Predicting crystal form stability under real-world conditions.

The physicochemical properties of molecular crystals, such as solubility, stability, compactability, melting behaviour and bioavailability, depend on their crystal form1. In silico crystal form selection has recently come much closer to realization because of the development of accurate and affordable free-energy calculations2-4. Here we redefine the state of the art, primarily by improving the accuracy of free-energy calculations, constructing a reliable experimental benchmark for solid-solid free-energy differences, quantifying statistical errors for the computed free energies and placing both hydrate crystal structures of different stoichiometries and anhydrate crystal structures on the same energy landscape, with defined error bars, as a function of temperature and relative humidity. The calculated free energies have standard errors of 1-2 kJ mol-1 for industrially relevant compounds, and the method to place crystal structures with different hydrate stoichiometries on the same energy landscape can be extended to other multi-component systems, including solvates. These contributions reduce the gap between the needs of the experimentalist and the capabilities of modern computational tools, transforming crystal structure prediction into a more reliable and actionable procedure that can be used in combination with experimental evidence to direct crystal form selection and establish control5.

How many ritonavir cases are there still out there?

Based on a thorough and critical analysis of the commercial crystal structure prediction studies of 41 pharmaceutical compounds, we conclude that for between 15 and 45% of all small-molecule drugs currently on the market the most stable experimentally observed polymorph is not the thermodynamically most stable crystal structure and that the appearance of the latter is kinetically hindered.

Crystallographic and Dynamic Aspects of Solid-State NMR Calibration Compounds: Towards ab Initio NMR Crystallography.

The excellent results of dispersion-corrected density functional theory (DFT-D) calculations for static systems have been well established over the past decade. The introduction of dynamics into DFT-D calculations is a target, especially for the field of molecular NMR crystallography. Four (13) C ss-NMR calibration compounds are investigated by single-crystal X-ray diffraction, molecular dynamics and DFT-D calculations. The crystal structure of 3-methylglutaric acid is reported. The rotator phases of adamantane and hexamethylbenzene at room temperature are successfully reproduced in the molecular dynamics simulations. The calculated (13) C chemical shifts of these compounds are in excellent agreement with experiment, with a root-mean-square deviation of 2.0 ppm. It is confirmed that a combination of classical molecular dynamics and DFT-D chemical shift calculation improves the accuracy of calculated chemical shifts.

Synthesis and Characterization of Two Novel Naphthalenediimide/Zinc Phosphonate Crystalline Materials Precipitated from Different Solvents.

Hybrid naphthalenediimide/zinc phosphonate materials (NDI/Zn) were prepared by mixing solutions of N,N'-bis(2-phosphonoethyl)-1,4,5,8-naphthalenediimide (PNDI) and zinc nitrate, resulting in the precipitation of the desired compounds. Samples precipitated from water and N,N-dimethylformamide (DMF) were produced. The obtained samples had the expected elemental composition, and the presence of naphthalenediimides (NDI) was ascertained by infrared and UV-visible spectroscopy. All the samples were crystalline, according to powder X-ray diffraction. Nitrogen adsorption isotherms showed the presence of porosity in the NDI/Zn samples. Mesopores with a diameter = 4.1 nm were present in the sample from DMF, with total pore volume reaching 0.13 cm3/g.

Structures of cefradine dihydrate and cefaclor dihydrate from DFT-D calculations.

The crystal structure of cefradine dihydrate, C16H19N3O4S·2H2O, is considered in the pharmaceutical sciences to be the epitome of an isolated-site hydrate. The structure from single-crystal X-ray data was described in 1976, but atomic coordinates were not published. The atomic coordinates are determined here by combining the information available from the published single-crystal data with a dispersion-corrected density functional theory (DFT-D) method that has been validated to reproduce molecular crystal structures very accurately. Additional proof for the correctness of the structure comes from comparison with cefaclor dihydrate, C15H14ClN3O4S·2H2O, which is isomorphous and for which more complete single-crystal data are available. H-atom positions have not previously been published for either compound. The DFT-D calculations confirm that both cefradine and cefaclor are present in the zwitterionic form in the two dihydrate structures. A potential ambiguity concerning the orientation of the cyclohexadienyl ring in cefradine dihydrate is also clarified, and on the basis of the calculated energies it is shown that disorder should not be expected at room temperature. The DFT-D methods can be applied to recover full structural data in cases where only partial information is available, and where it may not be possible or desirable to obtain new experimental data.

Hydrogen bonding patterns and C-H...π interactions in the structure of the antiparkinsonian drug (R)-rasagiline mesylate determined using laboratory and synchrotron X-ray powder diffraction data.

The structure of (R)-rasagiline mesylate [(R)-RasH+·Mes-], an active pharmaceutical ingredient used to treat Parkinson's disease, is presented. The structure was determined from laboratory and synchrotron powder diffraction data, refined using the Rietveld method, and validated and optimized using dispersion-corrected DFT calculations. The unit-cell parameters obtained in both experiments are in good agreement and the refinement with both datasets converged to good agreement factors. The final parameters obtained from laboratory data were a = 5.4905 (8), b = 6.536 (2), c = 38.953 (3) Å, V = 1398.0 (4) Å3 and from synchrotron powder data were a = 5.487530 (10) Å, b = 6.528939 (12) Å, c = 38.94313 (9) Å, V = 1395.245 (5) Å3 with Z = 4 and space group P212121. Preferred orientation was properly accounted for using the synchrotron radiation data, leading to a March-Dollase parameter of 1.140 (1) instead of the 0.642 (1) value obtained from laboratory data. In the structure, (R)-RasH+ moieties form layers parallel to the ab plane connected by mesylate ions through N-H...O and C-H...O hydrogen bonds. These layers stack along the c axis and are further connected by C-H...π interactions. Hirshfeld surface analysis and fingerprint plot calculations indicate that the main interactions are: H...H (50.9%), H...C/C...H (27.1%) and H...O/O...H (21.1%).

Ab-initio crystal structure analysis and refinement approaches of oligo p-benzamides based on electron diffraction data.

Ab-initio crystal structure analysis of organic materials from electron diffraction data is presented. The data were collected using the automated electron diffraction tomography (ADT) technique. The structure solution and refinement route is first validated on the basis of the known crystal structure of tri-p-benzamide. The same procedure is then applied to solve the previously unknown crystal structure of tetra-p-benzamide. In the crystal structure of tetra-p-benzamide, an unusual hydrogen-bonding scheme is realised; the hydrogen-bonding scheme is, however, in perfect agreement with solid-state NMR data.

Reinterpretation of the monohydrate of clarithromycin from X-ray powder diffraction data as a trihydrate.

Noguchi, Fujiki, Iwao, Miura & Itai [Acta Cryst. (2012), E68, o667-o668] recently reported the crystal structure of clarithromycin monohydrate from synchrotron X-ray powder diffraction data. Voids in the crystal structure suggested the possible presence of two more water molecules. After successful location of the two additional water molecules, the Rietveld refinement still showed minor problems. These were resolved by noticing that one of the chiral centres in the molecule had been inverted. The corrected crystal structure of clarithromycin trihydrate, refined against the original data, is now reported. Dispersion-corrected density functional theory calculations were used to check the final crystal structure and to position the H atoms.

Crystal structure from X-ray powder diffraction data, DFT-D calculation, Hirshfeld surface analysis, and energy frameworks of (RS)-trichlorme-thia-zide.

The structure of racemic (RS)-trichlorme-thia-zide [systematic name: (RS)-6-chloro-3-(di-chloro-meth-yl)-1,1-dioxo-3,4-di-hydro-2H-1λ6,2,4-benzo-thia-di-azine-7-sulfonamide], C8H8Cl3N3O4S2 (RS-TCMZ), a diuretic drug used in the treatment of oedema and hypertension, was determined from laboratory X-ray powder diffraction data using DASH [David et al. (2006 ▸). J. Appl. Cryst. 39, 910-915.], refined by the Rietveld method with TOPAS-Academic [Coelho (2018 ▸). J. Appl. Cryst. 51, 210-218], and optimized using DFT-D calculations. The extended structure consists of head-to-tail dimers connected by π-π inter-actions which, in turn, are connected by C-Cl⋯π inter-actions. They form chains propagating along [101], further connected by N-H⋯O hydrogen bonds to produce layers parallel to the ac plane that stack along the b-axis direction, connected by additional N-H⋯O hydrogen bonds. The Hirshfeld surface analysis indicates a major contribution of H⋯O and H⋯Cl inter-actions (32.2 and 21.7%, respectively). Energy framework calculations confirm the major contribution of electrostatic inter-actions (E elec) to the total energy (E tot). A comparison with the structure of S-TCMZ is also presented.

Progress in crystal structure prediction.

The results of the application of a density functional theory method incorporating dispersive corrections in the 2010 crystal structure prediction blind test are reported. The method correctly predicted four out of the six experimental structures. Three of the four correct predictions were found to have the lowest lattice energy of any crystal structure for that molecule. The experimental crystal structures for all six compounds were found during the structure generation phase of the simulations, indicating that the tailor-made force fields used for screening structures were valid and that the structure generation engine, which combines a Monte Carlo parallel tempering algorithm with an efficient lattice energy minimiser, was working effectively. For the three compounds for which the experimental crystal structures did not correspond to the lowest energy structures found, the method for calculating the lattice energy needs to be further refined or there may be other polymorphs that have not yet been found experimentally.

Towards crystal structure prediction of complex organic compounds--a report on the fifth blind test.

Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories - a larger, much more flexible molecule and a hydrate with more than one polymorph. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome.

Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations.

This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Š(0.084 Šfor the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 A either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect.

Rational modification of the hierarchy of intermolecular interactions in molecular crystal structures by using tunable halogen bonds.

A family of 16 isomolecular salts (3-XpyH)(2)[MX'(4)] (3-XpyH = 3-halopyridinium; M = Co, Zn; X = (F), Cl, Br, (I); X' = Cl, Br, I) each containing rigid organic cations and tetrahedral halometallate anions has been prepared and characterized by X-ray single crystal and/or powder diffraction. Their crystal structures reflect the competition and cooperation between non-covalent interactions: N-H...X'-M hydrogen bonds, C-X...X'-M halogen bonds and pi-pi stacking. The latter are essentially unchanged in strength across the series, but both halogen bonds and hydrogen bonds are modified in strength upon changing the halogens involved. Changing the organic halogen (X) from F to I strengthens the C-X...X'-M halogen bonds, whereas an analogous change of the inorganic halogen (X') weakens both halogen bonds and N-H...X'-M hydrogen bonds. By so tuning the strength of the putative halogen bonds from repulsive to weak to moderately strong attractive interactions, the hierarchy of the interactions has been modified rationally leading to systematic changes in crystal packing. Three classes of crystal structure are obtained. In type A (C-F...X'-M) halogen bonds are absent. The structure is directed by N-H...X'-M hydrogen bonds and pi-stacking interactions. In type B structures, involving small organic halogens (X) and large inorganic halogens (X'), long (weak) C-X...X'-M interactions are observed with type I halogen-halogen interaction geometries (C-X...X' approximately = X...X'-M approximately = 155 degrees), but hydrogen bonds still dominate. Thus, minor but quite significant perturbations from the type A structure arise. In type C, involving larger organic halogens (X) and smaller inorganic halogens (X'), stronger halogen bonds are formed with a type II halogen-halogen interaction geometry (C-X...X' approximately = 180 degrees; X...X'-M approximately = 110 degrees) that is electrostatically attractive. The halogen bonds play a major role alongside hydrogen bonds in directing the type C structures, which as a result are quite different from type A and B.

Structures of six industrial benzimidazolone pigments from laboratory powder diffraction data.

The crystal structures of six industrially produced benzimidazolone pigments [Pigment Orange 36 (beta phase), Pigment Orange 62, Pigment Yellow 151, Pigment Yellow 154 (alpha phase), Pigment Yellow 181 (beta phase) and Pigment Yellow 194] were determined from laboratory X-ray powder diffraction data by means of real-space methods using the programs DASH and MRIA, respectively. Subsequent Rietveld refinements were carried out with TOPAS. The crystal phases correspond to those produced industrially. Additionally, the crystal structures of the non-commercial compound 'BIRZIL' (a chloro derivative of Pigment Yellow 194) and of a dimethylsulfoxide solvate of Pigment Yellow 154 were determined by single-crystal structure analyses. All eight crystal structures are different; the six industrial pigments even exhibit five different hydrogen-bond topologies. Apparently, the good application properties of the benzimidazolone pigments are not the result of one specific hydrogen-bonding pattern, but are the result of a combination of efficient molecular packing and strong intermolecular hydrogen bonds.

Structure determination of seven phases and solvates of Pigment Yellow 183 and Pigment Yellow 191 from X-ray powder and single-crystal data.

The crystal structures of two industrially produced laked yellow pigments, Pigment Yellow 183 [P.Y. 183, Ca(C16H10Cl2N4O7S2), alpha phase] and Pigment Yellow 191 [P.Y. 191, Ca(C17H13ClN4O7S2), alpha and beta phases], were determined from laboratory X-ray powder diffraction data. The coordinates of the molecular fragments of the crystal structures were found by means of real-space methods (simulated annealing) with the program DASH. The coordinates of the calcium ions and the water molecules were determined by combining real-space methods (DASH and MRIA) and repeated Rietveld refinements (TOPAS) of the partially finished crystal structures. TOPAS was also used for the final Rietveld refinements. The crystal structure of beta-P.Y. 183 was determined from single-crystal data. The alpha phases of the two pigments are isostructural, whereas the beta phases are not. All four phases exhibit a double-layer structure, built from nonpolar layers containing the C/N backbone and polar layers containing the calcium ions, sulfonate groups and water molecules. Furthermore, the crystal structures of an N,N-dimethylformamide solvate of P.Y. 183, and of P.Y. 191 solvates with N,N-dimethylformamide and N,N-dimethylacetamide were determined by single-crystal X-ray analysis.

Electron diffraction, X-ray powder diffraction and pair-distribution-function analyses to determine the crystal structures of Pigment Yellow 213, C23H21N5O9.

The crystal structure of the nanocrystalline alpha phase of Pigment Yellow 213 (P.Y. 213) was solved by a combination of single-crystal electron diffraction and X-ray powder diffraction, despite the poor crystallinity of the material. The molecules form an efficient dense packing, which explains the observed insolubility and weather fastness of the pigment. The pair-distribution function (PDF) of the alpha phase is consistent with the determined crystal structure. The beta phase of P.Y. 213 shows even lower crystal quality, so extracting any structural information directly from the diffraction data is not possible. PDF analysis indicates the beta phase to have a columnar structure with a similar local structure as the alpha phase and a domain size in column direction of approximately 4 nm.

Significant progress in predicting the crystal structures of small organic molecules--a report on the fourth blind test.

We report on the organization and outcome of the fourth blind test of crystal structure prediction, an international collaborative project organized to evaluate the present state in computational methods of predicting the crystal structures of small organic molecules. There were 14 research groups which took part, using a variety of methods to generate and rank the most likely crystal structures for four target systems: three single-component crystal structures and a 1:1 cocrystal. Participants were challenged to predict the crystal structures of the four systems, given only their molecular diagrams, while the recently determined but as-yet unpublished crystal structures were withheld by an independent referee. Three predictions were allowed for each system. The results demonstrate a dramatic improvement in rates of success over previous blind tests; in total, there were 13 successful predictions and, for each of the four targets, at least two groups correctly predicted the observed crystal structure. The successes include one participating group who correctly predicted all four crystal structures as their first ranked choice, albeit at a considerable computational expense. The results reflect important improvements in modelling methods and suggest that, at least for the small and fairly rigid types of molecules included in this blind test, such calculations can be constructively applied to help understand crystallization and polymorphism of organic molecules.

A jumping crystal predicted with molecular dynamics and analysed with TLS refinement against powder diffraction data.

By running a temperature series of molecular dynamics (MD) simulations starting from the known low-temperature phase, the experimentally observed phase transition in a 'jumping crystal' was captured, thereby providing a prediction of the unknown crystal structure of the high-temperature phase and clarifying the phase-transition mechanism. The phase transition is accompanied by a discontinuity in two of the unit-cell parameters. The structure of the high-temperature phase is very similar to that of the low-temperature phase. The anisotropic displacement parameters calculated from the MD simulations readily identified libration as the driving force behind the phase transition. Both the predicted crystal structure and the phase-transition mechanism were verified experimentally using TLS (translation, libration, screw) refinement against X-ray powder diffraction data.

Crystal structure analysis of a star-shaped triazine compound: a combination of single-crystal three-dimensional electron diffraction and powder X-ray diffraction.

The solid-state structure of star-shaped 2,4,6-tris{(E)-2-[4-(dimethylamino)-phenyl]ethenyl}-1,3,5-triazine is determined from a powder sample by exploiting the respective strengths of single-crystal three-dimensional electron diffraction and powder X-ray diffraction data. The unit-cell parameters were determined from single crystal electron diffraction data. Using this information, the powder X-ray diffraction data were indexed, and the crystal structure was determined from the powder diffraction profile. The compound crystallizes in a noncentrosymmetric space group, P212121. The molecular conformation in the crystal structure was used to calculate the molecular dipole moment of 3.22 Debye, which enables the material to show nonlinear optical effects.

Reversible gas uptake by a nonporous crystalline solid involving multiple changes in covalent bonding.

Hydrogen chloride gas (HCl) is absorbed (and reversibly released) by a nonporous crystalline solid, [CuCl2(3-Clpy)2] (3-Clpy = 3-chloropyridine), under ambient conditions leading to conversion from the blue coordination compound to the yellow salt (3-ClpyH)2[CuCl4]. These reactions require substantial motions within the crystalline solid including a change in the copper coordination environment from square planar to tetrahedral. This process also involves cleavage of the covalent bond of the gaseous molecules (H-Cl) and of coordination bonds of the molecular solid compound (Cu-N) and formation of N-H and Cu-Cl bonds. These reactions are not a single-crystal-to-single-crystal transformation; thus, the crystal structure determinations have been performed using X-ray powder diffraction. Importantly, we demonstrate that these reactions proceed in the absence of solvent or water vapor, ruling out the possibility of a water-assisted (microscopic recrystallization) mechanism, which is remarkable given all the structural changes needed for the process to take place. Gas-phase FTIR spectroscopy has permitted us to establish that this process is actually a solid-gas equilibrium, and time-resolved X-ray powder diffraction (both in situ and ex situ) has been used for the study of possible intermediates as well as the kinetics of the reaction.