ainsi, nous avons développé un outil adapté aux contraintes de l’industrie pharmaceutique pouvant être transféré dans un laboratoire de recherche pour une utilisation de routine par des non-spécialistes de la microfluidique. La plateforme permet une approche de criblage à haut débit (HTS) et tend vers l’automatisation à la fois du criblage et de la DRX. / The aim of this work is the development of a versatile microfluidique platform for protein crystallization, combining statistical studies, material saving, speed of execution and ease of use. The aim is to develop a unique tool to address the different issues of proteins crystallization: identification of a robust crystallization condition via screening and optimization, and co-crystallization of a protein with ligands for structure-based drug design. For this purpose, a versatile droplet-based microfluidic method without adding any surfactant is used. It allows the generation of hundreds or even thousands of droplets of a few nanoliters in which the crystallization takes place independently. Droplets composition is controlled by the flow rates of the different solutions using programmable syringe pumps and checked on-line by UV-visible spectroscopy. Many different crystallization conditions can thus be tested quickly: nature and concentration of crystallization agent(s), addition of a ligand, etc. In addition, the crystals obtained using this microfluidic platform are characterized in situ and ex situ by X-ray diffraction.The platform is applied to the crystallization of two proteins, first a model protein, lysozyme, and then a protein of pharmaceutical interest, quinone reductase 2. Thus we have developed a tool suitable to constraints of pharmaceutical industry, in order to be transferred to research laboratories for routine use by non-specialists of microfluidics. This platform permits a high throughput screening approach, or HTS, and tends to the automation of both screening and X-ray diffraction.

Micro-reactors, enabling continuous processes at small scales, have been of growing interest due to their advantage over batch. These advantages include better scaling, as well as improved mass and heat transfer, though many new challenges arise due to the small scales involved such as non-negligible entrance effects and significant pressure drops. The flow in coils, rectangular channel serpentine plates, mix-and-reside plates, and complex liquid-liquid mixing plates was investigated and characterized using residence time distribution (RTD) tests. A pulse test was used to determine the RTD curve shape of these reactors at flowrates ranging from 20 to 100 g/min. A semi-empirical, multi-parameter model was used to describe the asymmetrical curves, while the axial dispersion model was used to describe the symmetrical ones. The Peclet number is given in function of the Reynolds number for the liquid-liquid plates that were found to be near-plug flow (Pe > 100). In a continuous mixing plate, the Pe ranged from 190 to 475 with Pe increasing as Re increased. The effect of straight channel sections in micro-reactors is also evaluated. Longer straight segments between micromixers resulted in the development of unidirectional flow and the occurrence of tailing in the RTD. Finally, the suitability of a liquid-liquid plate for a reactive liquid-solid system is evaluated. The plugging is determined visually and by measuring pressure increase; pressure started to increase after 5 minutes and the experiment had to be halted after 10 minutes due to plugging. Parallels between the particle size distribution and the residence time distribution curves are drawn. The particle size distribution of silver chloride at low flow rates is much wider than at high flowrates. The average particle size at high flowrates was also much lower (≈69nm) than at low flowrates (≈112nm).

This work presents a comprehensive study on the application of PAT tools to study, monitor and control polymorphism during batch cooling crystallization processes. For the first time, the same techniques were used to control and adjust polymorphic purity of the solid phase but also to investigate the relation between chemical equilibrium in solution and polymorphic outcome of cooling crystallization. Crystallization is an important unit operation used as separation and purification technique. It is widely employed in the pharmaceutical, chemical, agrochemical, food and cosmetics industries but also in the electronic, metallurgic and material industries. More than 90% of the APIs on the market are produced by crystallization, therefore, monitoring and control this process is fundamental to ensure the quality of the final product. The implementation of process analytical technology (PAT) tools during the development stage of APIs has largely helped in better understanding and optimizing both batch and, more recently, continuous crystallization. Polymorphism is the capacity of a compound to crystallize in more than one different crystalline structure, which can have different properties such as density, melting point, bioavailability and solubility. The choice of solvent, pH, kinetic conditions and presence of impurities has very strong effect on the polymorphic outcome of a cooling crystallization in solution. Understanding this phenomenon as well as being able to monitor and control it during industrial crystallization is one the biggest challenges for pharmaceutical industries.

Doctor of Philosophy / Department of Chemistry / Christer B. Aakeroy / The impact of the molecular electrostatic potential values (MEPs) in halogen and hydrogen bond interactions were explored using two acceptors with multiple acceptor sites with twelve hydrogen-bond donors, five halogen bond donors and four mixed halogen and hydrogen bond donors. The results suggested if the difference between the two acceptor sites is above 38 kJ/mol both hydrogen and halogen bond donors prefer the acceptor site with the highest MEP value and this selectivity was lost if the difference is below 26 kJ/mol. To examine the potential of halogen-bond donors in organocatalysis, a halogen-bond donor molecule was synthesized and the catalytic activity was measured using a benchmark Ritter type solvolysis reaction. Results suggested the catalytic activity of the halogen-bond donor molecule with > 90 % conversion of the product with the use of a stoichiometric amount of the catalyst for 96 hrs. Successful use of the control molecules confirm that the catalytic activity is an outcome of having halogen-bond donors in the molecule. The benefit of using a structural mimic in landscaping the structural outcomes of poorly soluble molecules was explored using an anticancer drug erlotinib. A structural mimic was synthesized by maintaining all binding sites that are important to design a structural landscape and the structural outcomes were analyzed using five FDA approved dicarboxylic acids. The results suggested that the structural outcomes of the mimic can be related to the actual drug erlotinib. Solubility and thermal behavior analysis of the co-crystals also suggested that with the systematic changes of the co-crystallization agent, it is possible to make predictable changes to the physical properties. To observe the effect of co-crystallization technology in reducing the chemical reactivity and sensitivity of an energetic compound dinitrobenzotriazole, a series of co-crystallization experiments was carried out using fourteen nitrogen and oxygen based acceptors. Four co-crystals were obtained and the acceptors were identified as supramolecular protecting groups which led to successful diminish of chemical instability and decreased impact sensitivity. Hygroscopicity and chemical reactivity of tetranitrobisimidazole, a potential RDX replacement, was successfully decreased by protecting the acidic N-H protons in the molecule by introducing suitable co-formers. Introduction of the N-oxide based acceptors into the system enhanced the stability while retaining most of the desirable energetic properties.

Masters of Science / The three-dimensional structures of proteins are important in understanding their function and interaction with ligands and other proteins. In this work, the structures of two proteins, ImuA’ from mycobacterium tuberculosis and GH9 C1 cellulase from a metagenomic library, were analysed using structural biological and modelling techniques. The gene encoding ImuA’ was amplified by two-step PCR, cloned, and expressed in E. coli. The recombinant ImuA’ produced was found to be largely insoluble. The insoluble protein was successfully solubilized in 8M urea but refolding the protein to its native structure was unsuccessful. By homology modelling, a 3D model of ImuA’ was obtained from a partly homologous protein RecA. In comparison to RecA, ImuA’ appears to lack some loop amino acids critical for DNA binding. Hence ImuA’ is postulated to not bind DNA. The second protein, GH9 C1 cellulase, was produced in E. coli. The protein was purified by chromatographic techniques and crystallized in a precipitant to protein ratio of 1:2 by hanging and sitting drop crystallization methods. The reservoir solution was made up of 15-30% (w/v) PEG 3350, 200 mM salt and 100 mM Tris-HCL pH 7.5-8.5. The protein crystals only diffracted x-rays to 4 å resolution which could not be used to obtain a crystal structure of the protein. The diffraction data, however, showed the crystal to be monoclinic with space group P2. Homology modelling revealed GH9 C1 cellulase to be a two domain protein with a smaller N-terminal Ig-like domain and a larger catalytic domain.The catalytic domain retains two ca2+ binding sites, which potentially stabilize the active site conformation and increase thermostability of the protein. Overall GH9 C1 cellulase is structurally similar to other GH9 cellulases, suggesting that its catalytic mechanism may be conserved.

Le potentiel de l'énergie solaire comme énergie renouvelable a été largement démontré depuis plusieurs années. Le stockage inter-saisonnier de cette énergie peut être réalisé au moyen d'un nouveau procédé basé sur l'absorption de la vapeur d'eau par une solution saline. L'innovation de ce procédé réside en la cristallisation du sel dans la cuve de stockage pour optimiser les capacités de stockage. Une étude préalable a été réalisée en utilisant le bromure de lithium (LiBr) comme absorbant avec des rendements thermiques très encourageants. Toutefois, son prix élevé ne permet pas d'envisager son utilisation dans un procédé industriel. L'objectif de cette thèse est d'évaluer et de déterminer de nouveaux couples d'absorption potentiellement utilisables industriellement dans ce procédé. Le premier chapitre présente une étude bibliographique des procédés de stockage, plus particulièrement ceux basés sur l'absorption. Les deuxième et troisième chapitres présentent les propriétés thermodynamiques des sels, obtenues par des mesures calorimétriques et de pressions de vapeur, et le calcul des paramètres procédés qui ont conduit au choix du couple de sorption permettant de répondre à l'ensemble des spécifications du procédé. Le quatrième chapitre présente l'étude de l'équilibre solide/liquide/vapeur de ce nouveau couple, pour obtenir l'ensemble des données de base nécessaires pour l'étude de la cristallisation du sel dans l'eau, et sa comparaison avec le couple LiBr/H20. Ce point est présenté dans le dernier chapitre en synergie avec des modélisations CFD des écoulements au sein de la cuve de stockage / The use of solar energy as a renewable energy has been widely demonstrated since many years. Thermal solar energy storage is an interesting way of reducing gas emissions. This storage can be achieved using water vapor absorption-desorption in a binary system with a desiccant salt. The innovation of this project is the crystallization of the salt solution as its temperature falls under the storage temperature to optimize the storage capacity. A previous work was realized using LiBr as absorbent. In spite of its interesting efficiency, two major drawbacks have been underlined: its price and its low storage capacity. This work is dedicated to evaluate and characterize new potential candidates of absorbent usable in the industrial process. The first chapter presents a bibliography report of the various thermal energy processes. The second and third chapters display the thermodynamical properties of the selected binary systems, calculated from calorimetric and vapor pressure measurements, and calculated process parameters which lead to select the new absorbent. The fourth chapter is based on the study of the solid/liquid/gas equilibrium of the new binary system and of LiBr/H20 to characterize the crystallized phases in many different equilibrium states. Finally, the last chapter presents a preliminary study of the CFD modeling of the non-isothermal flow in the storage tank and the suggested geometries tested for the crystallization of KHCOO in the storage tank

Long-chain molecules are widely used in many commercial products, including waxes, oils, fats and soaps. This study focuses on the primary n-alkylammonium chlorides that have applications as surfactants, detergents and as models for bio-membranes. The specific topic of this investigation is the polymorphism of three series of n-alkylammonium halides. Polymorphism is the ability of a substance to exist in more than one crystal form. Due to the conformational flexibility of the long alkyl chain and the forces (hydrogen bonding and van der Waals interactions) dictating the packing in these compounds, more than one type of molecular packing is possible, resulting in the crystallization of various polymorphs for each compound. Various investigations of the polymorphism of n-alkylammonium halides have been published in the scientific literature. This includes mainly studies on the polymorphism and structures of n-alkylammonium chlorides. Only a few reports on investigations of the polymorphism of n-alkylammonium bromides were found in the literature, but no investigation of the polymorphism of n-alkylammonium iodides could be located. This study is limited to the medium chain length primary n-alkylammonium halides, CnH2n+1N+H3X- where n = 11 to 18 (except 17) and X = Cl, Br and I. It is expected that in this chain length range, both packing forces (hydrogen bonding and van der Waals interactions) will play a role in dictating the molecular packing. It was attempted to crystallize the maximum number of polymorphs of each compound by extensive variation of the crystallization conditions. The parameters varied include crystallization temperature, solvent and crystallization method. Information regarding the polymorphism of a compound crystallized under specific conditions were collected by the complementary techniques of X-ray diffraction and thermal analysis. X-ray diffraction is the ideal technique to study polymorphism because the result of such an investigation is the three-dimensional packing in the crystal structure. Due to the wide scope of the investigation, only the polymorphic forms stable at room temperature were investigated. The single crystal X-ray technique allows the determination of the crystal structure of a polymorph, but due to the tendency of the compounds to crystallize in thin plates, very few single crystals of good diffraction quality were obtained. Nine crystal structures were, however, determined. Most polymorphic forms were available as polycrystalline powders. The new techniques for crystal structure determination from powder data were employed to determine two crystal structures from powder diffraction data, although at lower precision, and further refined them by the Rietveld technique. Conventional X-ray powder diffraction is well suited to the identification of polycrystalline materials. The technique does not give direct information regarding the structural nature of the polymorph, but gives a unique fingerprint for each polymorphic form. All polymorphs that were obtained by the various crystallization techniques were characterised by X-ray powder diffraction, and the unique long Summary iispacing of each polymorphic form was determined from the position of the low angle diffraction peaks in the diffraction pattern. Linear correlations between the chain lengths and long spacings were used to search for the presence of isostructural series amongst the phases. More than one isostructural series could be identified for each homologous series of compounds. Thermal analysis techniques were employed to determine the phase transition temperatures and enthalpies of phase transitions occurring at temperatures above room temperature. In this investigation the thermal behaviour of polymorphs were investigated by differential scanning calorimetry (DSC), thermo-gravimetric analysis (TGA) and hot stage microscopy (HSM). A stepwise melting behaviour that includes various solid-solid phase transitions was observed for all compounds studied. The sequence of phase transitions that occur with an increase in temperature were found to be unique to a specific polymorphic form. Thermogravimetric analysis provided information regarding the incorporation of solvent in the crystal lattice by monitoring the change of sample weight with increase in temperature. Hot stage microscopy allowed the visual observation of changes occurring in the morphology and texture of the sample with temperature. This investigation contributed a large amount of information to the pool of knowledge on the crystalline phases of the n-alkylammonium halides. Up to now, not much structural data on the crystal forms of these compounds were available in the literature. In this study, complex patterns of crystal packing and phase transitions were revealed. Six isostructural series of n-alkylammonium chlorides were identified, three of which have not been reported previously, and the crystal structure of one of the novel forms was determined. Four isostructural polymorphic forms of n-alkylammonium bromides were identified. Only two forms have been reported previously in the literature. Six crystal structures of compounds with a novel crystal form were determined. For the homologous series of n-alkylammonium iodides, four novel isostructural series were identified, and one structure was determined. Relationships between chain lengths and structural parameters like long spacings, unit cell parameters and phase transition temperatures were determined and expressed as mathematical functions. An analysis of all the known structures (structures reported in the literature and structures determined in this investigation) indicated that different molecular conformations and hydrogen bonds are responsible for differences in the packing, as expressed in the formation of polymorphs. A choice of anion for a specific compound (chloride, bromide or iodide) influenced not only the cell volume, as would be expected, but also dictated the preferential formation of pseudo-polymorphs and complex hydrogen bonding networks in the crystals themselves. Phase transition temperatures were found to be not simply a function of chain length, but to be significantly influenced by the anion and polymorphic form present. / Prof. G.J. Kruger

Two series monodispersed nanoparticles of hydroxylpropyl cellulose (HPC) and functionalized poly-N-isopropylamide (PNIPAM) particles have been synthesized and used as building blocks for creating three-dimensional networks, with two levels of structural hierarchy. The first level is HPC nanoparticles were made from methacrylated or degradable cross-linker attached HPC. These nanoparticles could be stabilized at room temperature by residual methacrylate or degradable groups are present both within and on the exterior of HPC nanoparticles. Controlled release studies have been performed on the particle and networks .The nearly monodispersed nanoparticles have been synthesized on the basis of a natural polymer of hydropropylcellulose (HPC) with a high molecular weight using the precipitation polymerization method and self-assembly of these particles in water results in bright colors. The HPC nanoparticles can be potential using as crosslinkers to increase the hydrogels mechanical properties, such as high transparency and rapid swelling/de-swelling kinetics. The central idea is to prepare colloidal particles containing C=C bonds and to use them as monomers - vinylparticles, to form stable particle assemblies with various architectures. This is accomplished by mixing an aqueous suspension of hydrogel nanoparticles (PNIPAM-co-allylamine) with the organic solvent (dichloromethane) to grow columnar crystals. The hydrogels with such a unique crystal structure behavior not only like the hydrogel opals, but also have a unique property: anisotropy.