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Synthesis and guest inclusion for molecular catcher-based structure determination

Nature Protocols (2026) Cite this article

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Abstract

Natural products and drugs containing long alkyl chains are difficult to grow in the form of single crystals. This makes it challenging, if not impossible, to determine their molecular structures through conventional single-crystal X-ray diffraction. We recently reported a ‘molecular catcher’ technique using a pillar[5]arene-incorporated metal–organic framework (MOF), namely a ‘molecular catcher’, that enables rapid and accurate determination of crystal structures for long-alkyl-chain compounds without a need to grow single crystals. In this approach, presynthesized pillar[5]arene-containing MOF crystals are soaked in a solution of the target compound. The compound is captured into the MOF crystals, which are then analyzed by X-ray diffraction, allowing the crystal structure of the guest to be determined. Here we describe detailed protocols for the synthesis of this pillar[5]arene-containing MOF and its further use in structure determinations. In brief, the MOF crystals required for this Protocol are prepared from an in-house synthesized pillar[5]arene derivative, a commercially available tetraphenyl ethylene derivative and zinc nitrate hexahydrate in N,N-dimethylformamide. The resulting crystals are washed with fresh N,N-dimethylformamide to remove unreacted starting materials and can be used directly for guest inclusion without further solvent exchange. The most critical step is selecting MOF crystals with suitable size and quality. We recommend using optical microscopy for preliminary screening to evaluate crystal size and quality as the selection criteria. By soaking the MOF crystals in a solution of the target compound, target-included MOF crystals suitable for X-ray diffraction analysis can be obtained. The entire process—from starting materials to determining the crystal structure—can be completed within 10 d.

Key points

  • ‘Molecular catcher’ technique using a pillar[5]arene-incorporated metal–organic framework for crystal structure determination.

  • The metal–organic framework crystals are prepared from an in-house synthesized pillar[5]arene derivative, a commercially available tetraphenyl ethylene derivative, and zinc nitrate hexahydrate in N,N-dimethylformamide.

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Fig. 1: A workflow schematic showing the synthesis and guest inclusion protocols required for molecular catcher-based structure determination.
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Fig. 2: Comparison of three MOF-based structure determination methods.
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Fig. 3: Photographs during the synthesis of EtP5.
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Fig. 4: Photographs during the synthesis of EtP4Q1.
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Fig. 5: Photographs during the synthesis of EtP5-2OH.
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Fig. 6: Photographs during the synthesis of EtP5-2OTf.
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Fig. 7: Photographs during the synthesis of EtP5BPPy.
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Fig. 8: Photographs during the synthesis and preparation of the MOF crystals.
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Fig. 9: Photographs during the preparation of guest-included MOF crystals.
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Fig. 10: 1H NMR (400 MHz, DMSO-d6:DCl = 100:1, 298 K) spectrum of EtP5-MOF-2 after digestion.
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Fig. 11: Porosity analysis of EtP5-MOF-2.
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Fig. 12: SCXRD data analyses of the guest-included EtP5-MOF-2 crystals.
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Fig. 13: Crystal structure analyses of EtP5-MOF-2-D, EtP5-MOF-2-B and EtP5-MOF-2-M.
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Data availability

Crystallographic data of the crystal structures reported in this Protocol are available from the Cambridge Crystallographic Data Centre (CCDC) with the following codes: SCXRD data for EtP5-MOF-2-D1 to EtP5-MOF-2-D15 (CIF), EtP5-MOF-2-B1 to EtP5-MOF-2-B9 (CIF) and EtP5-MOF-2-M1 to EtP5-MOF-2-M6 (CIF), CCDC numbers 2494643–2494650, 2526173–2526179, 2526203, 2526267, 2494958–2494960 and 2494962–2494971. Other data that support the findings of this Protocol are available in the Protocol and its Supplementary Information. Source data are provided with this paper.

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Acknowledgements

F.H. was supported by the Zhejiang Provincial Natural Science Foundation of China (grant no. LD26B020001), the ‘pioneer’ and ‘Leading Goose’ R&D Program of Zhejiang (grant no. 2025C04010), the National Natural Science Foundation of China (grant nos. 22320102001 and 22350007) and the Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China (grant no. JYB2025XDXM407). Y.W. was supported by the National Postdoctoral Program for Innovative Talents (grant no. BX20240316), China Postdoctoral Science Foundation for General Program (grant no. 2024M762793) and the National Natural Science Foundation of China (grant no. 22501251). J.L.S. was supported by the Robert A. Welch Foundation (grant no. F-0018) and the US National Science Foundation (grant no. CHE-2304731). We thank J. Liu, Y. Liu, X. Li and Q. He from the Chemistry Instrumentation Center of Zhejiang University for technical support. We thank W. Chen from Shiyanjia Lab (www.shiyanjia.com), eceshi (www.eceshi.com), D. Liu from SCI-GO (www.sci-go.com), ReadCrystal and NOGIN for the SCXRD measurements. We thank the staff at BL17B1 beamline of the National Facility for Protein Science in Shanghai (NFPS), Shanghai Advanced Research Institute and CAS for providing technical support in X-ray diffraction data collection and analysis. We thank BSD INSTRUMENT for the BET measurements. We thank Bidepharm for supplying the compound (Bidepharm, CAS 1610858-96-2, cat. no. BD765165), MACKLIN for supplying the compound (MACKLIN, CAS 1610858-96-2, cat. no. E856436-200mg), Yanshen Technology for supplying the compound (Jilin Chinese Academy of Sciences-Yanshen Technology, CAS 1610858-96-2, cat. no. YSWG130-5g) and LeYan for supplying the compound (LeYan, CAS 1045332-30-6, cat. no. 1061476).

Author information

Author notes

  1. These authors contributed equally: Yitao Wu, Lei Xu.

Authors and Affiliations

  1. State Key Laboratory of Soil Pollution Control and Safety, Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou, P. R. China

    Yitao Wu, Shang Li, Hongyan Zhang, Shiyuan Wang, Jiahao Yu, Jiyong Liu & Feihe Huang

  2. Key Laboratory of High-Performance Adhesion Functional Materials and Application Technology of Zhejiang, Zhejiang–Israel Joint Laboratory of Self-Assembling Functional Materials, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, P. R. China

    Yitao Wu, Shang Li, Hongyan Zhang, Shiyuan Wang, Jiahao Yu, Jiyong Liu & Feihe Huang

  3. Jiangsu Key Lab of Data Engineering and Knowledge Service, Laboratory of Data Intelligence and Interdisciplinary Innovation, School of Information Management, Nanjing University, Nanjing, P. R. China

    Lei Xu

  4. Department of Chemistry, The University of Texas at Austin, Austin, TX, USA

    Jonathan L. Sessler

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Contributions

Y.W. conceived the idea, designed and performed all the experiments, analyzed all the data, wrote the Protocol and Supplementary Information and led the project; L.X. conducted the SCXRD analyses and checked the SCXRD data; S.L. discussed the data; H.Z. discussed the data; S.W. discussed the data; J.Y. discussed the data; J.L. discussed the SCXRD data; J.L.S. provided guidance, discussed the data and revised the manuscript; and F.H. provided direct supervision and guidance, revised the manuscript, provided funding support and led the project.

Corresponding authors

Correspondence to Jonathan L. Sessler or Feihe Huang.

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Nature Protocols thanks Shengqian Ma, Ying-Wei Yang and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Key reference

Wu, Y. et al. Nature 640, 676–682 (2025): https://doi.org/10.1038/s41586-025-08833-2

Supplementary information

Supplementary Information (download PDF )

Supplementary Figs. 1–90 and Tables 1–32.

Reporting Summary (download PDF )

Supplementary Data 1 (download ZIP )

Crystallographic data of this Protocol.

Source data

Source Data Fig. 11 (download XLSX )

Statistical source data of Fig. 11b.

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Wu, Y., Xu, L., Li, S. et al. Synthesis and guest inclusion for molecular catcher-based structure determination. Nat Protoc (2026). https://doi.org/10.1038/s41596-026-01370-w

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