Searching for stereoisomerism in crystallographic databases: algorithm, analysis and chiral curiosities

Chirality determination in crystals

This tutorial review article discusses chirality determination in the solid state, both in single crystals and in crystal assemblies, with an emphasis on X-ray diffraction. The main principles of using X-ray diffraction to reliably determine absolute structure are summarized, and the complexity which can be encountered in chiral structures-kryptoracemates, scalemates, and inversion twinning-is illustrated with examples from our laboratories and the literature. We then address the problem of the bulk crystallization and discuss different techniques to determine chirality in a large assembly of crystal structures, with a special prominence given to an X-ray natural circular dichroism mapping technique that we recently reported.

Crystallization of chiral molecular compounds: what can be learned from the Cambridge Structural Database?

A detailed study on chiral compound structures found in the Cambridge Structural Database (CSD) is presented. Solvates, salts and co-crystals have intentionally been excluded, in order to focus on the most basic structures of single enantiomers, scalemates and racemates. Similarity between the latter and structures of achiral monomolecular compounds has been established and utilized to arrive at important conclusions about crystallization of chiral compounds. For example, the fundamental phenomenon of conglomerate formation and, in particular, their frequency of occurrence is addressed. In addition, rarely occurring kryptoracemates and scalemic compounds (anomalous racemates) are discussed. Finally, an extended search of enantiomer solid solutions in the CSD is performed to show that there are up to 1800 instances most probably hiding among the deposited crystal structures, while only a couple of dozen have been previously known and studied.

Kryptoracemic compound hunting and frequency in the Cambridge Structural Database

Determination of kryptoracemic compound frequency in the Cambridge Structural Database using CCDC Python API script.

Chirality and stereoisomerism of organic multicomponent crystals in the CSD

Multicomponent crystals in the CSD are classified into 49 subclasses based on chirality and residue type.

Binding of metal ions and water molecules to nucleic acid bases: the influence of water molecule coordination to a metal ion on water-nucleic acid base hydrogen bonds

The interactions of nucleic acid bases with non-coordinated and coordinated water molecules were studied by analyzing data in the Protein Data Bank (PDB) and by quantum chemical calculations. The analysis of the data in the crystal structures from the PDB indicates that hydrogen bonds involving oxygen or nitrogen atoms of nucleic acid bases and water molecules are shorter when water is bonded to a metal ion. These results are in agreement with the quantum chemical calculations on geometries and interaction energies of hydrogen bonds; the calculations on model systems show that hydrogen bonds of nucleic acid bases with water bonded to a metal ion are stronger than hydrogen bonds with non-coordinated water. These calculated values are similar to the strength of hydrogen bonds between nucleic acid bases. The results presented in this paper may be relevant to understand the role of water molecules and metal ions in the process of replication and stabilization of nucleic acids and also to understand the possible toxicity of metal ion interactions with nucleic acids.

Microbatch under-oil salt screening of organic cations: single-crystal growth of active pharmaceutical ingredients

Multicomponent solid forms of active pharmaceutical ingredients represent a modern method of tuning their physicochemical properties. Typically, salts are the most commonly used multicomponent solid form in the pharmaceutical industry. More than 38% are formulated as organic cations. Salt screening is an essential but demanding step when identifying the most appropriate formulation. The microbatch under-oil crystallization technique of proteins has been combined with the previously developed high-throughput vapour-diffusion screening for use as a novel method of primary salt screening of organic cations. The procedure allows the set up of about 100 crystallization experiments per 30 min. This requires between 17 and 564 mg of screened cationic active pharmaceutical ingredients, which were of moderate to very high water solublity. Five distinct organic salts, three of them diverse active pharmaceutical compounds or the other enantiomer thereof, in the form of chloride salts were tested. The screening was extremely successful; at least two new single-crystal structures could be obtained for each particular compound and many more salts as single crystals were formed compared with our previous vapour-diffusion method.