Towards automated crystallographic structure refinement with phenix.refine

phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods

Quantitative analysis of diffuse X-ray scattering in partially transformed 3C-SiC single crystals

International audienceThe X-ray scattering of partially transformed 3C-SiC single crystals is considered in details. Extended diffuse scattering streaks, originating from stacking faults (SFs) lying in the {111} planes, are clearly observed in the wide-range reciprocal space maps. The intensity distribution along the diffuse streaks is simulated with a model including the contributions of the diffuse scattering originating from the SFs [based on the pioneering theoretical description given by Kabra et al. (J. Mater. Sci. 21, 1654-1666 (1986))], the coherent scattering emanating from untransformed areas of the crystals, as well as all θ-dependent terms that affect the scattered intensity (the layer structure factor, the irradiated volume and the polarization of the beam). The quantitative simulation of the diffuse streaks reveals that the transformation occurs through the glide of partial dislocations and allows to derive the transformation level. It is shown that the 3C polytype is indeed unstable at high temperature. However, it is further shown that defect-free 3C-SiC single crystals remain stable at temperatures where it is known to be usually unstable (1900°C). The origin of this apparent stability is very likely of kinetic nature, i.e. the lack of crystalline defects inhibits the transformation

Hirshfeld surfaces identify inadequacies in computations of intermolecular interactions in crystals: pentamorphic 1,8-dihydroxyanthraquinone

Fingerprint plots of Hirshfeld surfaces were used to locate and analyze the deficiencies in various methodologies employed in the determination of the relative energies of five polymorphs of 1,8-dihydroxyanthraquinone. Nine crystallographically independent molecules were characterized by X-ray crystallography and Hirshfeld surfaces were derived from the X-ray structures. The space groups and number of independent molecules (Z') for each of the polymorphs (1-5) is as follows: (1) P41 (or P43),Z' ) 1; (2) Pca21, Z' ) 2; (3) P1 j, Z' ) 4; (4) P21/n, Z' ) 1; (5) P41212 (or P43212), Z' ) 0.5. Form 1 is the most thermodynamically stable among the reproducible structures, as established by competitive solubility tests, followed by 2 and then 4. The unrestrained structures of the five polymorphs were computed using the CVFF and COMPASS force fields as well as with the density functionalcode, SIESTA