Hydrogen-bond coordination in organic crystal structures: statistics, predictions and applications

Conglomerate Crystallization in the Cambridge Structural Database (2020-2021)

Conglomerate crystals are materials capable of undergoing spontaneous resolution and were responsible for the discovery of molecular chirality. Their relevance to modern chemical and crystallographic sciences has been hindered by the difficulty in identifying and searching materials with this characteristic ability to spontaneously bias their own enantioenrichment. With the release of the November 2021 distribution of the Cambridge Structural Database (CSD) (version 5.43), a fresh quantity of chiral conglomerate crystals is expected to have been published in the CSD without identification. Indeed, no crystals in the CSD have been identified as a spontaneously resolving conglomerate crystal in their crystallographic information file since the 2019 release, despite the deposition of over 108,000 new crystal structures into the database over the same time period. A manual inspection of crystals deposited between 2020 and 2021 was conducted to identify 343 new chiral materials which exhibit conglomerate crystallization behavior. It is hoped that the continued manual curation of this list will aid those in the crystallographic and synthetic communities to study and exploit this spontaneous enantioenrichment behavior.

Formation Thermodynamics of Carbamazepine with Benzamide, Para-Hydroxybenzamide and Isonicotinamide Cocrystals: Experimental and Theoretical Study

Formation thermodynamic parameters for three cocrystals of carbamazepine (CBZ) with structurally related coformers (benzamide (BZA), para-hydroxybenzamide (4-OH-BZA) and isonicotinamide (INAM)) were determined by experimental (cocrystal solubility and competitive reaction methods) and computational techniques. The experimental solubility values of cocrystal components at eutectic points and solubility product of cocrystals [CBZ + BZA], [CBZ + 4-OH-BZA], and [CBZ + INAM] in acetonitrile at 293.15 K, 298.15 K, 303.15 K, 308.15 K, and 313.15 K were measured. All the thermodynamic functions (Gibbs free energy, enthalpy, and entropy) of cocrystals formation were evaluated from the experimental data. The crystal structure of [CBZ + BZA] (1:1) cocrystal was solved and analyzed by the single crystal X-ray diffractometry. A correlation between the solubility products and pure coformers solubility values has been found for CBZ cocrystals. The relationship between the entropy term and the molecular volume of the cocrystal formation has been revealed. The effectiveness of the estimation of the cocrystal formation thermodynamic parameters, based on the knowledge of the melting temperatures of active pharmaceutical ingredients, coformers, cocrystals, as well as the sublimation Gibbs energies and enthalpies of the individual components, was proven. A new method for the comparative assessment of the cocrystal stability based on the H-bond propensity analysis was proposed. The experimental and theoretical results on the thermodynamic parameters of the cocrystal formation were shown to be in good agreement. According to the thermodynamic stability, the studied cocrystals can be arranged in the following order: [CBZ + 4-OH-BZA] > [CBZ + BZA] > [CBZ + INAM].

New Zinc-Based Active Chitosan Films: Physicochemical Characterization, Antioxidant, and Antimicrobial Properties

The improvement of the antioxidant and antimicrobial activities of chitosan (CS) films can be realized by incorporating transition metal complexes as active components. In this context, bioactive films were prepared by embedding a newly synthesized acylpyrazolonate Zn(II) complex, [Zn(Q^PhtBu)₂(MeOH)₂], into the eco-friendly biopolymer CS matrix. Homogeneous, amorphous, flexible, and transparent CS@Zn_n films were obtained through the solvent casting method in dilute acidic solution, using different weight ratios of the Zn(II) complex to CS and characterized by powder X-ray diffraction (PXRD), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), Fourier transform infrared (FT-IR), Raman, and scanning electron microscopy (SEM) techniques. The X-ray single-crystal analysis of [Zn(Q^PhtBu)₂(MeOH)₂] and the evaluation of its intermolecular interactions with a protonated glucosamine fragment through hydrogen bond propensity (HBP) calculations are reported. The effects of the different contents of the [Zn(Q^PhtBu)₂(MeOH)₂] complex on the CS biological proprieties have been evaluated, proving that the new CS@Zn_n films show an improved antioxidant activity, tested according to the DPPH method, with respect to pure CS, related to the concentration of the incorporated Zn(II) complex. Finally, the CS@Zn_n films were tried out as antimicrobial agents, showing an increase in antimicrobial activity against Gram-positive bacteria (Staphylococcus aureus) with respect to pure CS, when detected by the agar disk-diffusion method.

Effect of substituents in novel bioactive tavaborole derivatives on the intermolecular interaction hierarchy

Tavaborole, a molecule based on the benzoxaborole scaffold, is an effective antifungal drug marketed under the Kerydin® trademark.

Hydrogen Bond Patterns of Dipyridone and Bis(Hydroxypyridinium) Cations

Dipyridonyl-substituted derivatives 2-4 of benzene, pyridine, and pyrazine, respectively, were synthesized to examine the ability of 2-pyridone and its protonated species to direct the self-assembly by hydrogen bonding. Structural analysis by single-crystal X-ray diffraction (SCXRD) of 2 and 4 in trifluoroacetic acid demonstrated that salts are formed as a result of the transfer of protons from the acid to the base (organic species) to generate a bis(hydroxypyridinium) dication. However, if no proton transfer takes place like in the case of crystals of 3 grown from DMSO/H₂O, the self-assembly is mainly directed by the typical R ₂ ²(8) hydrogen bond motif of 2-pyridone. These results indicate that the process of converting a neutral 2-pyridonyl group into a hydroxypyridinium cation makes structure prediction difficult. Consequently, examination of proton transfer and assembly of dipyridone and its protonated species are of interest. In combination with SCXRD, Hirshfeld surface analysis (HSA) was also used to have a better understanding on the nature of intermolecular interactions within crystal structures of 2-4. The large number of F···H/H···F, H···O/O···H, H···H, and H···C/C···H contacts revealed by HSA indicates that hydrogen bonding and van der Waals interactions mainly contribute to crystal packing.

SMINBR: An Integrated Network and Chemoinformatics Tool Specialized for Prediction of Two-Component Crystal Formation

Two-component crystals such as pharmaceutical cocrystals and salts have been proven as an effective strategy to improve physicochemical and biopharmaceutical properties of drugs. It is not easy to select proper molecular combinations to form two-component crystals. The network-based models have been successfully utilized to guide cocrystal design. Yet, the traditional social network-derived methods based on molecular-interaction topology information cannot directly predict interaction partners for new chemical entities (NCEs) that have not been observed to form two-component crystals. Herein, we proposed an effective tool, namely substructure-molecular-interaction network-based recommendation (SMINBR), to prioritize potential interaction partners for NCEs. This in silico tool incorporates network and chemoinformatics methods to bridge the gap between NCEs and known molecular-interaction network. The high performance of 10-fold cross validation and external validation shows the high accuracy and good generalization capability of the model. As a case study, top 10 recommended coformers for apatinib were all experimentally confirmed and a new apatinib cocrystal with paradioxybenzene was obtained. The predictive capability of the model attributes to its accordance with complementary patterns driving the formation of intermolecular interactions. SMINBR could automatically recommend new interaction partners for a target molecule, and would be an effective tool to guide cocrystal design. A free web server for SMINBR is available at http://lmmd.ecust.edu.cn/sminbr/.

Contributions of secondary alcohol-ketone O-H...O=C and furan-acetate Csp2-H...OOC synthons to the supramolecular packings of two bioactive molecules

The crystal structures of rubescin D (1, C₂₆H₃₀O₅) and monadelphin A (2, C₃₀H₃₆O₁₁), bioactive molecules of the vilasinin and gedunin classes of limonoids, respectively, are reported for the first time and the synthons affecting their crystal packings are analyzed on the basis of their occurrences in molecules in the Cambridge Structural Database that share the same moieties. Rubescin D, 1, crystallizes in the space group P2₁ and its molecular structure consists of three six-membered rings A, C and D having, respectively, envelope, twist-boat and half-chair conformations, and three five-membered rings with half-chair (B and E) and planar conformations (F). Many synthons found in the crystal packing of 1 are in agreement with expectations derived from molecules displaying the same moieties. However, the secondary alcohol-ketone O-H...O=C synthon, which has a low occurrence (2.9%), contributes much to the layered packing, while the furan-ketone Csp²-H...O=C and secondary alcohol-epoxide O-H...OC₂ synthons usually found in these compounds (occurrences of 20.6 and 17.6%, respectively) are missing. The packing of 1 is close to that of ceramicine B (3), but is completely different from that of TS3 (4), suggesting that the absence of the epoxide group in 3 would have favoured the furan-secondary alcohol Csp²-H...OH synthon and that the missing hydroxy group in 4, a strong hydrogen-bond donor, would have favoured the involvement of water molecules in the crystal packing. The molecular structure of monadelphin A, 2, consists of four six-membered fused rings (A, B, C and D) and one five-membered ring (E); they have twist-boat (A and C), chair (B), screw-boat (D) and planar (E) conformations. The molecule crystallizes in the space group P2₁2₁2₁ with the contribution of many synthons usually found in compounds having the same moieties. However, the secondary alcohol-acetate O-H...OOC and secondary alcohol-ketone O-H...O=C synthons (occurrences of 16.7% each in these compounds) are missing. The furan-acetate Csp²-H...OOC synthon not observed in these compounds greatly contributes to the layered packing of 2. The layered packing is very close to those of 7-oxogedunin (5) and 6-dehydro-7-deacetoxy-7-oxogedunin (6), which both crystallize in the space group P2₁.

Assessment of Computational Tools for Predicting Supramolecular Synthons

The ability to predict the most likely supramolecular synthons in a crystalline solid is a valuable starting point for subsequently predicting the full crystal structure of a molecule with multiple competing molecular recognition sites. Energy and informatics-based prediction models based on molecular electrostatic potentials (MEPs), hydrogen-bond energies (HBE), hydrogen-bond propensity (HBP), and hydrogen-bond coordination (HBC) were applied to the crystal structures of twelve pyrazole-based molecules. HBE, the most successful method, correctly predicted 100% of the experimentally observed primary intermolecular-interactions, followed by HBP (87.5%), and HBC = MEPs (62.5%). A further HBC analysis suggested a risk of synthon crossover and synthon polymorphism in molecules with multiple binding sites. These easy-to-use models (based on just 2-D chemical structure) can offer a valuable risk assessment of potential formulation challenges.

Heteroleptic Cu(ii) saccharin complexes: intriguing coordination modes and properties

A new Cu(ii) O,S-coordinated saccharinate complex is reported, showing crystallochromism and NIR emission in the solid state, in silico ligand exchange reactions with N/S-donor ligands in the presence of model molecules mimicking biological targets.

Optimization and comparison of statistical tools for the prediction of multicomponent forms of a molecule: the antiretroviral nevirapine as a case study

A methodology is proposed to assess the propensity to obtain multicomponent forms of an API based on the combination of modified statistical analytical tools to order the possible co-formers in a ranking index.

Can solvated intermediates inform us about nucleation pathways? The case of β-pABA

Using crystallography to search for nucleation pathways: α and β polymorphs of p-aminobenzoic acid.

Intermolecular Interactions in Functional Crystalline Materials: From Data to Knowledge

Intermolecular interactions of organic, inorganic, and organometallic compounds are the key to many composition–structure and structure–property networks. In this review, some of these relations and the tools developed by the Cambridge Crystallographic Data Center (CCDC) to analyze them and design solid forms with desired properties are described. The potential of studies supported by the Cambridge Structural Database (CSD)-Materials tools for investigation of dynamic processes in crystals, for analysis of biologically active, high energy, optical, (electro)conductive, and other functional crystalline materials, and for the prediction of novel solid forms (polymorphs, co-crystals, solvates) are discussed. Besides, some unusual applications, the potential for further development and limitations of the CCDC software are reported.

A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts

The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.

The role of non-covalent interactions in some 2-trifluoromethylchromones in the solid state

Intermolecular interactions in chromone systems and criteria for the existence of C–H⋯F hydrogen bonds involving organic fluorine have been focused on in this work.

The integration of solid-form informatics into solid-form selection

OBJECTIVES

To demonstrate how the use of structural informatics during drug development assists with the assessment of the risk of polymorphism and the selection of a commercial solid form.

METHODS

The application of structural chemistry knowledge derived from the hundreds of thousands of crystal structures contained in the Cambridge Structural Database to drug candidates is described. Examples given show the comparison of intermolecular geometries to database-derived statistics, the use of Full Interaction Maps to assess polymorph stability and the calculation of hydrogen bond propensities to provide assurance of a stable solid form. The software tools used are included in the Cambridge Structural Database System and the Solid Form Module of Mercury.

KEY FINDINGS

The early identification of an unusual supramolecular motif in the development phase of maraviroc led to further experimental work to find the most stable polymorph. Analyses of two polymorphs of a pain candidate drug demonstrated how consideration of molecular conformation and intermolecular interactions were used for the assessment of relative stability. Informatics analysis confirmed that the solid form of crizotinib, a monomorphic system, had a low risk of polymorphism.

CONCLUSIONS

The application of informatics-based assessment of new chemical entities complements experimental studies and provides a deeper understanding of the qualities of the structure. The information provided by structural analyses is incorporated into the assessment of risk. Informatics techniques are quick to apply and are straightforward to use, allowing an assessment of progressing drug candidates.

A comprehensive classification and nomenclature of carboxyl-carboxyl(ate) supramolecular motifs and related catemers: implications for biomolecular systems

Carboxyl and carboxylate groups form important supramolecular motifs (synthons). Besides carboxyl cyclic dimers, carboxyl and carboxylate groups can associate through a single hydrogen bond. Carboxylic groups can further form polymeric-like catemer chains within crystals. To date, no exhaustive classification of these motifs has been established. In this work, 17 association types were identified (13 carboxyl-carboxyl and 4 carboxyl-carboxylate motifs) by taking into account the syn and anti carboxyl conformers, as well as the syn and anti lone pairs of the O atoms. From these data, a simple rule was derived stating that only eight distinct catemer motifs involving repetitive combinations of syn and anti carboxyl groups can be formed. Examples extracted from the Cambridge Structural Database (CSD) for all identified dimers and catemers are presented, as well as statistical data related to their occurrence and conformational preferences. The inter-carboxyl(ate) and carboxyl(ate)-water hydrogen-bond properties are described, stressing the occurrence of very short (strong) hydrogen bonds. The precise characterization and classification of these supramolecular motifs should be of interest in crystal engineering, pharmaceutical and also biomolecular sciences, where similar motifs occur in the form of pairs of Asp/Glu amino acids or motifs involving ligands bearing carboxyl(ate) groups. Hence, we present data emphasizing how the analysis of hydrogen-containing small molecules of high resolution can help understand structural aspects of larger and more complex biomolecular systems of lower resolution.