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.

Automated diffraction tomography combined with electron precession: a new tool for ab initio nanostructure analysis

2009 ◽  
Vol 1184 ◽  
Author(s):  
Ute Kolb ◽  
Tatiana Gorelik ◽  
Enrico Mugnaioli
Keyword(s):  
Electron Diffraction ◽  
Ab Initio ◽  
Crystal Structures ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Direct Methods ◽  
Electron Diffraction Data ◽  
Diffraction Tomography ◽  
Diffraction Mode ◽  
Structure Solution

AbstractThree-dimensional electron diffraction data was collected with our recently developed module for automated diffraction tomography and used to solve inorganic as well as organic crystal structures ab initio. The diffraction data, which covers nearly the full relevant reciprocal space, was collected in the standard nano electron diffraction mode as well as in combination with the precession technique and was subsequently processed with a newly developed automated diffraction analysis and processing software package. Non-precessed data turned out to be sufficient for ab initio structure solution by direct methods for simple crystal structures only, while precessed data allowed structure solution and refinement in all of the studied cases.

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.

Structure of the in on SI(111)4X1 Surface Determined by Applying Direct Phasing Methods to Transmission Electron Diffraction Data

1997 ◽  
Vol 3 (S2) ◽  
pp. 1041-1042
Author(s):  
C. Collazo-Davila ◽  
L. D. Marks ◽  
K. Nishii ◽  
Y. Tanishiro
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Direct Methods ◽  
Surface Structures ◽  
Electron Diffraction Data ◽  
Imaging Plate ◽  
Data Sets ◽  
Interface Formation ◽  
Transmission Electron Diffraction ◽  
Transmission Electron

Direct methods were applied to transmission electron diffraction data to solve the previously unknown In on Si(111)4x1 surface structure. The structure consists of zig-zag chains of In atoms separated by regions of silicon including dimer chains (Fig 1.). The 4x1 structure is one of several stable surface structures formed with increasing In coverages on the Si(111) surface. The √3x√3 structure consists of 1/3 of a monolayer of In, the √31x√31 occurs at a slightly higher coverage and the 4x1 structure appears before the formation of In islands on the surface . While the √3x√3 surface has been extensively studied, relatively little is known about the √31x√31 and 4x1 structures. Knowledge of the atomic positions in the 4x1 structure is an important step in understanding metal/semiconductor epitaxy and interface formation.Two data sets were used in this study -- the first recorded on film and reduced in Tokyo, the second recorded on Imaging Plate in Tokyo and reduced at Northwestern. Twenty-seven independent intensities were measured.

Crystal structure analysis of a star-shaped triazine compound: a combination of single-crystal three-dimensional electron diffraction and powder X-ray diffraction

2018 ◽  
Vol 74 (3) ◽  
pp. 287-294 ◽  
Author(s):  
Tatiana E. Gorelik ◽  
Jacco van de Streek ◽  
Herbert Meier ◽  
Lars Andernach ◽  
Till Opatz
Keyword(s):  
Crystal Structure ◽  
Electron Diffraction ◽  
Single Crystal ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Electron Diffraction Data ◽  
Dimensional Electron ◽  
X Ray Diffraction ◽  
Diffraction Profile ◽  
X Ray

The solid-state structure of star-shaped 2,4,6-tris{(E)-2-[4-(dimethylamino)-phenyl]ethenyl}-1,3,5-triazine is determined from a powder sample by exploiting the respective strengths of single-crystal three-dimensional electron diffraction and powder X-ray diffraction data. The unit-cell parameters were determined from single crystal electron diffraction data. Using this information, the powder X-ray diffraction data were indexed, and the crystal structure was determined from the powder diffraction profile. The compound crystallizes in a noncentrosymmetric space group,P212121. The molecular conformation in the crystal structure was used to calculate the molecular dipole moment of 3.22 Debye, which enables the material to show nonlinear optical effects.

scholarly journals Ab initiostructure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector

2016 ◽  
Vol 72 (2) ◽  
pp. 236-242 ◽  
Author(s):  
E. van Genderen ◽  
M. T. B. Clabbers ◽  
P. P. Das ◽  
A. Stewart ◽  
I. Nederlof ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Room Temperature ◽  
Dynamic Range ◽  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
Direct Methods ◽  
Liquid Nitrogen Temperature ◽  
High Dynamic Range ◽  
Electron Diffraction Data ◽  
High Signal

Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enablingab initiophasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e− Å−2 s−1) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS,SHELX) and for electron crystallography (ADT3D/PETS,SIR2014).

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 On the Completeness of Three-Dimensional Electron Diffraction Data for Structural Analysis of Metal-Organic Frameworks

2021 ◽  
Author(s):  
Meng Ge ◽  
Taimin Yang ◽  
Yanzhi Wang ◽  
Francesco Carraro ◽  
Weibin Liang ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Electron Diffraction ◽  
Structural Model ◽  
Metal Organic Frameworks ◽  
Three Dimensional ◽  
Electron Diffraction Data ◽  
Dimensional Electron ◽  
Data Completeness ◽  
Continuous Rotation ◽  
Metal Organic

<p>Three-dimensional electron diffraction (3DED) has been proven as an effective and accurate method for structure determination of nano-sized crystals. In the past decade, the crystal structures of various new complex metal-organic frameworks (MOFs) have been revealed by 3DED, which has been the key to understand their properties. However, due to the design of transmission electron microscopes (TEMs), one drawback of 3DED experiments is the limited tilt range of goniometer, which often leads to incomplete 3DED data, particularly when the crystal symmetry is low. This drawback can be overcome by high throughput data collection using continuous rotation electron diffraction (cRED), where data from a large number of crystals can be collected and merged. Here, we investigate the effects of improving completeness on structural analysis of MOFs. We use ZIF-EC1, a zeolitic imidazolate framework (ZIF), as an example. ZIF-EC1 crystallizes in a monoclinic system with a plate-like morphology. cRED data of ZIF-EC1 with different completeness and resolution were analyzed. The data completeness increased to 92.0% by merging ten datasets. Although the structures could be solved from individual datasets with a completeness as low as 44.5% and refined to a high precession (better than 0.04 Å), we demonstrate that a high data completeness could improve the structural model, especially on the electrostatic potential map. We further discuss the strategy adopted during data merging. We also show that ZIF-EC1 doped with cobalt can act as an efficient electrocatalyst for oxygen reduction reaction. </p>

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