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Development of serial electron crystallography methodology for quantitative phase analysis

English title Development of serial electron crystallography methodology for quantitative phase analysis
Applicant Smeets Stef
Number 177761
Funding scheme Advanced Postdoc.Mobility
Research institution Department of Materials and Environmental Chemistry Stockholm University
Institution of higher education Institution abroad - IACH
Main discipline Material Sciences
Start/End 01.01.2018 - 31.12.2018
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Keywords (5)

Polycrystalline materials; Structure determination; Serial crystallography; Electron diffraction; Quantitative phase analysis

Lay Summary (German)

Lead
Viele industriell und kommerziell wichtige Materialien, wie Katalysatoren, Pharmazeutika, Mineralien oder Halbleiter werden in polykristalliner Form synthetisiert und eingesetzt. Die Kenntnis der Anordnung der Atome in einem Material (die sogenannte Kristallstruktur) ist der Schlüssel für das Verständnis der chemischen und vor allem auch der physikalischen Eigenschaften dieser Materialien. Dies ermöglicht es dann auch, diese Eigenschaften durch gezielte Änderungen der Kristallstruktur zu verbessern. Es ist daher wichtig, Methoden zu entwickeln um solche Strukturen zu bestimmen. Die Kristallstrukturbestimmung von einem polykristallinen Material ist indes keine triviale Aufgabe und das Interesse an Methoden, mit denen die immer komplizierteren Materialien und deren Strukturen untersucht werden können, ist dementsprechend hoch.
Lay summary
Das Ziel dieses Projektes ist es, einen neuen Ansatz zu entwickeln, der es möglich macht, die Kristallstrukturen von komplexen polykristallinen Materialien zu bestimmen, insbesondere von solchen, die nur wenige Nanometer grosse Kristallen aufweisen. Alle Untersuchungsmethoden basieren auf Experimenten mit Röntgen- oder Elektronenstrahlen und die Strahlungsempfindlichkeit der Proben stellt bei den bestehenden Methoden ein grosses Problem dar. Die "Serial Snapshot Crystallography" wurde entwickelt um die Strukturen von komplizierten Proteinen mit den modernen Röntgenlaser zu lösen. Mit dieser Technik werden Beugungsbilder aus einer Vielzahl Kristallen zu einem einzigen Datensatz kombiniert. Diese Idee soll nun übertragen werden auf das Sammeln von dreidimensionalen Elektronenbeugungsdaten mit einem Elektronenmikroskop. Dies wird es ermöglichen, Strukturdaten aus einer großen Anzahl Kristallen zu sammeln, so dass die Wechselwirkung zwischen den Kristallen untersucht werden kann (z. B. Mineralien, Zemente, Pharmazeutika usw.).
Direct link to Lay Summary Last update: 16.12.2017

Responsible applicant and co-applicants

Publications

Publication
Synthesis and Structure Determination of SCM-15: A 3D Large Pore Zeolite with Interconnected Straight 12×12×10-Ring Channels
Luo Yi, Smeets Stef, Wang Zhendong, Sun Junliang, Yang Weimin (2019), Synthesis and Structure Determination of SCM-15: A 3D Large Pore Zeolite with Interconnected Straight 12×12×10-Ring Channels, in Chemistry - A European Journal, 0.
Quantitative Phase Analysis for Carbide Characterization in Steel Using Automated Electron Diffraction
Smeets Stef, Ångström Jonas, Olsson Claes-Olof A. (2019), Quantitative Phase Analysis for Carbide Characterization in Steel Using Automated Electron Diffraction, in steel research international, 90(1), 1800300-1800300.
High-throughput continuous rotation electron diffraction data acquisition via software automation
Cichocka Magdalena Ola, Ångström Jonas, Wang Bin, Zou Xiaodong, Smeets Stef (2018), High-throughput continuous rotation electron diffraction data acquisition via software automation, in Journal of Applied Crystallography, 51(6), 1652-1661.
Site-Specific Adsorption of CO 2 in Zeolite NaK-A
Rzepka Przemyslaw, Bacsik Zoltán, Smeets Stef, Hansen Thomas C., Hedin Niklas, Wardecki Dariusz (2018), Site-Specific Adsorption of CO 2 in Zeolite NaK-A, in The Journal of Physical Chemistry C, 122(47), 27005-27015.
Serial electron crystallography for structure determination and phase analysis of nanocrystalline materials
Smeets Stef, Zou Xiaodong, Wan Wei (2018), Serial electron crystallography for structure determination and phase analysis of nanocrystalline materials, in Journal of Applied Crystallography, 51(5), 1262-1273.
CO 2 -Induced Displacement of Na + and K + in Zeolite |NaK|-A
Rzepka Przemyslaw, Wardecki Dariusz, Smeets Stef, Müller Melanie, Gies Hermann, Zou Xiaodong, Hedin Niklas (2018), CO 2 -Induced Displacement of Na + and K + in Zeolite |NaK|-A, in The Journal of Physical Chemistry C, 122(30), 17211-17220.
Multidimensional Disorder in Zeolite IM-18 Revealed by Combining Transmission Electron Microscopy and X-ray Powder Diffraction Analyses
Cichocka Magdalena O., Lorgouilloux Yannick, Smeets Stef, Su Jie, Wan Wei, Caullet Philippe, Bats Nicolas, McCusker Lynne B., Paillaud Jean-Louis, Zou Xiaodong (2018), Multidimensional Disorder in Zeolite IM-18 Revealed by Combining Transmission Electron Microscopy and X-ray Powder Diffraction Analyses, in Crystal Growth & Design, 18(4), 2441-2451.

Datasets

serial electron diffraction data

Author Smeets, Stef
Publication date 24.01.2018
Persistent Identifier (PID) 10.5281/zenodo.1158420.
Repository Zenodo
Abstract
Raw serial electron diffraction data sets from 6 samples: Zeolite A Zeolite Y Ge-BEC Mordenite ECR-18 CAU-36(Co)Each zip file contains at least 3 directories: calib: contains the calibration files for the experiment data: contains the raw diffraction data for all the identified crystals in hdf5 format images: contains the image data used to locate crystals in hdf5 formatExperimental parameters (such as the crystal coordinates) are stored in the attributes on the data files. Worked out examples have been included for samples 1 and 2 in a jupyter notebook. The Python code to process the data can be found in the problematic-0.1.0.zip folder or on http://github.com/stefsmeets/problematic

Continuous rotation electron diffraction data for Zeolite Mordenite

Author Smeets, Stef; Cichocka, Magdalena
Publication date 26.07.2018
Persistent Identifier (PID) 10.5281/zenodo.1321880
Repository Zenodo
Abstract
Raw continuous rotation electron diffraction data for mordenite: - mordenite_cRED_1.zip - mordenite_cRED_2.zipThe zip file contains 3 directories - SMV: Diffraction data (stretch correction applied) in SMV format - Tiff: Raw diffraction data in 16-bit unsigned integer TIFF format - Defocused images in 16-bit unsigned integer TIFF formatExperimental parameters are stored in the header files of the SMV images, and in the file cRED_log.txtThe SMV data can be processed using XDS.Raw serial electron diffraction data sets for mordenite: - mordenite_SerialED.zipThe zip file contains at least 3 directories: - calib: contains the calibration files for the experiment - data: contains the raw diffraction data for all the identified crystals in hdf5 format - images: contains the image data used to locate crystals in hdf5 formatExperimental parameters (such as the crystal coordinates) are stored in the attributes on the data files. The Python code to process the data can be found in the problematic-0.1.0.zip folder or on http://github.com/stefsmeets/problematicPrediction scores for all diffraction patterns are given in `learning.csv`

Instamatic

Author Smeets, Stef; Wang, Bin; Cichocka, Magdalena; Ångström, Jonas; Wan, Wei
Publication date 07.12.2018
Persistent Identifier (PID) 10.5281/zenodo.1090388
Repository Zenodo
Abstract
Instamatic is a Python program that is being developed with the aim to automate the collection of electron diffraction data. At the core is a Python library for transmission electron microscope experimental control with bindings for the JEOL microscope and interfaces to the gatan/timepix cameras. Routines have been implemented for collecting serial electron diffraction (serialED), continuous rotation electron diffraction (cRED), and stepwise rotation electron diffraction (RED) data.Some of the methods implemented in Instamatic are described in: M.O. Cichocka, J. Ångström, B. Wang, X. Zou, and S. Smeets, High-throughput continuous rotation electron diffraction data acquisition via software automation, J. Appl. Cryst. (2018). 51, 1652-1661, S. Smeets, X. Zou, and W. Wan, Serial electron crystallography for structure determination and phase analysis of nanocrystalline materials, J. Appl. Cryst. (2018). 51, 1262-1273TEMs supported: JEOL JEM-2100 (tested), JEOL JEM-1400/3100/3200 (any JEOL TEM with the TEMCOM library)Cameras supported: ASI Timepix (including live-view GUI), Gatan cameras through DM plugin (no GUI)A DM script for collecting cRED data on a OneView camera (or any Gatan camera) can be found in the dmscript directory.

Collaboration

Group / person Country
Types of collaboration
Sandvik Materials Technology (Claes Olsson) Sweden (Europe)
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
European Crystallographic Meeting 31 Talk given at a conference High-Silica Zeolite SSZ-70: New Understanding of a Successful Catalytic Material 22.08.2018 Oviedo, Spain Smeets Stef;
European Powder Diffraction Conference 16 Talk given at a conference Structure determination of polycrystalline materials using X-rays and electrons 01.07.2018 Edinburgh, Great Britain and Northern Ireland Smeets Stef;


Awards

Title Year
EPDIC Award for Young Scientists for outstanding scientific achievements in the field of powder diffraction 2018

Associated projects

Number Title Start Funding scheme
165282 Development of serial crystallography methods for structure solution of polycrystalline materials using electron diffraction 01.01.2016 Early Postdoc.Mobility

Abstract

Many industrially and commercially important materials, such as catalysts, pharmaceuticals, minerals, building materials, and semiconductors, are produced and used in polycrystalline form. Understanding the regular arrangement of atoms within the crystal structure is key to understanding why and how these materials function, and to improve on the structural characteristics that make them useful. Sometimes the specific function of a material even depends on a precise composition of several phases. It is therefore essential to develop methods that allow the compositions and structures of these materials to be unraveled and studied. Our initial attempt at this problem lead to the development of serial electron crystallography (SNSF project 165282); a technique that enables automated collection of diffraction patterns on thousands of individual crystals on a transmission electron microscope (TEM). These electron diffraction data contain information about the orientation of a crystal, its phase, and its crystal structure. Until now, our work has been concentrated developing the data collection strategy, and optimizing data processing and merging algorithms for accurate structure determination. Phase analysis, on the other hand, is less demanding on the data quality than structure determination, but of high interest for industrial applications, e.g. screening and quality control. Phase analysis is typically the domain of X-ray powder diffraction (XPD). However, several characteristics are inherent to the material that can make the analysis of XPD data problematic, such as preferred orientation and reflection overlap from materials with low crystal symmetry and/or large unit cells. Serial electron diffraction data are collected crystal-by-crystal, and therefore free of this problem. The aim for this proposal is to extend the serial electron crystallography method to quantitative phase analysis, and to investigate the possibility of including energy-dispersive X-ray spectroscopy (EDS) data in the data collection routine to provide additional information. The method will be applied to cements, carbides, pharmaceuticals, and minerals. Ultimately, we hope to develop serial electron crystallography into a stand-alone technique that can be generally applicable for phase analysis, and structure determination of (beam-sensitive) materials. Electron microscopes are versatile enough that all kinds of data can be collected. By building on our serial electron crystallography platform, we expect to extend the capabilities of electron microscopes to include statistical analyses on a large number of crystals.
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