Serial electron crystallography: merging diffraction data through rank aggregation

2017 ◽  
Vol 50 (3) ◽  
pp. 885-892 ◽  
Author(s):  
Stef Smeets ◽  
Wei Wan

Serial electron crystallography is being developed as an alternative way to collect diffraction data on beam-sensitive polycrystalline materials. Merging serial diffraction data from a large number of snapshots is difficult, and the dynamical nature of electron diffraction prevents the use of existing methods that rely on precise measurement of kinematical reflection intensities. To overcome this problem, an alternative method that uses rank aggregation to combine the rankings of relative reflection intensities from a large number of snapshots has been developed. The method does not attempt to accurately model the diffraction intensity, but instead optimizes the most likely ranking of reflections. As a consequence, the problem of scaling individual snapshots is avoided entirely, and requirements for the data quality and precision are low. The method works best when reflections can be fully measured, but the benefit over measuring partial intensities is small. Since there were no experimental data available for testing rank-based merging, the validity of the approach was assessed through a series of simulated serial electron diffraction datasets with different numbers of frames and varying degrees of errors. Several programs have been used to show that these rank-merged simulated data are good enough forab initiostructure determination using several direct methods programs.

Author(s):  
Douglas L. Dorset

AbstractSingle crystal electron diffraction intensity data, analyzed by direct methods for determining crystallographic phases, have been employed to seek differences between the crystal structures of calcined MCM-22 and MCM-49. A direct comparison of


2018 ◽  
Vol 51 (5) ◽  
pp. 1262-1273 ◽  
Author(s):  
Stef Smeets ◽  
Xiaodong Zou ◽  
Wei Wan

Serial electron crystallography has been developed as a fully automated method to collect diffraction data on polycrystalline materials using a transmission electron microscope. This enables useful data to be collected on materials that are sensitive to the electron beam and thus difficult to measure using the conventional methods that require long exposure of the same crystal. The data collection strategy combines goniometer translation with electron beam shift, which allows the entire sample stage to be probed. At each position of the goniometer, the locations of the crystals are identified using image recognition techniques. Diffraction data are then collected on each crystal using a quasi-parallel focused beam with a predefined size (usually 300–500 nm). It is shown that with a fast and sensitive Timepix hybrid pixel area detector it is possible to collect diffraction data of up to 3500 crystals per hour. These data can be indexed using a brute-force forward-projection algorithm. Results from several test samples show that 100–200 frames are enough for structure determination using direct methods or dual-space methods. The large number of crystals examined enables quantitative phase analysis and automatic screening of materials for known and unknown phases.


Author(s):  
Douglas L. Dorset

AbstractThe prospect of carrying out quantitative crystal structure analyses by direct methods with electron diffraction intensity data from zeolites is evaluated for two related materials: ZSM-5 and ZSM-11. The stacked plate-like arrays of ZSM-5 induce intensity perturbations from secondary electron scattering; nevertheless, the T-site positions can be found by direct methods. Intensity data from smaller ZSM-11 microcrystals are more favorable for


1999 ◽  
Vol 06 (06) ◽  
pp. 1061-1065 ◽  
Author(s):  
D. GROZEA ◽  
E. BENGU ◽  
C. COLLAZO-DAVILA ◽  
L. D. MARKS

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 .


2013 ◽  
Vol 46 (4) ◽  
pp. 1017-1023 ◽  
Author(s):  
Stef Smeets ◽  
Lynne B. McCusker ◽  
Christian Baerlocher ◽  
Enrico Mugnaioli ◽  
Ute Kolb

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.


Author(s):  
J. R. FRYER

It is shown that it is possible to obtain structural information from small (<100 nm) phthalocyanine crystals by using crystallographic direct phasing methods applied to electron diffraction data. This technique is both quantitative and does not suffer from the difficulties associated with high-resolution electron microscopy. Structural information has been obtained from both tetra- and octa chloro-copper phthalocyanines, and the results compared with the hydrogenated and perchloro members of the series.


Author(s):  
Ron Anderson ◽  
M. J. Carr ◽  
V. L. Himes ◽  
A. D. Mighell

The identification of unknown phases using diffraction data and the JCPDS-ICDD Powder Diffraction File (PDF)[1] is a three-step process. First, the Search step rapidly screens the entire PDF to produce a list of candidate solutions that correspond to the unknown phase’s d-spacings and chemistry. Second, the Match step examines closely every aspect of each phase in the candidate list, vs. the unknown, to make the identification. Third, the Decision step: does the solution found make crystal-chemical-thermodynamic sense? A hindrance to the identification process for electron diffraction applications is that the PDF consists of X-ray powder diffraction data. There are two problems: First, while X-ray diffraction intensity data compares well to electron diffraction intensities for randomly-oriented, small-grained specimens, in the main, intensities from the two methods are not the same. The differing intensities exacerbate the problem of unknown phase searching for electron diffraction because X-ray derived Search/Matching methods rely heavily on intensity information.


Author(s):  
Douglas L. Dorset

Recently the direct 3D determination of an aluminosilicate structure was reported based on high-voltage, high resolution electron microscopy of thin slices representing several projections of the crystal. It was particularly interesting that the relatively light oxygen atom positions could be visualized along with those of heavier components (Al, Si, Fe) in the staurolite structure.Although this direct visualization of a crystal structure in the electron microscope certainly is a tour de force, representing a significant advance in microscopic instrumentation and technique, the electron crystallography of silicate structures at atomic resolution is, in itself, not particularly a new field of investigation. For example, in his book, B. B. Zvyagin outlines how he was able to use texture electron diffraction intensity data from several layer silicates in order to determine their crystal structures via interpretation of the Patterson function or construction of reasonable layer models suggested by the atomic stoichiometry.It is unfortunate that many of the early Russian electron diffraction structure analyses have been overlooked or even ignored by the crystallographic community.


Author(s):  
Z. G. Li ◽  
L. Liang ◽  
R. L. Harlow ◽  
K.E. Lehman ◽  
N. Herron

Recently, CCD camera has been more and more used in the electron microscopy particularly for electron crystallography [1]. Use of CCD camera in this field as a recording medium possesses many significant advantages over conventional photographic films. A CCD camera has a very high dynamic range (reliable) and produces images directly in digital form which can be conveniently processed and transferred. We have initiated a program to obtain crystal structural information of plate-like materials by processing electron diffraction data from a CCD detector. As part of our program, we have developed a complete and routine procedure to convert images to diffraction data (h, k, l’s and intensities).Figure 1 is a schematic representation of the procedure. Images are initially obtained using a 1024×1024 Gatan CCD camera (model 794) which was attached to JEM-2000EX electron microscope. The collection of the images is controlled by a MAC computer which also stores the data and allows the data to be viewed. Then, the digitized electron diffraction patterns are transferred to a Sun station computer where, using Khoros software, the CCD images are processed. The Khoros system is a very complete image analysis and image processing software developed by University of New Mexico [2].


Author(s):  
D. L. Dorset ◽  
M. P. McCourt

AbstractThe x-ray crystal structure of bacteriorhodopsin was used to generate model electron diffraction amplitudes and phases, referring to an electron crystallographic determination to isolate the details of a 52 Å-thick single layer in plane group p3 will cell constants:


Sign in / Sign up

Export Citation Format

Share Document