1
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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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2
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Jiao J, Li H, Xie W, Zhao Y, Lin C, Jiang J, Wang L. Host-guest system of a phosphorylated macrocycle assisting structure determination of oily molecules in single-crystal form. Chem Sci 2023; 14:11402-11409. [PMID: 37886082 PMCID: PMC10599484 DOI: 10.1039/d3sc02995f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/24/2023] [Indexed: 10/28/2023] Open
Abstract
X-ray crystallography is the most reliable method for structure elucidation and absolute configuration determination of organic molecules based on their single-crystal forms. However, many analytes are hard to crystallize because of their low melting points (an oily state at room temperature) or conformational flexibility. Here, we report the crystallization of a macrocycle, CTX[P(O)Ph] (host), which is a cyclotrixylohydroquinoylene (CTX) derivative, with 26 oily organic molecules (guests), which is applied for the structural determination of the guest with X-ray crystallography. With the aid of the host, CTX[P(O)Ph], the guest molecules were well-ordered with full occupancy in crystal structures. In most cases, at least one guest structure without any disorder could be observed; solvent masking was not necessary for the single crystal X-ray structural analysis, and thus the structures of the guests could be successfully determined, and the absolute configuration could be assigned reliably for chiral guests with this method. The crystallization mechanism was further discussed from theoretical and experimental perspectives, suggesting that the negative electrostatic potential surface of CTX[P(O)Ph] and noncovalent interactions between the host and guest were crucial for the ordered arrangements of the guest.
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Affiliation(s)
- Jianmin Jiao
- State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Heng Li
- State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Wang Xie
- State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Yue Zhao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Chen Lin
- State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Juli Jiang
- State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Leyong Wang
- State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
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3
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Carroll RC, Harrowven DC, Pearce JE, Coles SJ. A systematic study of the interplay between guest molecule structure and intermolecular interactions in crystalline sponges. IUCRJ 2023; 10:497-508. [PMID: 37409807 PMCID: PMC10324488 DOI: 10.1107/s2052252523005146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/08/2023] [Indexed: 07/07/2023]
Abstract
Utilization of the crystalline sponge {[(ZnI2)3(tpt)2·x(solvent)]n} method has enabled characterization of a novel family of synthetic organic oils. The systematic structural differences and diversity of functional groups offered by 13 related molecular adsorbates provide a detailed quantitative understanding of the relationship between the guest structure, its conformation, and the type of intermolecular interactions adopted with neighbouring guests and the host framework. This analysis is extended to assess the connection of these factors to the resulting quality indicators for a particular molecular structure elucidation.
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Affiliation(s)
- Robert C. Carroll
- School of Chemistry, University of Southampton, University Road, Southampton, Hampshire SO17 1BJ, United Kingdom
| | - David C. Harrowven
- School of Chemistry, University of Southampton, University Road, Southampton, Hampshire SO17 1BJ, United Kingdom
| | - James E. Pearce
- School of Chemistry, University of Southampton, University Road, Southampton, Hampshire SO17 1BJ, United Kingdom
| | - Simon J. Coles
- School of Chemistry, University of Southampton, University Road, Southampton, Hampshire SO17 1BJ, United Kingdom
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4
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Metherall JP, Carroll RC, Coles SJ, Hall MJ, Probert MR. Advanced crystallisation methods for small organic molecules. Chem Soc Rev 2023; 52:1995-2010. [PMID: 36857636 DOI: 10.1039/d2cs00697a] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Molecular materials based on small organic molecules often require advanced structural analysis, beyond the capability of spectroscopic techniques, to fully characterise them. In such cases, diffraction methods such as single crystal X-ray diffraction (SCXRD), are one of the most powerful tools available to researchers, providing molecular and structural elucidation at atomic level resolution, including absolute stereochemistry. However SCXRD, and related diffraction methods, are heavily dependent on the availability of suitable, high-quality crystals, thus crystallisation often becomes the major bottleneck in preparing samples. Following a summary of classical methods for the crystallisation of small organic molecules, this review will focus on a number of recently developed advanced methods for crystalline material sample preparation for SCXRD. This review will cover two main areas of modern small organic molecule crystallisation, namely the inclusion of molecules within host complexes (e.g., "crystalline sponge" and tetraaryladamantane based inclusion chaperones) and the use of high-throughput crystallisation, employing "under-oil" approaches (e.g., microbatch under-oil and ENaCt). Representative examples have been included for each technique, together with a discussion of their relative advantages and limitations to aid the reader in selecting the most appropriate technique to overcome a specific analytical challenge.
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Affiliation(s)
- J P Metherall
- Newcastle University, Chemistry - School of Natural Environmental Sciences, Newcastle upon Tyne, NE1 7RU, UK.
| | - R C Carroll
- University of Southampton, School of Chemistry, Southampton, SO17 1BJ, UK
| | - S J Coles
- University of Southampton, School of Chemistry, Southampton, SO17 1BJ, UK
| | - M J Hall
- Newcastle University, Chemistry - School of Natural Environmental Sciences, Newcastle upon Tyne, NE1 7RU, UK.
| | - M R Probert
- Newcastle University, Chemistry - School of Natural Environmental Sciences, Newcastle upon Tyne, NE1 7RU, UK.
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5
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Watanabe S, Kikuchi T, Iwai T, Matsushita R, Takatsu M, Honda S, Nakanishi T, Nakamura Y, Seto Y. Single crystal X-ray analysis using the crystalline sponge method for direct structure determination of new and earlier synthetic cannabinoids including OXIZIDs, AKB48, and JWH-424 from a trace sample. Forensic Chem 2023. [DOI: 10.1016/j.forc.2023.100480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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6
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Highly Luminescent Crystalline Sponge: Sensing Properties and Direct X-ray Visualization of the Substrates. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27228055. [PMID: 36432154 PMCID: PMC9692560 DOI: 10.3390/molecules27228055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/09/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022]
Abstract
A phenomenon of crystalline sponge is represented by guest-dependent structural fluidity of the host polymeric lattice in highly crystalline sorbents, such as metal-organic frameworks, driven by multiple weak intermolecular interactions. Such induced fitting in MOFs is a valuable property in selective adsorption, guest determination by single-crystal XRD and in-situ structural analysis under external stimuli. In this work, a porous three-dimensional metal-organic framework [Eu2(DMF)4(ttdc)3]·4.45DMF (1DMF; DMF = N,N-dimethylformamide, ttdc2- = trans-thienothiophenedicarboxylate anion) was applied as a crystalline sponge bearing luminescent functionality to couple its sensing properties with direct structural determination of the adsorbed molecules. As a result, the paper discusses crystal structures and luminescent properties for the successfully obtained new adducts with the crystallographic formulae [Eu2(DMSO)4(ttdc)3]·2.5DMSO·2.2H2O (1DMSO; DMSO = dimethylsulfoxide), [Eu2(DMF)4(ttdc)3]·3phet (1phet; phet = phenylethanal) and [Eu2(DMF)3.5(cin)0.5(ttdc)3]·1.64cin (1cin; cin = trans-cinnamaldehyde). As a result of inclusion of DMSO into 1, a slight increase in the quantum yield and excited state phosphorescence lifetime was observed, while the adsorption of phet leads to a considerable (up to three times) decrease in the corresponding values. The incorporation of cinnamal results in a full quenching of QY, from 20% down to zero, and a more than order of magnitude diminishing of the excited state lifetime compared to the initial 1DMF. The effective sensing of cinnamal was explained from the structural point of view by its direct coordination to the Eu3+ emitter, as well as by multiple weak intermolecular interactions with ttdc antenna ligand, both capable of enhancing the non-radiative energy dissipation.
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7
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A novel crystalline template for the structural determination of flexible chain compounds of nanoscale length. Chem 2022. [DOI: 10.1016/j.chempr.2022.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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8
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Chauhan P, Javed S. Crystallographic capture of caged diamondoids: Camphor and adamantanes’ guests‐encapsulation on specific recognition‐sites of host MOF. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Chauhan P, Javed S, Levendis DC, Fernandes M. Hydrophobicity directed guest-inclusion for structure-elucidation of enclatherated guests within a crystalline sponge by SC-XRD. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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10
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He W, Tashiro S, Shionoya M. Highly selective acid-catalyzed olefin isomerization of limonene to terpinolene by kinetic suppression of the overreactions in a confined space of porous metal-macrocycle framework. Chem Sci 2022; 13:8752-8758. [PMID: 35975147 PMCID: PMC9350587 DOI: 10.1039/d2sc01561g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/02/2022] [Indexed: 11/21/2022] Open
Abstract
Natural enzymes control the intrinsic reactivity of chemical reactions in the natural environment, giving only the necessary products. In recent years, challenging research on the reactivity control of terpenes with structural diversity using artificial host compounds that mimic such enzymatic reactions has been actively pursued. A typical example is the acid-catalyzed olefin isomerization of (+)-limonene, which generally gives a complex mixture due to over-isomerization to thermodynamically favored isomers. Herein we report a highly controlled conversion of (+)-limonene by kinetic suppression of over-isomerization in a confined space of a porous metal–macrocycle framework (MMF) equipped with a Brønsted acid catalyst. The terminal double bond of (+)-limonene migrated to one neighbor, preferentially producing terpinolene. This reaction selectivity was in stark contrast to the homogeneous acid-catalyzed reaction in bulk solution and to previously reported catalytic reactions. X-ray structural analysis and examination of the reaction with adsorption inhibitors suggest that the reactive substrates may bind non-covalently to specific positions in the confined space of the MMF, thereby inhibiting the over-isomerization reaction. The nanospaces of the MMF with substrate binding ability are expected to enable highly selective synthesis of a variety of terpene compounds. A porous metal–macrocycle framework (MMF) equipped with a Brønsted acid catalyst in nanochannels enables highly selective isomerization of limonene to terpinolene by kinetically suppressing over-isomerization at confined acid sites.![]()
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Affiliation(s)
- Wei He
- Department of Chemistry, Graduate School of Science, The University of Tokyo Tokyo 113-0033 Japan
| | - Shohei Tashiro
- Department of Chemistry, Graduate School of Science, The University of Tokyo Tokyo 113-0033 Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo Tokyo 113-0033 Japan
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11
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Wada N, Kageyama K, Jung Y, Mitsuhashi T, Fujita M. Solvent Effects in the Crystalline Sponge Method: Importance of Co-solvents for Ordering Absorbed Guests. Org Lett 2021; 23:9288-9291. [PMID: 34806896 DOI: 10.1021/acs.orglett.1c03660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the crystalline sponge method, the crucial step for ordering the absorbed guest is soaking of the guest into the pores of the crystalline sponge. Here, we find that the choice of solvent is particularly important for smooth guest soaking and ordering. Moderately polar solvents, such as ketones and esters, which we have previously avoided for the guest-soaking process, efficiently promote diffusion and guest ordering by filling the gaps in the pores through co-crystallization with the guests. Using this modified protocol, we successfully demonstrate the structural analysis of various steroids.
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Affiliation(s)
- Naoki Wada
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ko Kageyama
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Youngcheol Jung
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takaaki Mitsuhashi
- Division of Advanced Molecular Science, Institute for Molecular Science (IMS), Okazaki, Aichi 444-8787, Japan
| | - Makoto Fujita
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.,Division of Advanced Molecular Science, Institute for Molecular Science (IMS), Okazaki, Aichi 444-8787, Japan
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12
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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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13
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Taniguchi Y, Kikuchi T, Sato S, Fujita M. Comprehensive Structural Analysis of the Bitter Components in Beer by the HPLC-Assisted Crystalline Sponge Method. Chemistry 2021; 28:e202103339. [PMID: 34755407 DOI: 10.1002/chem.202103339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Indexed: 11/10/2022]
Abstract
Trans-iso-α-acid is one of the main contributors to the bitter taste of fresh beer and is known to transform into various derivatives during beer aging. However, structural characterization of the derivatives has been a challenging task because of the formation of too many components. Herein, we report that most of the transformation products of trans-iso-α-acid, isolated in this study in only small quantities by HPLC, can be structurally analyzed with the crystalline sponge method. Thirteen compounds, including eight that were previously unreported, have been successfully isolated and analyzed with complete assignment of their absolute configuration. This provides an improved understanding of the chemical transformations that occur during beer aging.
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Affiliation(s)
- Yoshimasa Taniguchi
- Kirin Central Research Institute, Research & Development Division, Kirin Holdings Company, Ltd., 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Takashi Kikuchi
- Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima-shi, Tokyo, 196-8666, Japan
| | - Sota Sato
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Integrated Molecular Structure Analysis Laboratory Social Cooperation Program, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Makoto Fujita
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Integrated Molecular Structure Analysis Laboratory Social Cooperation Program, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Division of Advanced Molecular Science, Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
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14
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Taniguchi Y, Miwa M, Kitada N. Crystalline sponge X-ray analysis coupled with supercritical fluid chromatography: a novel analytical platform for the rapid separation, isolation, and characterization of analytes. Analyst 2021; 146:5230-5235. [PMID: 34373868 DOI: 10.1039/d1an00948f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Crystalline sponge (CS) based X-ray diffraction (XRD) analysis allows for the observation of the structure of an analyte, including its absolute configuration. Herein we report a powerful analytical platform for the separation, isolation, and structural elucidation of a target analyte in a seamless way by coupling supercritical fluid chromatography (SFC) with CS-based XRD analysis (SFC-CSXRD). The efficacy of this methodology is demonstrated by the rapid characterization of regio- and stereoisomers using three types of CSs with differing tolerances to the solvents used in SFC and guest-soaking.
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Affiliation(s)
- Yoshimasa Taniguchi
- Kirin Central Research Institute, Research & Development Division, Kirin Holdings Company Ltd., 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.
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15
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Rosenberger L, von Essen C, Khutia A, Kühn C, Georgi K, Hirsch AKH, Hartmann RW, Badolo L. Crystalline sponge affinity screening: A fast tool for soaking condition optimization without the need of X-ray diffraction analysis. Eur J Pharm Sci 2021; 164:105884. [PMID: 34161782 DOI: 10.1016/j.ejps.2021.105884] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/07/2021] [Accepted: 05/14/2021] [Indexed: 11/28/2022]
Abstract
Structural elucidation of small molecules only available in low quantity (nanogram) is one of the big advantages of the crystalline sponge method. The optimization of various soaking parameters is crucial for effective analyte absorption and repetitive positioning in the pores of the crystal. Time-consuming X-ray diffraction measurements are necessary for data collection and confirmation of successful guest inclusion. In this work, we report a screening method to select optimal soaking conditions without the need of single-crystal X-ray diffraction analysis for individual compounds and mixtures. 14 substances were chosen as test compounds. Parallel guest soaking of individual compounds and mixtures was conducted using various soaking conditions. After evaporation of solvent, excessive material was removed, and guest molecules released through dissolution of the framework. Liquid chromatography-tandem mass spectrometry allowed the estimation of analyte trapped in the pores and the selection of optimal soaking condition dependent on the highest amount of analyte to crystal size (affinity factor). The tool allowed subsequent crystallographic analysis of ten compounds with minimal experiment time. Additionally, a study to examine the lower limit of detection of the crystalline sponge method was conducted. Determination of two target analytes was possible using only 5 ng of sample. Our study shows the potential of an affinity screening to prioritize soaking parameters by estimation of the guest concentration in a single crystal for one or multiple target compounds within a short period of time.
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Affiliation(s)
- Lara Rosenberger
- Discovery and Development Technologies (DDTech), Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; Department of Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Carolina von Essen
- Innovation Center, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Anupam Khutia
- Innovation Center, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Clemens Kühn
- Innovation Center, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany.
| | - Katrin Georgi
- Discovery and Development Technologies (DDTech), Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Anna K H Hirsch
- Department of Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Rolf W Hartmann
- Department of Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Lassina Badolo
- Discovery and Development Technologies (DDTech), Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
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16
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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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17
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Lunn RJ, Tocher DA, Sidebottom PJ, Montgomery MG, Keates AC, Carmalt CJ. Applying the Crystalline Sponge Method to Agrochemicals: Obtaining X-ray Structures of the Fungicide Metalaxyl-M and Herbicide S-Metolachlor. CRYSTAL GROWTH & DESIGN 2021; 21:3024-3036. [PMID: 34054355 PMCID: PMC8154245 DOI: 10.1021/acs.cgd.1c00196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/29/2021] [Indexed: 06/12/2023]
Abstract
The crystalline sponge method is a technique that provides the ability to elucidate the absolute structure of noncrystalline or hard to crystallize compounds through single-crystal X-ray diffraction by removing the need to obtain crystals of the target compound. In this study the crystalline sponges {[(ZnX2)3(2,4,6-tris(4-pyridyl)-1,3,5-trazine)2].x(solvent)} n (X = I, Br) were used to obtain X-ray structures of the agrochemical active ingredients metalaxyl-M and S-metolachlor. The effect of the temperature used during guest uptake and the influence of changing the host framework ZnX2 nodes on guest encapsulation were investigated. Additionally, three compounds containing chemical fragments similar to those of metalaxyl-M and S-metolachlor (phenylacetaldehyde, N-ethyl-o-toluidine, and methyl phenylacetate) were also encapsulated. This allowed for the effect of guest size on the position that guests occupy within the host frameworks to be examined. The disorder experienced by the guest compounds was documented, and an analysis of the intermolecular host-guest interactions (CH···π and π ···π) used for guest ordering within the host frameworks was also undertaken in this study.
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Affiliation(s)
- Richard
D. J. Lunn
- University
College London, Department of Chemistry, 20 Gordon Street, London WC1H 0AJ, U.K.
| | - Derek A. Tocher
- University
College London, Department of Chemistry, 20 Gordon Street, London WC1H 0AJ, U.K.
| | - Philip J. Sidebottom
- Syngenta,
Jealott’s Hill International Research Centre, Bracknell, Berkshire RG42 6EY, U.K.
| | - Mark G. Montgomery
- Syngenta,
Jealott’s Hill International Research Centre, Bracknell, Berkshire RG42 6EY, U.K.
| | - Adam C. Keates
- Syngenta,
Jealott’s Hill International Research Centre, Bracknell, Berkshire RG42 6EY, U.K.
| | - Claire J. Carmalt
- University
College London, Department of Chemistry, 20 Gordon Street, London WC1H 0AJ, U.K.
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18
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Cardenal A, Ramadhar TR. Application of Crystalline Matrices for the Structural Determination of Organic Molecules. ACS CENTRAL SCIENCE 2021; 7:406-414. [PMID: 33791424 PMCID: PMC8006175 DOI: 10.1021/acscentsci.0c01492] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Indexed: 06/12/2023]
Abstract
While single-crystal X-ray diffraction (SC-XRD) is one of the most powerful structural determination techniques for organic molecules, the requirement of obtaining a suitable crystal for analysis limits its applicability, particularly for liquids and amorphous solids. The emergent use of preformed porous crystalline matrices that can absorb organic compounds and stabilize them via host-guest interactions for observation via SC-XRD offers a way to overcome this hindrance. A topical and current discussion of SC-XRD in organic chemistry and the use of preformed matrices for the in crystallo analysis of organic compounds, with a particular focus on the absolute structure determination of chiral molecules, is presented. Preformed crystalline matrices that are covered include metal-organic frameworks (MOFs) as used in the crystalline sponge method, metal-organic polyhedra (MOPs, coordination cages), porous organic materials (POMs)/porous organic molecular crystals (POMCs), and biological scaffolds. An outlook and perspective on the current technology and on its future directions is provided.
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Affiliation(s)
- Ashley
D. Cardenal
- Department of Chemistry, Howard University, Washington, DC 20059, United States
| | - Timothy R. Ramadhar
- Department of Chemistry, Howard University, Washington, DC 20059, United States
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19
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Abstract
The crystalline sponge (CS) method was developed as an X-ray crystallographic molecular structure analysis method that can be performed without the need for crystallization of the analyte. CS has strong molecular-recognition properties and a highly flexible framework. The amount of analyte can be reduced to a sub-milligram level. These features of the crystalline nano-space allow for determining the absolute structure of a trace analyte. In this review, we focus on the discovery of the CS method and its applications to biosynthetic products in combination with NMR spectroscopy. We also describe some examples of the CS method that are used mainly in combination with mass spectrometry (MS). Both approaches demonstrate the potential of microanalysis to determine the molecular structure of an unknown sample. Finally, we mention the use of a crystalline "nano-surface" rather than a crystalline nano-space in MS, which can detect small metabolites as well as post-translation biomolecules.
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Affiliation(s)
- Kazuaki Ohara
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa, 769-2193, Japan
| | - Kentaro Yamaguchi
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa, 769-2193, Japan
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20
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Yu MH, Liu XT, Space B, Chang Z, Bu XH. Metal-organic materials with triazine-based ligands: From structures to properties and applications. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213518] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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21
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Albalad J, Sumby CJ, Maspoch D, Doonan CJ. Elucidating pore chemistry within metal–organic frameworks via single crystal X-ray diffraction; from fundamental understanding to application. CrystEngComm 2021. [DOI: 10.1039/d1ce00067e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The application of metal–organic frameworks (MOFs) to diverse chemical sectors is aided by their crystallinity, which permits the use of X-ray crystallography to characterise their pore chemistry and provides invaluable insight into their properties.
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Affiliation(s)
- Jorge Albalad
- Department of Chemistry and Centre for Advanced Nanomaterials
- The University of Adelaide
- Adelaide
- Australia
| | - Christopher J. Sumby
- Department of Chemistry and Centre for Advanced Nanomaterials
- The University of Adelaide
- Adelaide
- Australia
| | - Daniel Maspoch
- Catalan Institute of Nanoscience and Nanotechnology (ICN2)
- CSIC
- Barcelona Institute of Science and Technology
- Barcelona
- Spain
| | - Christian J. Doonan
- Department of Chemistry and Centre for Advanced Nanomaterials
- The University of Adelaide
- Adelaide
- Australia
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22
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Kawahata M, Tominaga M, Komatsu A, Hyodo T, Yamaguchi K. Structural elucidation of liquid cyclooctatetraene and cyclooctadienes in inclusion crystals. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Krupp F, Frey W, Richert C. Absolute Configuration of Small Molecules by Co-Crystallization. Angew Chem Int Ed Engl 2020; 59:15875-15879. [PMID: 32441841 PMCID: PMC7540501 DOI: 10.1002/anie.202004992] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Indexed: 12/18/2022]
Abstract
The most reliable method to determine the absolute configuration of chiral molecules is X-ray crystallography, but small molecules can be difficult to crystallize. We report rapid co-crystallization of tetraaryladamantanes with small molecules as different as n-decane to nicotine to produce crystals for X-ray analysis and the assignment of absolute configuration when the molecules are chiral. A screen of 52 diverse compounds gave inclusion in co-crystals for 88 % of all cases and a high-resolution structure in 77 % of cases. Furthermore, starting from three milligrams of analyte, a combination of NMR spectroscopy and X-ray crystallography produced a full structure in less than three days using an adamantane crystallization chaperone that encapsulates the analyte at room temperature.
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Affiliation(s)
- Felix Krupp
- Institute of Organic ChemistryUniversity of Stuttgart70569StuttgartGermany
| | - Wolfgang Frey
- Institute of Organic ChemistryUniversity of Stuttgart70569StuttgartGermany
| | - Clemens Richert
- Institute of Organic ChemistryUniversity of Stuttgart70569StuttgartGermany
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24
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Saito F, Schreiner PR. Determination of the Absolute Configurations of Chiral Alkanes – An Analysis of the Available Tools. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000711] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Fumito Saito
- Institute of Organic Chemistry Justus Liebig University Heinrich‐Buff‐Ring 17 35392 Giessen Germany
| | - Peter R. Schreiner
- Institute of Organic Chemistry Justus Liebig University Heinrich‐Buff‐Ring 17 35392 Giessen Germany
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25
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Krupp F, Frey W, Richert C. Absolute Configuration of Small Molecules by Co‐Crystallization. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004992] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Felix Krupp
- Institute of Organic Chemistry University of Stuttgart 70569 Stuttgart Germany
| | - Wolfgang Frey
- Institute of Organic Chemistry University of Stuttgart 70569 Stuttgart Germany
| | - Clemens Richert
- Institute of Organic Chemistry University of Stuttgart 70569 Stuttgart Germany
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26
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Saito F, Gerbig D, Becker J, Schreiner PR. Absolute Configuration of trans-Perhydroazulene. Org Lett 2020; 22:3895-3899. [DOI: 10.1021/acs.orglett.0c01184] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fumito Saito
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Dennis Gerbig
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Jonathan Becker
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Peter R. Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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27
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Schwartz HA, Laurenzen H, Kerschbaumer S, Werker M, Olthof S, Kopacka H, Huppertz H, Meerholz K, Ruschewitz U. High fatigue resistance of a photochromic dithienylethene embedded into the pores of a metal–organic framework (MOF). Photochem Photobiol Sci 2020; 19:1730-1740. [DOI: 10.1039/d0pp00002g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The incorporation of photochromic dyes into porous metal–organic frameworks (MOFs) is an attractive way to transfer the photochromic properties of the dye to a solid crystalline material.
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Affiliation(s)
- Heidi A. Schwartz
- Institute of Inorganic Chemistry
- University of Cologne
- D-50939 Cologne
- Germany
- Institute of General, Inorganic, and Theoretical Chemistry
| | - Hannah Laurenzen
- Institute of Inorganic Chemistry
- University of Cologne
- D-50939 Cologne
- Germany
| | - Samuel Kerschbaumer
- Institute of General, Inorganic, and Theoretical Chemistry
- University of Innsbruck
- Center for Chemistry and Biomedicine
- A-6020 Innsbruck
- Austria
| | - Melanie Werker
- Institute of Inorganic Chemistry
- University of Cologne
- D-50939 Cologne
- Germany
| | - Selina Olthof
- Institute of Physical Chemistry
- University of Cologne
- D-50939 Cologne
- Germany
| | - Holger Kopacka
- Institute of General, Inorganic, and Theoretical Chemistry
- University of Innsbruck
- Center for Chemistry and Biomedicine
- A-6020 Innsbruck
- Austria
| | - Hubert Huppertz
- Institute of General, Inorganic, and Theoretical Chemistry
- University of Innsbruck
- Center for Chemistry and Biomedicine
- A-6020 Innsbruck
- Austria
| | - Klaus Meerholz
- Institute of Physical Chemistry
- University of Cologne
- D-50939 Cologne
- Germany
| | - Uwe Ruschewitz
- Institute of Inorganic Chemistry
- University of Cologne
- D-50939 Cologne
- Germany
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28
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Schwartz HA, Schaniel D, Ruschewitz U. Tracking the light-induced isomerization processes and the photostability of spiropyrans embedded in the pores of crystalline nanoporous MOFs via IR spectroscopy. Photochem Photobiol Sci 2020; 19:1433-1441. [DOI: 10.1039/d0pp00267d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Difference IR spectroscopy of spiropyran@MOF systems to obtain the characteristic signatures of the spiropyran and merocyanine form at ambient conditions.
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Affiliation(s)
- Heidi A. Schwartz
- Institute of General
- Inorganic and Theoretical Chemistry
- University of Innsbruck
- A-6020 Innsbruck
- Austria
| | | | - Uwe Ruschewitz
- Department of Chemistry
- University of Cologne
- D-50939 Cologne
- Germany
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29
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Abstract
Host-guest interactions are the key to the supramolecular chemistry and the further application of the receptors to study the structural details of the small guest molecules. Crystalline sponges as a kind of supramolecular receptor need to be investigated in terms of the binding ability with the guests. We found in this work that one guest with σ-hole donors and another with electron-donating species were separately entrapped in two distinct channels of the host framework via the crystalline sponge method. Halogen bonding and weak hydrogen bonding were detected between the host and the two guests, respectively. The ability of the crystalline sponge to absorb and sort guests of different types was unambiguously confirmed by X-ray crystallography.
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Affiliation(s)
- Liangqian Yuan
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis, College of Chemistry , Central China Normal University , Luoyu Road 152 , Wuhan 430079 , People's Republic of China
| | - Siyu Li
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis, College of Chemistry , Central China Normal University , Luoyu Road 152 , Wuhan 430079 , People's Republic of China
| | - Fangfang Pan
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis, College of Chemistry , Central China Normal University , Luoyu Road 152 , Wuhan 430079 , People's Republic of China
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30
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Kunde T, Schmidt BM. Microcrystal Electron Diffraction (MicroED) for Small-Molecule Structure Determination. Angew Chem Int Ed Engl 2018; 58:666-668. [PMID: 30548517 DOI: 10.1002/anie.201813215] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Indexed: 01/08/2023]
Abstract
The development of new methods to analyze and determine molecular structures parallels the ability to accelerate synthetic research. For many decades, single-crystal analysis by X-ray diffraction (SXRD) has been the definitive tool for structural analysis at the atomic level; the drawback, however, is that a suitable single crystal of the analyte needs to be grown. The recent innovation of the crystalline sponge (CS) method allows the microanalysis of compounds simply soaked in a readily prepared CS crystal, thus circumventing the need to screen crystallization conditions while also using only a trace amount of the sample. In this context, electron diffraction for the structure determination of small molecules is discussed as potentially the next big development in this field.
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Affiliation(s)
- Tom Kunde
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Bernd M Schmidt
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
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31
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Kunde T, Schmidt BM. Mikrokristalline Elektronenbeugung (MicroED) zur Strukturaufklärung niedermolekularer Verbindungen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201813215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Tom Kunde
- Institut für Organische Chemie und Makromolekulare ChemieHeinrich-Heine-Universität Düsseldorf Universitätsstraße 1 40225 Düsseldorf Deutschland
| | - Bernd M. Schmidt
- Institut für Organische Chemie und Makromolekulare ChemieHeinrich-Heine-Universität Düsseldorf Universitätsstraße 1 40225 Düsseldorf Deutschland
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32
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Du Q, Peng J, Wu P, He H. Review: Metal-organic framework based crystalline sponge method for structure analysis. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.02.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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33
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Wada N, Kersten RD, Iwai T, Lee S, Sakurai F, Kikuchi T, Fujita D, Fujita M, Weng JK. Crystalline-Sponge-Based Structural Analysis of Crude Natural Product Extracts. Angew Chem Int Ed Engl 2018; 57:3671-3675. [DOI: 10.1002/anie.201713219] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Naoki Wada
- Department of Applied Chemistry; Graduate School of Engineering; The University of Tokyo, and JST- ACCEL; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Roland D. Kersten
- Whitehead Institute for Biomedical Research; 455 Main Street Cambridge MA USA
| | - Takahiro Iwai
- Department of Applied Chemistry; Graduate School of Engineering; The University of Tokyo, and JST- ACCEL; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Shoukou Lee
- Department of Applied Chemistry; Graduate School of Engineering; The University of Tokyo, and JST- ACCEL; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Fumie Sakurai
- Department of Applied Chemistry; Graduate School of Engineering; The University of Tokyo, and JST- ACCEL; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Takashi Kikuchi
- Rigaku Corporation; 3-9-12 Matsubara-cho, Akishima-shi Tokyo 196-8628 Japan
| | - Daishi Fujita
- Department of Applied Chemistry; Graduate School of Engineering; The University of Tokyo, and JST- ACCEL; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
- Whitehead Institute for Biomedical Research; 455 Main Street Cambridge MA USA
| | - Makoto Fujita
- Department of Applied Chemistry; Graduate School of Engineering; The University of Tokyo, and JST- ACCEL; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research; 455 Main Street Cambridge MA USA
- Department of Biology; Massachusetts Institute of Technology; Cambridge MA USA
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34
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Wada N, Kersten RD, Iwai T, Lee S, Sakurai F, Kikuchi T, Fujita D, Fujita M, Weng JK. Crystalline-Sponge-Based Structural Analysis of Crude Natural Product Extracts. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713219] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Naoki Wada
- Department of Applied Chemistry; Graduate School of Engineering; The University of Tokyo, and JST- ACCEL; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Roland D. Kersten
- Whitehead Institute for Biomedical Research; 455 Main Street Cambridge MA USA
| | - Takahiro Iwai
- Department of Applied Chemistry; Graduate School of Engineering; The University of Tokyo, and JST- ACCEL; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Shoukou Lee
- Department of Applied Chemistry; Graduate School of Engineering; The University of Tokyo, and JST- ACCEL; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Fumie Sakurai
- Department of Applied Chemistry; Graduate School of Engineering; The University of Tokyo, and JST- ACCEL; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Takashi Kikuchi
- Rigaku Corporation; 3-9-12 Matsubara-cho, Akishima-shi Tokyo 196-8628 Japan
| | - Daishi Fujita
- Department of Applied Chemistry; Graduate School of Engineering; The University of Tokyo, and JST- ACCEL; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
- Whitehead Institute for Biomedical Research; 455 Main Street Cambridge MA USA
| | - Makoto Fujita
- Department of Applied Chemistry; Graduate School of Engineering; The University of Tokyo, and JST- ACCEL; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research; 455 Main Street Cambridge MA USA
- Department of Biology; Massachusetts Institute of Technology; Cambridge MA USA
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35
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de Poel W, Tinnemans PT, Duchateau ALL, Honing M, Rutjes FPJT, Vlieg E, de Gelder R. Racemic and Enantiopure Camphene and Pinene Studied by the Crystalline Sponge Method. CRYSTAL GROWTH & DESIGN 2018; 18:126-132. [PMID: 29317854 PMCID: PMC5754839 DOI: 10.1021/acs.cgd.7b00942] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 11/28/2017] [Indexed: 05/31/2023]
Abstract
The use of an achiral metal-organic framework for structure determination of chiral compounds is demonstrated for camphene and pinene. The structure of enantiopure β-pinene can be resolved using the crystalline sponge method. However, α-pinene cannot be resolved using enantiopure material alone because no ordering of guest molecules takes place in that case. Interestingly, enantiomeric pairs order inside the channels of the host framework when impure (+)-camphene is offered to the host, which is also the case when a racemic mixture of α-pinene is used. A mixture of (+)-α-pinene and (-)-β-pinene also leads to ordered incorporation in the host, showing the influence of the presence of an inversion center in the host framework. We further show that powder X-ray diffraction provides a direct view on incorporation of ordered guest molecules. This technique, therefore, provides a way to determine the optimal and/or minimal soaking time. In contrast, color change of the crystal only demonstrates guest uptake, not ordering. Moreover, we show that color change can also be caused by guest-induced host degradation.
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Affiliation(s)
- Wester de Poel
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Paul T. Tinnemans
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | | | - Maarten Honing
- DSM,
Resolve, Urmonderbaan
22, Geleen, 6160 MD, The Netherlands
| | - Floris P. J. T. Rutjes
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Elias Vlieg
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - René de Gelder
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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36
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Sakurai F, Khutia A, Kikuchi T, Fujita M. X‐ray Structure Analysis of N‐Containing Nucleophilic Compounds by the Crystalline Sponge Method. Chemistry 2017; 23:15035-15040. [DOI: 10.1002/chem.201704176] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Fumie Sakurai
- Department of Applied Chemistry School of Engineering The University of Tokyo 7-3-1 Hongo Tokyo Bunkyo-ku 113–8656 Japan
| | - Anupam Khutia
- Department of Applied Chemistry School of Engineering The University of Tokyo 7-3-1 Hongo Tokyo Bunkyo-ku 113–8656 Japan
| | - Takashi Kikuchi
- Rigaku Corporation 3-9-12 Matsubara-cho Tokyo Akishima-shi 196–8628 Japan
| | - Makoto Fujita
- Department of Applied Chemistry School of Engineering The University of Tokyo 7-3-1 Hongo Tokyo Bunkyo-ku 113–8656 Japan
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