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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

DOI: 10.1107/S2052252522004237 DOI Help

Authors: Carina Schlesinger (Johann Wolfgang Goethe University) , Arnd Fitterer (Johann Wolfgang Goethe University) , Christian Buchsbaum (Johann Wolfgang Goethe University) , Stefan Habermehl (Johann Wolfgang Goethe University) , Michele R. Chierotti (University of Torino) , Carlo Nervi (University of Torino) , Martin U. Schmidt (Johann Wolfgang Goethe University)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Iucrj , VOL 9

State: Published (Approved)
Published: July 2022

Open Access Open Access

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.

Journal Keywords: ambiguous structures; structure determination from powder data; pair distribution function refinement; Rietveld refinement; solid-state NMR; lattice-energy minimization; DFT; quinacridone

Subject Areas: Technique Development, Chemistry

Instruments: I15-1-X-ray Pair Distribution Function (XPDF)

Added On: 26/05/2022 09:29


Discipline Tags:

Technique Development - Chemistry Chemistry Organic Chemistry

Technical Tags:

Scattering Pair Distribution Function (PDF)