PDXLstructure analysis wizard

Abstract

The reflection overlap problem is the primary limitation in structure determination from powder diffraction data, and over the last decade, a procedure that addresses this problem experimentally by exploiting preferred orientation has been developed [1]. The intensity variation in the X-ray diffraction pattern obtained from a textured sample as a function of sample orientation (tilt χ and rotation ϕ) can be applied to resolve the relative intensities of reflections that overlap in a conventional powder diffraction pattern. The availability of a new version of the 1-dimensional Si-microstrip detector (Mythen II) on the Materials Science Beamline at SLS [2] and new features in the computer program Maud [3] have allowed both the experimental and the data analysis procedures to be redesigned. By applying these modifications, it was expected that a significant improvement in the quality of the extracted reflection intensities could be achieved.To test this modified method, two samples of a zirconium phosphate framework material (ZrPOF-pyr) with a known crystal structure [4] were measured: (1) a textured sample using the revised experimental setup and data collection strategy, and (2) an untextured sample in a 0.5mm capillary. Both datasets were collected at the SLS using the Mythen II detector. For the analysis, reflections up to a minimum dspacing of 1.0 Å were considered, and a reflection separation factor of 0.5*FWHM was used to define the overlap groups.Comparison of the structure factors extracted from conventionally measured powder diffraction data with those derived from a textured sample indeed shows the latter to be significantly better. The agreement between the amplitudes obtained with a LeBail extraction using Maud for the untextured data and those calculated from the refined crystal structure [4] can be expressed as an R value of 0.453. For overlapping reflections (80.2% of the reflections) an R value of 0.547 was obtained. Amplitudes derived in a joint extraction using 32 powder patterns collected on a textured sample yielded R values of 0.380 and 0.408 for all and overlapping reflections, respectively. This improvement was obtained even though the peaks in these patterns are broader (presumably a result of multiple measurements of this particular sample) and have 91.9% overlap.The quality of the extraction could be further improved by combining the amplitudes derived from the textured sample with those derived from the sharper untextured one. This combination results in R values of 0.326 for all and 0.385 for overlapping reflections. This obvious improvement in the estimation of the structure factor amplitudes should allow some crystal structures that were previously inaccessible to be solved. If the remaining difficulties with the estimation of the background and the description of the peak shapes can also be solved, the method would become even more powerful.[1] Ch. Baerlocher et al

Zn(NH3)2Cl2, a Mineral-like Anthropogenic Phase with Ammine Complexes from the Burned Dumps of the Chelyabinsk Coal Basin, South Urals, Russia: Crystal Structure, Spectroscopy and Thermal Evolution

“…The sample was studied in the temperature range 30-250 • C with 10 • C steps (Figure S1). The room-temperature data were loaded into PDXL [21] to check the phase composition. The TOPAS software package [22] was used for the refinement of unit-cell parameters at all temperatures using the Pawley method.…”

Ca3SiO4Cl2—An Anthropogenic Phase from Burnt Mine Dumps of the Chelyabinsk Coal Basin: Crystal Structure Refinement, Spectroscopic Study and Thermal Evolution

“…A thin powder sample was deposited on a Pt sample holder (20 × 12 × 2 mm 3 ) from an ethanol suspension. The data concerning room temperature were loaded into PDXL [18] to refine the phase composition, then the TOPAS software package [19] was used for refining the unit cell parameters for all temperatures via the Rietveld method (Table S1). The coordinates of atoms, site scattering, and isotropic displacement parameters were fixed.…”