scholarly journals Automated serial rotation electron diffraction combined with cluster analysis: an efficient multi-crystal workflow for structure determination

IUCrJ ◽  
2019 ◽  
Vol 6 (5) ◽  
pp. 854-867 ◽  
Author(s):  
Bin Wang ◽  
Xiaodong Zou ◽  
Stef Smeets
Keyword(s):  
Cluster Analysis ◽  
Electron Diffraction ◽  
Data Collection ◽  
Structure Analysis ◽  
Structure Determination ◽  
Hierarchical Cluster ◽  
Electron Diffraction Data ◽  
Data Sets ◽  
Analysis Tool ◽  
Continuous Rotation

Serial rotation electron diffraction (SerialRED) has been developed as a fully automated technique for three-dimensional electron diffraction data collection that can run autonomously without human intervention. It builds on the previously established serial electron diffraction technique, in which submicrometre-sized crystals are detected using image processing algorithms. Continuous rotation electron diffraction (cRED) data are collected on each crystal while dynamically tracking the movement of the crystal during rotation using defocused diffraction patterns and applying a set of deflector changes. A typical data collection screens up to 500 crystals per hour, and cRED data are collected from suitable crystals. A data processing pipeline is developed to process the SerialRED data sets. Hierarchical cluster analysis is implemented to group and identify the different phases present in the sample and to find the best matching data sets to be merged for subsequent structure analysis. This method has been successfully applied to a series of zeolites and a beam-sensitive metal–organic framework sample to study its capability for structure determination and refinement. Two multi-phase samples were tested to show that the individual crystal phases can be identified and their structures determined. The results show that refined structures obtained using automatically collected SerialRED data are indistinguishable from those collected manually using the cRED technique. At the same time, SerialRED has lower requirements of expertise in transmission electron microscopy and is less labor intensive, making it a promising high-throughput crystal screening and structure analysis tool.

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.

scholarly journals High-throughput continuous rotation electron diffraction data acquisition via software automation

2018 ◽  
Vol 51 (6) ◽  
pp. 1652-1661 ◽  
Author(s):  
Magdalena Ola Cichocka ◽  
Jonas Ångström ◽  
Bin Wang ◽  
Xiaodong Zou ◽  
Stef Smeets
Keyword(s):  
Electron Diffraction ◽  
Data Collection ◽  
High Throughput ◽  
Diffraction Data ◽  
Human Error ◽  
Electron Diffraction Data ◽  
Transmission Electron ◽  
Electron Diffraction Technique ◽  
Continuous Rotation ◽  
Crystal Electron

Single-crystal electron diffraction (SCED) is emerging as an effective technique to determine and refine the structures of unknown nano-sized crystals. In this work, the implementation of the continuous rotation electron diffraction (cRED) method for high-throughput data collection is described. This is achieved through dedicated software that controls the transmission electron microscope and the camera. Crystal tracking can be performed by defocusing every nth diffraction pattern while the crystal rotates, which addresses the problem of the crystal moving out of view of the selected area aperture during rotation. This has greatly increased the number of successful experiments with larger rotation ranges and turned cRED data collection into a high-throughput method. The experimental parameters are logged, and input files for data processing software are written automatically. This reduces the risk of human error, and makes data collection more reproducible and accessible for novice and irregular users. In addition, it is demonstrated how data from the recently developed serial electron diffraction technique can be used to supplement the cRED data collection by automatic screening for suitable crystals using a deep convolutional neural network that can identify promising crystals through the corresponding diffraction data. The screening routine and cRED data collection are demonstrated using a sample of the zeolite mordenite, and the quality of the cRED data is assessed on the basis of the refined crystal structure.

scholarly journals Can 3D Electron Diffraction Provide Accurate Atomic Structures of Metal-Organic Frameworks?

2020 ◽  
Author(s):  
Zhehao Huang ◽  
meng ge ◽  
Francesco Carraro ◽  
Christian Doonan ◽  
paolo falcaro ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Data Collection ◽  
Single Crystal ◽  
Structure Determination ◽  
Metal Organic Frameworks ◽  
X Ray Diffraction ◽  
X Ray ◽  
Continuous Rotation ◽  
Metal Organic ◽  
3D Electron

Many framework materials such as metal-organic frameworks (MOFs) or porous coordination polymers (PCPs) are synthesized as polycrystalline powders, which are too small for structure determination by single crystal X-ray diffraction (SCXRD). Here, we show that a three-dimensional (3D) electron diffraction method, namely continuous rotation electron diffraction (cRED), can be used for <i>ab initio</i> structure determination of such materials. As an example, we present a complete structural analysis of a biocomposite, denoted BSA@ZIF-C, where Bovin Serum Albumin (BSA) was encapsulated in a zeolitic imidazolate framework (ZIF). Low electron dose was combined with ultrafast cRED data collection to minimize electron beam damage of the sample. We demonstrate that the atomic structure obtained by cRED is as reliable and accurate as that obtained by single crystal X-ray diffraction. The high accuracy and fast data collection open new opportunities for investigation of cooperative phenomena in framework structures at atomic level.

scholarly journals Single Crystal 3D Rotation Electron Diffraction from Nano-sized Crystals

2014 ◽  
Vol 70 (a1) ◽  
pp. C366-C366
Author(s):  
Xiaodong Zou
Keyword(s):  
Electron Diffraction ◽  
Data Collection ◽  
Data Processing ◽  
Single Crystal ◽  
Diffraction Data ◽  
Structure Determination ◽  
Reciprocal Lattice ◽  
Electron Diffraction Data ◽  
Electron Crystallography ◽  
Structure Solution

Electron crystallography is an important technique for structure analysis of nano-sized materials. Crystals too small or too complicated to be studied by X-ray diffraction can be investigated by electron crystallography. However, conventional TEM methods requires high TEM skills and strong crystallographic knowledge, which many synthetic materials scientists and chemists do not have. We recently developed the software-based Rotation Electron Diffraction (RED) method for automated collection and processing of 3D electron diffraction data. Complete single crystal 3D electron diffraction data can be collected from nano- and micron-sized crystals in less than one hour by combining electron beam tilt and goniometer tilt, which are controlled by the RED – data collection software.3 The unit cell, possible space groups and electron diffraction intensities can be obtained from the RED data using the RED data processing software. The figure below illustrates the data collection and data processing of a zeolite silicalite-1 by RED. 1427 ED frames were collected in less than 1 hour from a crystal of 800 x 400 x 200 nm in size. A 3D reciprocal lattice of silicalite-1 was reconstructed from the ED frames, from which the unit cell parameters and space group were determined (P21/n, a=20.02Å, b=20.25Å, c=13.35Å, alfa=90.130, beta=90.740, gamma=90.030. It was possible to cut the 3D reciprocal lattice perpendicular to any directions and study the reflection conditions. The reflection intensities could be extracted. The structure of the calcined silicalite-1 could be solved from the RED data by routine direct methods using SHELX-97. All 78 unique Si and O atoms could be located and refined to an accuracy better than 0.08 Å. The RED method has been applied for structure solution of a wide range of crystals and shown to be very powerful and efficient. Now a structure determination can be achieved within a few hours, from the data collection to structure solution. We will present several examples including unknown inorganic compounds, metal-organic frameworks and organic structures solved from the RED data. Different parameters that affect the RED data quality and thus the structure determination will be discussed. The methods are general and can be applied to any crystalline materials.

scholarly journals Can 3D Electron Diffraction Provide Accurate Atomic Structures of Metal-Organic Frameworks?

2020 ◽  
Author(s):  
Zhehao Huang ◽  
meng ge ◽  
Francesco Carraro ◽  
Christian Doonan ◽  
paolo falcaro ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Data Collection ◽  
Single Crystal ◽  
Structure Determination ◽  
Metal Organic Frameworks ◽  
X Ray Diffraction ◽  
X Ray ◽  
Continuous Rotation ◽  
Metal Organic ◽  
3D Electron

Many framework materials such as metal-organic frameworks (MOFs) or porous coordination polymers (PCPs) are synthesized as polycrystalline powders, which are too small for structure determination by single crystal X-ray diffraction (SCXRD). Here, we show that a three-dimensional (3D) electron diffraction method, namely continuous rotation electron diffraction (cRED), can be used for <i>ab initio</i> structure determination of such materials. As an example, we present a complete structural analysis of a biocomposite, denoted BSA@ZIF-C, where Bovin Serum Albumin (BSA) was encapsulated in a zeolitic imidazolate framework (ZIF). Low electron dose was combined with ultrafast cRED data collection to minimize electron beam damage of the sample. We demonstrate that the atomic structure obtained by cRED is as reliable and accurate as that obtained by single crystal X-ray diffraction. The high accuracy and fast data collection open new opportunities for investigation of cooperative phenomena in framework structures at atomic level.

scholarly journals InsteaDMatic: towards cross-platform automated continuous rotation electron diffraction

2020 ◽  
Vol 53 (5) ◽  
pp. 1217-1224
Author(s):  
Maria Roslova ◽  
Stef Smeets ◽  
Bin Wang ◽  
Thomas Thersleff ◽  
Hongyi Xu ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Data Collection ◽  
Data Acquisition ◽  
Diffraction Data ◽  
Electron Diffraction Data ◽  
Electron Dose ◽  
Structure Solution ◽  
Continuous Rotation ◽  
Thermo Fisher Scientific ◽  
Cross Platform

A DigitalMicrograph script, InsteaDMatic, has been developed to facilitate rapid automated 3D electron diffraction/microcrystal electron diffraction data acquisition by continuous rotation of a crystal with a constant speed, denoted as continuous rotation electron diffraction. The script coordinates microscope functions, such as stage rotation, and camera functions relevant for data collection, and stores the experiment metadata. The script is compatible with any microscope that can be controlled by DigitalMicrograph and has been tested on both JEOL and Thermo Fisher Scientific microscopes. A proof of concept has been performed through employing InsteaDMatic for data collection and structure determination of a ZSM-5 zeolite. The influence of illumination settings and electron dose rate on the quality of diffraction data, unit-cell determination and structure solution has been investigated in order to optimize the data acquisition procedure.

Crystal Structure Determination of Glycerol-Containing Lipids from Electron Diffraction Data. Use of Analog Compounds Based upon Configurational Isomers of Cyclopentane-1, 2, 3-TRIOL

1977 ◽  
Vol 35 ◽  
pp. 24-25
Author(s):  
Douglas L. Dorset ◽  
Anthony J. Hancock
Keyword(s):  
Crystal Structure ◽  
Electron Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Crystal Surface ◽  
Coherent Scattering ◽  
Crystal Structure Determination ◽  
Electron Diffraction Data ◽  
Polar Group ◽  
Axis Orientation

Lipids containing long polymethylene chains were among the first compounds subjected to electron diffraction structure analysis. It was only recently realized, however, that various distortions of thin lipid microcrystal plates, e.g. bends, polar group and methyl end plane disorders, etc. (1-3), restrict coherent scattering to the methylene subcell alone, particularly if undistorted molecular layers have well-defined end planes. Thus, ab initio crystal structure determination on a given single uncharacterized natural lipid using electron diffraction data can only hope to identify the subcell packing and the chain axis orientation with respect to the crystal surface. In lipids based on glycerol, for example, conformations of long chains and polar groups about the C-C bonds of this moiety still would remain unknown.One possible means of surmounting this difficulty is to investigate structural analogs of the material of interest in conjunction with the natural compound itself. Suitable analogs to the glycerol lipids are compounds based on the three configurational isomers of cyclopentane-1,2,3-triol shown in Fig. 1, in which three rotameric forms of the natural glycerol derivatives are fixed by the ring structure (4-7).

scholarly journals High-resolution structure determination by continuous-rotation data collection in MicroED

2014 ◽  
Vol 11 (9) ◽  
pp. 927-930 ◽  
Author(s):  
Brent L Nannenga ◽  
Dan Shi ◽  
Andrew G W Leslie ◽  
Tamir Gonen
Keyword(s):  
High Resolution ◽  
Data Collection ◽  
Structure Determination ◽  
Continuous Rotation ◽  
High Resolution Structure ◽  
Resolution Structure

scholarly journals Molecular Structure of Pyrazinamide: a Critical Assessment of Modern Gas Electron Diffraction Data from Three Laboratories

2020 ◽  
Author(s):  
Arseniy A. Otlyotov ◽  
Georgiy V. Girichev ◽  
Anatolii N. Rykov ◽  
Timo Glodde ◽  
Yury Vishnevskiy
Keyword(s):  
Molecular Structure ◽  
Electron Diffraction ◽  
Structure Refinement ◽  
Diffraction Method ◽  
Detailed Examination ◽  
Gas Electron Diffraction ◽  
Electron Diffraction Data ◽  
Data Sets ◽  
Background Elimination ◽  
Diffraction Patterns

<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>

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