Calculation of Diamagnetic Susceptibility Tensors of Organic Crystals: From Coronene to Pharmaceutical Polymorphs

Understanding why crystallization in strong magnetic fields can lead to new polymorphs requires methods to calculate the diamagnetic response of organic molecular crystals. We develop the calculation of the macroscopic diamagnetic susceptibility tensor, χ^{cryst}, for organic molecular crystals using periodic density functional methods. The crystal magnetic susceptibility tensor, χ^{cryst}, for all experimentally known polymorphs, and its molecular counterpart, χ^{mol}, are calculated for flexible pharmaceuticals such as carbamazepine, flufenamic acid, and chalcones, and rigid molecules, such as benzene, pyridine, acridine, anthracene, and coronene, whose molecular magnetic properties have been traditionally studied. A tensor addition method is developed to approximate the crystal diamagnetic susceptibility tensor, χ^{cryst}, from the molecular one, χ^{mol}, giving good agreement with those calculated directly using the more costly periodic density functional method for χ^{cryst}. The response of pharmaceutical molecules and crystals to magnetic fields, as embodied by χ^{cryst}, is largely determined by the packing in the crystal, as well as the molecular conformation. The anisotropy of χ^{cryst} can vary considerably between polymorphs though the isotropic terms are fairly constant. The implications for developing a computational method for predicting whether crystallization in a magnetic field could produce a novel or different polymorph are discussed

Reducing crystal structure overprediction of ibuprofen with large scale molecular dynamics simulations

The control of the crystal form is a central issue in the pharmaceutical industry. The identification of putative polymorphs through Crystal Structure Prediction (CSP) methods is based on lattice energy calculations, which are known to significantly over-predict the number of plausible crystal structures. A valuable tool to reduce overprediction is to employ physics-based, dynamic simulations to coalesce lattice energy minima separated by small barriers into a smaller number of more stable geometries once thermal effects are introduced. Molecular dynamics simulations and enhanced sampling methods can be employed in this context to simulate crystal structures at finite temperature and pressure. Here we demonstrate the applicability of approaches based on molecular dynamics to systematically process realistic CSP datasets containing several hundreds of crystal structures. The system investigated is ibuprofen, a conformationally flexible active pharmaceutical ingredient that crystallises both in enantiopure forms and as a racemic mixture. By introducing a hierarchical approach in the analysis of finite-temperature supercell configurations, we can post-process a dataset of 555 crystal structures, identifying 65% of the initial structures as labile, while maintaining all the experimentally known crystal structures in the final, reduced set. Moreover, the extensive nature of the initial dataset allows one to gain quantitative insight into the persistence and the propensity to transform of crystal structures containing common hydrogen-bonded intermolecular interaction motifs

Systematic Finite-Temperature Reduction of Crystal Energy Landscapes

Crystal structure prediction methods are prone to overestimate the number of potential polymorphs of organic molecules. In this work, we aim to reduce the overprediction by systematically applying molecular dynamics simulations and biased sampling methods to cluster subsets of structures that can easily interconvert at finite temperature and pressure. Following this approach, we rationally reduce the number of predicted putative polymorphs in crystal structure prediction (CSP)-generated crystal energy landscapes. This uses an unsupervised clustering approach to analyze independent finite-temperature molecular dynamics trajectories and hence identify a representative structure of each cluster of distinct lattice energy minima that are effectively equivalent at finite temperature and pressure. Biased simulations are used to reduce the impact of limited sampling time and to estimate the work associated with polymorphic transformations. We demonstrate the proposed systematic approach by studying the polymorphs of urea and succinic acid, reducing an initial set of over 100 energetically plausible CSP structures to 12 and 27 respectively, including the experimentally known polymorphs. The simulations also indicate the types of disorder and stacking errors that may occur in real structures

The Crystal Structure of 5-Aminouracil and the Ambiguity of Alternative Polymorphs

The nucleobase derivative 5-aminouracil (AUr, C4H5N3O2) is of interest for its biological activity, yet the solid state structure of this compound has remained elusive owing to its propensity to crystallize as aggregates of microcrystalline particles. Here we report the first single-crystal structure of AUr determined from synchrotron x-ray diffraction data. An early crystal structure prediction effort, which assumed that AUr was rigid in the isolated molecule optimized conformation, provided several poor matches to the simulated PXRD pattern. Revisiting these crystal structures, by periodic electronic level modelling (PBE-TS optimization) gave more realistic relative lattice energies, but a good match to the experimental powder pattern required using the experimental cell parameters. PXRD and Raman spectroscopy suggest that phase impurities may be present in the bulk crystallization product, though the identity of alternative polymorphs could not be confirmed on the basis of the data available

A strategy for producing predicted polymorphs: catemeric carbamazepine form V

A computationally assisted approach has enabled the first catemeric polymorph of carbamazepine (form V) to be selectively formed by templating the growth of carbamazepine from the vapour phase onto the surface of a crystal of dihydrocarbamazepine form II

A Prolific Solvate Former, Galunisertib, under the Pressure of Crystal Structure Prediction, Produces Ten Diverse Polymorphs

The solid form screening of galunisertib produced many solvates, prompting an extensive investigation into possible risks to the development of the favored monohydrate form. Inspired by crystal structure prediction, the search for neat polymorphs was expanded to an unusual range of experiments, including melt crystallization under pressure, to work around solvate formation and the thermal instability of the molecule. Ten polymorphs of galunisertib were found; however, the structure predicted to be the most stable has yet to be obtained. We present the crystal structures of all ten unsolvated polymorphs of galunisertib, showing how state-of-the-art characterization methods can be combined with emerging computational modeling techniques to produce a complete structure landscape and assess the risk of late-appearing, more stable polymorphs. The exceptional conformational polymorphism of this prolific solvate former invites further development of methods, computational and experimental, that are applicable to larger, flexible molecules with complex solid form landscapes

Serendipitous isolation of a disappearing conformational polymorph of succinic acid challenges computational polymorph prediction

A conformational polymorph (γ) of succinic acid was discovered in an attempt to purify a leucine dipeptide by cocrystallization from a methanol solution in the presence of various impurities, such as trifluoroacetic acid. The new γ form was found to have crystallized concomitantly with the most stable β form. In light of this situation, a crystal structure prediction study was undertaken to examine the polymorph landscape. These studies reveal that the γ polymorph is thermodynamically competitive with the other observed polymorphs; having a more stable folded conformation than the planar crystalline conformation in the β form, but being stabilized less by the intermolecular interactions. Simulations and experiment show that the folded conformation is dominant in solution, but that trapping long-lived crystals of the new metastable polymorph may be challenging. Thus the γ polymorph provides a stringent test of theories for predicting which thermodynamically plausible structures may be practically important polymorphs

The solid state forms of the sex hormone 17-β-estradiol

The crystal structure of the single component form of the primary female sex hormone, 17-β-estradiol (BES), is reported, solved from single crystals obtained by sublimation. The Z′ = 2 P2₁2₁2₁ structure was computationally predicted as one of the thermodynamically plausible structures. It appears that the dehydration process for the very stable hemihydrate structure is a complex process, strongly affected by particle size and conditions. An experimental polymorph screen has produced six solid forms of BES, including novel acetonitrile and highly labile ethylene dichloride solvates, and reproduced previously reported methanol and propanol solvates. These have been characterized, as far as possible given the metastability relative to the hemihydrate (BES·0.5H₂O), by single-crystal X-ray diffraction (SCXRD), powder X-ray diffraction (PXRD), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), hot-stage microscopy and Fourier transform infrared spectroscopy (FT-IR), sorting out some of the confusion in the earlier literature

A molecular picture of the problems in ensuring structural purity of tazofelone

Almost twenty years after the crystal polymorphism of tazofelone was first studied at Lilly, the compound was revisited by calculating the crystal energy landscape and complementing the calculations with experimental work for calibration purposes. The crystal structure prediction study confirmed the stability of racemic form II (RCII) and showed that the racemic compound had greater potential for polymorphism than the single enantiomer. The seeding experiment that has previously been shown to produce a racemic solid solution (SS) correlates with the isostructurality between some low energy racemic structures and the enantiopure form. Other low energy structures have the same layer structure as both racemic polymorphs and the newly-discovered, but closely related, polymorph RCIII, which accounts for the difficulty in obtaining phase pure samples of the metastable RCI and RCIII and the problems of structural purity evidenced by streaked diffraction spots for RCI–III in the single crystal diffraction. This molecular picture of the problems in ensuring structural purity in the layer structure polymorphs of tazofelone not only explains the crystal dependent thermochemistry measurements of tazofelone, but also shows the value of combining a range of experimental and computational techniques to investigate the organic solid state

Successful computationally-directed templating of metastable pharmaceutical polymorphs

A strategy of using crystal structure prediction (CSP) methods to determine which, if any, isostructural template could facilitate the first crystallization of a predicted polymorph by vapor deposition, is extended to the fenamate family. Mefenamic acid (MFA) and tolfenamic acid (TFA) are used as molecules with minimal chemical differences, whereas flufenamic acid (FFA) shows greater differences in the substituents. The three crystal energy landscapes were calculated and periodic electronic structure calculations used to confirm the thermodynamic plausibility of possible isostructural polymorphs to experimentally obtainable crystals of the other molecules. As predicted, a new polymorph, TFA form VI was found by sublimation onto isomorphous MFA form I, using a recently developed technique. MFA and TFA form a continuous solid solution with the structure of MFA I and TFA VI at the limits, but the isomorphous MFA:FFA solid solution does not extended to a new polymorph of FFA. The novel solid solution structure of TFA and FFA was found and a new isomorphous polymorph TFA VII was found by sublimation onto this new solid solution template. Sublimation of TFA onto a metal surface at the early stage of deposition gave TFA form VIII. We rationalize the formation of new polymorphs of only TFA