Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Development of rotation electron diffraction as a fully automated and accurate method for structure determination
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). (Xiaodong Zou)ORCID iD: 0000-0002-4327-6424
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 [en]
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: urn:nbn:se:su:diva-168157ISBN: 978-91-7797-646-2 (print)ISBN: 978-91-7797-647-9 (electronic)OAI: oai:DiVA.org:su-168157DiVA, id: diva2:1306254
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
List of papers
1. A Porous Cobalt Tetraphosphonate Metal-Organic Framework: Accurate Structure and Guest Molecule Location Determined by Continuous-Rotation Electron Diffraction
Open this publication in new window or tab >>A Porous Cobalt Tetraphosphonate Metal-Organic Framework: Accurate Structure and Guest Molecule Location Determined by Continuous-Rotation Electron Diffraction
Show others...
2018 (English)In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 24, no 66, p. 17429-17433Article in journal (Refereed) Published
Abstract [en]

Single-crystal electron diffraction has shown to be powerful for structure determination of nano- and submicron-sized crystals that are too small to be studied by single-crystal X-ray diffraction. However, it has been very challenging to obtain high quality electron diffraction data from beam sensitive crystals such as metal-organic frameworks (MOFs). It is even more difficult to locate guest species in the pores of MOF crystals. Here, we present synthesis of a novel porous cobalt MOF with 1D channels, [Co-2(Ni-H4TPPP)]center dot 2DABCO center dot 6H(2)O, (denoted Co-CAU-36; DABCO=1,4-diazabicyclo[2.2.2]octane), and its structure determination using continuous rotation electron diffraction (cRED) data. By combining a fast hybrid electron detector with low sample temperature (96 K), high resolution (0.83-1.00 angstrom) cRED data could be obtained from eight Co-CAU-36 crystals. Independent structure determinations were conducted using each of the eight cRED datasets. We show that all atoms in the MOF framework could be located. More importantly, we demonstrate for the first time that organic molecules in the pores, which were previously difficult to find, could be located using the cRED data. A comparison of eight independent structure determinations using different datasets shows that structural models differ only on average by 0.03(2) angstrom for the framework atoms and 0.10(6) and 0.16(12) angstrom for DABCO and water molecules, respectively.

Keywords
cobalt phosphonate, electron diffraction, metal-organic frameworks, structure determination, structure refinement
National Category
Chemical Sciences
Research subject
Inorganic Chemistry
Identifiers
urn:nbn:se:su:diva-163614 (URN)10.1002/chem.201804133 (DOI)000451901200007 ()30288800 (PubMedID)
Available from: 2019-01-09 Created: 2019-01-09 Last updated: 2019-04-23Bibliographically approved
2. Automated serial rotation electron diffraction combined with cluster analysis: an efficient multi-crystal workflow for structure determination
Open this publication in new window or tab >>Automated serial rotation electron diffraction combined with cluster analysis: an efficient multi-crystal workflow for structure determination
(English)In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525Article in journal (Refereed) Submitted
Keywords
Serial crystallography, automated data collection, hierarchical cluster analysis, structure determination, electron diffraction, microED
National Category
Inorganic Chemistry
Research subject
Inorganic Chemistry
Identifiers
urn:nbn:se:su:diva-168148 (URN)
Funder
Swedish Research Council, 2017-04321Knut and Alice Wallenberg Foundation, 2012.0112
Available from: 2019-04-23 Created: 2019-04-23 Last updated: 2019-04-23Bibliographically approved
3. High-throughput continuous rotation electron diffraction data acquisition via software automation
Open this publication in new window or tab >>High-throughput continuous rotation electron diffraction data acquisition via software automation
Show others...
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.

Keywords
single-crystal electron diffraction, high throughput, crystal screening, structure analysis
National Category
Inorganic Chemistry
Research subject
Inorganic Chemistry
Identifiers
urn:nbn:se:su:diva-162656 (URN)10.1107/S1600576718015145 (DOI)000451833600016 ()
Available from: 2018-12-05 Created: 2018-12-05 Last updated: 2019-04-23Bibliographically approved
4. A method for accurate orientation determination for rotation electron diffraction patterns
Open this publication in new window or tab >>A method for accurate orientation determination for rotation electron diffraction patterns
Show others...
(English)Manuscript (preprint) (Other academic)
Abstract [en]

A numerical method for calculating the frame orientation of a crystal from indexed electron diffraction patterns is developed. The algorithm uses the observed reflection indices and unit cell parameters of the crystal, and operates by minimizing the summed distances in reciprocal space between the observed reflections and the Ewald sphere. Partiality correction is proposed by making use of the information about the rotation axis. The accuracy of the orientations is found to be around 0.01° for each of the frames in a rotation dataset.

National Category
Inorganic Chemistry
Research subject
Inorganic Chemistry
Identifiers
urn:nbn:se:su:diva-168150 (URN)
Available from: 2019-04-23 Created: 2019-04-23 Last updated: 2019-04-23Bibliographically approved
5. A method for determination of angular accuracy of the goniometer on a transmission electron microscope
Open this publication in new window or tab >>A method for determination of angular accuracy of the goniometer on a transmission electron microscope
(English)Manuscript (preprint) (Other academic)
Abstract [en]

For collection and reconstruction of 3D electron diffraction or electron tomography data, it is essential to have reliable goniometer tilt angles. Thus, it is important to know the accuracy of tilt angles a goniometer can provide on a transmission electron microscope (TEM).  In this paper, a method to determine the angular accuracy of a goniometer is presented, which is based on the orientation determination of rotation electron diffraction (RED) data from a crystal with known unit cell. The method was demonstrated on a JEOL JEM 2100 LaB6 TEM. The result showed that the uncertainty for the goniometer was 1.75% from the expected rotation angle. Meanwhile, the readout error from the TEM hardware followed a combination of sinusoidal and linear components, indicating a more complicated readout error source than only linear errors. A quality assessment method for general TEM goniometers is proposed.

National Category
Inorganic Chemistry
Research subject
Inorganic Chemistry
Identifiers
urn:nbn:se:su:diva-168151 (URN)
Available from: 2019-04-23 Created: 2019-04-23 Last updated: 2019-05-08Bibliographically approved
6. Instamatic
Open this publication in new window or tab >>Instamatic
Show others...
2018 (English)Other (Other academic)
National Category
Inorganic Chemistry
Research subject
Inorganic Chemistry
Identifiers
urn:nbn:se:su:diva-168156 (URN)10.5281/zenodo.2026774 (DOI)
Note

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.

Available from: 2019-04-23 Created: 2019-04-23 Last updated: 2019-04-25Bibliographically approved

Open Access in DiVA

Development of rotation electron diffraction as a fully automated and accurate method for structure determination(3876 kB)88 downloads
File information
File name FULLTEXT01.pdfFile size 3876 kBChecksum SHA-512
1f1a6768f0893e8f6e87cc3a01587b8ee3234592b3cf3a7ac2afe5f5b53f2f02fe3779b288c0b51b8c97ec868e9bab94bfb89f7a15dc1384d37766edf764892f
Type fulltextMimetype application/pdf

Search in DiVA

By author/editor
Wang, Bin
By organisation
Department of Materials and Environmental Chemistry (MMK)
Inorganic Chemistry

Search outside of DiVA

GoogleGoogle Scholar
Total: 88 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

isbn
urn-nbn

Altmetric score

isbn
urn-nbn
Total: 358 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf