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Single-crystal structure determination of nanosized metal–organic frameworks by three-dimensional electron diffraction

Nature Protocols volume 17, pages 2389–2413 (2022)Cite this article

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Abstract

Metal–organic frameworks (MOFs) have attracted considerable interest due to their well-defined pore architecture and structural tunability on molecular dimensions. While single-crystal X-ray diffraction (SCXRD) has been widely used to elucidate the structures of MOFs at the atomic scale, the formation of large and well-ordered crystals is still a crucial bottleneck for structure determination. To alleviate this challenge, three-dimensional electron diffraction (3D ED) has been developed for structure determination of nano- (submicron-)sized crystals. Such 3D ED data are collected from each single crystal using transmission electron microscopy. In this protocol, we introduce the entire workflow for structural analysis of MOFs by 3D ED, from sample preparation, data acquisition and data processing to structure determination. We describe methods for crystal screening and handling of crystal agglomerates, which are crucial steps in sample preparation for single-crystal 3D ED data collection. We further present how to set up a transmission electron microscope for 3D ED data acquisition and, more importantly, offer suggestions for the optimization of data acquisition conditions. For data processing, including unit cell and space group determination, and intensity integration, we provide guidelines on how to use electron and X-ray crystallography software to process 3D ED data. Finally, we present structure determination from 3D ED data and discuss the important features associated with 3D ED data that need to be considered. We believe that this protocol provides critical details for implementing and utilizing 3D ED as a structure determination platform for nano- (submicron-)sized MOFs as well as other crystalline materials.

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Fig. 1: Workflow for 3D ED structural analysis of nanosized MOFs using a standard TEM setup.
Fig. 2: Crystal handling and grid preparation.
Fig. 3: ED patterns obtained at different camera lengths defining the magnification of the diffraction pattern as set by the projector lenses.
Fig. 4: The data collection procedure.
Fig. 5: Low-magnification TEM images showing an overview of the crystal distribution on the grid.
Fig. 6: Procedures for bringing a crystal to the mechanical eucentric height.
Fig. 7: Example of crystal tracking using Instamatic.
Fig. 8: Reconstruction of 3D reciprocal space using REDp software.
Fig. 9: Data statistics produced by XDS.
Fig. 10: Comparison of peak integration.
Fig. 11: Hierarchical clustering analysis.
Fig. 12: An example SHELXT input file for structure solution of MOF CAU-3653.
Fig. 13: An example SHELXL input file for structure refinement of MOF CAU-36 (ref. 53).
Fig. 14: Electrostatic potential maps calculated based on the refinement of ZIF-EC1 against 3D ED data.

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Data availability

CCDC 1865990-1865999, 2004306, 2020844 and 2063952 contain the example crystallographic data as part of the supporting primary research publications. These data can be obtained free of charge from www.ccdc.cam.ac.uk/data_request/cif, or by emailing data_request@ccdc.cam.ac.uk, or by contacting The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK; fax: +44 1223 336033. Additional reasonable requests for data supporting this publication should be addressed to the corresponding authors.

Code availability

Reasonable requests for the code and scripts used in this publication should be addressed to the corresponding authors.

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Acknowledgements

This work was supported by the Swedish research council Formas (2020-00831 to Z.H.), the Swedish Research Council (VR 2016-04625 to Z.H., VR 2017-04321 and 2019-00815 to X.Z., VR 2017-05333 to H.X. and VR 2019-05465 to T.W.), the Knut and Alice Wallenberg Foundation (2012.0112 and 2018.0237 to X.Z.) and the MicroED@SciLifeLab project (H.X.)

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  1. Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden

    Taimin Yang, Tom Willhammar, Hongyi Xu, Xiaodong Zou & Zhehao Huang

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  1. Taimin Yang
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T.Y., T.W., H.X., X.Z. and Z.H. wrote the manuscript. Z.H. initiated this manuscript. All authors read, discussed and approved the manuscript.

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Correspondence to Hongyi Xu, Xiaodong Zou or Zhehao Huang.

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Nature Protocols thanks Jessica Bruhn, Russell E. Morris and Enrico Mugnaioli for their contribution to the peer review of this work.

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Key references using this protocol

Ge, M. et al. Angew. Chem. Int. Ed. 60, 11391–11397 (2021): https://doi.org/10.1002/anie.202016882

Samperisi, L. et al. J. Am. Chem. Soc. 143, 17947–17952 (2021): https://doi.org/10.1021/jacs.1c08354

Cichocka, M. O. et al. J. Am. Chem. Soc. 142, 15386–15395 (2020): https://doi.org/10.1021/jacs.0c06329

Yuan, S. et al. ACS Cent. Sci. 4, 105–111 (2018): https://doi.org/10.1021/acscentsci.7b00497

Wang, B. et al. Chem. Eur. J. 24, 17429–17433 (2018): https://doi.org/10.1002/chem.201804133

Key data used in this protocol

Wang, B. et al. Chem. Eur. J. 24, 17429–17433 (2018): https://doi.org/10.1002/chem.201804133

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Yang, T., Willhammar, T., Xu, H. et al. Single-crystal structure determination of nanosized metal–organic frameworks by three-dimensional electron diffraction. Nat Protoc 17, 2389–2413 (2022). https://doi.org/10.1038/s41596-022-00720-8

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