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.

Ab initio structure determination of interlayer expanded zeolites by single crystal rotation electron diffraction

2014 ◽  
Vol 43 (27) ◽  
pp. 10593-10601 ◽  
Author(s):  
Peng Guo ◽  
Leifeng Liu ◽  
Yifeng Yun ◽  
Jie Su ◽  
Wei Wan ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Single Crystal ◽  
Ab Initio ◽  
Diffraction Data ◽  
Structure Determination ◽  
Electron Diffraction Data ◽  
Crystal Rotation ◽  
Ab Initio Structure ◽  
Crystal Electron

Rotation electron diffraction (RED) combines the beam tilt and goniometer tilt to obtain single crystal electron diffraction data, which has been used forab initiostructure determination of interlayer expanded zeolites.

scholarly journals Quasicrystal approximants solved by Rotation Electron Diffraction (RED)

2014 ◽  
Vol 70 (a1) ◽  
pp. C1195-C1195 ◽  
Author(s):  
Sven Hovmöller ◽  
Devinder SINGH ◽  
Wei Wan ◽  
Yifeng Yun ◽  
Benjamin Grushko ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Data Processing ◽  
Single Crystal ◽  
Crystal Structures ◽  
Reciprocal Lattice ◽  
Electron Diffraction Data ◽  
Data Set ◽  
X Ray ◽  
X Ray Crystallography ◽  
3D Electron

We have developed single crystal electron diffraction for powder-sized samples, i.e. < 0.1μm in all dimensions. Complete 3D electron diffraction is collected by Rotation Electron Diffraction (RED) in about one hour. Data processing takes another hour. The crystal structures are solved by standard crystallographic techniques. X-ray crystallography requires crystals several micrometers big. For nanometer sized crystals, electron diffraction and electron microscopy (EM) are the only possibilities. Modern transmission EMs are equipped with the two things that are necessary for turning them into automatic single crystal diffractometers; they have CCD cameras and all lenses and the sample stage are computer-controlled. Two methods have been developed for collecting complete (except for a missing cone) 3D electron diffraction data; the Rotation Electron Diffraction (RED) [1] and Automated Electron Diffraction Tomography (ADT) by Kolb et al. [2]. Because of the very strong interaction between electrons and matter, an electron diffraction pattern with visible spots is obtained in one second from a submicron sized crystal in the EM. By collecting 1000-2000 electron diffraction patterns, a complete 3D data set is obtained. The geometry in RED is analogous to the rotation method in X-ray crystallography; the sample is rotated continuously along one rotation axis. The data processing results in a list of typically over 1000 reflections with h,k,l and Intensity. The unit cell is typically obtained correctly to within 1%. Space group determination is done as in X-ray crystallography from systematically absent reflections, but special care must be taken because occasionally multiple electron diffraction can give rise to very strong forbidden reflections. At +/-60° tilt with 0.1° steps, a complete data collection will be some 1200 frames. With one second exposures this takes about one hour. There is no need to align the crystal orientation. The reciprocal lattice can be rotated and displayed at any direction of view. Sections such as hk0, hk1, hk2, h0l and so on can easily be cut out and displayed. We have solved over 50 crystal structures by RED in one year. These include the most complex zeolites ever solved and quasicrystal approximants, such as the pseudo-decagonal approximants PD2 [3] and PD1 in AlCoNi. Observed and calculated sections of reciprocal space (cut at 1.0Å) are shown in Fig. 1. Notice the 10-fold symmetry of strong reflections.

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).

Challenging structure determination from powder diffraction data: two pharmaceutical salts and one cocrystal with Z′ = 2

2019 ◽  
Vol 234 (4) ◽  
pp. 257-268 ◽  
Author(s):  
Carina Schlesinger ◽  
Michael Bolte ◽  
Martin U. Schmidt
Keyword(s):  
Single Crystal ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Real Space ◽  
Powder Diffraction Data ◽  
The Real ◽  
Pharmaceutical Salts ◽  
Structure Solution ◽  
Space Method

Abstract Structure solution of molecular crystals from powder diffraction data by real-space methods becomes challenging when the total number of degrees of freedom (DoF) for molecular position, orientation and intramolecular torsions exceeds a value of 20. Here we describe the structure determination from powder diffraction data of three pharmaceutical salts or cocrystals, each with four molecules per asymmetric unit on general position: Lamivudine camphorsulfonate (1, P 21, Z=4, Z′=2; 31 DoF), Theophylline benzamide (2, P 41, Z=8, Z′=2; 23 DoF) and Aminoglutethimide camphorsulfonate hemihydrate [3, P 21, Z=4, Z′=2; 31 DoF (if the H2O molecule is ignored)]. In the salts 1 and 3 the cations and anions have two intramolecular DoF each. The molecules in the cocrystal 2 are rigid. The structures of 1 and 2 could be solved without major problems by DASH using simulated annealing. For compound 3, indexing, space group determination and Pawley fit proceeded without problems, but the structure could not be solved by the real-space method, despite extensive trials. By chance, a single crystal of 3 was obtained and the structure was determined by single-crystal X-ray diffraction. A post-analysis revealed that the failure of the real-space method could neither be explained by common sources of error such as incorrect indexing, wrong space group, phase impurities, preferred orientation, spottiness or wrong assumptions on the molecular geometry or other user errors, nor by the real-space method itself. Finally, is turned out that the structure solution failed because of problems in the extraction of the integrated reflection intensities in the Pawley fit. With suitable extracted reflection intensities the structure of 3 could be determined in a routine way.

scholarly journals Procedure and Computer Programs for the Structure Determination of Gaseous Molecules from Electron Diffraction Data.

1969 ◽  
Vol 23 ◽  
pp. 3224-3234 ◽  
Author(s):  
B. Andersen ◽  
H. M. Seip ◽  
T. G. Strand ◽  
R. Stølevik ◽  
Gunner Borch ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Computer Programs ◽  
Electron Diffraction Data

STRUCTURE DETERMINATION OF THE Ge(111)-(3×1)Ag SURFACE RECONSTRUCTION

1999 ◽  
Vol 06 (06) ◽  
pp. 1061-1065 ◽  
Author(s):  
D. GROZEA ◽  
E. BENGU ◽  
C. COLLAZO-DAVILA ◽  
L. D. MARKS
Keyword(s):  
Electron Diffraction ◽  
Surface Reconstruction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Heavy Atom ◽  
Direct Methods ◽  
Electron Diffraction Data ◽  
Transmission Electron ◽  
First Time

For the first time, during the investigation of the Ag submonolayer on the Ge(111) system, large, independent domains of the Ge (111)-(3×1) Ag phase were imaged and investigated. Previous studies have reported it only as small insets between Ge (111)-(4×4) Ag and Ge (111)- c (2×8) domains. The transmission electron diffraction data were analyzed using a Direct Methods approach and "heavy-atom holography," with the result of an atomic model of the structure similar to that of Ge (111)-(3×1) Ag .

scholarly journals A tutorial for learning and teaching macromolecular crystallography

2008 ◽  
Vol 41 (6) ◽  
pp. 1161-1172 ◽  
Author(s):  
Annette Faust ◽  
Santosh Panjikar ◽  
Uwe Mueller ◽  
Venkataraman Parthasarathy ◽  
Andrea Schmidt ◽  
...  
Keyword(s):  
Data Collection ◽  
Data Processing ◽  
Diffraction Data ◽  
Structure Determination ◽  
Macromolecular Crystallography ◽  
Data Set ◽  
Learning And Teaching

Five experiments have been designed to be used for teaching macromolecular crystallography. The three proteins used in this tutorial are all commercially available; they can be easily and reproducibly crystallized and mounted for diffraction data collection. For each of the five experiments the raw images and the processed data of a sample diffraction data set as well as the refined coordinates and phases are provided for teaching the steps of data processing and structure determination.

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