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.

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.

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).

Essential features of the polytypic charoite-96 structure compared to charoite-90

2011 ◽  
Vol 75 (6) ◽  
pp. 2833-2846 ◽  
Author(s):  
I. V. Rozhdestvenskaya ◽  
E. Mugnaioli ◽  
M. Czank ◽  
W. Depmeier ◽  
U. Kolb ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Ab Initio ◽  
Direct Methods ◽  
Diffraction Tomography ◽  
Space Group ◽  
Sakha Republic ◽  
Alkaline Intrusion ◽  
Different Types

AbstractCharoite, ideally (K,Sr,Ba,Mn)15–16(Ca,Na)32[(Si70(O,OH)180)](OH,F)4·nH20, is a rock-forming mineral from the Murun massif in Yakutia, Sakha Republic, Siberia, Russia, where it occurs in a unique alkaline intrusion. Charoite occurs as four different polytypes, which are commonly intergrown in nanocrystallme fibres. We report the structure of charoite-96 (a = 32.11(6), b = 19.77(4), c = 7.23(1) Å, β = 95.85(9)°, V = 4565(24) Å3, space group P21/m), which was solved ab initio by direct methods on the basis of 2676 unique electron diffraction reflections collected by automated diffraction tomography and refined to R1/wR2 = 0.34/0.37. The structure of charoite-96 is related to that of the charoite-90, which was also solved recently. Both structures are composed of three different types of dreier silicate chains running along [001] and separated by ribbons of edge-sharing Ca- and Na-centred octahedra. In the structure of charoite-96, adjacent blocks formed by three different silicate chains and stacked along the x axis, are shifted by a translation of 1/2 c. The shifts involve a hybrid dreier quadruple chain, [Si17O43]18– and a double dreier chain, [Si6O17]10–. In charoite-90 adjacent blocks are stacked without shifts.

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 .

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