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

Abstract

Four different structural models, which all fit the same X-ray powder pattern, were obtained in the structure determination of 4,11-difluoroquinacridone (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.

Improving the Accuracy of Small‐Molecule Crystal Structures Solved from Powder X‐Ray Diffraction Data by Using External Sources

“…Noteworthy, these different minima can sometimes be far apart from each other, as described above in the case of four structure models of an organic dye (Figure 4). [48] The Rietveld refinement modifies the crystal structure model along the line of steepest descent in a least squares refinement. The descent to the global minimum may in some cases be achieved from a range of starting points, but this cannot be expected to be valid for the majority of molecular crystal structures.…”

“…Noteworthy, these different minima can sometimes be far apart from each other, as described above in the case of four structure models of an organic dye ( Figure 4). [48] …”

Quantitative matching of crystal structures to experimental powder diffractograms

“…While debate over how to interpret the refinement metrics is not new, 5 recent publication of four unique crystal structure models that are able to yield a reasonable refined fit to a powder diffractogram obtained from synchrotron X-ray diffraction has highlighted the inherent ambiguity that may accompany a structure solution from powder diffraction data. 6 Crystal structure prediction (CSP) uses theoretical and physical chemistry to deduce the crystal structure(s) of a given molecule or elemental composition. 7 CSP has become notable in material science as an aid to the development of porous solids 8,9 and organic semiconductors, 10 among other materials with desirable properties.…”

“…While debate over how to interpret the refinement metrics is not new, 5 recent publication of four unique crystal structure models that are able to yield a reasonable refined fit to a powder diffractogram obtained from synchrotron X-ray diffraction has highlighted the inherent ambiguity that may accompany a structure solution from powder diffraction data. 6 …”

Solving molecular compounds from powder diffraction data: are results always reliable?

“…Powder X-ray diffraction (PXRD) is a powerful tool for solving microcrystalline powder structures. Writing in IUCrJ, Schlesinger et al (2022) report intriguing results demonstrating that, in the case of poor-quality PXRD data, starting from one experimental pattern, we can obtain different structure solutions, all crystallochemically plausible and satisfying the reliability criteria currently adopted in the solution process. This unexpected situation suggests adopting a more critical attitude towards structure determination from powders.…”