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High-throughput continuous rotation electron diffraction data acquisition via software automation
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).ORCID iD: 0000-0002-7829-1974
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
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2018 (English)In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 51, no 6, p. 1652-1661Article in journal (Refereed) Published
Abstract [en]

Single-crystal electron diffraction (SCED) is emerging as an effective technique to determine and refine the structures of unknown nano-sized crystals. In this work, the implementation of the continuous rotation electron diffraction (cRED) method for high-throughput data collection is described. This is achieved through dedicated software that controls the transmission electron microscope and the camera. Crystal tracking can be performed by defocusing every nth diffraction pattern while the crystal rotates, which addresses the problem of the crystal moving out of view of the selected area aperture during rotation. This has greatly increased the number of successful experiments with larger rotation ranges and turned cRED data collection into a high-throughput method. The experimental parameters are logged, and input files for data processing software are written automatically. This reduces the risk of human error, and makes data collection more reproducible and accessible for novice and irregular users. In addition, it is demonstrated how data from the recently developed serial electron diffraction technique can be used to supplement the cRED data collection by automatic screening for suitable crystals using a deep convolutional neural network that can identify promising crystals through the corresponding diffraction data. The screening routine and cRED data collection are demonstrated using a sample of the zeolite mordenite, and the quality of the cRED data is assessed on the basis of the refined crystal structure.

Place, publisher, year, edition, pages
2018. Vol. 51, no 6, p. 1652-1661
Keywords [en]
single-crystal electron diffraction, high throughput, crystal screening, structure analysis
National Category
Inorganic Chemistry
Research subject
Inorganic Chemistry
Identifiers
URN: urn:nbn:se:su:diva-162656DOI: 10.1107/S1600576718015145ISI: 000451833600016OAI: oai:DiVA.org:su-162656DiVA, id: diva2:1268362
Available from: 2018-12-05 Created: 2018-12-05 Last updated: 2019-04-23Bibliographically approved
In thesis
1. Unraveling the structures of complex nanocrystalline materials by combining TEM and XRPD – development and application
Open this publication in new window or tab >>Unraveling the structures of complex nanocrystalline materials by combining TEM and XRPD – development and application
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Knowledge of the three-dimensional (3D) atomic structure of materials is essential to a fundamental understanding of their properties. The key to understanding the functionality of many materials, particularly those of commercial and industrial interest, is often hidden in the details at the nanoscale. For this reason, it is very important to choose the right strategy to analyze the structure of challenging materials with complex disordered framework structures, or of the layered materials that are the subject of this thesis. Structure analysis of beam-sensitive or uniquely disordered materials can be complicated. Although there are already existing methods such as X-ray powder diffraction (XRPD), the data may exhibit reflection overlap or other problems that make structure determination difficult. To overcome these limitations for nanocrystalline materials, complementary characterization techniques can be used. Here, I will focus on 3D electron crystallography (continuous rotation electron diffraction and high-resolution electron microscopy) methods that have grown during the past years as hybrid methods for structure determination. Based on the presented materials, I will also emphasize that any kind of challenges can be a driving force for method development.  Furthermore, some of the insights gained lead to better understanding of how to collect and process 3D electron diffraction data, which could be applied to make data collection of challenging samples easier and obtain higher quality structure refinements from the data. Finally, I will try to describe the general procedures for ab initio structure elucidation of disordered nanocrystals and layered materials.

Place, publisher, year, edition, pages
Stockholm: Department of Materials and Environmental Chemistry (MMK), Stockholm University, 2019. p. 82
Keywords
Structure determination, 3D electron diffraction, Complex materials, X-ray powder diffraction, Transmission electron microscopy
National Category
Inorganic Chemistry
Research subject
Inorganic Chemistry
Identifiers
urn:nbn:se:su:diva-162710 (URN)978-91-7797-532-8 (ISBN)978-91-7797-533-5 (ISBN)
Public defence
2019-02-08, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.

Available from: 2019-01-16 Created: 2018-12-07 Last updated: 2019-01-15Bibliographically approved
2. Development of rotation electron diffraction as a fully automated and accurate method for structure determination
Open this publication in new window or tab >>Development of rotation electron diffraction as a fully automated and accurate method for structure determination
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Over the past decade, electron diffraction methods have aroused more and more interest for micro-crystal structure determination. Compared to traditional X-ray diffraction, electron diffraction breaks the size limitation of the crystals studied, but at the same time it also suffers from much stronger dynamical effects. While X-ray crystallography has been almost thoroughly developed, electron crystallography is still under active development. To be able to perform electron diffraction experiments, adequate skills for using a TEM are usually required, which makes ED experiments less accessible to average users than X-ray diffraction. Moreover, the relatively poor data statistics from ED data prevented electron crystallography from being widely accepted in the crystallography community.

The thesis focused on both application and method development of continuous rotation electron diffraction (cRED) technique. The cRED method was first applied to a beam sensitive metal-organic framework sample, Co-CAU-36, and the structure was determined and refined within one working day. More importantly, the guest molecules in the pores were also located using only electron diffraction data. To facilitate general users to perform cRED data collection for useful data, software was developed to automate the overall data collection procedure. Through combination of hierarchical cluster analysis tools, the automatically collected data showed comparable quality to those from recent publications, and thus were useful for structure determination and even phase identification. To deal with dynamical refinement for ED data, a frame orientation refinement algorithm was designed to calculate accurate frame orientations for rotation data. Accuracy for the method was validated and compared to an existing software, and the behavior of TEM goniometer was studied by applying the method to an experimental data set.

Place, publisher, year, edition, pages
Department of Materials and Environmental Chemistry (MMK), Stockholm University, 2019. p. 81
Keywords
electron crystallography, structure determination, structure refinement, metal-organic framework, guest molecules, software development, automation, hierarchical cluster analyses, high-throughput data processing, data merging, frame orientations, least-squares optimization, data processing, TEM goniometer
National Category
Inorganic Chemistry
Research subject
Inorganic Chemistry
Identifiers
urn:nbn:se:su:diva-168157 (URN)978-91-7797-646-2 (ISBN)978-91-7797-647-9 (ISBN)
Public defence
2019-06-10, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 13:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Submitted. Paper 4: Manuscript. Paper 5: Manuscript.

Available from: 2019-05-16 Created: 2019-04-23 Last updated: 2019-05-08Bibliographically approved

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