Explanation of the stacking disorder in the β-phase of Pigment Red 170

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.

Automated electron diffraction tomography - development and applications

Electron diffraction tomography (EDT) has gained increasing interest, starting with the development of automated electron diffraction tomography (ADT) which enables the collection of three-dimensional electron diffraction data from nano-sized crystals suitable for ab initio structure analysis. A basic description of the ADT method, nowadays recognized as a reliable and established method, as well as its special features and general applicability to different transmission electron microscopes is provided. In addition, the usability of ADT for crystal structure analysis of single nano-sized crystals with and without special crystallographic features, such as twinning, modulations and disorder is demonstrated.

Structure analysis of materials at the order–disorder borderline using three-dimensional electron diffraction

Diffuse scattering, observed as intensity distribution between the Bragg peaks, is associated with deviations from the average crystal structure, generally referred to as disorder. In many cases crystal defects are seen as unwanted perturbations of the periodic structure and therefore they are often ignored. Yet, when it comes to the structure analysis of nano-volumes, what electron crystallography is designed for, the significance of defects increases. Twinning and polytypic sequences are other perturbations from ideal crystal structure that are also commonly observed in nanocrystals. Here we present an overview of defect types and review some of the most prominent studies published on the analysis of defective nanocrystalline structures by means of three-dimensional electron diffraction.

Disorder in molecular crystals justified with the help of statistical mechanics: a case of two enantiomer solid solutions

An elegant statistical mechanics approach has been exploited in combination with accurate quantum chemical calculations to justify the disorder in two previously reported racemic solids.

Rapid Structure Determination of Microcrystalline Molecular Compounds Using Electron Diffraction

Chemists of all fields currently publish about 50 000 crystal structures per year, the vast majority of which are X‐ray structures. We determined two molecular structures by employing electron rather than X‐ray diffraction. For this purpose, an EIGER hybrid pixel detector was fitted to a transmission electron microscope, yielding an electron diffractometer. The structure of a new methylene blue derivative was determined at 0.9 Å resolution from a crystal smaller than 1×2 μm². Several thousand active pharmaceutical ingredients (APIs) are only available as submicrocrystalline powders. To illustrate the potential of electron crystallography for the pharmaceutical industry, we also determined the structure of an API from its pill. We demonstrate that electron crystallography complements X‐ray crystallography and is the technique of choice for all unsolved cases in which submicrometer‐sized crystals were the limiting factor.

Azulene revisited: solid-state structure, invariom modeling and lattice-energy minimization of a classical example of disorder

The molecular and solid-state structure of azulene both raise fundamental questions. Therefore, the disordered crystal structure of azulene was re-refined with invariom non-spherical atomic scattering factors from new single-crystal X-ray diffraction data with a resolution of d = 0.45 Å. An unconstrained refinement results in a molecular geometry with C s symmetry. Refinements constrained to fulfill C 2v symmetry, as observed in the gas phase and in high-level ab initio calculations, lead to similar figures of merit and residual densities as unconstrained ones. Such models are consistent with the structures from microwave spectroscopy and electron diffraction, albeit they are not the same. It is shown that for the disorder present in azulene, the invariom model describes valence electron density as successfully as it does for non-disordered structures, although the disorder still leads to high correlations mainly between positional parameters. Lattice-energy minimizations on a variety of ordered model structures using dispersion-corrected DFT calculations reveal that the local deviations from the average structure are small. Despite the molecular dipole moment there is no significant molecular ordering in any spatial direction. A superposition of all ordered model structures leads to a calculated average structure, which explains not only the experimental determined atomic coordinates, but also the apparently unusual experimental anisotropic displacement parameters.

On the structural aspects of solid solutions of enantiomers: an intriguing case study of enantiomer recognition in the solid state

The structural aspects of type 1 and type 2 solid solutions have been revised.

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.

Rationalization of the Color Properties of Fluorescein in the Solid State: A Combined Computational and Experimental Study

Fluorescein is known to exist in three tautomeric forms defined as quinoid, zwitterionic, and lactoid. In the solid state, the quinoid and zwitterionic forms give rise to red and yellow materials, respectively. The lactoid form has not been crystallized pure, although its cocrystal and solvate forms exhibit colors ranging from yellow to green. An explanation for the observed colors of the crystals is found using a combination of UV/Vis spectroscopy and plane-wave DFT calculations. The role of cocrystal coformers in modifying crystal color is also established. Several new crystal structures are determined using a combination of X-ray and electron diffraction, solid-state NMR spectroscopy, and crystal structure prediction (CSP). The protocol presented herein may be used to predict color properties of materials prior to their synthesis.

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.

Crystal structure of disordered nanocrystalline αII-quinacridone determined by electron diffraction

The nanocrystalline α^II-phase of the industrially produced organic pigment quinacridone was studied by 3D electron diffraction. The average crystal structure was obtained directly from the data and validated by energy minimization. A model describing the experimentally observed diffuse scattering was proposed.

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.