High Temperature Electron Diffraction on Organic Crystals: In Situ Crystal Structure Determination of Pigment Orange 34

Small molecule structures and their applications rely on good knowledge of their atomic arrangements. However, the crystal structures of these compounds and materials, which are often composed of fine crystalline domains, cannot be determined with single-crystal X-ray diffraction. Three-dimensional electron diffraction (3D ED) is already becoming a reliable method for the structure analysis of submicrometer-sized organic materials. The reduction of electron beam damage is essential for successful structure determination and often prevents the analysis of organic materials at room temperature, not to mention high temperature studies. In this work, we apply advanced 3D ED methods at different temperatures enabling the accurate structure determination of two phases of Pigment Orange 34 (C34H28N8O2Cl2), a biphenyl pyrazolone pigment that has been industrially produced for more than 80 years and used for plastics application. The crystal structure of the high-temperature phase, which can be formed during plastic coloration, was determined at 220 °C. For the first time, we were able to observe a reversible phase transition in an industrial organic pigment in the solid state, even with atomic resolution, despite crystallites being submicrometer in size. By localizing hydrogen atoms, we were even able to detect the tautomeric state of the molecules at different temperatures. This demonstrates that precise, fast, and low-dose 3D ED measurements enable high-temperature studies the door for general in situ studies of nanocrystalline materials at the atomic level.

Leucopterin, the white pigment in butterfly wings: structural analysis by PDF fit, FIDEL fit, Rietveld refinement, solid-state NMR and DFT-D

Leucopterin (C₆H₅N₅O₃) is the white pigment in the wings of Pieris brassicae butterflies, and other butterflies; it can also be found in wasps and other insects. Its crystal structure and its tautomeric form in the solid state were hitherto unknown. Leucopterin turned out to be a variable hydrate, with 0.5 to about 0.1 molecules of water per leucopterin molecule. Under ambient conditions, the preferred state is the hemihydrate. Initially, all attempts to grow single crystals suitable for X-ray diffraction were to no avail. Attempts to determine the crystal structure by powder diffraction using the direct-space method failed, because the trials did not include the correct, but rare, space group P2/c. Attempts were made to solve the crystal structure by a global fit to the pair distribution function (PDF-Global-Fit), as described by Prill and co-workers [Schlesinger et al. (2021). J. Appl. Cryst. 54, 776-786]. The approach worked well, but the correct structure was not found, because again the correct space group was not included. Finally, tiny single crystals of the hemihydrate could be obtained, which allowed at least the determination of the crystal symmetry and the positions of the C, N and O atoms. The tautomeric state of the hemihydrate was assessed by multinuclear solid-state NMR spectroscopy. ¹⁵N CPMAS spectra showed the presence of one NH₂ and three NH groups, and one unprotonated N atom, which agreed with the ¹H MAS and ¹³C CPMAS spectra. Independently, the tautomeric state was investigated by lattice-energy minimizations with dispersion-corrected density functional theory (DFT-D) on 17 different possible tautomers, which also included the prediction of the corresponding ¹H, ¹³C and ¹⁵N chemical shifts in the solid. All methods showed the presence of the 2-amino-3,5,8-H tautomer. The DFT-D calculations also confirmed the crystal structure. Heating of the hemihydrate results in a slow release of water between 130 and 250 °C, as shown by differential thermal analysis and thermogravimetry (DTA-TG). Temperature-dependent powder X-ray diffraction (PXRD) showed an irreversible continuous shift of the reflections upon heating, which reveals that leucopterin is a variable hydrate. This observation was also confirmed by PXRD of samples obtained under various synthetic and drying conditions. The crystal structure of a sample with about 0.2 molecules of water per leucopterin was solved by a fit with deviating lattice parameters (FIDEL), as described by Habermehl et al. [Acta Cryst. (2022), B78, 195-213]. A local fit, starting from the structure of the hemihydrate, as well as a global fit, starting from random structures, were performed, followed by Rietveld refinements. Despite dehydration, the space group remains P2/c. In both structures (hemihydrate and variable hydrate), the leucopterin molecules are connected by 2-4 hydrogen bonds into chains, which are connected by further hydrogen bonds to neighbouring chains. The molecular packing is very efficient. The density of leucopterin hemihydrate is as high as 1.909 kg dm^-3, which is one of the highest densities for organic compounds consisting of C, H, N and O only. The high density might explain the good light-scattering and opacity properties of the wings of Pieris brassicae and other butterflies.

Analysis of diffuse scattering in electron diffraction data for the crystal structure determination of Pigment Orange 13, C32H24Cl2N8O2

The crystallographic study of two polymorphs of the industrial pyrazolone Pigment Orange 13 (P.O.13) is reported. The crystal structure of the β phase was determined using single-crystal X-ray analysis of a tiny needle. The α phase was investigated using three-dimensional electron diffraction. The electron diffraction data contain sharp Bragg reflections and strong diffuse streaks, associated with severe stacking disorder. The structure was solved by careful analysis of the diffuse scattering, and similarities of the unit-cell parameters with the β phase. The structure solution is described in detail and this provides a didactic example of solving molecular crystal structures in the presence of diffuse scattering. Several structural models were constructed and optimized by lattice-energy minimization with dispersion-corrected DFT. A four-layer model was found, which matches the electron diffraction data, including the diffuse scattering, and agrees with X-ray powder data. Additionally, five further phases of P.O.13 are described.

Ambiguous structure determination from powder data: four different structural models of 4,11-di-fluoro-quinacridone with similar X-ray powder patterns, fit to the PDF, SSNMR and DFT-D

Four different structural models, which all fit the same X-ray powder pattern, were obtained in the structure determination of 4,11-di-fluoro-quinacridone (C₂₀H₁₀N₂O₂F₂) from unindexed X-ray powder data by a global fit. The models differ in their lattice parameters, space groups, Z, Z', molecular packing and hydrogen bond patterns. The molecules form a criss-cross pattern in models A and B, a layer structure built from chains in model C and a criss-cross arrangement of dimers in model D. Nevertheless, all models give a good Rietveld fit to the experimental powder pattern with acceptable R-values. All molecular geometries are reliable, except for model D, which is slightly distorted. All structures are crystallochemically plausible, concerning density, hydrogen bonds, intermolecular distances etc. All models passed the checkCIF test without major problems; only in model A a missed symmetry was detected. All structures could have probably been published, although 3 of the 4 structures were wrong. The investigation, which of the four structures is actually the correct one, was challenging. Six methods were used: (1) Rietveld refinements, (2) fit of the crystal structures to the pair distribution function (PDF) including the refinement of lattice parameters and atomic coordinates, (3) evaluation of the colour, (4) lattice-energy minimizations with force fields, (5) lattice-energy minimizations by two dispersion-corrected density functional theory methods, and (6) multinuclear CPMAS solid-state NMR spectroscopy (¹H, ¹³C, ¹⁹F) including the comparison of calculated and experimental chemical shifts. All in all, model B (perhaps with some disorder) can probably be considered to be the correct one. This work shows that a structure determination from limited-quality powder data may result in totally different structural models, which all may be correct or wrong, even if they are chemically sensible and give a good Rietveld refinement. Additionally, the work is an excellent example that the refinement of an organic crystal structure can be successfully performed by a fit to the PDF, and the combination of computed and experimental solid-state NMR chemical shifts can provide further information for the selection of the most reliable structure among several possibilities.

Structure determination from unindexed powder data from scratch by a global optimization approach using pattern comparison based on cross-correlation functions

A method of ab initio crystal structure determination from powder diffraction data for organic and metal-organic compounds, which does not require prior indexing of the powder pattern, has been developed. Only a reasonable molecular geometry is required, needing knowledge of neither unit-cell parameters nor space group. The structures are solved from scratch by a global fit to the powder data using the new program FIDEL-GO (`FIt with DEviating Lattice parameters - Global Optimization'). FIDEL-GO uses a similarity measure based on cross-correlation functions, which allows the comparison of simulated and experimental powder data even if the unit-cell parameters deviate strongly. The optimization starts from large sets of random structures in various space groups. The unit-cell parameters, molecular position and orientation, and selected internal degrees of freedom are fitted simultaneously to the powder pattern. The optimization proceeds in an elaborate multi-step procedure with built-in clustering of duplicate structures and iterative adaptation of parameter ranges. The best structures are selected for an automatic Rietveld refinement. Finally, a user-controlled Rietveld refinement is performed. The procedure aims for the analysis of a wide range of `problematic' powder patterns, in particular powders of low crystallinity. The method can also be used for the clustering and screening of a large number of possible structure candidates and other application scenarios. Examples are presented for structure determination from unindexed powder data of the previously unknown structures of the nanocrystalline phases of 4,11-difluoro-, 2,9-dichloro- and 2,9-dichloro-6,13-dihydro-quinacridone, which were solved from powder patterns with 14-20 peaks only, and of the coordination polymer dichloro-bis(pyridine-N)copper(II).

Solid-State NMR-Driven Crystal Structure Prediction of Molecular Crystals: The Case of Mebendazole

Among all possible NMR crystallography approaches for crystal-structure determination, crystal structure prediction - NMR crystallography (CSP-NMRX) has recently turned out to be a powerful method. In the latter, the original procedure exploited solid-state NMR (SSNMR) information during the final steps of the prediction. In particular, it used the comparison of computed and experimental chemical shifts for the selection of the correct crystal packing. Still, the prediction procedure, generally carried out with DFT methods, may require important computational resources and be quite time-consuming, especially if there are no available constraints to use at the initial stage. Herein, the successful application of this combined prediction method, which exploits NMR information also in the input step to reduce the search space of the predictive algorithm, is presented. Herein, this method was applied on mebendazole, which is characterized by desmotropism. The use of SSNMR data as constraints for the selection of the right tautomer and the determination of the number of independent molecules in the unit cell led to a considerably faster process, reducing the number of calculations to be performed. In this way, the crystal packing was successfully predicted for the three known phases of mebendazole. To evaluate the quality of the predicted structures, these were compared to the experimental ones. The crystal structure of phase B of mebendazole, in particular, was determined de novo by powder diffraction and is presented for the first time in this paper.

Crystal structure of copper perchlorophthalocyanine analysed by 3D electron diffraction

The structure of copper perchlorophthalo­cyanine (CuC₃₂N₈Cl₁₆, Pigment Green 7) was solved from three-dimensional electron diffraction data (3D ED) and placed into the series of known copper phthalo­cyanine crystal structures.

Copper perchlorophthalo­cyanine (CuPcCl₁₆, CuC₃₂N₈Cl₁₆, Pigment Green 7) is one of the commercially most important green pigments. The compound is a nanocrystalline fully insoluble powder. Its crystal structure was first addressed by electron diffraction in 1972 [Uyeda et al. (1972). J. Appl. Phys.43, 5181–5189]. Despite the commercial importance of the compound, the crystal structure remained undetermined until now. Using a special vacuum sublimation technique, micron-sized crystals could be obtained. Three-dimensional electron diffraction (3D ED) data were collected in two ways: (i) in static geometry using a combined stage-tilt/beam-tilt collection scheme and (ii) in continuous rotation mode. Both types of data allowed the crystal structure to be solved by direct methods. The structure was refined kinematically with anisotropic displacement parameters for all atoms. Due to the pronounced crystal mosaicity, a dynamic refinement was not feasible. The unit-cell parameters were verified by Rietveld refinement from powder X-ray diffraction data. The crystal structure was validated by many-body dispersion density functional theory (DFT) calculations. CuPcCl₁₆ crystallizes in the space group C2/m (Z = 2), with the molecules arranged in layers. The structure agrees with that proposed in 1972.

First crystal structure of a Pigment Red 52 compound: DMSO solvate hydrate of the monosodium salt

Pigment Red 52, Na2[C18H11ClN2O6S], is an industrially produced hydrazone-laked pigment. It serves as an inter-mediate in the synthesis of the corresponding Ca2+ and Mn2+ salts, which are used commercially for printing inks and lacquers. Hitherto, no crystal structure of any salt of Pigment Red 52 is known. Now, single crystals have been obtained of a dimethyl sulfoxide solvate hydrate of the monosodium salt of Pigment Red 52, namely, monosodium 2-[2-(3-carb-oxy-2-oxo-1,2-di-hydro-naphthalen-1-yl-idene)hydrazin-1-yl]-5-chloro-4-methyl-benz-ene-sulfonate dimethyl sulfoxide monosolvate monohydrate, Na+·C18H12ClN2O6S-·H2O·C2H6OS, obtained from in-house synthesized Pigment Red 52. The crystal structure was determined by single-crystal X-ray diffraction at 173 K. In this monosodium salt, the SO3 - group is deprotonated, whereas the COOH group is protonated. The residues form chains via ionic inter-actions and hydrogen bonds. The chains are arranged in polar/non-polar double layers.

Sustained-release hot melt extrudates of the weak acid TMP-001: A case study using PBB modelling

Over the last 30 years, hot melt extrusion has become a leading technology in the manufacture of amorphous drug delivery systems. Mostly applied as an 'enabling formulation' for poorly soluble compounds, application in the design of sustained-release formulations increasingly attracts the attention of the pharmaceutical industry. The drug candidate TMP-001 is currently under evaluation for the early treatment of Multiple Sclerosis. Although this weak acid falls into class II of the Biopharmaceutics Classification System, the compound exhibits high solubility in the upper intestine resulting in high peroral bioavailability. In the present studies, four different formulation prototypes varying in their sustained-release behavior were developed, using L-arginine as a pore-forming agent in concentrations ranging between 0 and 20%. Initially, biorelevant release testing was applied to assess the dissolution behavior of the prototypes. For these formulations, a total drug release of 44.7%, 64.6%, 75%, and 90.5% was achieved in FaSSIF-v2 after 24 h. Two candidates were selected for further characterization considering the crystal structure and the physical stability of the amorphous state of TMP-001 in the formulations together with the release behavior in Level II biorelevant media. Our findings indicate L-arginine as a valuable excipient in the formulation of hot melt extrudates, as its presence led to a considerable stabilization of the amorphous state and favorably impacted the milling process and release behavior of TMP-001. To properly evaluate the proposed formulations and the importance of colonic dissolution and absorption on the overall bioavailability, a physiologically-based biopharmaceutics model was used.

Orientational disorder of monomethyl-quinacridone investigated by Rietveld refinement, structure refinement to the pair distribution function and lattice-energy minimizations

The crystal structure of the organic pigment 2-monomethyl-quinacridone (Pigment Red 192, C₂₁H₁₄N₂O₂) was solved from X-ray powder diffraction data. The resulting average structure is described in space group P\overline 1, Z = 1 with the molecule on the inversion centre. The molecules are arranged in chains. The molecules, which have no inversion symmetry, show orientational head-to-tail disorder. In the average structure, the methyl group is disordered and found on both ends of the molecule with an occupancy of 0.5 each. The disorder and the local structure were investigated using various ordered structural models. All models were analysed by three approaches: Rietveld refinement, structure refinement to the pair distribution function (PDF) and lattice-energy minimization. All refinements converged well. The Rietveld refinement provided the average structure and gave no indication of a long-range ordering. The refinement to the PDF turned out to be very sensitive to small structural details, giving insight into the local structure. The lattice-energy minimizations revealed a significantly preferred local ordering of neighbouring molecules along the [0\bar 11] direction. In conclusion, all methods indicate a statistical orientational disorder with a preferred parallel orientation of molecules in one direction. Additionally, electron diffraction revealed twinning and faint diffuse scattering.

4-Cyanopyridine complexes [MX2(4-CNpy)x]n (with X = Cl, Br and x = 1, 2): crystal structures, thermal properties and a comparison with [MX2(3-CNpy)x]n complexes

Crystal structures of [MX₂(4-CNpy)_x] with X = Cl and Br, M = Mn, Fe, Co, Ni, Cu, and Zn, and x = 1 and 2 were determined by X-ray powder diffraction. 4-Cyanopyridine can build chain and net structures.

Crystal structure of sodium ethoxide (C2H5ONa), unravelled after 180 years

180 years after Liebig's synthesis, the crystal structures of C₂H₅ONa and C₂H₅ONa·2C₂H₅OH were finally determined.

Two new polymorphs of cis-perinone: crystal structures, physical and electric properties

The crystal structures of two polymorphs of cis-perinone (bisbenzimidazo[2,1-b:1',2'-j]benzo[lmn][3,8]phenanthroline-6,9-dione, Pigment Red 194) were solved from single crystals obtained solvothermally from 1,2-dichlorobenzene or n-butanol at 220°C. Both crystal structures (space group P2₁/c) derive from stacking of flat molecules arranged due to π-π interaction. The melting points of these two polymorphs are 471°C and 468°C and their respective optical bandgaps are 1.94 eV and 1.71 eV. One of the polymorphs demonstrates drift and hopping mechanisms of electric conductivity, whereas the other one is dominated by the drift conductivity. The direct current (DC) electric conductivity of the samples are 4.77 × 10^-13 S m^-1 and 6.84 × 10^-10 S m^-1 at room temperature. The significant difference in DC conductivities can be explained by the dependence of the mobility and concentration of charge carriers on the structure of the samples.

Coordination compounds built up from MIICl2 and 3-cyanopyridine: double chains, single chains and isolated complexes

Crystal structures of [M^IICl₂(3-CNpy)_x], with M = Mn, Fe, Co, Ni, Cu, Zn and x = 1, 2, were determined by X-ray powder diffraction. Surprisingly, 3-cyanopyridine coordinates monodentately only.

Challenging structure determination from powder diffraction data: two pharmaceutical salts and one cocrystal with Z′ = 2

Structure solution of molecular crystals from powder diffraction data by real-space methods becomes challenging when the total number of degrees of freedom (DoF) for molecular position, orientation and intramolecular torsions exceeds a value of 20. Here we describe the structure determination from powder diffraction data of three pharmaceutical salts or cocrystals, each with four molecules per asymmetric unit on general position: Lamivudine camphorsulfonate (1, P 21, Z=4, Z′=2; 31 DoF), Theophylline benzamide (2, P 41, Z=8, Z′=2; 23 DoF) and Aminoglutethimide camphorsulfonate hemihydrate [3, P 21, Z=4, Z′=2; 31 DoF (if the H2O molecule is ignored)]. In the salts 1 and 3 the cations and anions have two intramolecular DoF each. The molecules in the cocrystal 2 are rigid. The structures of 1 and 2 could be solved without major problems by DASH using simulated annealing. For compound 3, indexing, space group determination and Pawley fit proceeded without problems, but the structure could not be solved by the real-space method, despite extensive trials. By chance, a single crystal of 3 was obtained and the structure was determined by single-crystal X-ray diffraction. A post-analysis revealed that the failure of the real-space method could neither be explained by common sources of error such as incorrect indexing, wrong space group, phase impurities, preferred orientation, spottiness or wrong assumptions on the molecular geometry or other user errors, nor by the real-space method itself. Finally, is turned out that the structure solution failed because of problems in the extraction of the integrated reflection intensities in the Pawley fit. With suitable extracted reflection intensities the structure of 3 could be determined in a routine way.

3-Cyanopyridine as a bridging and terminal ligand in coordination polymers

Crystal structures of [M^IIBr₂(3-CNpy)_x]_(n) with M = Mn, Fe, Co, Ni and x = 1, 2, 4 were determined by powder diffraction. For x = 1, the 3-cyanopyridine ligand is bridging two metal atoms.

Crystal structures of ordered and plastic-crystalline phases of iso-butyllithium by X-ray powder diffraction

The crystal structures of solid, donor-free i-BuLi at different temperatures were determined from X-ray powder diffraction data.

On the stacking disorder of DL-norleucine

DL-Norleucine (2-aminohexanoic acid, C6H13NO2) forms a double-layer structure in all known phases (α, β, γ). The crystal structure of the β-phase was redetermined at 173 K. Diffraction patterns of the α- and β-phases frequently show diffuse streaks parallel to c*, which indicates a stacking disorder of the layers. A symmetry analysis was carried out to derive possible stacking sequences. Lattice-energy minimizations by force fields and by dispersion-corrected density functional theory (DFT-D) were performed on a set of ordered model structures with Z = 4, 8 and 16 with different stacking sequences. The calculated energies depend not only on the arrangement of neighbouring double layers, but also of next-neighbouring double layers. Stacking probabilities were calculated from the DFT-D energies. According to the calculated stacking probabilities large models containing 100 double layers were constructed. Their simulated diffraction patterns show sharp reflections for h + k = 2n and diffuse streaks parallel to c* through all reflections with h + k = 2n + 1. Experimental single-crystal X-ray diffraction revealed that at 173 K norleucine exists in the β-phase with stacking disorder. After reheating to room temperature, the investigated crystal showed a diffraction pattern with strong diffuse scattering parallel to c* through all reflections with h + k = 2n + 1, which is in good agreement with the simulated disordered structure.

Local structure and stacking disorder of chloro(phthalocyaninato)aluminium

Chloro(phthalocyaninato)aluminium [(C₃₂H₁₆N₈)AlCl, Pigment Blue 79] is a molecular compound which crystallizes in a layer structure with stacking disorder. Order-disorder theory was applied to analyse and explain the stacking disorder and to determine the symmetry operations, which generate subsequent layers from a given one. Corresponding ordered structural models were constructed and optimized by force field and dispersion-corrected density functional theory methods. The superposition of the four lowest-energy stackings lead to a structure in which every second double layer looks to be ordered; in the other double layers the molecules occupy one of two lateral positions. This calculated superposition structure agrees excellently with an (incomplete) experimental structure determined from single-crystal data. From the optimized ordered models, the stacking probabilities and the preferred local arrangements were derived. Packing effects such as the distortion of the molecules depending on the arrangement of neighbouring molecules could also be determined.

Validation of missed space-group symmetry in X-ray powder diffraction structures with dispersion-corrected density functional theory

More than 600 molecular crystal structures with correct, incorrect and uncertain space-group symmetry were energy-minimized with dispersion-corrected density functional theory (DFT-D, PBE-D3). For the purpose of determining the correct space-group symmetry the required tolerance on the atomic coordinates of all non-H atoms is established to be 0.2 Å. For 98.5% of 200 molecular crystal structures published with missed symmetry, the correct space group is identified; there are no false positives. Very small, very symmetrical molecules can end up in artificially high space groups upon energy minimization, although this is easily detected through visual inspection. If the space group of a crystal structure determined from powder diffraction data is ambiguous, energy minimization with DFT-D provides a fast and reliable method to select the correct space group.

The structure of denisovite, a fibrous nanocrystalline polytypic disordered 'very complex' silicate, studied by a synergistic multi-disciplinary approach employing methods of electron crystallography and X-ray powder diffraction

Denisovite is a rare mineral occurring as aggregates of fibres typically 200-500 nm diameter. It was confirmed as a new mineral in 1984, but important facts about its chemical formula, lattice parameters, symmetry and structure have remained incompletely known since then. Recently obtained results from studies using microprobe analysis, X-ray powder diffraction (XRPD), electron crystallography, modelling and Rietveld refinement will be reported. The electron crystallography methods include transmission electron microscopy (TEM), selected-area electron diffraction (SAED), high-angle annular dark-field imaging (HAADF), high-resolution transmission electron microscopy (HRTEM), precession electron diffraction (PED) and electron diffraction tomography (EDT). A structural model of denisovite was developed from HAADF images and later completed on the basis of quasi-kinematic EDT data by ab initio structure solution using direct methods and least-squares refinement. The model was confirmed by Rietveld refinement. The lattice parameters are a = 31.024 (1), b = 19.554 (1) and c = 7.1441 (5) Å, β = 95.99 (3)°, V = 4310.1 (5) ų and space group P12/a1. The structure consists of three topologically distinct dreier silicate chains, viz. two xonotlite-like dreier double chains, [Si₆O₁₇]^10-, and a tubular loop-branched dreier triple chain, [Si₁₂O₃₀]^12-. The silicate chains occur between three walls of edge-sharing (Ca,Na) octahedra. The chains of silicate tetrahedra and the octahedra walls extend parallel to the z axis and form a layer parallel to (100). Water molecules and K⁺ cations are located at the centre of the tubular silicate chain. The latter also occupy positions close to the centres of eight-membered rings in the silicate chains. The silicate chains are geometrically constrained by neighbouring octahedra walls and present an ambiguity with respect to their z position along these walls, with displacements between neighbouring layers being either Δz = c/4 or -c/4. Such behaviour is typical for polytypic sequences and leads to disorder along [100]. In fact, the diffraction pattern does not show any sharp reflections with l odd, but continuous diffuse streaks parallel to a* instead. Only reflections with l even are sharp. The diffuse scattering is caused by (100) nano-lamellae separated by stacking faults and twin boundaries. The structure can be described according to the order-disorder (OD) theory as a stacking of layers parallel to (100).

4-Cyanopyridine, a versatile mono- and bidentate ligand. Crystal structures of related coordination polymers determined by X-ray powder diffraction

4-Cyanopyridine (4-CNpy) as a monodentate ligand in single or double chains or as a bidentate ligand in two-dimensional networks.

Local structure in the disordered solid solution ofcis- andtrans-perinones

Thecis- andtrans-isomers of the polycyclic aromatic compound perinone, C26H12N4O2, form a solid solution (Vat Red 14). This solid solution is isotypic to the crystal structures ofcis-perinone (Pigment Red 194) andtrans-perinone (Pigment Orange 34) and exhibits a combined positional and orientational disorder: In the crystal, each molecular position is occupied by either acis- ortrans-perinone molecule, both of which have two possible molecular orientations. The structure ofcis-perinone exhibits a twofold orientational disorder, whereas the structure oftrans-perinone is ordered. The crystal structure of the solid solution was determined by single-crystal X-ray analysis. Extensive lattice-energy minimizations with force-field and DFT-D methods were carried out on combinatorially complete sets of ordered models. For the disordered systems, local structures were calculated, including preferred local arrangements, ordering lengths, and probabilities for the arrangement of neighbouring molecules. The superposition of the atomic positions of all energetically favourable calculated models corresponds well with the experimentally determined crystal structures, explaining not only the atomic positions, but also the site occupancies and anisotropic displacement parameters.

The challenging case of the theophylline–benzamide cocrystal

Theophylline has been used as an active pharmaceutical ingredient (API) in the treatment of pulmonary diseases, but due to its low water solubility reveals very poor bioavailability. Based on its different hydrogen-bond donor and acceptor groups, theophylline is an ideal candidate for the formation of cocrystals. The crystal structure of the 1:1 benzamide cocrystal of theophylline, C7H8N4O2·C7H7NO, was determined from synchrotron X-ray powder diffraction data. The compound crystallizes in the tetragonal space groupP41with four independent molecules in the asymmetric unit. The molecules form a hunter's fence packing. The crystal structure was confirmed by dispersion-corrected DFT calculations. The possibility of salt formation was excluded by the results of Raman and1H solid-state NMR spectroscopic analyses.

Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function

A method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may be used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure inP1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.

Determination of crystal structures and tautomeric states of 2-ammoniobenzenesulfonates by laboratory X-ray powder diffraction

The crystal structures of 4-chloro-5-methyl-2-ammoniobenzenesulfonate and of the corresponding derivatives 4,5-dimethyl- and 4,5-dichloro-2-ammoniobenzenesulfonates have been determined from laboratory X-ray powder diffraction data. The tautomeric state of all three compounds could also be unequivocally determined from laboratory data, using careful Rietveld refinements. The tautomeric state was confirmed by IR spectroscopy. The compounds are neither isostructural to each other nor to the 5-chloro-4-methyl derivate, despite the similar size of the chloro and methyl substituents. The influence of the chloro and methyl substituents on the packing and on the thermal stability is demonstrated. All crystal structures were confirmed by dispersion-corrected DFT calculations. For the 4-chloro-5-methyl and the 4,5-dichloro derivatives the DFT calculations indicated that the observed polymorph should not be the thermodynamical one. However, no other polymorphs could be found in experimental polymorph screening, even using seeding with the corresponding isostructural phases. Obviously the DFT methods need further improvements.

Total-scattering pair-distribution function of organic material from powder electron diffraction data

This paper shows that pair-distribution function (PDF) analyses can be carried out on organic and organometallic compounds from powder electron diffraction data. Different experimental setups are demonstrated, including selected area electron diffraction and nanodiffraction in transmission electron microscopy or nanodiffraction in scanning transmission electron microscopy modes. The methods were demonstrated on organometallic complexes (chlorinated and unchlorinated copper phthalocyanine) and on purely organic compounds (quinacridone). The PDF curves from powder electron diffraction data, called ePDF, are in good agreement with PDF curves determined from X-ray powder data demonstrating that the problems of obtaining kinematical scattering data and avoiding beam damage of the sample are possible to resolve.

The determination of crystal structures of active pharmaceutical ingredients from X-ray powder diffraction data: a brief, practical introduction, with fexofenadine hydrochloride as example

OBJECTIVES

This study describes the general method for the determination of the crystal structures of active pharmaceutical ingredients (API) from powder diffraction data and demonstrates its use to determine the hitherto unknown crystal structure of fexofenadine hydrochloride, a third-generation antihistamine drug.

METHODS

Fexofenadine hydrochloride was subjected to a series of crystallisation experiments using re-crystallisation from solvents, gas diffusion, layering with an antisolvent and gel crystallisation. Powder diffraction patterns of all samples were recorded and inspected for polymorphism and for crystallinity.

KEY FINDINGS

All samples corresponded to the same polymorph. The crystal structure was determined from an X-ray powder diffraction pattern using a real-space method with subsequent Rietveld refinement. The structure exhibits a two-dimensional hydrogen bond network.

CONCLUSION

Crystal structures of API can be determined from X-ray powder diffraction data with good reliability. Fexofenadine exhibits only one polymorphic form, which is stabilised in the crystal by strong hydrogen bonds of the type (+)N-H···Cl(-), O-H···Cl(-), and between COOH groups.

Modelling pair distribution functions (PDFs) of organic compounds: describing both intra- and intermolecular correlation functions in calculated PDFs

The methods currently used to calculate atomic pair distribution functions (PDFs) from organic structural models do not distinguish between the intramolecular and intermolecular distances. Owing to the stiff bonding between atoms within a molecule, the PDF peaks arising from intramolecular atom–atom distances are much sharper than those of the intermolecular atom–atom distances. This work introduces a simple approach to calculate PDFs of molecular systems without building a supercell model by using two different isotropic displacement parameters to describe atomic motion: one parameter is used for the intramolecular, the other one for intermolecular atom–atom distances. Naphthalene, quinacridone and paracetamol were used as examples. Calculations were done with theDiffPy-CMIcomplex modelling infrastructure. The new modelling approach produced remarkably better fits to the experimental PDFs, confirming the higher accuracy of this method for organic materials.

Prediction of molecular crystal structures by a crystallographic QM/MM model with full space-group symmetry

A crystallographic quantum-mechanical/molecular-mechanical model (c-QM/MM model) with full space-group symmetry has been developed for molecular crystals. The lattice energy was calculated by quantum-mechanical methods for short-range interactions and force-field methods for long-range interactions. The quantum-mechanical calculations covered the interactions within the molecule and the interactions of a reference molecule with each of the surrounding 12-15 molecules. The interactions with all other molecules were treated by force-field methods. In each optimization step the energies in the QM and MM shells were calculated separately as single-point energies; after adding both energy contributions, the crystal structure (including the lattice parameters) was optimized accordingly. The space-group symmetry was maintained throughout. Crystal structures with more than one molecule per asymmetric unit, e.g. structures with Z' = 2, hydrates and solvates, have been optimized as well. Test calculations with different quantum-mechanical methods on nine small organic molecules revealed that the density functional theory methods with dispersion correction using the B97-D functional with 6-31G* basis set in combination with the DREIDING force field reproduced the experimental crystal structures with good accuracy. Subsequently the c-QM/MM method was applied to nine compounds from the CCDC blind tests resulting in good energy rankings and excellent geometric accuracies.

Average structures of the disordered β-phase of Pigment Red 170: a single-crystal X-ray diffraction study

The β-phase of the industrially important Pigment Red 170 (β-P.R. 170) has a structure with severe layer stacking disorder. The single-crystal X-ray diffraction pattern consists of a difficult-to-disentangle mix of Bragg diffraction superimposed on rods of diffuse scattering which impede the estimation of accurate Bragg intensities. Two average monoclinic structure models with the same unit-cell dimensions, but different extents of disorder in the layers and different space groups seem plausible, one with the non-conventional space group setting B2(1)/g (No. 14, Z' = 2) and one in P2(1)/a (No. 14, Z' = 4). Disordered molecules related by a translation of 0.158b are present in all layers of the B2(1)/g model and in every second layer of the P2(1)/a model. Layer-to-layer contacts are practically the same in both models. According to order-disorder theory, both models are valid superposition structures. Structure-factor calculations show that the pattern of strong and weak Bragg reflections is very similar for the two models. R factors indicate that the B2(1)/g model is the most economic representation of the average structure. However, given the limitations in data processing, the P2(1)/a model should not be discarded and further insight sought from a detailed analysis of the experimental diffuse scattering. The difficulties encountered in this analysis raise the question of whether or not the concept of an average structure is applicable in practice to β-P.R. 170.