scholarly journals Discrimination of Aluminum from Silicon by Electron Crystallography with the JUNGFRAU Detector

Crystals ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1148
Author(s):  
Erik Fröjdh ◽  
Julian T. C. Wennmacher ◽  
Przemyslaw Rzepka ◽  
Aldo Mozzanica ◽  
Sophie Redford ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Structure Function ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Electron Diffraction Data ◽  
Chiral Molecules ◽  
Type Zeolite ◽  
Energy Discrimination ◽  
Further Development

The crystal structure of a chemical compound serves several purposes: its coordinates represent three-dimensional information about the connectivity between the atoms; it is the only technique that determines the absolute configuration of chiral molecules; it enables determining structure–function relations; and crystallographic data at atomic resolution distinguish between element types and serve as a confirmation of synthesis protocols. Here, we collected electron diffraction data from albite and from a Linde Type A (LTA) type zeolite. Both compounds are aluminosilicates with well-defined silicon and aluminum crystallographic sites. Data were recorded with the “adJUstiNg Gain detector FoR the Aramis User station” (JUNGFRAU detector) and we made use of its capability of energy discrimination to suppress noise. For both compounds, crystallographic refinement distinguishes correctly between silicon and aluminum, even though these elements have very similar electron scattering factors. These results highlight the quality of the electron diffraction data and the reliability of the models for chemical interpretation. Further development in this direction will provide enormous opportunities for structure–function studies by 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.

scholarly journals Gently does it for submicron crystals

eLife ◽  
2013 ◽  
Vol 2 ◽  
Author(s):  
Oliver B Zeldin ◽  
Axel T Brunger
Keyword(s):  
Electron Beam ◽  
Protein Structure ◽  
Electron Diffraction ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Electron Diffraction Data ◽  
Large Numbers ◽  
Diffraction Patterns ◽  
Weak Electron

A protein structure has been refined with electron diffraction data obtained by using a very weak electron beam to collect large numbers of diffraction patterns from a few sub-micron-sized three-dimensional crystals.

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.

scholarly journals A Medipix quantum area detector allows rotation electron diffraction data collection from submicrometre three-dimensional protein crystals

2013 ◽  
Vol 69 (7) ◽  
pp. 1223-1230 ◽  
Author(s):  
Igor Nederlof ◽  
Eric van Genderen ◽  
Yao-Wang Li ◽  
Jan Pieter Abrahams
Keyword(s):  
Electron Diffraction ◽  
Data Collection ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Protein Crystal ◽  
Protein Crystals ◽  
Electron Diffraction Data ◽  
Single Shot ◽  
X Ray ◽  
Area Detector

When protein crystals are submicrometre-sized, X-ray radiation damage precludes conventional diffraction data collection. For crystals that are of the order of 100 nm in size, at best only single-shot diffraction patterns can be collected and rotation data collection has not been possible, irrespective of the diffraction technique used. Here, it is shown that at a very low electron dose (at most 0.1 e− Å−2), a Medipix2 quantum area detector is sufficiently sensitive to allow the collection of a 30-frame rotation series of 200 keV electron-diffraction data from a single ∼100 nm thick protein crystal. A highly parallel 200 keV electron beam (λ = 0.025 Å) allowed observation of the curvature of the Ewald sphere at low resolution, indicating a combined mosaic spread/beam divergence of at most 0.4°. This result shows that volumes of crystal with low mosaicity can be pinpointed in electron diffraction. It is also shown that strategies and data-analysis software (MOSFLMandSCALA) from X-ray protein crystallography can be used in principle for analysing electron-diffraction data from three-dimensional nanocrystals of proteins.

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.

EDIFF: a program for automated unit-cell determination and indexing of electron diffraction data

2011 ◽  
Vol 44 (5) ◽  
pp. 1132-1136 ◽  
Author(s):  
Linhua Jiang ◽  
Dilyana Georgieva ◽  
Jan Pieter Abrahams
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Unit Cell ◽  
Electron Diffraction Data ◽  
Cell Determination ◽  
Diffraction Patterns ◽  
Inorganic Molecules ◽  
User Friendly

EDIFFis a new user-friendly software suite for unit-cell determination of three-dimensional nanocrystals from randomly oriented electron diffraction patterns with unknown independent orientations. It can also be used for three-dimensional cell reconstruction from diffraction tilt series. In neither case is exact knowledge of the angular relationship between the patterns required. The unit cell can be validated and the crystal system assigned.EDIFFcan index the reflections in electron diffraction patterns. Thus,EDIFFcan be employed as a first step in reconstructing the three-dimensional atomic structure of organic and inorganic molecules and of proteins from diffraction data. An example illustrates the viability of theEDIFFapproach.

scholarly journals UsingFOCUSto solve zeolite structures from three-dimensional electron diffraction data

2013 ◽  
Vol 46 (4) ◽  
pp. 1017-1023 ◽  
Author(s):  
Stef Smeets ◽  
Lynne B. McCusker ◽  
Christian Baerlocher ◽  
Enrico Mugnaioli ◽  
Ute Kolb
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Direct Methods ◽  
Electron Diffraction Data ◽  
Chemical Information ◽  
Data Sets ◽  
Dimensional Electron ◽  
Specific Chemical ◽  
Structure Solution

The programFOCUS[Grosse-Kunstleve, McCusker & Baerlocher (1997).J. Appl. Cryst.30, 985–995] was originally developed to solve zeolite structures from X-ray powder diffraction data. It uses zeolite-specific chemical information (three-dimensional 4-connected framework structure with known bond distances and angles) to supplement the diffraction data. In this way, it is possible to compensate, at least in part, for the ambiguity of the reflection intensities resulting from reflection overlap, and the program has proven to be quite successful. Recently, advances in electron microscopy have led to the development of automated diffraction tomography (ADT) and rotation electron diffraction (RED) techniques for collecting three-dimensional electron diffraction data on very small crystallites. Reasoning that such data are also less than ideal (dynamical scattering, low completeness, beam damage) and that this can lead to failure of structure solution by conventional direct methods for very complex zeolite frameworks,FOCUSwas modified to accommodate electron diffraction data. The modified program was applied successfully to five different data sets (four ADT and one RED) collected on zeolites of different complexities. One of these could not be solved completely by direct methods but emerged easily in theFOCUStrials.

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.

SIR2011: a new package for crystal structure determination and refinement

2012 ◽  
Vol 45 (2) ◽  
pp. 357-361 ◽  
Author(s):  
Maria Cristina Burla ◽  
Rocco Caliandro ◽  
Mercedes Camalli ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Protein Structures ◽  
Three Dimensional ◽  
Molecular Geometry ◽  
Electron Diffraction Data ◽  
Medium Size ◽  
Molecular Replacement ◽  
Density Maps ◽  
Difficult Cases

SIR2011, the successor ofSIR2004, is the latest program of theSIRsuite. It can solveab initiocrystal structures of small- and medium-size molecules, as well as protein structures, using X-ray or electron diffraction data. With respect to the predecessor the program has several new abilities:e.g.a new phasing method (VLD) has been implemented, it is able to exploit prior knowledge of the molecular geometryviasimulated annealing techniques, it can use molecular replacement methods for solving proteins, it includes new tools like free lunch and new approaches for electron diffraction data, and it visualizes three-dimensional electron density maps. The graphical interface has been further improved and allows the straightforward use of the program even in difficult cases.

Sign in / Sign up

Export Citation Format

Share Document