Linking solid-state phenomena via energy differences in `archetype crystal structures'

Categorization underlies understanding. Conceptualizing solid-state structures of organic molecules with `archetype crystal structures' bridges established categories of disorder, polymorphism and solid solutions and is herein extended to special position and high-Z' structures. The concept was developed in the context of disorder modelling [Dittrich, B. (2021). IUCrJ, 8, 305-318] and relies on adding quantum chemical energy differences between disorder components to other criteria as an explanation as to why disorder - and disappearing disorder - occurs in an average structure. Part of the concept is that disorder, as probed by diffraction, affects entire molecules, rather than just the parts of a molecule with differing conformations, and the finding that an R·T energy difference between disorder archetypes is usually not exceeded. An illustrative example combining disorder and special positions is the crystal structure of oestradiol hemihydrate analysed here, where its space-group/subgroup relationship is required to explain its disorder of hydrogen-bonded hydrogen atoms. In addition, we show how high-Z' structures can also be analysed energetically and understood via archetypes: high-Z' structures occur when an energy gain from combining different rather than overall alike conformations in a crystal significantly exceeds R·T, and this finding is discussed in the context of earlier explanations in the literature. Twinning is not related to archetype structures since it involves macroscopic domains of the same crystal structure. Archetype crystal structures are distinguished from crystal structure prediction trial structures in that an experimental reference structure is required for them. Categorization into archetype structures also has practical relevance, leading to a new practice of disorder modelling in experimental least-squares refinement alluded to in the above-mentioned publication.

Revisiting Homochiral versus Heterochiral Interactions through a Long Detective Story of a Useful Azobis-Nitrile and Puzzling Racemate

This paper documents and reinvestigates the solid-state and crystal structures of 4,4'-azobis-4-cyanopentanoic acid (ACPA), a water-soluble azobis-nitrile of immense utility as a radical initiator in living polymerizations and a labile mechanophore that can be embedded within long polymer chains to undergo selective scission under mechanical activation. Surprisingly, for such applications, both the commercially available reagent and their derivatives are used as "single initiators" when this azonitrile is actually a mixture of stereoisomers. Although the racemate and meso compounds were identified more than half a century ago and their enantiomers were separated by classical resolution, there have been confusing narratives dealing with their characterization, the existence of a conglomeratic phase, and fractional crystallization. Our results report on the X-ray crystal structures of all stereoisomers for the first time, along with further details on enantiodiscrimination and the always intriguing arguments accounting for the stability of homochiral versus heterochiral crystal aggregates. To this end, metadynamic (MTD) simulations on stereoisomer molecular aggregates were performed to capture the incipient nucleation events at the picosecond time scale. This analysis sheds light on the driving homochiral aggregation of ACPA enantiomers.

Schiff Base in Ketoamine Form and Rh(η4-cod)-Schiff Base Complex with Z' = 2 Structure from Pairwise C-H···Metallochelate-π Contacts

Condensation of 2-hydroxybenzaldehyde (salicylaldehyde) or 2-hydroxy-1-naphthaldehyde with 2-ethylaniline yields the Schiff base compound of (E)-2-(((2-ethylphenyl)imino)methyl)phenol (HL¹) or (E)-1-(((2-ethylphenyl)imino)methyl)naphthalen-2-ol (HL²), which in turn react with the dinuclear complex of [Rh(η⁴-cod)(µ-O₂CCH₃)]₂ (cod = cycloocta-1,5-diene) to afford the mononuclear (η⁴-cod){(E)-2-(((2-ethylphenyl)imino)methyl)phenolato-κ²N,O}rhodium(I), [Rh(η⁴-cod)(L¹)] (1) or (η⁴-cod){(E)-1-(((2-ethylphenyl)imino)methyl)naphthalen-2-olato-κ²N,O}rhodium(I), [Rh(η⁴-cod)(L²)] (2) (L¹ or L² = deprotonated Schiff base ligand). The X-ray structure determination revealed that the HL² exists in the solid state not as the usual (imine)N···H-O(phenol) form (enolamine form) but as the zwitterionic (imine)N-H⁺···^-O(phenol) form (ketoamine form). ¹H NMR spectra for HL² in different solvents demonstrated the existence of keto-enol tautomerism (i.e., keto ⇆ enol equilibrium) in solution. The structure for 1 and 2 showed that the deprotonated Schiff base ligand coordinates to the Rh(η⁴-cod)-fragment as a six-membered N^O-chelate around the rhodium atom with a close-to-square-planar geometry. Two symmetry-independent molecules (with Rh1 and Rh2) were found in the asymmetric unit in 1 in a structure with Z' = 2. The supramolecular packing in HL² was organized by π-π and C-H···π contacts, while only two recognized C-H···π contacts were revealed in 1 and 2. Remarkably, there were reciprocal or pairwise C-H···π contacts between a pair of each of the symmetry-independent molecules in 1. This pairwise C-H contact to the Rh-N^O chelate (metalloaromatic) ring may be a reason for the two symmetry-independent molecules in 1. Differential scanning calorimetry (DSC) analyses revealed an irreversible phase transformation from the crystalline-solid to the isotropic-liquid phase and subsequently confirmed the thermal stability of the compounds. Absorption spectra in solution were explained by excited state properties from DFT/TD-DFT calculations.

Crystalline salts of a diuretic drug torasemide with improved solubility and dissolution properties

Two novel pharmaceutical crystalline salts of a diuretic drug torasemide with improved solubility and dissolution profiles are disclosed in this manuscript.

Organic Salts of p-Coumaric Acid and Trans-Ferulic Acid with Aminopicolines

p-Coumaric acid (pCA) and trans-ferulic acid (TFA) were co-crystallised with 2-amino-4-picoline (2A4MP) and 2-amino-6-picoline (2A6MP) producing organic salts of (pCA^-)(2A4MP⁺) (1), (pCA^̶ )(2A6MP⁺) (2) and (TFA^̶ )(2A4MP⁺)·( 3 2 H₂O) (3). For salt 3, water was included in the crystal structure fulfilling a bridging role. pCA formed a 1:1 salt with 2A4MP (Z' = 1) and a 4:4 salt with 2A6MP (Z' = 4). The thermal stability of the salts was determined using differential scanning calorimetry (DSC). Salt 2 had the highest thermal stability followed by salt 1 and salt 3. The salts were also characterised using Fourier transform infrared (FTIR) spectroscopy. Hirshfeld surface analysis was used to study the different intermolecular interactions in the three salts. Solvent-assisted grinding was also investigated in attempts to reproduce the salts.

Exploring concomitant/conformational dimorphism in a difluoro-substituted phosphoramidate derivative

The concomitant occurrence of dimorphs of diphenyl (3,4-difluorophenyl)phosphoramidate, C₁₈H₁₄F₂NO₃P, was observed via a solution-mediated crystallization process with variation in the symmetry-free molecules (Z'). The existence of two forms, i.e. Form I (block, Z' = 1) and Form II (needle, Z' = 2), was characterized by single-crystal X-ray diffraction, differential scanning calorimetry and powder X-ray diffraction. Furthermore, a quantitative analysis of the energetics of the different intermolecular interactions was carried out via the energy decomposition method (PIXEL), which corroborates with inputs from the energy framework and looks at the topology of the various intermolecular interactions present in both forms. The unequivocally distinguished contribution of strong N-H...O hydrogen bonds along with other interactions, such as C-H...O, C-H...F, π-π and C-H...π, mapped on the Hirshfeld surface is depicted by two-dimensional fingerprint plots. Apart from the major electrostatic contribution from N-H...O hydrogen bonds, the crystal structures are stabilized by contributions from the dispersion energy. The closely related melting points and opposite trends in the calculated lattice energies are interesting to investigate with respect to the thermodynamic stability of the observed dimorphs. The significant variation in the torsion angles in both forms helps in classifying them in the category of conformational polymorphs.

Separation or combination of non-covalently linked partners provides polymorphs of N-(aryl)-2-(propan-2-ylidene)hydrazine carbothioamides

Polymorphs of N-(2-methoxyphenyl)-2-(propan-2ylidene)hydrazine carbothioamide and N-(4-nitrophenyl)-2-(propan-2-ylidene)hydrazine carbothioamide differing in homomeric assemblies are described.

Evaluating the importance of fractional Z′ polymorphs in a trifluoromethylated N,N′-diphenyloxalamide derivative

A curious case of crystal dimorphism reveals an adjusted fractional number of molecules in their respective crystallographic asymmetric units.

Conformational variation of ligands in mercury halide complexes; high and low Z′ structures

Small changes in the ligand resulted in a conformational variation of L^Py to L^Pz which led to high and low Z′ structures in the corresponding metal complexes.

Using crystal structure prediction to rationalize the hydration propensities of substituted adamantane hydrochloride salts

The crystal energy landscapes of the salts of two rigid pharmaceutically active molecules reveal that the experimental structure of amantadine hydrochloride is the most stable structure with the majority of low-energy structures adopting a chain hydrogen-bond motif and packings that do not have solvent accessible voids. By contrast, memantine hydrochloride which differs in the substitution of two methyl groups on the adamantane ring has a crystal energy landscape where all structures within 10 kJ mol−1of the global minimum have solvent-accessible voids ranging from 3 to 14% of the unit-cell volume including the lattice energy minimum that was calculated after removing water from the hydrated memantine hydrochloride salt structure. The success in using crystal structure prediction (CSP) to rationalize the different hydration propensities of these substituted adamantane hydrochloride salts allowed us to extend the model to predict under blind test conditions the experimental crystal structures of the previously uncharacterized 1-(methylamino)adamantane base and its corresponding hydrochloride salt. Although the crystal structure of 1-(methylamino)adamantane was correctly predicted as the second ranked structure on the static lattice energy landscape, the crystallization of aZ′ = 3 structure of 1-(methylamino)adamantane hydrochloride reveals the limits of applying CSP when the contents of the crystallographic asymmetric unit are unknown.

Chirality at metal and helical ligand folding in optical isomers of chiral bis(naphthaldiminato)nickel(ii) complexes

Ni-Schiff base complexes combine ligand chirality, chirality at metal, and helical ligand folding in a concerted way.

Insight to the thermodynamic stability of molecular crystals through crystallographic studies of a multipolymorph system

Five solvent-free polymorphs of a pharmaceutical compound were discovered during polymorph screening. Out of the five polymorphs, only one has strong intermolecular N-H···N hydrogen bonding, whereas the others exhibit only weak C-H···N and π-π stacking interactions in addition to all the other weak C-H···X and van der Waals interactions. The relative thermodynamic stability relationships among the polymorphs are not intuitive and quite complex due to enantiotropic phase behavior. For instance, the polymorph with the most efficient packing (i.e., highest density) is not always the most thermodynamically stable form, and the polymorph with strong intermolecular interactions is not thermodynamically more stable than the polymorph with weak intermolecular interactions at all temperatures. Nevertheless, systematic examination and comparison of the molecular packing and intermolecular interactions of these polymorphs provide insight into the importance of H-bonding and packing efficiency to the thermodynamic stability of a crystalline form, and how these effects are dependent on temperature. This study seeks to correlate single-crystal structure features with experimentally established thermodynamic stability, and provides an example where a polymorph with only van der Waals forces and weak intermolecular interactions can be more stable than a polymorph that displays strong H-bonding in its structural make-up.

A supramolecular ladder-like network from trimesic acid and pyrazineN,N′-dioxide

In the title complex, benzene-1,3,5-tricarboxylic acid–pyrazineN,N′-dioxide (2/1), C9H6O6·0.5C4H4N2O2, cocrystallized trimesic acid (TMA) and pyrazineN,N′-dioxide (PNO) molecules form strong O—H...O hydrogen bonds, but also important weak C—H...O and dipole–dipole intermolecular interactions, to generate a densely packed three-dimensional network. PNO molecules lie on inversion centres where they connect pairs of TMA sheets into distinct two-dimensional hydrogen-bonded layers perpendicular to the crystallographicabdiagonal.

Unusual co-crystal of isonicotinamide: the structural landscape in crystal engineering

The idea of a structural landscape is based on the fact that a large number of crystal structures can be associated with a particular organic molecule. Taken together, all these structures constitute the landscape. The landscape includes polymorphs, pseudopolymorphs and solvates. Under certain circumstances, it may also include multi-component crystals (or co-crystals) that contain the reference molecule as one of the components. Under still other circumstances, the landscape may include the crystal structures of molecules that are closely related to the reference molecule. The idea of a landscape is to facilitate the understanding of the process of crystallization. It includes all minima that can, in principle, be accessed by the molecule in question as it traverses the path from solution to the crystal. Isonicotinamide is a molecule that is known to form many co-crystals. We report here a 2:1 co-crystal of this amide with 3,5-dinitrobenzoic acid, wherein an unusual N-H···N hydrogen-bonded pattern is observed. This crystal structure offers some hints about the recognition processes between molecules that might be implicated during crystallization. Also included is a review of other recent results that illustrate the concept of the structural landscape.

Polymorphs and polymorphic cocrystals of temozolomide

Crystal polymorphism in the antitumor drug temozolomide (TMZ), cocrystals of TMZ with 4,4'-bipyridine-N,N'-dioxide (BPNO), and solid-state stability were studied. Apart from a known X-ray crystal structure of TMZ (form 1), two new crystalline modifications, forms 2 and 3, were obtained during attempted cocrystallization with carbamazepine and 3-hydroxypyridine-N-oxide. Conformers A and B of the drug molecule are stabilized by intramolecular amide N--HN(imidazole) and N--HN(tetrazine) interactions. The stable conformer A is present in forms 1 and 2, whereas both conformers crystallized in form 3. Preparation of polymorphic cocrystals I and II (TMZBPNO 1:0.5 and 2:1) were optimized by using solution crystallization and grinding methods. The metastable nature of polymorph 2 and cocrystal II is ascribed to unused hydrogen-bond donors/acceptors in the crystal structure. The intramolecularly bonded amide N-H donor in the less stable structure makes additional intermolecular bonds with the tetrazine C==O group and the imidazole N atom in stable polymorph 1 and cocrystal I, respectively. All available hydrogen-bond donors and acceptors are used to make intermolecular hydrogen bonds in the stable crystalline form. Synthon polymorphism and crystal stability are discussed in terms of hydrogen-bond reorganization.

Conformational polymorphism in organic crystals

Polymorphs are different crystalline modifications of the same chemical substance. When different conformers of the same molecule occur in different crystal forms, the phenomenon is termed conformational polymorphism. Occasionally, more than one conformer is present in the same crystal structure. The influence of molecular conformation changes on the formation and stability of polymorphs is the focus of this Account. X-ray crystal structures of conformational polymorphs were analyzed to understand the interplay of intramolecular (conformer) and intermolecular (lattice) energy in the crystallization and stability of polymorphs. Polymorphic structures stabilized by strong O-H...O/N-H...O hydrogen bonds, weak C-H...O interactions, and close packing were considered. 4,4-Diphenyl-2,5-cyclohexadienone (1) and bis(p-tolyl) ketone p-tosylhydrazone (3) are prototypes of C-H...O and N-H...O hydrogen-bonded structures. Distance-angle scatter plots of O-H...O and C-H...O hydrogen bonds extracted from the Cambridge Structural Database indicate that polymorphs with a larger number of symmetry-independent molecules (high Z') generally have better interactions when compared with the polymorphs with lower Z' values, with the implication that these symmetry-independent molecules have different conformations. Since molecular conformer (E(conf)) and crystal lattice (U(latt)) energy differences are of the same magnitude in organic crystals (typically <5 kcal mol(-1)), situations wherein these two factors compensate or cancel one another are illustrative. Calculation of conformer and lattice energies using Gaussian 03 and Cerius(2) in 23 recently published polymorph sets shows that a strained conformer (higher E(conf)) is stabilized by stronger interactions or better crystal packing (lower U(latt)) in two-thirds of the cases, whereas there is no energy balance in the remaining structures. Organic molecules with flexible torsions and low-energy conformers have a greater likelihood of exhibiting polymorphism because (1) different conformations lead to new hydrogen-bonding and close-packing modes and (2) the tradeoff reduces the total energy difference between alternative crystal structures. As a test case, polymorph promiscuity in fuchsones (6) is related to the conformational diversity at the exo-methylene phenyl rings and the small energy difference computed for dimethyl fuchsone polymorphs. These ideas find application in the design of putative pharmaceutical polymorphs and crystal structure prediction.