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26 citations found for Smeets, S
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A semi-automated routine for continuous rotation electron diffraction has been developed, enabling high-throughput data collection. Serial electron crystallography combined with a deep convolutional network are used to screen for suitable crystals.
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We have mimicked the 4%-energy-bandpass mode of the SwissFEL beam at a synchrotron facility, collected snapshots of randomly oriented multi-crystal samples, and developed a methodology to index and process such non-monochromatic data for materials science applications.
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In the title compound, [Cu(SO4)(C2H8N2)2]n, the Cu, S and two O atoms lie on a mirror plane. The Cu atom is in a distorted octahedral environment and the ethylenediamine ligand is in a gauche conformation. The sulfate dianion is bridging, forming a one-dimensional chain. A two-dimensional net parallel to (001) is generated by N—H
O hydrogen bonding between the chains.
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The synthesis of the polycrystalline niobium silicate catalyst AM-11 was first reported in 1998 [1], but its structure proved to be elusive. In 2007 we received two samples from the Aveiro group. At the time, we were looking for a material suitable for the application of the texture method of structure solution, and AM-11 seemed to be ideal for this purpose. One of the samples had needle and the other platelet morphology, and textured samples could be prepared in both cases. The conventional powder diffraction pattern could be indexed on a hexagonal, an orthorhombic or a monoclinic unit cell, so this was the first issue to be resolved. The texture measurements quickly revealed that the crystal system was orthorhombic, but the structure resisted solution. We then tried applying the precession electron diffraction technique in combination with high-resolution powder diffraction data, but beyond confirming the orthorhombic symmetry, these data did not help us to solve the structure. Another attempt was made with a new sample and an improved texture setup, but to no avail. Rotation electron diffraction data and high-resolution transmission electron microscopy images showed that some disorder was present and helped to define the space group, but the structure remained a mystery. The powder charge-flipping routine in Superflip [2], yielded tantalizingly clear electron density maps, but they could not be interpreted sensibly. The unit cell parameters were seen to be related to those of the titanium silicate zorite [3] (one axis doubled in AM-11), so the problem was taken up once again last year. By starting with a simplified zorite framework structure with Nb in place of Ti, and performing what amounts to manual Fourier recycling, the surprisingly simple structure (1Nb, 3 Si, 9 O), which is significantly different from zorite, finally revealed itself. There is some stacking disorder, but the structure is otherwise innocuous. What made it so difficult to solve?
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A DigitalMicrograph script named InsteaDMatic has been developed for automated continuous rotation electron diffraction (cRED) data acquisition. InsteaDMatic coordinates functions of the transmission electron microscope goniometer and camera in order to tune up diffraction-frame recording simultaneously with crystal rotation. Exploiting fast and automated data collection, the influence of the electron dose rate on the quality of cRED data was studied, and structural models obtained for two different parallel-beam illumination modes (aperture selection and nanoprobe) were compared.
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High-resolution synchrotron X-ray powder diffraction (SXPD) data alone are sometimes not enough to solve the structure of a complex polycrystalline material. Such was the case for the high-silica zeolites SSZ-61 and SSZ-87, where combining data from different sources, in particular XPD and electron microscopy, was vital to success. For SSZ-61, the SXPD data feature broad peaks and a resolution of ca. 1.2 Å. Although the pattern could be indexed, structure determination failed both with the charge flipping routine in SUPERFLIP [1] and with the zeolite-specific program FOCUS [2]. The unit cell parameters and HRTEM images indicated a relationship with ZSM-12 (MTW) and SSZ-59 (SFN), so several models derived from these two frameworks were built. Eventually, after considering Si-29 MAS NMR data and the size of the organic structure directing agent (SDA), a framework model that fits all the data emerged. To complete the structure, the SDA was included as a rigid-body, and its location and orientation optimized using simulated annealing. Subsequent Rietveld refinement confirmed the structure. In contrast to SSZ-61, the SXPD pattern for SSZ-87 was quite good, and it could be indexed with a C-centered cell. However, structure solution failed, probably because of the very high degree of reflection overlap (93%). Therefore, rotation electron diffraction (RED) data [3] were collected, but they proved to be of low resolution and poor quality. Only 2 of the 7 data sets could be indexed, and these had different unit cells. Neither fit the XPD pattern directly. The problem was traced to large errors in the RED cell parameters, and eventually one RED cell could be transformed to one similar to the SXPD cell. The RED data with this cell was only 15% complete up to a resolution of 1.22 Å. Even so, the structure could be solved using a recently developed version of FOCUS that works with ED data. The SDA was found as for SSZ-61, and the structure then confirmed by Rietveld refinement.
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The structures of the isostructural title compounds have been determined at multiple temperatures. The disorder in the cation due to hydrogen bonding and/or ring puckering and the Jahn–Teller effect were analyzed using a rigid-body model and normal coordinate analysis.
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Serial crystallography using electron diffraction has been developed as a fully automated method for collecting electron diffraction data from a large number of crystals. It is demonstrated how the data can be used for structure determination and phase analysis.
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The crystal structure of the title compound, [Zn{CO(NH2)2}6](NO3)2, has been determined at 110 and 250 K. The structure is stabilized by 12 individual hydrogen bonds, both intra- and intermolecular. Analysis of the thermal expansion tensor, based on unit cells determined over a temperature range of 180 K, shows uniaxial compression in the direction of the b axis during warming. The hydrogen bonds form layers perpendicular to this axis and these layers are connected by coordinative bonds parallel to the axis. As expected, the intermolecular hydrogen bonds expand during warming. Surprisingly, the coordinative bonds contract, accompanied by changes in the O—Zn—O angles. Overall, this behaviour can be described as an accordion-like effect.
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The zeolite-specific structure solution program FOCUS has been modified to work with three-dimensional electron diffraction data. The method was applied successfully to five different zeolite materials using data sets collected with either automated diffraction tomography or the rotation electron diffraction technique.