Conformational polymorphism

A spontaneous single-crystal-to-single-crystal polymorphic transition involving major packing changes

4,6-O-Benzylidene-α-d-galactosyl azide crystallizes into two morphologically distinct polymorphs depending on the solvent. While the α form appeared as thick rods and crystallized in P21 space group (monoclinic) with a single molecule in the asymmetric unit, the β form appeared as thin fibers and crystallized in P1 space group (triclinic) with six molecules in the asymmetric unit. Both the polymorphs appeared to melt at the same temperature. Differential scanning calorimetry analysis revealed that polymorph α irreversibly undergoes endothermic transition to polymorph β much before its melting point, which accounts for their apparently same melting points. Variable temperature powder X-ray diffraction (PXRD) experiments provided additional proof for the polymorphic transition. Single-crystal XRD analyses revealed that α to β transition occurs in a single-crystal-to-single-crystal (SCSC) fashion not only under thermal activation but also spontaneously at room temperature. The SCSC nature of this transition is surprising in light of the large structural differences between these polymorphs. Polarized light microscopy experiments not only proved the SCSC nature of the transition but also suggested nucleation and growth mechanism for the transition.

Epitaxial Retrieval of a Disappearing Polymorph

Recrystallization of [PdCl2([9]aneS2O)] ([9]aneS2O = 1-oxa-4,7-dithiacyclononane), 1, and [PtCl2([9]aneS2O)], 2, by diffusion of Et2O vapor into solutions of the complexes in MeNO2 yielded three phases of 1 and two phases of 2. The known phase of 1, herein designated α-1, was obtained under ambient conditions. A second phase, designated β-1, was initially also obtained by this method; however, following the advent of a third phase, γ-1, all subsequent efforts over a period of a year to crystallize β-1 yielded either γ-1, obtained by carrying out the recrystallization at elevated temperature, or α-1, commonly found throughout the study. This persistent absence of a phase which could initially be crystallized with ease led us to the conclusion that β-1 was an example of a "disappearing polymorph". The first phase obtained of 2, designated α-2, was obtained by recrystallization under ambient conditions and is isomorphous and isostructural with α-1. The second phase β-2 was obtained by slight elevation of the recrystallization temperature and was found to be isomorphous and isostructural with β-1. Subsequently, β-2 was used to seed the growth of the disappearing polymorph β-1. No third phase of 2 (γ-2) has been isolated thus far.

Crystallization of triple- and quadruple-stranded dinuclear bis-β-diketonate-Dy(iii) helicates: single molecule magnetic behavior

Quadruple-stranded Dy-helicates are crystallographically locked through deliberate design on the bis-β-diketonate ligand. The triple-stranded helicates could be tuned by the incorporation of phenanthroline, which contributes to strengthening the anisotropy barrier as well.

Conformational behaviour of 3-methyl-4-(4-methylbenzoyl)-1-phenyl-pyrazol-5-one: a sudden story of three desmotropes

The conformational behaviour of 3-methyl-4-(4-methylbenzoyl)-1-phenyl-pyrazol-5-one was studied using a combination of X-ray diffraction, NMR spectroscopy in solution and the solid state, and DFT calculations in the gas phase.

Reversible piezochromism in a molecular wine-rack

Coupling of a ‘wine-rack’ lattice motif with molecular flexibility leads to a large piezochromic response in an organic material.

Static and lattice vibrational energy differences between polymorphs

Lattice energy, entropy and free energy differences for over 500 pairs of known polymorphs are computed and discussed.

Polymorphism and solid-to-solid phase transitions of a simple organic molecule, 3-chloroisonicotinic acid

Three polymorphs have been discovered for 3-chloroisonicotinic acid. Its thermal properties appear to be eventful, including sublimation, melting and recrystallization, and solid-to-solid phase transition. The polymorphism seemingly results from the disruption of molecular symmetry by chlorine substitution.

Crystalline arrays of molecular rotors with TIPS-trityl and phenolic-trityl stators using phenylene, 1,2-difluorophenylene and pyridine rotators

Molecular rotors based on substituted-trityl stators provide crystalline arrays capable of supporting different rotators through non-covalent interactions.

Polymorphism in anti-hyperammonemic agent N-carbamoyl-l-glutamic acid

Solid form screen of anti-hyperammonemic drug carglumic acid (CGA) resulted in two polymorphs, Form-I and Form-II. The crystal structure of Form-I is sustained by an acid catemer synthon, whereas Form-II has an acid–amide heterosynthon. Slurry grinding, thermal stress, stability measurements, and DVS analysis confirm the thermodynamic stability of Form-I.

The effects of molecular flexibility and substituents on conformational polymorphism in a series of 2,5-diamino-3,6-dicyanopyrazine dyes with highly flexible groups

The flexibility of the dibenzylamino groups and the terminal substituents played an important role in the conformational polymorphism of diaminodicyanopyrazine dyes.

Analysis of the conformational profiles of fenamates shows route towards novel, higher accuracy, force-fields for pharmaceuticals

The conformational barriers of the fenamates which lead to conformational polymorphism can be represented by a novel, physically motivated, model intramolecular potential suitable for extension to other pharmaceuticals.

Structural insights into the hexamorphic system of an isoniazid derivative

The compound isonicotinic acid (E)-(1-phenylethylidene)hydrazide exists in 6 different structural forms isolated through complex manipulations on a Kofler hot stage.

X-ray studies of conformation: observation of conformational polymorphism of a glycoluril clip

In this report, molecular modeling, X-ray crystallography and NMR spectroscopy were used to study the conformational behavior of a novel glycoluril based clip.

Concomitant conformational dimorphism in 1,2-bis(9-anthryl)acetylene

The structure of a concomitant conformational polymorph of an opto-electronic material raises questions about polymorphism.

Bis(paracetamol) pyridine – a new elusive paracetamol solvate: from modeling the phase diagram to successful single-crystal growth and structure–property relations

In addition to the synthon approach, it is equally important to consider phase diagrams when searching for practical methods of crystallising multi-component crystals, either as single crystals or as powders.

Polymorphism control in the mechanochemical and solution-based synthesis of a thermochromic Schiff base

Three crystal forms of a thermochromic Schiff base derived fromo-vanillin and 3-aminoacetophenone were obtained by conventional solution-based methods. Two polymorphs out of three were synthesized by mechanochemical syntheses, under solvent-free conditions.

Chemical design enables the control of conformational polymorphism in functional 2,3-thieno(bis)imide-ended materials

We introduce a chemical design strategy to control conformational polymorphism in 2,3-thienoimide based molecular materials.

Crystal nucleation from solutions – transition states, rate determining steps and complexity

This introductory paper offers a contemporary view of crystal nucleation. We begin with a molecular interpretation of the transition state and then revisit the use of classical nucleation theory as a means of obtaining molecular scale information from kinetic data. Traditional physical organic chemistry has always utilised the combination of kinetics and thermodynamics in order to gain insight over reaction pathways. Here we demonstrate for the cases of sucrose and p-aminobenzoic acid how solution chemistry, crystallography and kinetics come together to provide self-consistent pictures of the molecular scale processes occurring during nucleation. In this and a number of other systems desolvation of specific functional groups is highlighted as the rate determining step. Finally we move on to discuss the question of complexity, both from a phase and molecular perspective.

Two polymorphs of 4-hydroxypiperidine with different NH configurations

4-Hydroxypiperidine 1 exists in two crystal forms, tetragonal 1t with axial NH and orthorhombic 1o with equatorial NH.

A mechanophysical phase transition provides a dramatic example of colour polymorphism: the tribochromism of a substituted tri(methylene)tetrahydrofuran-2-one

Background

Derivatives of fulgides have been shown to have interesting photochromic properties. We have synthesised a number of such derivatives and have found, in some cases, that crystals can be made to change colour on crushing, a phenomenon we have termed “tribochromism”. We have studied a number of derivatives by X-ray crystallography, to see if the colour is linked to molecular structure or crystal packing, or both, and our structural results have been supported by calculation of molecular and lattice energies.

Results

A number of 5-dicyanomethylene-4-diphenylmethylene-3-disubstitutedmethylene-tetrahydrofuran-2-one compounds have been prepared and structurally characterised. The compounds are obtained as yellow or dark red crystals, or, in one case, both. In two cases where yellow crystals were obtained, we found that crushing the crystals gave a deep red powder. Structure determinations, including those of the one compound which gave both coloured forms, depending on crystallisation conditions, showed that the yellow crystals contained molecules in which the structure comprised a folded conformation at the diphenylmethylene site, whilst the red crystals contained molecules in a twisted conformation at this site. Lattice energy and molecular conformation energies were calculated for all molecules, and showed that the conformational energy of the molecule in structure IIIa (yellow) is marginally higher, and the conformation thus less stable, than that of the molecule in structure IIIb (red). However, the van der Waals energy for crystal structure IIIa, is slightly stronger than that of structure IIIb – which may be viewed as a hint of a metastable packing preference for IIIa, overcome by the contribution of a more stabilising Coulomb energy to the overall more favourable lattice energy of structure IIIb.

Conclusions

Our studies have shown that the crystal colour is correlated with one of two molecular conformations which are different in energy, but that the less stable conformation can be stabilised by its host crystal lattice.

Graphical abstract

Low-Cost Quantum Chemical Methods for Noncovalent Interactions

The efficient and reasonably accurate description of noncovalent interactions is important for various areas of chemistry, ranging from supramolecular host-guest complexes and biomolecular applications to the challenging task of crystal structure prediction. While London dispersion inclusive density functional theory (DFT-D) can be applied, faster "low-cost" methods are required for large-scale applications. In this Perspective, we present the state-of-the-art of minimal basis set, semiempirical molecular-orbital-based methods. Various levels of approximations are discussed based either on canonical Hartree-Fock or on semilocal density functionals. The performance for intermolecular interactions is examined on various small to large molecular complexes and organic solids covering many different chemical groups and interaction types. We put the accuracy of low-cost methods into perspective by comparing with first-principle density functional theory results. The mean unsigned deviations of binding energies from reference data are typically 10-30%, which is only two times larger than those of DFT-D. In particular, for neutral or moderately polar systems, many of the tested methods perform very well, while at the same time, computational savings of up to 2 orders of magnitude can be achieved.

Solid-state supramolecular synthesis based on the N-H…O heterosynthon: an approach to solve the polymorphism problem in famotidine

Famotidine (FMT), a histamine H2 -receptor antagonist, is a drug commonly used in treatments of gastroesophageal diseases that presents solid-state polymorphism (A and B forms), the marketed form being the metastable polymorph B. A new stable salt was obtained by combination of FMT and maleic acid as coformer. FMT maleate (FMT-MLT) was prepared either by solvent evaporation or comilling methods. Single-crystal X-ray diffraction reveals that (FMT)(+) in FMT-MLT adopts an extended conformation that is stabilized by classical and nonclassical H-bonds. The three-dimensional packing consists of tapes along the axis b that further develop a columnar array based on H-bonds involving (FMT)(+) side chain. Nonconventional π-stacking interactions between adjacent tapes were also identified. Fourier transform infrared, differential scanning calorimetry, thermogravimetric analysis, polarized light thermal microscopy, and scanning electron microscopy were employed to characterize the multicomponent complex. According to the solubility values in water and simulated gastric fluid, FMT-MLT exhibits such a performance that improves on the solubility of the commercially available polymorph. Finally, the higher stability of FMT-MLT regarding both FMT forms, as well as its easy preparation from either A or B forms or a mixture of them, also allows to consider this salt as a valuable alternative to avoid the polymorphism issue in marketed formulations containing FMT.

Accurate Modeling of Organic Molecular Crystals by Dispersion-Corrected Density Functional Tight Binding (DFTB)

The ambitious goal of organic crystal structure prediction challenges theoretical methods regarding their accuracy and efficiency. Dispersion-corrected density functional theory (DFT-D) in principle is applicable, but the computational demands, for example, to compute a huge number of polymorphs, are too high. Here, we demonstrate that this task can be carried out by a dispersion-corrected density functional tight binding (DFTB) method. The semiempirical Hamiltonian with the D3 correction can accurately and efficiently model both solid- and gas-phase inter- and intramolecular interactions at a speed up of 2 orders of magnitude compared to DFT-D. The mean absolute deviations for interaction (lattice) energies for various databases are typically 2-3 kcal/mol (10-20%), that is, only about two times larger than those for DFT-D. For zero-point phonon energies, small deviations of <0.5 kcal/mol compared to DFT-D are obtained.

Are racemic crystals favored over homochiral crystals by higher stability or by kinetics? Insights from comparative studies of crystalline stereoisomers

The crystal and molecular structures of 134 pairs of diastereoisomers and of 279 racemic-homochiral pairs were retrieved from the Cambridge Structural Database. Lattice and intramolecular energies are calculated. Density differences between crystals of stereoisomers of all kind are mostly within 5%, as observed also for crystal polymorphs. Racemic crystals are predominantly, but not exclusively, more stable and more dense. Denser crystals are predominantly more stable, but there is no quantitative correlation between density and energy differences between partners in the chosen pairs. Second-order symmetry operators are neither ubiquitous in the racemic nor patently superior to first-order operators in promoting crystal cohesion. Thermodynamic, energetic factors in the final crystalline products are not enough to explain the (largely) predominant occurrence of racemic crystallization from racemic solution. At least for homogeneous nucleation, a probabilistic factor, from kinetics or from statistical predominance of mixed versus enantiopure aggregates, must be in action during the early separation of liquid-like particles, which are thought to be the precursors of crystal nucleation.

Which conformations make stable crystal structures? Mapping crystalline molecular geometries to the conformational energy landscape

Flexible organic molecules often do not adopt their lowest energy conformer in crystal structures. We find that there is a preference for molecules to crystallise with high surface area conformers.

Trimorphism of N-(3-pyridyl)-benzamide

Three polymorphic modifications of N-(3-pyridyl)-benzamide were structurally characterized and investigated for their transition behavior and thermodynamic relations.

Capturing a novel metastable polymorph of the anticancer drug gefitinib

The anticancer drug gefitinib exhibited conformational polymorphism, revealing 3D isostructurality in the molecular organization, and slight differences in the stacking pattern. The kinetic (red) polymorph undergoes a crystal-to-crystal thermal phase transition to the thermodynamic (blue) form.

Predicting crystal structures of organic compounds

Organic Crystal Structure Prediction methods generate the thermodynamically plausible crystal structures of a molecule. There are often many more such structures than experimentally observed polymorphs.