The use of co-crystals for the determination of absolute stereochemistry: an alternative to salt formation

Cocrystal Synthesis through Crystal Structure Prediction

Crystal structure prediction (CSP) is an invaluable tool in the pharmaceutical industry because it allows to predict all the possible crystalline solid forms of small-molecule active pharmaceutical ingredients. We have used a CSP-based cocrystal prediction method to rank ten potential cocrystal coformers by the energy of the cocrystallization reaction with an antiviral drug candidate, MK-8876, and a triol process intermediate, 2-ethynylglyclerol. For MK-8876, the CSP-based cocrystal prediction was performed retrospectively and successfully predicted the maleic acid cocrystal as the most likely cocrystal to be observed. The triol is known to form two different cocrystals with 1,4-diazabicyclo[2.2.2]octane (DABCO), but a larger solid form landscape was desired. CSP-based cocrystal screening predicted the triol-DABCO cocrystal as rank one, while a triol-l-proline cocrystal was predicted as rank two. Computational finite-temperature corrections enabled determination of relative crystallization propensities of the triol-DABCO cocrystals with different stoichiometries and prediction of the triol-l-proline polymorphs in the free-energy landscape. The triol-l-proline cocrystal was obtained during subsequent targeted cocrystallization experiments and was found to exhibit an improved melting point and deliquescence behavior over the triol-free acid, which could be considered as an alternative solid form in the synthesis of islatravir.

Thermal Expansion Properties and Mechanochemical Synthesis of Stoichiometric Cocrystals Containing Tetrabromobenzene as a Hydrogen- and Halogen-Bond Donor

The solution and mechanochemical synthesis of two cocrystals that differ in the stoichiometric ratio of the components (stoichiometric cocrystals) is reported. The components in the stoichiometric cocrystals interact through hydrogen or hydrogen/halogen bonds and differ in π-stacking arrangements. The difference in structure and noncovalent interactions affords dramatically different thermal expansion behaviors in the two cocrystals. At certain molar ratios, the cocrystals are obtained concomitantly; however, by varying the ratios, a single stoichiometric cocrystal is achieved using mechanochemistry.

Systematic comparison of racemic and enantiopure multicomponent crystals of phenylsuccinic acid—the role of chirality

Comparison of binary cocrystals of chiral and racemic carboxylic acids showed that the introduction of chiral building blocks may lead to the formation of subclasses of multicomponent crystals with unique Z′′/Z^r values combined with complex protonation stages of the molecules.

Structural similarity in chiral-achiral multi-component crystals

Understanding the structural similarities between co-crystals formed with racemic mixture and enantiopure chiral components with an achiral co-former.

Temperature-induced phase transition of isonicotinamide-malonic acid (2/1) and supramolecular construct analysis of isonicotinamide structures

The isonicotinamide-malonic acid (2/1) co-crystal salt (2IN·C3) exhibits a first-order displacive structural phase transition from low-temperature triclinic P1̅ crystal structure to high-temperature monoclinic C2/c crystal structure and vice versa at the transition temperatures of 298 (1) and 295 (1) K, respectively, as determined by variable-temperature SCXRD analysis and DSC measurements. The asymmetric unit of 2IN·C3 comprises three malonic acid molecules and six isonicotinamide molecules at the low-temperature phase, and this is reduced to a half-molecule of malonic acid and an isonicotinamide molecule in the high-temperature phase. The carboxyl and pyridinium H atoms are disordered at both phases. The observed phase transition near room temperature is triggered by the molecular displacement of the isonicotinamide molecule and the syn-anti conformational transformation of the malonic acid molecule with deviation angles of 10.4 and 11.7°, respectively, which induced an energy change of 19.1 kJ mol−1 in the molecular cluster comprising a central isonicotinamide molecule and eight neighboring molecules. However, the total interaction energy of the molecular cluster of a central malonic acid molecule and eight neighboring molecules does not change significantly upon the phase transition. The molecules of isonicotinamide structures except IN·IN+·triazole ‒ form zero-dimensional finite arrays or one-dimensional chains as the primary supramolecular construct by carboxyl···pyridyl (−35.9 to −56.7 kJ mol−1) and carboxamide···carboxamide (−53.6 to −68.7 kJ mol−1) or carboxyl···carboxamide (−52.6 to −67.1 kJ mol−1) synthons.

Binary co-crystals of the active pharmaceutical ingredient 1,4-bis(4-pyridyl)-2,3-diaza-1,3-butadiene and camphoric acid

Co-crystals comprising the active pharmaceutical ingredient 1,4-bis(4-pyridyl)-2,3-diaza-1,3-butadiene, C12H10N4, and the chiral co-formers (+)-, (-)- and (rac)-camphoric acid (cam), C10H16O4, have been synthesized. Two different stoichiometries of the API and co-former are obtained, namely 1:1 and 3:2. Crystallization experiments suggest that the 3:2 co-crystal is kinetically favoured over the 1:1 co-crystal. Single-crystal X-ray diffraction analysis of the co-crystals reveals N-H...O hydrogen bonding as the primary driving force for crystallization of the supramolecular structures. The 1:1 co-crystal contains undulating hydrogen-bonded ribbons, in which the chiral cam molecules impart a helical twist. The 3:2 co-crystal contains discrete Z-shaped motifs comprising three molecules of the API and two molecules of cam. The 3:2 co-crystals with (+)-cam, (-)-cam (space group P21) and (rac)-cam (space group P21/n) are isostructural. The enantiomeric co-crystals contain pseudo-symmetry consistent with space group P21/n, and the co-crystal with (rac)-cam represents a solid solution between the co-crystals containing (+)-cam and (-)-cam.

Determination of absolute configuration using single crystal X-ray diffraction

Single crystal X-ray crystallography is the most powerful structural method for the determination of the 3D structures of molecules. While the results of a routine diffraction experiment readily provide unambiguous determination of the relative configuration of all stereogenic centers in the molecule, determination of absolute configuration is more challenging. This chapter provides some helpful tips towards increasing the chances of success in the determination of the absolute configuration of a chiral, enantiomerically pure natural product using X-ray crystallography.

Crystal engineering rescues a solution organic synthesis in a cocrystallization that confirms the configuration of a molecular ladder

Treatment of an achiral molecular ladder of C(2h) symmetry composed of five edge-sharing cyclobutane rings, or a [5]-ladderane, with acid results in cis- to trans-isomerization of end pyridyl groups. Solution NMR spectroscopy and quantum chemical calculations support the isomerization to generate two diastereomers. The NMR data, however, could not lead to unambiguous configurational assignments of the two isomers. Single-crystal X-ray diffraction was employed to determine each configuration. One isomer readily crystallized as a pure form and X-ray diffraction revealed the molecule as being achiral based on C(i) symmetry. The second isomer resisted crystallization under a variety of conditions. Consequently, a strategy based on a cocrystallization was developed to generate single crystals of the second isomer. Cocrystallization of the isomer with a carboxylic acid readily afforded single crystals that confirmed a chiral ladderane based on C(2) symmetry. The chiral ladderane and acid self-assembled to generate a five-component hydrogen-bonded complex that packs to form large solvent-filled homochiral channels of nanometer-scale dimensions. Whereas cocrystallizations are frequently applied to structure determinations of proteins, our study represents the first application of a cocrystallization to confirm the relative configuration of a small-molecule diastereomer generated in a solution-phase organic synthesis.