Accurate lattice-parameter determination from electron diffraction tomography data using two-dimensional diffraction vectors

2018 ◽  
Vol 51 (4) ◽  
pp. 982-989 ◽  
Author(s):  
Jonas Ångström ◽  
Hong Chen ◽  
Wei Wan

Electron diffraction tomography (EDT) has emerged as a successful tool for ab initio atomic structure determination of nanometre-sized crystals. However, lattice parameters obtained from EDT data are often of lower accuracy than those from powder X-ray data, owing to experimental errors and data-processing methods. This work describes a lattice-parameter refinement method for EDT data using two-dimensional diffraction vectors and shows that the accuracy of lattice-parameter determination can be improved significantly. It is also shown that the method is tolerant to sample displacement during data collection and to geometric distortions in the electron diffraction patterns due to lens imperfections. For the data sets tested, the method reduces the 95% confidence interval of the worst errors in angles from ±1.98 to ±0.82° and the worst relative errors of the unit-cell lengths from ±1.8% to ±1.3%, compared with the conventional method using clustering of three-dimensional diffraction vectors. The improvement is attributed to the fact that the new method makes use of the positions of two-dimensional diffraction spots, which can be determined with high accuracy, and disregards the position of the central beam, the orientation of the rotation axis and the angles of the diffraction frames, whose errors all contribute to the errors for lattice-parameter determination using the three-dimensional method.

2015 ◽  
Vol 71 (2) ◽  
pp. 235-244 ◽  
Author(s):  
Lukáš Palatinus ◽  
Václav Petříček ◽  
Cinthia Antunes Corrêa

Accurate structure refinement from electron-diffraction data is not possible without taking the dynamical-diffraction effects into account. A complete three-dimensional model of the structure can be obtained only from a sufficiently complete three-dimensional data set. In this work a method is presented for crystal structure refinement from the data obtained by electron diffraction tomography, possibly combined with precession electron diffraction. The principle of the method is identical to that used in X-ray crystallography: data are collected in a series of small tilt steps around a rotation axis, then intensities are integrated and the structure is optimized by least-squares refinement against the integrated intensities. In the dynamical theory of diffraction, the reflection intensities exhibit a complicated relationship to the orientation and thickness of the crystal as well as to structure factors of other reflections. This complication requires the introduction of several special parameters in the procedure. The method was implemented in the freely available crystallographic computing systemJana2006.


2020 ◽  
Author(s):  
Arseniy A. Otlyotov ◽  
Georgiy V. Girichev ◽  
Anatolii N. Rykov ◽  
Timo Glodde ◽  
Yury Vishnevskiy

<div><div>Accuracy and precision of molecular parameters determined by modern gas electron diffraction method</div><div>have been investigated. Diffraction patterns of gaseous pyrazinamide have been measured independently in three laboratories, in Bielefeld (Germany), Ivanovo (Russia) and Moscow (Russia). All data sets have been analysed in equal manner using highly controlled background elimination procedure and flexible restraints in molecular structure refinement. In detailed examination and comparison of the obtained results we have determined the average experimental precision of 0.004 Å for bond lengths and 0.2 degrees for angles. The corresponding average deviations of the refined parameters from the ae-CCSD(T)/ccpwCVTZ theoretical values were 0.003 Å and 0.2 degrees. The average precision for refined amplitudes of interatomic vibrations was determined to be 0.005 Å. It is recommended to take into account these values in calculations of total errors for refined parameters of other molecules with comparable complexity.</div></div><div><br></div>


IUCrData ◽  
2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Kai-Long Zhong ◽  
Guo-Qing Cao ◽  
Wei Song ◽  
Chao Ni

In the complex cation of the title salt, [Co(C12H8N2)3](C10H5O8)2·H2O, the CoII cation is situated on a twofold rotation axis and is coordinated in a distorted octahedral manner by six N atoms from three chelating 1,10-phenanthroline (phen) ligands. In the crystal, the non-coordinating 2,4,5-tricarboxybenzoate anions interact with each other via O—H...O hydrogen bonds, generating a two-dimensional network parallel to (100). Adjacent sheets are connected by waterO—H...Ocarboxylate hydrogen bonds, resulting in a three-dimensional network structure that surrounds the complex cations.


2003 ◽  
Vol 10 (04) ◽  
pp. 669-675
Author(s):  
F. S. Gard ◽  
J. D. Riley ◽  
R. Leckey ◽  
B. F. Usher

ZnSe epilayers have been grown under various Se/Zn atomic flux ratios in the range of 0.22–2.45 at a substrate temperature of 350°C on Zn pre-exposed GaAs (111) A surfaces. Real time reflection high energy electron diffraction (RHEED) observations have shown a transition from a two-dimensional (2D) to a three-dimensional (3D) growth mode. The transition time depends directly upon the growth rate. A detailed discussion is presented to explore the cause of this change in the growth mode.


2009 ◽  
Vol 65 (3) ◽  
pp. m118-m120
Author(s):  
Olha Sereda ◽  
Helen Stoeckli-Evans

The title coordination polymer, [Cd3Co2(CN)12(C2H8N2)4]n, has an infinite two-dimensional network structure. The asymmetric unit is composed of two crystallographically independent CdIIatoms, one of which is located on a twofold rotation axis. There are two independent ethylenediamine (en) ligands, one of which bis-chelates to the Cd atom that sits in a general position, while the other bridges this Cd atom to that sitting on the twofold axis. The Cd atom located on the twofold rotation axis is linked to four equivalent CoIIIatomsviacyanide bridges, while the Cd atom that sits in a general position is connected to three equivalent CoIIIatomsviacyanide bridges. In this way, a series of trinuclear, tetranuclear and pentanuclear macrocycles are linked to form a two-dimensional network structure lying parallel to thebcplane. In the crystal structure, these two-dimensional networks are linkedviaN—H...N hydrogen bonds involving an en NH2H atom and a cyanide N atom, leading to the formation of a three-dimensional structure. This coordination polymer is only the second example involving a cyanometallate where the en ligand is present in both chelating and bridging coordination modes.


1991 ◽  
Vol 12 (1) ◽  
pp. 11-16 ◽  
Author(s):  
W. Wrazidlo ◽  
H.J. Brambs ◽  
W. Lederer ◽  
S. Schneider ◽  
B. Geiger ◽  
...  

2003 ◽  
Vol 2 (1) ◽  
pp. 31-39 ◽  
Author(s):  
Frank van Ham ◽  
Jarke J. van Wijk

Beamtrees are a new method for the visualization of large hierarchical data sets, such as directory structures and organization structures. Nodes are shown as stacked circular beams such that both the hierarchical structure as well as the size of nodes are depicted. The dimensions of beams are calculated using a variation of the treemap algorithm. Both a two-dimensional and a three-dimensional variant are presented. A small user study indicated that beamtrees are significantly more effective than nested treemaps and cushion treemaps for the extraction of global hierarchical information.


1996 ◽  
Vol 437 ◽  
Author(s):  
D.P. Piotrowski ◽  
S.R. Stock ◽  
A. Guvenilir ◽  
J.D. Haase ◽  
Z.U. Rek

AbstractIn order to understand the macroscopic response of polycrystalline structural materials to loading, it is frequently essential to know the spatial distribution of strain as well as the variation of micro-texture on the scale of 100 μm. The methods must be nondestructive, however, if the three-dimensional evolution of strain is to be studied. This paper describes an approach to high resolution synchrotron x-ray diffraction tomography of polycrystalline materials. Results from model samples of randomly-packed, millimeter-sized pieces of Si wafers and of similarly sized single-crystal Al blocks have been obtained which indicate that polychromatic beams collimated to 30 μm diameter can be used to determine the depth of diffracting volume elements within ± 70 μm. The variation in the two-dimensional distribution of diffracted intensity with changing sample to detector separation is recorded on image storage plates and used to infer the depth of diffracting volume elements.


2015 ◽  
Vol 48 (6) ◽  
pp. 1943-1955 ◽  
Author(s):  
Antonios Vamvakeros ◽  
Simon D. M. Jacques ◽  
Marco Di Michiel ◽  
Vesna Middelkoop ◽  
Christopher K. Egan ◽  
...  

This paper reports a simple but effective filtering approach to deal with single-crystal artefacts in X-ray diffraction computed tomography (XRD-CT). In XRD-CT, large crystallites can produce spots on top of the powder diffraction rings, which, after azimuthal integration and tomographic reconstruction, lead to line/streak artefacts in the tomograms. In the simple approach presented here, the polar transform is taken of collected two-dimensional diffraction patterns followed by directional median/mean filtering prior to integration. Reconstruction of one-dimensional diffraction projection data sets treated in such a way leads to a very significant improvement in reconstructed image quality for systems that exhibit powder spottiness arising from large crystallites. This approach is not computationally heavy which is an important consideration with big data sets such as is the case with XRD-CT. The method should have application to two-dimensional X-ray diffraction data in general where such spottiness arises.


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