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Wada Y, Usov PM, Chan B, Mukaida M, Ohmori K, Ando Y, Fuwa H, Ohtsu H, Kawano M. Atomic-resolution structure analysis inside an adaptable porous framework. Nat Commun 2024; 15:81. [PMID: 38167264 PMCID: PMC10762011 DOI: 10.1038/s41467-023-44401-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
We introduce a versatile metal-organic framework (MOF) for encapsulation and immobilization of various guests using highly ordered internal water network. The unique water-mediated entrapment mechanism is applied for structural elucidation of 14 bioactive compounds, including 3 natural product intermediates whose 3D structures are clarified. The single-crystal X-ray diffraction analysis reveals that incorporated guests are surrounded by hydrogen-bonded water networks inside the pores, which uniquely adapt to each molecule, providing clearly defined crystallographic sites. The calculations of host-solvent-guest structures show that the guests are primarily interacting with the MOF through weak dispersion forces. In contrast, the coordination and hydrogen bonds contribute less to the total stabilization energy, however, they provide highly directional point interactions, which help align the guests inside the pore.
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Affiliation(s)
- Yuki Wada
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Pavel M Usov
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Bun Chan
- Graduate School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki-shi, Nagasaki, 852-8521, Japan
| | - Makoto Mukaida
- Asahi Kasei Pharma Corporation, 632-1 Mifuku Izunokuni, Shizuoka, 410-2321, Japan
| | - Ken Ohmori
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Yoshio Ando
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Haruhiko Fuwa
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Hiroyoshi Ohtsu
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Masaki Kawano
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
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Zigon N, Duplan V, Wada N, Fujita M. Crystalline Sponge Method: X‐ray Structure Analysis of Small Molecules by Post‐Orientation within Porous Crystals—Principle and Proof‐of‐Concept Studies. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Nicolas Zigon
- Department of Applied Chemistry Graduate School of Engineering The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Vincent Duplan
- Department of Applied Chemistry Graduate School of Engineering The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Naoki Wada
- Department of Applied Chemistry Graduate School of Engineering The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Makoto Fujita
- Department of Applied Chemistry Graduate School of Engineering The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
- Division of Advanced Molecular Science Institute for Molecular Science (IMS) 5-1 Higashiyama Myodaiji Okazaki Aichi 444-8787 Japan
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Zigon N, Duplan V, Wada N, Fujita M. Crystalline Sponge Method: X-ray Structure Analysis of Small Molecules by Post-Orientation within Porous Crystals-Principle and Proof-of-Concept Studies. Angew Chem Int Ed Engl 2021; 60:25204-25222. [PMID: 34109717 DOI: 10.1002/anie.202106265] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Indexed: 01/05/2023]
Abstract
This Review discusses, along with the historical background, the principles as well as proof-of-concept studies of the crystalline sponge (CS) method, a new single-crystal X-ray diffraction (SCXRD) method for the analysis of the structures of small molecules without sample crystallization. The method uses single-crystalline porous coordination networks (crystalline sponges) that can absorb small guest molecules within their pores. The absorbed guest molecules are ordered in the pores through molecular recognition and become observable by conventional SCXRD analysis. The complex {[(ZnI2 )3 (tpt)2 ]⋅x(solvent)}n (tpt=tris(4-pyridyl)-1,3,5-triazine) was first proposed as a crystalline sponge and has been most generally used. Crystalline sponges developed later are also discussed here. The principle of the CS method can be described as "post-crystallization" of the absorbed guest, whose ordering is templated by the pre-latticed cavities. The method has been widely applied to synthetic chemistry as well as natural product studies, for which proof-of-concept examples will be shown here.
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Affiliation(s)
- Nicolas Zigon
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Vincent Duplan
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Naoki Wada
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Makoto Fujita
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Division of Advanced Molecular Science, Institute for Molecular Science (IMS), 5-1 Higashiyama Myodaiji, Okazaki, Aichi, 444-8787, Japan
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Balestri D, Mazzeo PP, Perrone R, Fornari F, Bianchi F, Careri M, Bacchi A, Pelagatti P. Deciphering the Supramolecular Organization of Multiple Guests Inside a Microporous MOF to Understand their Release Profile. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202017105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Davide Balestri
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale Università di Parma Parco Area delle Scienze 17A 43124 Parma Italy
- Biopharmanet-TEC Università di Parma Parco Area delle Scienze 27/A 43124 Parma Italy
| | - Paolo P. Mazzeo
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale Università di Parma Parco Area delle Scienze 17A 43124 Parma Italy
- Biopharmanet-TEC Università di Parma Parco Area delle Scienze 27/A 43124 Parma Italy
| | - Roberto Perrone
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale Università di Parma Parco Area delle Scienze 17A 43124 Parma Italy
| | - Fabio Fornari
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale Università di Parma Parco Area delle Scienze 17A 43124 Parma Italy
| | - Federica Bianchi
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale Università di Parma Parco Area delle Scienze 17A 43124 Parma Italy
- Centro Interdipartimentale per l'Energia e l'Ambiente (CIDEA) Università di Parma Parco Area delle Scienze 42 43124 Parma Italy
| | - Maria Careri
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale Università di Parma Parco Area delle Scienze 17A 43124 Parma Italy
- Centro Interdipartimentale sulla Sicurezza, Tecnologie e Innovazione Agroalimentare (SITEIA.PARMA) Università di Parma Parco Area delle Scienze 181/A 43124 Parma Italy
| | - Alessia Bacchi
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale Università di Parma Parco Area delle Scienze 17A 43124 Parma Italy
- Biopharmanet-TEC Università di Parma Parco Area delle Scienze 27/A 43124 Parma Italy
| | - Paolo Pelagatti
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale Università di Parma Parco Area delle Scienze 17A 43124 Parma Italy
- Centro Interuniversitario di Reattività Chimica e Catalisi (CIRCC) Via Celso Ulpiani 27 70126 Bari Italy
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Balestri D, Mazzeo PP, Perrone R, Fornari F, Bianchi F, Careri M, Bacchi A, Pelagatti P. Deciphering the Supramolecular Organization of Multiple Guests Inside a Microporous MOF to Understand their Release Profile. Angew Chem Int Ed Engl 2021; 60:10194-10202. [PMID: 33512039 DOI: 10.1002/anie.202017105] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Indexed: 11/09/2022]
Abstract
Metal-organic frameworks (MOFs) give the opportunity of confining guest molecules into their pores even by a post-synthetic protocol. PUM168 is a Zn-based MOF characterized by microporous cavities that allows the encapsulation of a significant number of guest molecules. The pores engineered with different binding sites show a remarkable guest affinity towards a series of natural essential oils components, such as eugenol, thymol and carvacrol, relevant for environmental applications. Exploiting single crystal X-ray diffraction, it was possible to step-wisely monitor the rather complex three-components guest exchange process involving dimethylformamide (DMF, the pristine solvent) and binary mixtures of the flavoring agents. A picture of the structural evolution of the DMF-to-guest replacement occurring inside the MOF crystal was reached by a detailed single-crystal-to-single-crystal monitoring. The relation of the supramolecular arrangement in the pores with selective guests release was then investigated as a function of time and temperature by static headspace GC-MS analysis.
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Affiliation(s)
- Davide Balestri
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17A, 43124, Parma, Italy.,Biopharmanet-TEC, Università di Parma, Parco Area delle Scienze 27/A, 43124, Parma, Italy
| | - Paolo P Mazzeo
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17A, 43124, Parma, Italy.,Biopharmanet-TEC, Università di Parma, Parco Area delle Scienze 27/A, 43124, Parma, Italy
| | - Roberto Perrone
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17A, 43124, Parma, Italy
| | - Fabio Fornari
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17A, 43124, Parma, Italy
| | - Federica Bianchi
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17A, 43124, Parma, Italy.,Centro Interdipartimentale per l'Energia e l'Ambiente (CIDEA), Università di Parma, Parco Area delle Scienze 42, 43124, Parma, Italy
| | - Maria Careri
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17A, 43124, Parma, Italy.,Centro Interdipartimentale sulla Sicurezza, Tecnologie e Innovazione Agroalimentare (SITEIA.PARMA), Università di Parma, Parco Area delle Scienze 181/A, 43124, Parma, Italy
| | - Alessia Bacchi
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17A, 43124, Parma, Italy.,Biopharmanet-TEC, Università di Parma, Parco Area delle Scienze 27/A, 43124, Parma, Italy
| | - Paolo Pelagatti
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17A, 43124, Parma, Italy.,Centro Interuniversitario di Reattività Chimica e Catalisi (CIRCC), Via Celso Ulpiani 27, 70126, Bari, Italy
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Alkaş A, Friche LES, Harris SN, Telfer SG. Thermal Elimination of Ethylene from Cyclobutyl Groups Characterized by X-ray Crystallography in a Metal-Organic Framework Matrix. Chemistry 2020; 26:10321-10329. [PMID: 32686872 DOI: 10.1002/chem.202001466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/11/2020] [Indexed: 11/07/2022]
Abstract
Methods to synthesize and characterize aromatic molecules with vinyl substituents are sought after yet limited in the literature. Here, we introduce cyclobutyl groups into a metal-organic framework (MOF) matrix that are poised to produce ethylene upon heating. The expulsion of ethylene produces vinyl groups on an aromatic core, which are isolated by the crystalline matrix of the framework. This enables full characterization of the thermolysis by single-crystal X-ray diffraction. Further, we modify the vinyl groups by a bromine addition reaction. Importantly, the two transformations happen in a single-crystal-to-single-crystal manner without changing the overall network structure of the parent framework. New insights into the structural and synthetic chemistry of this important class of compound are generated. Installing reactive vinyl tags in materials by the high temperature thermolysis of cyclobutyl groups is a powerful strategy for altering their physicochemical characteristics.
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Affiliation(s)
- Adil Alkaş
- MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Laurine E S Friche
- MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Shikeale N Harris
- MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Shane G Telfer
- MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
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