Supramolecular Pharmacy 6. Crystals and co-crystals Ondřej Jurček 1 Introduction to Crystallography 2 • The weak intermolecular interactions form supramolecules or supramolecular self-assemblies • The same forces also act in the formation of crystals • Dunitz referred to organic crystals as supramolecular chemistry par excellence • Crystallography determines arrangement and bonding of atoms in crystalline solids • Crystallography studies small molecules with ease with weight of the asymmetric unit (Wau) 100-700 or with possible difficulties also larger up to 100 000 Wau • Agreement factor, R-factor or residual factor, shows the agreement between properly scaled observed structural factors and calculated structure factors (for small Wau R < 0.07, 7%, large Wau R ~ 15%) Book: Analytical methods in supramolecular chemistry, 2nd edition, Wiley, Kari Rissanen – chapter Crystallography and crystal engineering, book edited by C. Schalley Crystallization 3 • Obtaining a single crystal might be the most challenging task • Solvent evaporation, diffusion, layering method, sublimation, etc. • 0.05 × 0.05 × 0.05 mm crystal can provide good data for solving the structure, usually 0.1-0.4 mm in at least two dimensions • Good crystal = good enough periodicity of the crystal lattice in the crystal • The heavier and the more ordered the atoms are the better will be diffraction • Importance of crystal stability – keep the crystals in mother liqueur! General consideration 4 • Purify your compound! • Factors affecting crystallization: solubility of the compound in the solvent used, time, temperature, mechanical agitation, and the number of nucleation sides • Consider the physicochemical properties of your compounds (thermal stability, sensitivity, etc.) • Make solubility profile of your compound (mild solvent is good) • Use clean glassware • Set up number of crystallizations at the same time under different conditions Crystallization techniques 5 • Slow solvent evaporation • Controlling evaporation, choice of vessel, single solvent or mixtures • Don‘t let it fully dry! T https://www.unifr.ch/chem/de/assets/public/PDFWordDocuments/Guide%20for%20crystallization.pdf Crystallization techniques 6 • Slow cooling • Soluble in hot, insoluble in cold https://www.unifr.ch/chem/de/assets/public/PDFWordDocuments/Guide%20for%20crystallization.pdf Crystallization techniques 7 • Sublimation • The sample is heated under reduced pressure until it vaporizes and then it deposits on cold surface Crystallization techniques 8 • Soxhlet extraction • Crystals can appear during extraction or more often later during cooling Crystallization techniques 9 • Solvent diffusion • Solvent layering method • Good for small amounts of sample https://www.unifr.ch/chem/de/assets/public/PDFWordDocuments/Guide%20for%20crystallization.pdf Crystallization techniques 10 • Vapor diffusion • Good for small amounts of sample https://www.unifr.ch/chem/de/assets/public/PDFWordDocuments/Guide%20for%20crystallization.pdf Crystallization techniques 11 • Reactant diffusion https://www.unifr.ch/chem/de/assets/public/PDFWordDocuments/Guide%20for%20crystallization.pdf in solvent 1 in solvent 2 Crystallization techniques 12 • Convection https://www.unifr.ch/chem/de/assets/public/PDFWordDocuments/Guide%20for%20crystallization.pdf Crystallization techniques 13 • Hydrothermal (solvothermal) method https://www.unifr.ch/chem/de/assets/public/PDFWordDocuments/Guide%20for%20crystallization.pdf Crystallization techniques 14 • Alternative methods • Counterions – problematic Et4N+, Bu4N+, BF4 -, and PF6 -, by counter ions that are usually ordered are triflate, BPh4 -, Me4N+, (Ph4P)2N+, and Ph4As+ • Co-crystals • Seeding • Melting • Gel https://www.unifr.ch/chem/de/assets/public/PDFWordDocuments/Guide%20for%20crystallization.pdf Crystal Structure Determination 15 • Crystal → selecting and mounting crystal → unit cell determination and preliminary space group selection → data collection (measurement of the intensity data), data processing, and final space determination → data reduction, structure solution, and refinement → analysis of the structure • Obtaining a single crystal, placing in magic oil in nylon loop • Mounting the crystal on brass pin into goniometer in diffractometer Book: Analytical methods in supramolecular chemistry, 2nd edition, Wiley, Kari Rissanen – chapter Crystallography and crystal engineering, book edited by C. Schalley Crystal Structure Determination 16 • Does sample diffract? Does the diffraction pattern indicate twinning? How high is the resolution of diffraction? • Unit cell determination, the smallest imaginary 3D unit in which the atoms are placed and multiplying this unit will build the whole macroscopic crystal • Unit cell is defined by axes a, b, c, and angles α, β, γ – volume of unit cell • Due to crystal symmetry seven types of primitive unit cells can exist • Bravais lattices Book: Analytical methods in supramolecular chemistry, 2nd edition, Wiley, Kari Rissanen – chapter Crystallography and crystal engineering, book edited by C. Schalley Crystal Structure Determination 17 • Measurement – data collection – X-ray beam is diffracted by electrons of atoms • Reflection planes are described by integers h, k, l so called Miller indices • Goniometer enables to collect many reflections (thousands, measured in hours) which are then computationally combined and converted into format for space group determination • Space group = mathematically derived set of symmetry operation within given unit cell (crystal lattice), there are 230 space groups • Asymmetric unit A. P. Davis et al.: Nature Chemistry 2016, 8, 24–32. → → Crystal Structure Determination 18 • Data reduction – obtaining structure factor • Structure solution, refinement • Supramolecular structures are challenging: • Poor crystal quality • Large supramolecules do not form wellordered crystal lattices (periodicity) • Crystal density is low • Wau is large • Unit cell usually contains large amount of (different) solvent molecules, which are disordered (further decreasing the quality of single crystals) • Output file is Crystallographic information file (cif) – save to database Cambridge Crystallographic Data Centre Book: Analytical methods in supramolecular chemistry, 2nd edition, Wiley, Kari Rissanen – chapter Crystallography and crystal engineering, book edited by C. Schalley With thanks to Kari Rissanen and Matti Haukka Crystal Structure Analysis 21 • Detailed analysis of intra- and intermolecular interactions • Plot of data with their van der Waals radii (CPK model) • Crystal preparation J. F. Stoddart: J. Am. Chem. Soc. 2012, 134, 406–417. Asymmetric unit Unit cell Crystal packing CD-MOF-1 Crystal Structure Analysis 22 • Detailed analysis of intra- and intermolecular interactions • Plot of data with their van der Waals radii (CPK model) J. F. Stoddart: J. Am. Chem. Soc. 2012, 134, 406–417. Non-covalent interactions Thermal elipsoids CPK (space filling) model Crystal Structure Analysis 23 • Detailed analysis of intra- and intermolecular interactions • Plot of data with their van der Waals radii (CPK model) J. F. Stoddart: J. Am. Chem. Soc. 2012, 134, 406–417. Crystal Engineering 24 • A set of designed processes which aim to form a crystalline material utilizing the supramolecular interactions and self-assembly of the components • Simultaneous development of supramolecular chemistry and crystallographic techniques led to development of novel field Crystal Engineering • Crystal engineering term mentioned already in 1955, but in article by Schmidt (1971) was used as explicit term – the article also postulated, that under suitable conditions, the molecular recognition events, viz. self-assembly, could be the major factor leading to crystal formation • Journals dealing with this phenomena Crystal Engineering Communication or Crystal Growth and Design, etc. • Over 39 000 publications on Web of Knowledge by now Crystal Engineering 25 • Using supramolecular synthons and good knowledge of non-covalent interactions Co-crystals 26 • Co-crystal is a multicomponent molecular crystal; that is, a crystalline substance comprising two or more chemically different molecules (although includes solvates, hydrates, and both stoichiometric and non-stoichiometric lattice inclusion compounds) • Crystalline, structurally homogeneous materials in which the two or more component molecules are present in a well-defined stoichiometric ratio • A pharmaceutical co-crystal is simply a co-crystal in which at least one of the molecular components is an API in conjunction with another type of molecule termed a cocrystal former. Co-crystal former should be included on the US FDA ‘The Substances Added to Food’ (formerly EAFUS) list, which comprises over 3000 substances that are suitable as food additives. a) J. Steed: Trends Pharmacol. Sci. 2013, 34, No. 3. b) A. S. Myerson et al. Cryst. Growth Des. 2011, 11, 887–895 https://www.cfsanappsexternal.fda.gov/scripts/fdcc/?set=FoodSubstances Co-crystals 27 • Co-crystals have different physical properties such as habit, bulk density, solubility, compressibility, friability, melting point, hygroscopy, and dissolution rate. J. Steed: Trends Pharmacol. Sci. 2013, 34, No. 3. Benefits of Co-crystals 28 • Co-crystal formation transform an amorphous or hard-to-crystalize active pharmaceutical ingredient (API) into a readily handled, stable crystalline solid • Crystalline products are generally preferred because of their easier and more reproducible characterization, lower hygroscopicity, and greater chemical stability • It is far more likely poor biopharmaceutical characteristics rather than toxicity or lack of efficacy that prevent a candidate active compound from progressing in clinical trials • The 1:1 co-crystal of a candidate sodium channel blocker and glutaric acid proved to dissolve 18 times faster than the pure drug crystal and the co-crystal has three times the bioavailability • Although, solubility measurements on highly soluble co-crystals must be treated with caution because the substance can undergo recrystallisation to the most stable pure API form on contact with solvent • Solvate forms are the least soluble forms in the solvent they contain a) J. Steed: Trends Pharmacol. Sci. 2013, 34, No. 3. b) D. P. McNamara Pharm. Res. 2006, 23, 1888–1897. Co-crystals and Legal Issues 29 • Useful co-crystal solid form also offers new opportunities for the exploitation of intelectual property (IP) and there are now numerous patents covering cocrystals – novel, useful, non-obvious – new patent. • In legal terms, patent protection for co-crystals is thought to be significantly easier to enforce than that of other solid-form IP (solvates, salts), because allegations of obviousness are more difficult to establish • Of particular relevance to co-crystal research is the issue of proton transfer; a stoichiometric crystal containing a neutral acid such as carboxylic acid along with a free-base drug substance is a co-crystal. However, proton transfer from acid to base would give a carboxylate salt, which is not a cocrystal – IP or regulatory relevance. • Example: Valproic acid is an approved medication for epilepsy. It exists as an acid form and a sodium salt (sodium valproate) form. The acid form is liquid at ambient conditions and sodium salt is highly hygroscopic. The cocrystal form contains both valproic acid and sodium valproate. a) J. Steed: Trends Pharmacol. Sci. 2013, 34, No. 3. b) A. V. Trask Mol. Pharm. 2007, 4 (3), 301-309. Synthesis of Co-crystals 30 • Easiest is to crystallise the API from a supersaturated solution in the presence of (varying amounts of) the co-crystal former • Most commonly (in ~40% of cases), supersaturation is achieved by slowly cooling an undersaturated mixture until the solubility limit is reached • Key to the rational synthesis of co-crystals is an understanding of the binary or ternary phase diagrams for the equilibria involving the solvent (if present) and two-solute mixture J. Steed: Trends Pharmacol. Sci. 2013, 34, No. 3. Region A, component 1 and solvent; B, component 1 + co-crystal; C, co-crystal; D, component 2 + co-crystal; E, component 2 and solvent; F, solution. Synthesis of Co-crystals 31 (i) use of an excess of one of the co-crystal components with a consequent reduction in the solubility of the co-crystal in the presence of the excess component; (ii) slurry crystallisation to access the low percentage solvent region of the phase diagram; (iii) careful tuning of solvent identity or composition to maximise the pure co-crystal regions in the phase diagram; (iv) wet milling of the solid components in the presence of just a few drops of solvent; (v) involving an intermediate phase such as a hydrate or amorphous form as part of a solid-state synthesis; (vi) use of a metastable polymorph to give an unstable intermediate that can trigger co-crystal growth; (vii) seeding solutions using co-crystal seeds derived from melt crystallisation using hot-stage microscopy J. Steed: Trends Pharmacol. Sci. 2013, 34, No. 3. N. Blagden et al. New J. Chem. 2008, 32, 1659–1672. Region A, component 1 and solvent; B, component 1 + co-crystal; C, co-crystal; D, component 2 + co-crystal; E, component 2 and solvent; F, solution. Synthesis of Co-crystals 32 (viii) mechanical grinding (ix) supercritical fluid co-crystallization (x) forming host-guest inclusion complexes, e.g., with cyclodextrins, cucurbiturils (xi) spray-drying method a) J. Steed: Trends Pharmacol. Sci. 2013, 34, No. 3. b) R. K. Bandaru et al. Front. Pharm. 2021, 12, 780582. Paroxetin (antidepressant) Oxaliplatin (chemoterapeutics) Analysis of Co-crystals 33 • Obvious change of properties of crystalline materials, e.g., solubility, melting point, etc. • Visual • Single crystal X-ray diffraction • Powder X-ray diffraction • Differential scanning calorimetry • Thermogravimetry • Vibrational spectroscopy (IR, Raman) • Solid state magic angle spinning NMR • Polarised optical hot-stage microscopy, e.g., barbiturates – nembutal, phenobarbital • Neutron diffraction J. Steed: Trends Pharmacol. Sci. 2013, 34, No. 3. 1:1 acetaminophen (paracetamol) and 2,4-pyridine dicarboxylic acid Ternary and Salt Co-crystals 34 • Usually ternary multicomponent solids are ‘co-crystal hydrates’, in which water is one of three types of molecule present in the material. For example, mechanochemically grinding theophylline results in the formation of a co-crystal hydrate with citric acid. • An interesting related example is the formation of a 1:1:2 ‘co-gel’ of melamine (M), uric acid (U), and water. Sonication of an aqueous suspension of M and U gives a solid gel that was shown by crystal structure calculation and X-ray powder diffraction to comprise co-crystal fibres of composition M:U:2H2O. J. Steed: Trends Pharmacol. Sci. 2013, 34, No. 3. Uric acid Melamine Cyanuric acid purine Ternary and Salt Co-crystals 35 • Salt co-crystals: Valproic acid is an approved medication for epilepsy. It exists as an acid form and a sodium salt (sodium valproate) form. The acid form is liquid at ambient conditions and sodium salt is highly hygroscopic. The cocrystal form contains both valproic acid and sodium valproate in 1:1 ratio. This cocrystal form is less hygroscopic than the components. Commercially, it is called by different names, such as Depakote®, Epilim, and divalproex sodium. This structure is considered salt–cocrystal. R. K. Bandaru et al. Front. Pharm. 2021, 12, 780582. Co-crystals and Market 36 • Does it still fall within current guidelines or is this a new chemical entity (safety, toxicology - expensive)? • Drug-drug co-crystals, e.g., co-crystallization of quercetin (a plant-derived flavonoid, used as a nutritional supplement and reputed to have anticancer properties) with antidiabetic agents such as metformin or tolazamide. The combination drug has been suggested to have physical properties and biological activity that are distinct from the individual properties of the two components X. Wang et al. Asian J. Pharm. Sci. 2021, 16, 307–317. Polymorphism and co-crystallization 37 • Walter McCrone once famously said ‘every compound has different polymorphic forms, and that, in general, the number of forms known for a given compound is proportional to the time and money spent in research on that compound’ In the next class… Polymorphism Thank you for your attention!