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

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

Published: 2022-07-26 DOI: 10.1038/s41596-022-00720-8

Data processing

Metal–organic frameworks

3D electron diffraction

Single-crystal structure determination

Nano-sized crystals

AI 解读

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Metal–nobreakorganic 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 eluci
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ACKNOWLEDGMENTS

Smeets, S., Wang, B. & Hogenbirk, E. instamatic-dev/instamatic: 1.7.0 (Zenodo, 2021); https://doi.org/10.5281/zenodo.5175957
Yaghi, O. M., Li, G. & Li, H. Selective binding and removal of guests in a microporous metal–organic framework. Nature 378, 703–706 (1995).
Kitagawa, S., Kitaura, R. & Noro, S. Functional porous coordination polymers. Angew. Chem. Int. Ed. 43, 2334–2375 (2004).
Lee, J. et al. Metal–organic framework materials as catalysts. Chem. Soc. Rev. 38, 1450–1459 (2009).
Yoon, M., Srirambalaji, R. & Kim, K. Homochiral metal–organic frameworks for asymmetric heterogeneous catalysis. Chem. Rev. 112, 1196–1231 (2012).
Li, H., Eddaoudi, M., Groy, T. L. & Yaghi, O. M. Establishing microporosity in open metal–organic frameworks: gas sorption isotherms for Zn(BDC) (BDC = 1,4-benzenedicarboxylate). J. Am. Chem. Soc. 120, 8571–8572 (1998).
Li, Q. et al. Docking in metal–organic frameworks. Science 325, 855–859 (2009).
Ma, S. & Zhou, H.-C. Gas storage in porous metal–organic frameworks for clean energy applications. Chem. Commun. 46, 44–53 (2010).
Trickett, C. A. et al. The chemistry of metal–organic frameworks for CO2 capture, regeneration and conversion. Nat. Rev. Mater. 2, 1–16 (2017).
Li, J.-R., Sculley, J. & Zhou, H.-C. Metal–organic frameworks for separations. Chem. Rev. 112, 869–932 (2012).
Duan, J., Jin, W. & Kitagawa, S. Water-resistant porous coordination polymers for gas separation. Coord. Chem. Rev. 332, 48–74 (2017).
Bobbitt, N. S. et al. Metal–organic frameworks for the removal of toxic industrial chemicals and chemical warfare agents. Chem. Soc. Rev. 46, 3357–3385 (2017).
Lin, R.-B., Xiang, S., Xing, H., Zhou, W. & Chen, B. Exploration of porous metal–organic frameworks for gas separation and purification. Coord. Chem. Rev. 378, 87–103 (2019).
Zhang, T. & Lin, W. Metal–organic frameworks for artificial photosynthesis and photocatalysis. Chem. Soc. Rev. 43, 5982–5993 (2014).
Xia, W., Mahmood, A., Zou, R. & Xu, Q. Metal–organic frameworks and their derived nanostructures for electrochemical energy storage and conversion. Energy Environ. Sci. 8, 1837–1866 (2015).
Sheberla, D. et al. Conductive MOF electrodes for stable supercapacitors with high areal capacitance. Nat. Mater. 16, 220–224 (2017).
Feng, D. et al. Robust and conductive two-dimensional metal–organic frameworks with exceptionally high volumetric and areal capacitance. Nat. Energy 3, 30–36 (2018).
Park, J. et al. High thermopower in a Zn-based 3D semiconductive metal–organic framework. J. Am. Chem. Soc. 142, 20531–20535 (2020).
Della Rocca, J., Liu, D. & Lin, W. Nanoscale metal–organic frameworks for biomedical imaging and drug delivery. Acc. Chem. Res. 44, 957–968 (2011).
Horcajada, P. et al. Metal–organic frameworks in biomedicine. Chem. Rev. 112, 1232–1268 (2012).
Doonan, C., Riccò, R., Liang, K., Bradshaw, D. & Falcaro, P. Metal–organic frameworks at the biointerface: synthetic strategies and applications. Acc. Chem. Res. 50, 1423–1432 (2017).
Cichocka, M. O. et al. A porphyrinic zirconium metal–organic framework for oxygen reduction reaction: tailoring the spacing between active-sites through chain-based inorganic building units. J. Am. Chem. Soc. 142, 15386–15395 (2020).
Ge, M. et al. High-throughput electron diffraction reveals a hidden novel metal–organic framework for electrocatalysis. Angew. Chem. Int. Ed. 60, 11391–11397 (2021).
Dorset, D. L. & Hauptman, H. A. Direct phase determination for quasi-kinematical electron diffraction intensity data from organic microcrystals. Ultramicroscopy 1, 195–201 (1976).
Dorset, D. L. Electron crystallography—accomplishments and challenges. Acta Crystallogr. A 54, 750–757 (1998).
Gemmi, M. et al. 3D electron diffraction: the nanocrystallography revolution. ACS Cent. Sci. 5, 1315–1329 (2019).
Gruene, T., Holstein, J. J., Clever, G. H. & Keppler, B. Establishing electron diffraction in chemical crystallography. Nat. Rev. Chem. 5, 660–668 (2021).
Gruene, T. & Mugnaioli, E. 3D electron diffraction for chemical analysis: instrumentation developments and innovative applications. Chem. Rev. 121, 11823–11834 (2021).
Huang, Z., Willhammar, T. & Zou, X. Three-dimensional electron diffraction for porous crystalline materials: structural determination and beyond. Chem. Sci. 12, 1206–1219 (2021).
Huang, Z., Grape, E. S., Li, J., Inge, A. K. & Zou, X. 3D electron diffraction as an important technique for structure elucidation of metal-organic frameworks and covalent organic frameworks. Coord. Chem. Rev. 427, 213583 (2021).
Kolb, U., Gorelik, T., Kübel, C., Otten, M. T. & Hubert, D. Towards automated diffraction tomography: Part I—data acquisition. Ultramicroscopy 107, 507–513 (2007).
Kolb, U., Gorelik, T. & Otten, M. T. Towards automated diffraction tomography. Part II—cell parameter determination. Ultramicroscopy 108, 763–772 (2008).
Mugnaioli, E., Gorelik, T. & Kolb, U. “Ab initio” structure solution from electron diffraction data obtained by a combination of automated diffraction tomography and precession technique. Ultramicroscopy 109, 758–765 (2009).
Zhang, D., Oleynikov, P., Hovmöller, S. & Zou, X. Collecting 3D electron diffraction data by the rotation method. Z. Krist. 225, 94–102 (2010).
Wan, W., Sun, J., Su, J., Hovmöller, S. & Zou, X. Three-dimensional rotation electron diffraction: software RED for automated data collection and data processing. J. Appl. Crystallogr. 46, 1863–1873 (2013).
Jiang, J. et al. Synthesis and structure determination of the hierarchical meso-microporous zeolite ITQ-43. Science 333, 1131–1134 (2011).
Willhammar, T. et al. EMM-23: a stable high-silica multidimensional zeolite with extra-large trilobe-shaped channels. J. Am. Chem. Soc. 136, 13570–13573 (2014).
Guo, P. et al. A zeolite family with expanding structural complexity and embedded isoreticular structures. Nature 524, 74–78 (2015).
Birkel, C. S. et al. Solution synthesis of a new thermoelectric Zn1+xSb nanophase and its structure determination using automated electron diffraction tomography. J. Am. Chem. Soc. 132, 9881–9889 (2010).
Feyand, M. et al. Automated diffraction tomography for the structure elucidation of twinned, sub-micrometer crystals of a highly porous, catalytically active bismuth metal–organic framework. Angew. Chem. Int. Ed. 51, 10373–10376 (2012).
Cichocka, M. O., Ångström, J., Wang, B., Zou, X. & Smeets, S. High-throughput continuous rotation electron diffraction data acquisition via software automation. J. Appl. Crystallogr. 51, 1652–1661 (2018).
Nannenga, B. L., Shi, D., Leslie, A. G. W. & Gonen, T. High-resolution structure determination by continuous-rotation data collection in MicroED. Nat. Methods 11, 927–930 (2014).
Plana-Ruiz, S. et al. Fast-ADT: a fast and automated electron diffraction tomography setup for structure determination and refinement. Ultramicroscopy 211, 112951 (2020).
Gemmi, M., La Placa, M. G. I., Galanis, A. S., Rauch, E. F. & Nicolopoulos, S. Fast electron diffraction tomography. J. Appl. Crystallogr. 48, 718–727 (2015).
Nederlof, I., van Genderen, E., Li, Y.-W. & Abrahams, J. P. A Medipix quantum area detector allows rotation electron diffraction data collection from submicrometre three-dimensional protein crystals. Acta Crystallogr. D. 69, 1223–1230 (2013).
van Genderen, E. et al. Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector. Acta Crystallogr. Sect. Found. Adv. 72, 236–242 (2016).
Yuan, S. et al. [Ti8Zr2O12(COO)16] cluster: an ideal inorganic building unit for photoactive metal–organic frameworks. ACS Cent. Sci. 4, 105–111 (2018).
Hynek, J., Brázda, P., Rohlíček, J., Londesborough, M. G. S. & Demel, J. Phosphinic acid based linkers: building blocks in metal–organic framework chemistry. Angew. Chem. Int. Ed. 57, 5016–5019 (2018).
Portolés-Gil, N. et al. Crystalline curcumin bioMOF obtained by precipitation in supercritical CO2 and structural determination by electron diffraction tomography. ACS Sustain. Chem. Eng. 6, 12309–12319 (2018).
Lenzen, D. et al. A metal–organic framework for efficient water-based ultra-low-temperature-driven cooling. Nat. Commun. 10, 3025 (2019).
Leubner, S. et al. Expanding the variety of zirconium-based inorganic building units for metal–organic frameworks. Angew. Chem. Int. Ed. 58, 10995–11000 (2019).
Dou, J.-H. et al. Atomically precise single-crystal structures of electrically conducting 2D metal–organic frameworks. Nat. Mater. 20, 222–228 (2021).
Shi, D. et al. The collection of microED data for macromolecular crystallography. Nat. Protoc. 11, 895–904 (2016).
Wang, B. et al. A porous cobalt tetraphosphonate metal–organic framework: accurate structure and guest molecule location determined by continuous-rotation electron diffraction. Chem. Eur. J. 24, 17429–17433 (2018).
Samperisi, L. et al. Probing molecular motions in metal–organic frameworks by three-dimensional electron diffraction. J. Am. Chem. Soc. 143, 17947–17952 (2021).
Gao, C. et al. Isostructural three-dimensional covalent organic frameworks. Angew. Chem. Int. Ed. 58, 9770–9775 (2019).
Sun, T., Wei, L., Chen, Y., Ma, Y. & Zhang, Y.-B. Atomic-level characterization of dynamics of a 3D covalent organic framework by cryo-electron diffraction tomography. J. Am. Chem. Soc. 141, 10962–10966 (2019).
Kapaca, E. et al. Synthesis and structure of a 22 × 12 × 12 extra-large pore zeolite ITQ-56 determined by 3D electron diffraction. J. Am. Chem. Soc. 143, 8713–8719 (2021).
Fröjdh, E. et al. Discrimination of aluminum from silicon by electron crystallography with the JUNGFRAU detector. Crystals 10, 1148 (2020).
Seo, S. et al. Two aluminophosphate molecular sieves built from pairs of enantiomeric structural building units. Angew. Chem. Int. Ed. 57, 3727–3732 (2018).
Huang, Z. et al. 3D–3D topotactic transformation in aluminophosphate molecular sieves and its implication in new zeolite structure generation. Nat. Commun. 11, 3762 (2020).
Gruene, T. et al. Rapid structure determination of microcrystalline molecular compounds using electron diffraction. Angew. Chem. Int. Ed. 57, 16313–16317 (2018).
Jones, C. G. et al. The cryoEM method microED as a powerful tool for small molecule structure determination. ACS Cent. Sci. 4, 1587–1592 (2018).
Broadhurst, E. T. et al. Polymorph evolution during crystal growth studied by 3D electron diffraction. IUCrJ 7, 5–9 (2020).
Broadhurst, E. T., Xu, H., Parsons, S. & Nudelman, F. Revealing the early stages of carbamazepine crystallization by cryoTEM and 3D electron diffraction. IUCrJ 8, (2021).
Palatinus, L. et al. Hydrogen positions in single nanocrystals revealed by electron diffraction. Science 355, 166–169 (2017).
Brázda, P., Palatinus, L. & Babor, M. Electron diffraction determines molecular absolute configuration in a pharmaceutical nanocrystal. Science 364, 667–669 (2019).
Yang, L. et al. Ligand-directed conformational control over porphyrinic zirconium metal–organic frameworks for size-selective catalysis. J. Am. Chem. Soc. 143, 12129–12137 (2021).
Smeets, S., Wang, B. & Hogenbirk, E. Instamatic (2021); https://doi.org/10.5281/zenodo.1090388
edtools — edtools 1.0.1 documentation; https://edtools.readthedocs.io/en/latest/
Installation - XDSwiki; https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Installation
Sheldrick, G. M. SHELXT – Integrated space-group and crystal-structure determination. Acta Crystallogr. Sect. Found. Adv. 71, 3–8 (2015).
Sheldrick, G. M. A short history of SHELX. Acta Crystallogr. A 64, 112–122 (2008).
Oracle VM VirtualBox; https://www.virtualbox.org/
Install WSL; https://docs.microsoft.com/en-us/windows/wsl/install
Palatinus, L. et al. Specifics of the data processing of precession electron diffraction tomography data and their implementation in the program PETS2.0. Acta Crystallogr. B 75, 512–522 (2019).
Winter, G. et al. DIALS: implementation and evaluation of a new integration package. Acta Crystallogr. Sect. Struct. Biol. 74, 85–97 (2018).
CrysAlis Pro | Rigaku global website; https://www.rigaku.com/products/crystallography/crysalis
Burla, M. C. et al. Crystal structure determination and refinement via SIR2014. J. Appl. Crystallogr. 48, 306–309 (2015).
Petříček, V., Dušek, M. & Palatinus, L. Crystallographic computing system JANA2006: general features. Z. Krist. Cryst. Mater. 229, 345–352 (2014).
Palatinus, L., Petříček, V. & Corrêa, C. A. Structure refinement using precession electron diffraction tomography and dynamical diffraction: theory and implementation. Acta Crystallogr. Sect. Found. Adv. 71, 235–244 (2015).
Roslova, M. et al. InsteaDMatic: towards cross-platform automated continuous rotation electron diffraction. J. Appl. Crystallogr. 53, 1217–1224 (2020).
Mugnaioli, E. & Gemmi, M. Single-crystal analysis of nanodomains by electron diffraction tomography: mineralogy at the order-disorder borderline. Z. Krist. Cryst. Mater. 233, 163–178 (2018).
Nannenga, B. L., Shi, D., Leslie, A. G. W. & Gonen, T. High-resolution structure determination by continuous-rotation data collection in MicroED. Nat. Methods 11, 927–930 (2014).
Wang, B., Zou, X. & Smeets, S. Automated serial rotation electron diffraction combined with cluster analysis: an efficient multi-crystal workflow for structure determination. IUCrJ 6, 854–867 (2019).
de la Cruz, M. J., Martynowycz, M. W., Hattne, J. & Gonen, T. MicroED data collection with SerialEM. Ultramicroscopy 201, 77–80 (2019).
Yonekura, K., Ishikawa, T. & Maki-Yonekura, S. A new cryo-EM system for electron 3D crystallography by eEFD. J. Struct. Biol. 206, 243–253 (2019).
Carragher, B. et al. Leginon: An automated system for acquisition of images from vitreous ice specimens. J. Struct. Biol. 132, 33–45 (2000).
Electron Microscopy | Software Updates - SE; http://www.thermofisher.com/uk/en/home/electron-microscopy/products/software-em-3d-vis/software-updates.html
cctbx - Determination of lattice symmetry; http://cci.lbl.gov/cctbx/lattice_symmetry.html
Grosse-Kunstleve, R. W., Sauter, N. K., Moriarty, N. W. & Adams, P. D. The Computational Crystallography Toolbox: crystallographic algorithms in a reusable software framework. J. Appl. Crystallogr. 35, 126–136 (2002).
xds; https://xds.mr.mpg.de/html_doc/xds_prepare.html
Xu, H. XDS input template for 3D ED/MicroED data processing. (2021); https://doi.org/10.5281/zenodo.5574261
Doyle, P. A. & Turner, P. S. Relativistic Hartree–Fock X-ray and electron scattering factors. Acta Crystallogr. A 24, 390–397 (1968).
Peng, L.-M. Electron scattering factors of ions and their parameterization. Acta Crystallogr. A 54, 481–485 (1998).
Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. OLEX2: a complete structure solution, refinement and analysis program. J. Appl. Crystallogr. 42, 339–341 (2009).
FAES: Factors of Atomic Electron Scattering; https://srv.mbi.ucla.edu/faes/
Hübschle, C. B., Sheldrick, G. M. & Dittrich, B. ShelXle: a Qt graphical user interface for SHELXL. J. Appl. Crystallogr. 44, 1281–1284 (2011).
International Tables for Crystallography. C: Mathematical, Physical and Chemical Tables (ed. Prince, E.) (Kluwer Academic, 2004).
CheckCIF; https://checkcif.iucr.org/
Spek, A. L. Single-crystal structure validation with the program PLATON. J. Appl. Crystallogr. 36, 7–13 (2003).
Spek, A. L. checkCIF validation ALERTS: what they mean and how to respond. Acta Crystallogr. E 76, 1–11 (2020).
Case: Electron Diffraction Data in the CSD - The Cambridge Crystallographic Data Centre (CCDC); https://www.ccdc.cam.ac.uk/support-and-resources/support/case/?caseid=ceb813f7-aca7-e911-8cce-005056975d8a
Wang, Y., Yang, T., Xu, H., Zou, X. & Wan, W. On the quality of the continuous rotation electron diffraction data for accurate atomic structure determination of inorganic compounds. J. Appl. Crystallogr. 51, 1094–1101 (2018).
Huang, Z. et al. Can 3D electron diffraction provide accurate atomic structures of metal–organic frameworks? Faraday Discuss. 225, 118–132 (2021).
Latitude D software | Gatan; https://www.gatan.com/products/tem-imaging-spectroscopy/latitude-d-software
Ge, M. et al. On the completeness of three-dimensional electron diffraction data for structural analysis of metal–organic frameworks. Faraday Discuss. 231, 66–80 (2021).

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

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