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Crystal Structure Determination by 3D Electron Diffraction — New Software for Facilitating Data Processing
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stockholm University. (Xiaodong Zou)ORCID iD: 0000-0002-6020-9178
2022 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

Three-Dimensional Electron Diffraction (3DED) is a useful technique for determining crystal structures from very small crystals (hundreds of \si{\nano\meter} or less). Examples of such crystals are zeolites, metal-organic frameworks (MOFs), pharmaceuticals, and proteins. Knowledge of the structure is useful for understanding and potentially changing how the material or substance functions.

    This thesis includes the structure determination of the MOFs CAU-42 and CAU-45 as well as the development of the software \emph{Scipion-ED} in response to challenges during the processing of 3DED data from the two MOFs. Both MOFs displayed correlated disorder, where disorder in one part of the structure influences the configuration of disorder in nearby parts. The influence of the solvent during synthesis on the final structured is also discussed.

    The development and design of the software \emph{Scipion-ED} is described. It is a graphical user interface based on \emph{scipion-pyworkflow} for workflow-centric data processing. The described implementation includes the foundation for using \emph{Scipion} to process 3DED data, as well as a plugin for processing with \emph{DIALS}. Approaches are also described for extending the software to use \emph{XDS} or other programs.

Place, publisher, year, edition, pages
Stockholm: Stockholm University, 2022.
National Category
Inorganic Chemistry
Research subject
Inorganic Chemistry
Identifiers
URN: urn:nbn:se:su:diva-204708ISBN: 978-91-7911-001-7 (print)OAI: oai:DiVA.org:su-204708DiVA, id: diva2:1658988
Presentation
2022-06-15, Magnéli hall, Stockholm, 10:00 (English)
Opponent
Supervisors
Available from: 2022-05-18 Created: 2022-05-18 Last updated: 2022-05-18Bibliographically approved
List of papers
1. Hexahydroxytriphenylene for the synthesis of group 13 MOFs - a new inorganic building unit in a beta-cristobalite type structure
Open this publication in new window or tab >>Hexahydroxytriphenylene for the synthesis of group 13 MOFs - a new inorganic building unit in a beta-cristobalite type structure
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2020 (English)In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 49, no 10, p. 3088-3092Article in journal (Refereed) Published
Abstract [en]

Two new, microporous MOFs of framework composition ((CH3)(2)NH2)(2)[M3O(HHTP)(HHTP center dot)], M = Al3+, Ga3+, H6HHTP = 2,3,6,7,10,11-hexahydroxytriphenylene, are described. Electron diffraction combined with molecular simulations show that these compounds crystallize in the beta-cristobalite structure, containing a new type of trinuclear inorganic building unit for MOFs and radical anions.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:su:diva-181175 (URN)10.1039/d0dt00235f (DOI)000519895500033 ()32051978 (PubMedID)
Available from: 2020-05-09 Created: 2020-05-09 Last updated: 2022-05-18Bibliographically approved
2. Synthesis and Exfoliation of a New Layered Mesoporous Zr-MOF Comprising Hexa- and Dodecanuclear Clusters as Well as a Small Organic Linker Molecule
Open this publication in new window or tab >>Synthesis and Exfoliation of a New Layered Mesoporous Zr-MOF Comprising Hexa- and Dodecanuclear Clusters as Well as a Small Organic Linker Molecule
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2020 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 142, no 37, p. 15995-16000Article in journal (Refereed) Published
Abstract [en]

A new layered mesoporous Zr-MOF of composition [Zr30O20(OH)26(OAc)18L18] was synthesized by employing 5-acetamidoisophthalic acid (H2L) using acetic acid as the solvent. The new MOF, denoted as CAU-45, exhibits a honeycomb structure of stacked layers which comprise both hexa- and dodecanucelar zirconium clusters. Its structure was solved from submicrometer-sized crystals by continuous rotation electron diffraction (cRED). Liquid phase exfoliation and size selection were successfully performed on the material.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:su:diva-187335 (URN)10.1021/jacs.0c06978 (DOI)000573374400040 ()32820922 (PubMedID)
Available from: 2020-12-14 Created: 2020-12-14 Last updated: 2022-05-18Bibliographically approved
3. Scipion-ED: a graphical user interface for batch processing and analysis of 3D ED/MicroED data
Open this publication in new window or tab >>Scipion-ED: a graphical user interface for batch processing and analysis of 3D ED/MicroED data
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2022 (English)In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 55, no 3, p. 638-646Article in journal (Refereed) Published
Abstract [en]

Three-dimensional electron diffraction (3D ED)/microcrystal electron diffraction (MicroED) techniques are gaining in popularity. However, the data processing often does not fit existing graphical user interface software, instead requiring the use of the terminal or scripting. Scipion-ED, described in this article, provides a graphical user interface and extendable framework for processing of 3D ED/MicroED data. An illustrative project is described, in which multiple 3D ED/MicroED data sets collected on tetragonal lysozyme were processed with DIALS through the Scipion-ED interface. The ability to resolve unmodelled features in the electrostatic potential map was compared between three strategies for merging data sets.

Keywords
electron diffraction; 3D ED; MicroED; data processing; computer programs.
National Category
Inorganic Chemistry
Research subject
Inorganic Chemistry
Identifiers
urn:nbn:se:su:diva-204705 (URN)10.1107/s1600576722002758 (DOI)000810763300022 ()
Funder
Swedish Research Council, 2017-05333Swedish Research Council, 2019-00815Knut and Alice Wallenberg Foundation, 2018.0237Science for Life Laboratory, SciLifeLab, MicroED@SciLifeLab
Available from: 2022-05-18 Created: 2022-05-18 Last updated: 2025-04-03Bibliographically approved

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Bengtsson, Viktor E. G.

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