Quantitative Electron Diffraction for Crystal Structure Determination

2009 ◽  
Vol 1184 ◽  
Author(s):  
Peter Oleynikov ◽  
Daniel Grüner ◽  
Daliang Zhang ◽  
Junliang Sun ◽  
Xiaodong Zou ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Data Quality ◽  
Diffraction Data ◽  
Ccd Camera ◽  
Electron Diffraction Data ◽  
X Ray Diffraction ◽  
Quantitative Investigation ◽  
Critical Question ◽  
Selected Area Electron Diffraction

AbstractWe present a quantitative investigation of data quality using electron precession, compared to standard selected-area electron diffraction (SAED). Data can be collected on a CCD camera and automatically extracted by computer. The critical question of data quality is addressed – can electron diffraction data compete with X-ray diffraction data in terms of resolution, completeness and quality of intensities?

On the quality of the continuous rotation electron diffraction data for accurate atomic structure determination of inorganic compounds

2018 ◽  
Vol 51 (4) ◽  
pp. 1094-1101 ◽  
Author(s):  
Yunchen Wang ◽  
Taimin Yang ◽  
Hongyi Xu ◽  
Xiaodong Zou ◽  
Wei Wan
Keyword(s):  
Electron Diffraction ◽  
Single Crystal ◽  
Diffraction Data ◽  
Structural Models ◽  
Electron Diffraction Data ◽  
Data Sets ◽  
X Ray Diffraction ◽  
X Ray ◽  
Continuous Rotation

The continuous rotation electron diffraction (cRED) method has the capability of providing fast three-dimensional electron diffraction data collection on existing and future transmission electron microscopes; unknown structures could be potentially solved and refined using cRED data collected from nano- and submicrometre-sized crystals. However, structure refinements of cRED data using SHELXL often lead to relatively high R1 values when compared with those refined against single-crystal X-ray diffraction data. It is therefore necessary to analyse the quality of the structural models refined against cRED data. In this work, multiple cRED data sets collected from different crystals of an oxofluoride (FeSeO3F) and a zeolite (ZSM-5) with known structures are used to assess the data consistency and quality and, more importantly, the accuracy of the structural models refined against these data sets. An evaluation of the precision and consistency of the cRED data by examination of the statistics obtained from the data processing software DIALS is presented. It is shown that, despite the high R1 values caused by dynamical scattering and other factors, the refined atomic positions obtained from the cRED data collected for different crystals are consistent with those of the reference models refined against single-crystal X-ray diffraction data. The results serve as a reference for the quality of the cRED data and the achievable accuracy of the structural parameters.

Structures of nanometre-size crystals determined from selected-area electron diffraction data

2000 ◽  
Vol 56 (1) ◽  
pp. 29-35 ◽  
Author(s):  
Thomas E. Weirich ◽  
Xiaodong Zou ◽  
Reiner Ramlau ◽  
Arndt Simon ◽  
Giovanni Luca Cascarano ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Electron Diffraction Data ◽  
Selected Area Electron Diffraction

A complex pseudo-decagonal quasicrystal approximant, Al37(Co,Ni)15.5, solved by rotation electron diffraction

2014 ◽  
Vol 47 (1) ◽  
pp. 215-221 ◽  
Author(s):  
Devinder Singh ◽  
Yifeng Yun ◽  
Wei Wan ◽  
Benjamin Grushko ◽  
Xiaodong Zou ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Single Crystal ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Basic Structure ◽  
Electron Diffraction Data ◽  
Dimensional Electron ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Patterns

Electron diffraction is a complementary technique to single-crystal X-ray diffraction and powder X-ray diffraction for structure solution of unknown crystals. Crystals too small to be studied by single-crystal X-ray diffraction or too complex to be solved by powder X-ray diffraction can be studied by electron diffraction. The main drawbacks of electron diffraction have been the difficulties in collecting complete three-dimensional electron diffraction data by conventional electron diffraction methods and the very time-consuming data collection. In addition, the intensities of electron diffraction suffer from dynamical scattering. Recently, a new electron diffraction method, rotation electron diffraction (RED), was developed, which can overcome the drawbacks and reduce dynamical effects. A complete three-dimensional electron diffraction data set can be collected from a sub-micrometre-sized single crystal in less than 2 h. Here the RED method is applied forab initiostructure determination of an unknown complex intermetallic phase, the pseudo-decagonal (PD) quasicrystal approximant Al37.0(Co,Ni)15.5, denoted as PD2. RED shows that the crystal is F-centered, witha= 46.4,b= 64.6,c= 8.2 Å. However, as with other approximants in the PD series, the reflections with oddlindices are much weaker than those withleven, so it was decided to first solve the PD2 structure in the smaller, primitive unit cell. The basic structure of PD2 with unit-cell parametersa= 23.2,b= 32.3,c= 4.1 Å and space groupPnmmhas been solved in the present study. The structure withc= 8.2 Å will be taken up in the near future. The basic structure contains 55 unique atoms (17 Co/Ni and 38 Al) and is one of the most complex structures solved by electron diffraction. PD2 is built of characteristic 2 nm wheel clusters with fivefold rotational symmetry, which agrees with results from high-resolution electron microscopy images. Simulated electron diffraction patterns for the structure model are in good agreement with the experimental electron diffraction patterns obtained by RED.

Electron-diffraction patterns from frozen hydrate protein microcrystals: A new tool instructural studies

1994 ◽  
Vol 52 ◽  
pp. 102-103
Author(s):  
Christoph Burmester ◽  
Kenneth C. Holmes ◽  
Rasmus R. Schröder
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Heavy Atom ◽  
Atomic Resolution ◽  
Protein Crystals ◽  
Electron Diffraction Data ◽  
Phase Information ◽  
Isomorphous Replacement ◽  
Diffraction Patterns

Electron crystallography of 2D protein crystals can yield models with atomic resolution by taking Fourier amplitudes from electron diffraction and phase information from processed images. Imaging at atomic resolution is more difficult than the recording of corresponding electron diffraction patterns. Therefore attempts have been made to recover phase information from diffraction data from 2-D and 3-D crystals by the method of isomorphous replacement using heavy atom labelled protein crystals. These experiments, however, have so far not produced usable phase information, partly because of the large experimental error in the spot intensities. Here we present electron diffraction data obtained from frozen hydrated 3-D protein crystals with an energy-filter microscope and a specially constructed Image Plate scanner which are of considerably better crystallographic quality (as evidenced in much smaller values for the crystallographic R-factors Rsym and Rmerge) than those reported before. The quality of this data shows that the method of isomorphous replacement could indeed be used for phase determination for diffraction data obtained from 3-D microcrystals by electron diffraction.

Single-crystal x-ray diffraction structures of covalent organic frameworks

Science ◽  
2018 ◽  
Vol 361 (6397) ◽  
pp. 48-52 ◽  
Author(s):  
Tianqiong Ma ◽  
Eugene A. Kapustin ◽  
Shawn X. Yin ◽  
Lin Liang ◽  
Zhengyang Zhou ◽  
...  
Keyword(s):  
Single Crystal ◽  
Single Crystals ◽  
Diffraction Data ◽  
General Procedure ◽  
Three Dimensional ◽  
Electron Diffraction Data ◽  
Covalent Organic Frameworks ◽  
X Ray Diffraction ◽  
X Ray

The crystallization problem is an outstanding challenge in the chemistry of porous covalent organic frameworks (COFs). Their structural characterization has been limited to modeling and solutions based on powder x-ray or electron diffraction data. Single crystals of COFs amenable to x-ray diffraction characterization have not been reported. Here, we developed a general procedure to grow large single crystals of three-dimensional imine-based COFs (COF-300, hydrated form of COF-300, COF-303, LZU-79, and LZU-111). The high quality of the crystals allowed collection of single-crystal x-ray diffraction data of up to 0.83-angstrom resolution, leading to unambiguous solution and precise anisotropic refinement. Characteristics such as degree of interpenetration, arrangement of water guests, the reversed imine connectivity, linker disorder, and uncommon topology were deciphered with atomic precision—aspects impossible to determine without single crystals.

Generation, Processing, and Transferring of CCD Camera Images in Electron Crystallography

1996 ◽  
Vol 54 ◽  
pp. 426-427
Author(s):  
Z. G. Li ◽  
L. Liang ◽  
R. L. Harlow ◽  
K.E. Lehman ◽  
N. Herron
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Dynamic Range ◽  
Structural Information ◽  
Ccd Camera ◽  
High Dynamic Range ◽  
Electron Diffraction Data ◽  
Electron Crystallography ◽  
Camera Model ◽  
University Of New Mexico

Recently, CCD camera has been more and more used in the electron microscopy particularly for electron crystallography [1]. Use of CCD camera in this field as a recording medium possesses many significant advantages over conventional photographic films. A CCD camera has a very high dynamic range (reliable) and produces images directly in digital form which can be conveniently processed and transferred. We have initiated a program to obtain crystal structural information of plate-like materials by processing electron diffraction data from a CCD detector. As part of our program, we have developed a complete and routine procedure to convert images to diffraction data (h, k, l’s and intensities).Figure 1 is a schematic representation of the procedure. Images are initially obtained using a 1024×1024 Gatan CCD camera (model 794) which was attached to JEM-2000EX electron microscope. The collection of the images is controlled by a MAC computer which also stores the data and allows the data to be viewed. Then, the digitized electron diffraction patterns are transferred to a Sun station computer where, using Khoros software, the CCD images are processed. The Khoros system is a very complete image analysis and image processing software developed by University of New Mexico [2].

Applications of the maximum entropy method to powder diffraction and electron crystallography

1993 ◽  
Vol 442 (1914) ◽  
pp. 97-111 ◽  
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Direct Methods ◽  
Entropy Method ◽  
Electron Diffraction Data ◽  
Directed Search ◽  
X Ray Diffraction ◽  
Entropy Maximization ◽  
X Ray ◽  
Trial Phase

A new multisolution phasing method based on entropy maximization and likelihood ranking, proposed for the specific purpose of increasing the accuracy and sensitivity of probabilistic phase indications compared with conventional direct methods, has been implemented and applied to a wide variety of problems. The latter comprise the determination of small crystal structures from X-ray diffraction data obtained from single crystals or from powders, and from electron diffraction data, both with and without partial phase information obtained by image processing of electron micrographs; the ranking of phase sets for a small protein; and the improvement of poor quality phases for a larger protein at medium resolution under constraint of solvent flatness. The main components of the method are (1) a tree-directed search through a space of trial phase sets; (2) the saddlepoint method for calculating joint probabilities of structure factors, using entropy maximization; (3) likelihood-based scores to rank trial phase sets and prune the search tree; (4) a statistical analysis of the scores for automatically selecting reliable phase indications. Their use is illustrated here on structure determinations from powder X-ray diffraction data and from electron diffraction data.

Daliranite, PbHgAs2S5: determination of the incommensurately modulated structure and revision of the chemical formula

2019 ◽  
Vol 75 (4) ◽  
pp. 711-716 ◽  
Author(s):  
Arianna E. Lanza ◽  
Mauro Gemmi ◽  
Luca Bindi ◽  
Enrico Mugnaioli ◽  
Werner H. Paar
Keyword(s):  
Crystal Structure ◽  
Electron Diffraction ◽  
Diffraction Data ◽  
Structural Model ◽  
Electron Diffraction Data ◽  
Chemical Formula ◽  
Modulated Structure ◽  
X Ray

The incommensurately modulated crystal structure of the mineral daliranite has been determined using 3D electron diffraction data obtained on nanocrystalline domains. Daliranite is orthorhombic with a = 21, b = 4.3, c = 9.5 Å and shows modulation satellites along c. The solution of the average structure in the Pnma space group together with energy-dispersive X-ray spectroscopy data obtained on the same domains indicate a chemical formula of PbHgAs2S5, which has one S fewer than previously reported. The crystal structure of daliranite is built from columns of face-sharing PbS8 bicapped trigonal prisms laterally connected by [2+4]Hg polyhedra and (As3+ 2S5)4− groups. The excellent quality of the electron diffraction data allows a structural model to be built for the modulated structure in superspace, which shows that the modulation is due to an alternated occupancy of a split As site.

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