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

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.

Structural Analysis of Molecular Materials Using the Pair Distribution Function

This is a review of atomic pair distribution function (PDF) analysis as applied to the study of molecular materials. The PDF method is a powerful approach to study short- and intermediate-range order in materials on the nanoscale. It may be obtained from total scattering measurements using X-rays, neutrons, or electrons, and it provides structural details when defects, disorder, or structural ambiguities obscure their elucidation directly in reciprocal space. While its uses in the study of inorganic crystals, glasses, and nanomaterials have been recently highlighted, significant progress has also been made in its application to molecular materials such as carbons, pharmaceuticals, polymers, liquids, coordination compounds, composites, and more. Here, an overview of applications toward a wide variety of molecular compounds (organic and inorganic) and systems with molecular components is presented. We then present pedagogical descriptions and tips for further implementation. Successful utilization of the method requires an interdisciplinary consolidation of material preparation, high quality scattering experimentation, data processing, model formulation, and attentive scrutiny of the results. It is hoped that this article will provide a useful reference to practitioners for PDF applications in a wide realm of molecular sciences, and help new practitioners to get started with this technique.

Structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing

A method for the ab initio crystal structure determination of organic compounds by a fit to the pair distribution function (PDF), without prior knowledge of lattice parameters and space group, has been developed. The method is called 'PDF-Global-Fit' and is implemented by extension of the program FIDEL (fit with deviating lattice parameters). The structure solution is based on a global optimization approach starting from random structural models in selected space groups. No prior indexing of the powder data is needed. The new method requires only the molecular geometry and a carefully determined PDF. The generated random structures are compared with the experimental PDF and ranked by a similarity measure based on cross-correlation functions. The most promising structure candidates are fitted to the experimental PDF data using a restricted simulated annealing structure solution approach within the program TOPAS, followed by a structure refinement against the PDF to identify the correct crystal structure. With the PDF-Global-Fit it is possible to determine the local structure of crystalline and disordered organic materials, as well as to determine the local structure of unindexable powder patterns, such as nanocrystalline samples, by a fit to the PDF. The success of the method is demonstrated using barbituric acid as an example. The crystal structure of barbituric acid form IV solved and refined by the PDF-Global-Fit is in excellent agreement with the published crystal structure data.