1
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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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2
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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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3
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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: 8] [Impact Index Per Article: 8.0] [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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4
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Li H, Li Y, Jiao J, Lin C. Recent research progress on crystallization strategies for difficult-to-crystallize organic molecules. RESULTS IN CHEMISTRY 2023. [DOI: 10.1016/j.rechem.2023.100859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
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5
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Guo ST, Cui PF, Liu XR, Jin GX. Synthesis of Carborane-Backbone Metallacycles for Highly Selective Capture of n-Pentane. J Am Chem Soc 2022; 144:22221-22228. [PMID: 36442076 DOI: 10.1021/jacs.2c10201] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The specific recognition and separation of alkanes with similar molecular structures and close boiling points face significant scientific challenges and industrial demands. Here, rectangular carborane-based metallacycles were designed to selectively encapsulate n-pentane from n-pentane, iso-pentane, and cyclo-pentane mixtures in a simple-to-operate and more energy-efficient way. Metallacycle 1, bearing 1,2-di(4-pyridyl) ethylene, can selectively separate n-pentane from these three-component mixtures with a purity of 97%. The selectivity is ascribed to the capture of the preferred guest with matching size, C-H···π interactions, and potential B-Hδ-···Hδ+-C interactions. Besides, the removal of n-pentane gives rise to original guest-free carborane-based metallacycles, which can be recycled without losing performance. Considering the variety of substituted carborane derivatives, metal ions, and organic linkers, these new carborane-based supramolecular coordination complexes (SCCs) may be broadly applicable to other challenging recognition and separation systems with good performance.
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Affiliation(s)
- Shu-Ting Guo
- State Key Laboratory of Molecular Engineering of Polymers, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, 2005 Songhu Road, Shanghai 200433, P. R. China
| | - Peng-Fei Cui
- State Key Laboratory of Molecular Engineering of Polymers, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, 2005 Songhu Road, Shanghai 200433, P. R. China
| | - Xin-Ran Liu
- State Key Laboratory of Molecular Engineering of Polymers, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, 2005 Songhu Road, Shanghai 200433, P. R. China
| | - Guo-Xin Jin
- State Key Laboratory of Molecular Engineering of Polymers, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, 2005 Songhu Road, Shanghai 200433, P. R. China.,State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China
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6
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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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7
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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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8
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Meurer F, von Essen C, Kühn C, Puschmann H, Bodensteiner M. The benefits of Cu Kβ radiation for the single-crystal X-ray structure determination of crystalline sponges. IUCRJ 2022; 9:349-354. [PMID: 35546798 PMCID: PMC9067116 DOI: 10.1107/s2052252522002147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/23/2022] [Indexed: 06/15/2023]
Abstract
The crystalline sponge method facilitates the X-ray structure determination of samples that do not crystallize or are too sparsely available to afford viable crystallization. By including these materials in a metal-organic framework, the structure of the guest molecules can be determined. Some of the inherent difficulties of this method are discussed and the use of Cu Kβ radiation is presented as a simple and effective means to improve the quality of the diffraction data that can be obtained from a sponge crystal.
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Affiliation(s)
- Florian Meurer
- University of Regensburg, Universitätsstrasse 31, Regensburg, 93053 Bayern, Germany
| | - Carolina von Essen
- Merck Innovation Center, Merck KGaA, Frankfurter Strasse 250, Darmstadt, 64293 Hessen, Germany
| | - Clemens Kühn
- Merck Innovation Center, Merck KGaA, Frankfurter Strasse 250, Darmstadt, 64293 Hessen, Germany
| | - Horst Puschmann
- OlexSys Ltd, Chemistry Department, Durham University, Durham DH1 3LE, United Kingdom
| | - Michael Bodensteiner
- University of Regensburg, Universitätsstrasse 31, Regensburg, 93053 Bayern, Germany
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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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Chaikittisilp W, Yamauchi Y, Ariga K. Material Evolution with Nanotechnology, Nanoarchitectonics, and Materials Informatics: What will be the Next Paradigm Shift in Nanoporous Materials? ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2107212. [PMID: 34637159 DOI: 10.1002/adma.202107212] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/05/2021] [Indexed: 05/27/2023]
Abstract
Materials science and chemistry have played a central and significant role in advancing society. With the shift toward sustainable living, it is anticipated that the development of functional materials will continue to be vital for sustaining life on our planet. In the recent decades, rapid progress has been made in materials science and chemistry owing to the advances in experimental, analytical, and computational methods, thereby producing several novel and useful materials. However, most problems in material development are highly complex. Here, the best strategy for the development of functional materials via the implementation of three key concepts is discussed: nanotechnology as a game changer, nanoarchitectonics as an integrator, and materials informatics as a super-accelerator. Discussions from conceptual viewpoints and example recent developments, chiefly focused on nanoporous materials, are presented. It is anticipated that coupling these three strategies together will open advanced routes for the swift design and exploratory search of functional materials truly useful for solving real-world problems. These novel strategies will result in the evolution of nanoporous functional materials.
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Affiliation(s)
- Watcharop Chaikittisilp
- JST-ERATO Yamauchi Materials Space-Tectonics Project, National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
- Research and Services Division of Materials Data and Integrated System (MaDIS), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
| | - Yusuke Yamauchi
- JST-ERATO Yamauchi Materials Space-Tectonics Project, National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
- Australian Institute for Bioengineering and Nanotechnology (AIBN) and School of Chemical Engineering, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Katsuhiko Ariga
- JST-ERATO Yamauchi Materials Space-Tectonics Project, National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
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11
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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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12
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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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13
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Elyashberg M, Argyropoulos D. Computer Assisted Structure Elucidation (CASE): Current and future perspectives. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:669-690. [PMID: 33197069 DOI: 10.1002/mrc.5115] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/31/2020] [Accepted: 11/08/2020] [Indexed: 06/11/2023]
Abstract
The first efforts for the development of methods for Computer-Assisted Structure Elucidation (CASE) were published more than 50 years ago. CASE expert systems based on one-dimensional (1D) and two-dimensional (2D) Nuclear Magnetic Resonance (NMR) data have matured considerably by now. The structures of a great number of complex natural products have been elucidated and/or revised using such programs. In this article, we discuss the most likely directions in which CASE will evolve. We act on the premise that a synergistic interaction exists between CASE, new NMR experiments, and methods of computational chemistry, which are continuously being improved. The new developments in NMR experiments (long-range correlation experiments, pure-shift methods, coupling constants measurement and prediction, residual dipolar couplings [RDCs]), and residual chemical shift anisotropies [RCSAs], evolution of density functional theory (DFT), and machine learning algorithms will have an influence on CASE systems and vice versa. This is true also for new techniques for chemical analysis (Atomic Force Microscopy [AFM], "crystalline sponge" X-ray analysis, and micro-Electron Diffraction [micro-ED]), which will be used in combination with expert systems. We foresee that CASE will be utilized widely and become a routine tool for NMR spectroscopists and analysts in academic and industrial laboratories. We believe that the "golden age" of CASE is still in the future.
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14
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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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15
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Update on sesquiterpenes from red macroalgae of the Laurencia genus and their biological activities (2015–2020). ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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16
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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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17
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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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18
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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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19
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20
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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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21
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Abstract
This review covers the literature published between January and December in 2018 for marine natural products (MNPs), with 717 citations (706 for the period January to December 2018) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1554 in 469 papers for 2018), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. The proportion of MNPs assigned absolute configuration over the last decade is also surveyed.
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Affiliation(s)
- Anthony R Carroll
- School of Environment and Science, Griffith University, Gold Coast, Australia. and Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Brent R Copp
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Rohan A Davis
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia and School of Environment and Science, Griffith University, Brisbane, Australia
| | - Robert A Keyzers
- Centre for Biodiscovery, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Michèle R Prinsep
- Chemistry, School of Science, University of Waikato, Hamilton, New Zealand
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22
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Tashiro S, Umeki T, Kubota R, Shionoya M. Face-selective adsorption of a prochiral compound on the chiral pore-surface of a metal-macrocycle framework (MMF) directed towards stereoselective reactions. Faraday Discuss 2021; 225:197-209. [PMID: 33104769 DOI: 10.1039/d0fd00019a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular adsorption on a surface is a unique way to break the mirror-symmetry of prochiral molecules, and therefore the use of chiral surfaces is an effective strategy for achieving highly selective chiral separation and asymmetric catalytic reactions based on molecular adsorption with high diastereoselectivity. We have previously reported a porous metal-macrocycle framework (MMF) with an enantiomeric pair of chiral pore-surfaces derived from Pd-helical macrocycles as the ingredients of the framework. Aiming at applying the chiral pore-surface of the MMF to asymmetric reactions and chiral separation, herein we propose a strategy to utilize one of the enantiomerically paired pore-surfaces as a homochiral pore-surface with the aid of chiral auxiliaries that can block only one side of the enantiomeric pore-surfaces in a site-selective manner. Single-crystal X-ray diffraction analysis revealed that a chiral auxiliary, (1R)- or (1S)-1-(3-chlorophenyl)ethanol, and a prochiral guest molecule, 2'-hydroxyacetophenone, were cooperatively arranged in each pore unit so that the prochiral guest molecule can face-selectively bind to the homochiral pore-surface.
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Affiliation(s)
- Shohei Tashiro
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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23
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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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24
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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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25
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Taniguchi Y, Matsumoto R, Kadota T. An Expansion of Crystalline Sponge X-ray Analysis to Elucidate the Molecular Structure of Reactive Compounds via Ion Pair Formation. Chemistry 2020; 26:15799-15803. [PMID: 32729166 DOI: 10.1002/chem.202002504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/28/2020] [Indexed: 12/17/2022]
Abstract
The crystalline sponge (CS) method allows structural elucidation of a target compound (guest) in solution by single crystal X-ray diffraction through trapping the guest into the CS framework. In principle, the CS method is inapplicable to reactive compounds that break the CS framework, such as acidic, basic, or nucleophilic ones. Here, a solution to this problem is disclosed wherein an ion pair of the guest compound is formed during the guest-soaking step by adding a suitable reagent. The ion pair can be observed and does not damage the CS framework. Using the developed method, amino, guanidino, and amidino compounds have been successfully analyzed as ion pairs with sulfonic acids. Practical utility has been shown because the absolute configurations of optically resolved amine derivatives were revealed with only a few micrograms. This demonstrates that the ion-pair-soaking method is simple and expands the range of compounds applicable to the CS method.
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Affiliation(s)
- Yoshimasa Taniguchi
- Kirin Central Research Institute, Research & Development Division, Kirin Holdings Company, Ltd., 1-13-5, Fukuura, Kanazawa-ku, Yokohama-shi, Kanagawa, 236-0004, Japan
| | - Rie Matsumoto
- Kirin Central Research Institute, Research & Development Division, Kirin Holdings Company, Ltd., 1-13-5, Fukuura, Kanazawa-ku, Yokohama-shi, Kanagawa, 236-0004, Japan
| | - Tomoyuki Kadota
- Kirin Central Research Institute, Research & Development Division, Kirin Holdings Company, Ltd., 1-13-5, Fukuura, Kanazawa-ku, Yokohama-shi, Kanagawa, 236-0004, Japan
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26
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Pilgrim BS, Champness NR. Metal-Organic Frameworks and Metal-Organic Cages - A Perspective. Chempluschem 2020; 85:1842-1856. [PMID: 32833342 DOI: 10.1002/cplu.202000408] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/31/2020] [Indexed: 12/20/2022]
Abstract
The fields of metal-organic cages (MOCs) and metal-organic frameworks (MOFs) are both highly topical and continue to develop at a rapid pace. Despite clear synergies between the two fields, overlap is rarely observed. This article discusses the peculiarities and similarities of MOCs and MOFs in terms of synthetic strategies and approaches to system characterisation. The stability of both classes of material is compared, particularly in relation to their applications in guest storage and catalysis. Lastly, suggestions are made for opportunities for each field to learn and develop in partnership with the other.
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Affiliation(s)
- Ben S Pilgrim
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Neil R Champness
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
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27
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Rosenberger L, von Essen C, Khutia A, Kühn C, Urbahns K, Georgi K, Hartmann RW, Badolo L. Crystalline Sponges as a Sensitive and Fast Method for Metabolite Identification: Application to Gemfibrozil and its Phase I and II Metabolites. Drug Metab Dispos 2020; 48:587-593. [DOI: 10.1124/dmd.120.091140] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/20/2020] [Indexed: 11/22/2022] Open
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28
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Cui PF, Lin YJ, Li ZH, Jin GX. Dihydrogen Bond Interaction Induced Separation of Hexane Isomers by Self-Assembled Carborane Metallacycles. J Am Chem Soc 2020; 142:8532-8538. [DOI: 10.1021/jacs.0c03176] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Peng-Fei Cui
- State Key Laboratory of Molecular Engineering of Polymers, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, 2005 Songhu Road, Shanghai 200433, People’s Republic of China
| | - Yue-Jian Lin
- State Key Laboratory of Molecular Engineering of Polymers, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, 2005 Songhu Road, Shanghai 200433, People’s Republic of China
| | - Zhen-Hua Li
- State Key Laboratory of Molecular Engineering of Polymers, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, 2005 Songhu Road, Shanghai 200433, People’s Republic of China
| | - Guo-Xin Jin
- State Key Laboratory of Molecular Engineering of Polymers, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, 2005 Songhu Road, Shanghai 200433, People’s Republic of China
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29
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Morita I, Mori T, Mitsuhashi T, Hoshino S, Taniguchi Y, Kikuchi T, Nagae K, Nasu N, Fujita M, Ohwada T, Abe I. Exploiting a C–N Bond Forming Cytochrome P450 Monooxygenase for C–S Bond Formation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916269] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Iori Morita
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan
| | - Takaaki Mitsuhashi
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Shotaro Hoshino
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Yoshimasa Taniguchi
- Central Laboratories for Key Technologies Kirin Holdings Co. Ltd. 1-13-5, Fukuura Kana-zawa-ku Yokohama-shi Kanagawa 236-0004 Japan
| | - Takashi Kikuchi
- Rigaku Corporation 3-9-12 Matsubara-cho, Akishima-shi Tokyo 196-8666 Japan
| | - Kei Nagae
- Nissan Chemical Corporation 2-10-1 Tsuboi-nishi, Funabashi-shi Chiba 274-8507 Japan
| | - Norihiro Nasu
- Mitsui Chemical Analysis & Consulting Service, Inc. 580-32 Nagaura, Sodegaura-city Chiba 299-0265 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 National Institutes of Natural Sciences 5-1 Higashiyama Myodaiji, Okazaki 444-8787 Japan
| | - Tomohiko Ohwada
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan
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30
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Morita I, Mori T, Mitsuhashi T, Hoshino S, Taniguchi Y, Kikuchi T, Nagae K, Nasu N, Fujita M, Ohwada T, Abe I. Exploiting a C-N Bond Forming Cytochrome P450 Monooxygenase for C-S Bond Formation. Angew Chem Int Ed Engl 2020; 59:3988-3993. [PMID: 31886618 DOI: 10.1002/anie.201916269] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Indexed: 01/01/2023]
Abstract
C-S bond formation reactions are widely distributed in the biosynthesis of biologically active molecules, and thus have received much attention over the past decades. Herein, we report intramolecular C-S bond formation by a P450 monooxygenase, TleB, which normally catalyzes a C-N bond formation in teleocidin biosynthesis. Based on the proposed reaction mechanism of TleB, a thiol-substituted substrate analogue was synthesized and tested in the enzyme reaction, which afforded the unprecedented sulfur-containing thio-indolactam V, in addition to an unusual indole-fused 6/5/8-tricyclic product whose structure was determined by the crystalline sponge method. Interestingly, conformational analysis revealed that the SOFA conformation is stable in thio-indolactam V, in sharp contrast to the major TWIST form in indolactam V, resulting in differences in their biological activities.
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Affiliation(s)
- Iori Morita
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takaaki Mitsuhashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Shotaro Hoshino
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yoshimasa Taniguchi
- Central Laboratories for Key Technologies, Kirin Holdings Co. Ltd., 1-13-5, Fukuura Kana-zawa-ku, Yokohama-shi, Kanagawa, 236-0004, Japan
| | - Takashi Kikuchi
- Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima-shi, Tokyo, 196-8666, Japan
| | - Kei Nagae
- Nissan Chemical Corporation, 2-10-1 Tsuboi-nishi, Funabashi-shi, Chiba, 274-8507, Japan
| | - Norihiro Nasu
- Mitsui Chemical Analysis & Consulting Service, Inc., 580-32 Nagaura, Sodegaura-city, Chiba, 299-0265, 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, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
| | - Tomohiko Ohwada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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31
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Liu Y, Chen P, Shi B, Jiao T, Ju H, Liu P, Huang F. Cocrystallization with a clip-type molecule catcher: a new method to determine structures of liquid molecules. Org Chem Front 2020. [DOI: 10.1039/c9qo01526d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In order to measure the precise structure of liquid molecules by X-ray single-crystal diffraction, we report a new and easy method using a glycoluril-derived molecular clip as a molecule catcher to form cocrystals with liquid molecules.
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Affiliation(s)
- Yuezhou Liu
- State Key Laboratory of Chemical Engineering
- Center for Chemistry of High Performance & Novel Materials
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
| | - Panpan Chen
- State Key Laboratory of Chemical Engineering
- Center for Chemistry of High Performance & Novel Materials
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
| | - Bingbing Shi
- State Key Laboratory of Chemical Engineering
- Center for Chemistry of High Performance & Novel Materials
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
| | - Tianyu Jiao
- State Key Laboratory of Chemical Engineering
- Center for Chemistry of High Performance & Novel Materials
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
| | - Huaqiang Ju
- State Key Laboratory of Chemical Engineering
- Center for Chemistry of High Performance & Novel Materials
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
| | - Peiren Liu
- State Key Laboratory of Chemical Engineering
- Center for Chemistry of High Performance & Novel Materials
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
| | - Feihe Huang
- State Key Laboratory of Chemical Engineering
- Center for Chemistry of High Performance & Novel Materials
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
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32
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Alvarez R, Nievergelt PP, Slyshkina E, Müller P, Alberto R, Spingler B. Single crystal growth of water-soluble metal complexes with the help of the nano-crystallization method. Dalton Trans 2020; 49:9632-9640. [DOI: 10.1039/d0dt01236j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Let pipetting robots set up nano crystallization trials of water-soluble metal complexes in order to obtain single crystals!
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Affiliation(s)
- Ricardo Alvarez
- Department of Chemistry
- University of Zurich
- 8057 Zurich
- Switzerland
| | | | | | - Peter Müller
- Department of Chemistry
- University of Zurich
- 8057 Zurich
- Switzerland
| | - Roger Alberto
- Department of Chemistry
- University of Zurich
- 8057 Zurich
- Switzerland
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33
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Balestri D, Mazzeo PP, Carraro C, Demitri N, Pelagatti P, Bacchi A. Stepwise Evolution of Molecular Nanoaggregates Inside the Pores of a Highly Flexible Metal-Organic Framework. Angew Chem Int Ed Engl 2019; 58:17342-17350. [PMID: 31549464 DOI: 10.1002/anie.201907621] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/30/2019] [Indexed: 11/12/2022]
Abstract
The crystalline sponge method (CSM) is primarily used for structural determination by single-crystal X-ray diffraction of a single analyte encapsulated inside a porous MOF. As the host-guest systems often show severe disorder, reliable crystallographic determination is demanding; thus the dynamics of the guest entering and the formation of nanoconfined molecular aggregates has not been in the spotlight. Now, the concept is investigated of the CSM for monitoring the structural evolution of nanoconfined supramolecular aggregates of eugenol guests with displacement of DMF inside the cavities of the flexible MOF, PUM168. The interpretation of the electron density provides a series of unique detailed snapshots depicting the supramolecular guest aggregation, thus showing the tight interplay between the host flexible skeleton and the molecular guests through the DMF-to-eugenol exchange process.
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Affiliation(s)
- Davide Balestri
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Viale delle Scienze, 17A, 43124, Parma, Italy
| | - Paolo P Mazzeo
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Viale delle Scienze, 17A, 43124, Parma, Italy.,Biopharmanet-TEC, Università degli studi di Parma, via Parco Area delle Scienze 27/A, 43124, Parma, Italy
| | - Claudia Carraro
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Viale delle Scienze, 17A, 43124, Parma, Italy
| | - Nicola Demitri
- Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5 in Area Science Park, 34149 Basovizza-, Trieste, Italy
| | - Paolo Pelagatti
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Viale delle Scienze, 17A, 43124, Parma, Italy.,Centro Interuniveristario di Reattività Chimica e Catalisi (CIRCC), Via Celso Ulpiani 27, 70126, Bari, Italy
| | - Alessia Bacchi
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Viale delle Scienze, 17A, 43124, Parma, Italy.,Biopharmanet-TEC, Università degli studi di Parma, via Parco Area delle Scienze 27/A, 43124, Parma, Italy
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34
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Balestri D, Mazzeo PP, Carraro C, Demitri N, Pelagatti P, Bacchi A. Stepwise Evolution of Molecular Nanoaggregates Inside the Pores of a Highly Flexible Metal–Organic Framework. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907621] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Davide Balestri
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità AmbientaleUniversità di Parma Viale delle Scienze, 17A 43124 Parma Italy
| | - Paolo P. Mazzeo
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità AmbientaleUniversità di Parma Viale delle Scienze, 17A 43124 Parma Italy
- Biopharmanet-TECUniversità degli studi di Parma via Parco Area delle Scienze 27/A 43124 Parma Italy
| | - Claudia Carraro
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità AmbientaleUniversità di Parma Viale delle Scienze, 17A 43124 Parma Italy
| | - Nicola Demitri
- Elettra—Sincrotrone Trieste S.S. 14 Km 163.5 in Area Science Park 34149 Basovizza— Trieste Italy
| | - Paolo Pelagatti
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità AmbientaleUniversità di Parma Viale delle Scienze, 17A 43124 Parma Italy
- Centro Interuniveristario di Reattività Chimica e Catalisi (CIRCC) Via Celso Ulpiani 27 70126 Bari Italy
| | - Alessia Bacchi
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità AmbientaleUniversità di Parma Viale delle Scienze, 17A 43124 Parma Italy
- Biopharmanet-TECUniversità degli studi di Parma via Parco Area delle Scienze 27/A 43124 Parma Italy
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35
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Pavlović RZ, Border SE, Finnegan TJ, Zhiquan L, Gunther MJ, Mu̅noz E, Moore CE, Hadad CM, Badjić JD. Twist–Turn–Twist Motif Chaperoned Inside Molecular Baskets. J Am Chem Soc 2019; 141:16600-16604. [PMID: 31592662 DOI: 10.1021/jacs.9b09003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Radoslav Z. Pavlović
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Sarah E. Border
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Tyler J. Finnegan
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Lei Zhiquan
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Michael J. Gunther
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Eva Mu̅noz
- Affinimeter, Edificio Emprendia, Campus Vida, Santiago de Compostela, Spain
| | - Curtis E. Moore
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Christopher M. Hadad
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Jovica D. Badjić
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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36
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Abstract
Many natural products have been used as drugs for the treatment of diverse indications. Although most U.S. pharmaceutical companies have reduced or eliminated their in-house natural-product research over the years, new approaches for compound screening and chemical synthesis are resurrecting interest in exploring the therapeutic value of natural products. The aim of this commentary is to review emerging strategies and techniques that have made natural products a viable strategic choice for inclusion in drug discovery programs. Published 2019. U.S. Government.
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Affiliation(s)
- John A Beutler
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
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37
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Fox Ramos AE, Pavesi C, Litaudon M, Dumontet V, Poupon E, Champy P, Genta-Jouve G, Beniddir MA. CANPA: Computer-Assisted Natural Products Anticipation. Anal Chem 2019; 91:11247-11252. [PMID: 31369240 DOI: 10.1021/acs.analchem.9b02216] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Traditional natural products discovery workflows implying a combination of different targeting strategies, including structure- and/or bioactivity-based approaches, afford no information about new compound structures until late in the discovery pipeline. By integrating a MS/MS prediction module and a collaborative library of (bio)chemical transformations, we have developed a new platform, coined MetWork, that is capable of anticipating the structural identity of metabolites starting from any identified compound. In our quest to discover new monoterpene indole alkaloids, we demonstrate the utility of the MetWork platform by anticipating the structures of five previously undescribed sarpagine-like N-oxide alkaloids that have been targeted and isolated from the leaves of Alstonia balansae using a molecular networking-based dereplication strategy fueled by computer-generated annotations. This study constitutes the first example of nonpeptidic molecular networking-based natural product discovery workflow, in which the targeted structures were initially generated, and therefore anticipated by a computer prior to their isolation.
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Affiliation(s)
- Alexander E Fox Ramos
- Équipe "Pharmacognosie-chimie des substances naturelles" BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay , 5 rue J.-B. Clément , 92290 Châtenay-Malabry , France
| | - Coralie Pavesi
- Équipe "Pharmacognosie-chimie des substances naturelles" BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay , 5 rue J.-B. Clément , 92290 Châtenay-Malabry , France
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS, ICSN UPR 2301, Université Paris-Saclay , 21 avenue de la Terrasse , 91198 , Gif-sur-Yvette , France
| | - Vincent Dumontet
- Institut de Chimie des Substances Naturelles, CNRS, ICSN UPR 2301, Université Paris-Saclay , 21 avenue de la Terrasse , 91198 , Gif-sur-Yvette , France
| | - Erwan Poupon
- Équipe "Pharmacognosie-chimie des substances naturelles" BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay , 5 rue J.-B. Clément , 92290 Châtenay-Malabry , France
| | - Pierre Champy
- Équipe "Pharmacognosie-chimie des substances naturelles" BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay , 5 rue J.-B. Clément , 92290 Châtenay-Malabry , France
| | - Grégory Genta-Jouve
- C-TAC UMR CNRS 8038 CiTCoM, Faculté de Pharmacie de Paris, Université Paris Descartes , 4 avenue de l'Observatoire , 75006 Paris , France.,Muséum National d'Histoire Naturelle, Unité Molécules de Communication et Adaptation des Micro-organismes (UMR 7245) , Sorbonne Universités, CNRS , 75006 Paris , France
| | - Mehdi A Beniddir
- Équipe "Pharmacognosie-chimie des substances naturelles" BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay , 5 rue J.-B. Clément , 92290 Châtenay-Malabry , France
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38
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Hoshino S, Mitsuhashi T, Kikuchi T, Wong CP, Morita H, Awakawa T, Fujita M, Abe I. Structural Elucidation of Tenebrathin: Cytotoxic C-5-Substituted γ-Pyrone with a Nitroaryl Side Chain from Streptoalloteichus tenebrarius. Org Lett 2019; 21:6519-6522. [DOI: 10.1021/acs.orglett.9b02443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Shotaro Hoshino
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takaaki Mitsuhashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takashi Kikuchi
- Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima-shi, Tokyo 196-8666, Japan
| | - Chin Piow Wong
- Institute of Natural Medicine, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Hiroyuki Morita
- Institute of Natural Medicine, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, 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, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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39
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Adam R, Mon M, Greco R, Kalinke LHG, Vidal-Moya A, Fernandez A, Winpenny REP, Doménech-Carbó A, Leyva-Pérez A, Armentano D, Pardo E, Ferrando-Soria J. Self-Assembly of Catalytically Active Supramolecular Coordination Compounds within Metal-Organic Frameworks. J Am Chem Soc 2019; 141:10350-10360. [PMID: 31194534 DOI: 10.1021/jacs.9b03914] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Supramolecular coordination compounds (SCCs) represent the power of coordination chemistry methodologies to self-assemble discrete architectures with targeted properties. SCCs are generally synthesized in solution, with isolated fully coordinated metal atoms as structural nodes, thus severely limited as metal-based catalysts. Metal-organic frameworks (MOFs) show unique features to act as chemical nanoreactors for the in situ synthesis and stabilization of otherwise not accessible functional species. Here, we present the self-assembly of PdII SCCs within the confined space of a pre-formed MOF (SCCs@MOF) and its post-assembly metalation to give a PdII-AuIII supramolecular assembly, crystallography underpinned. These SCCs@MOFs catalyze the coupling of boronic acids and/or alkynes, representative multi-site metal-catalyzed reactions in which traditional SCCs tend to decompose, and retain their structural integrity as a consequence of the synergetic hybridization between SCCs and MOFs. These results open new avenues in both the synthesis of novel SCCs and their use in heterogeneous metal-based supramolecular catalysis.
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Affiliation(s)
- Rosa Adam
- Instituto de Tecnología Química , Universidad Politècnica de València-Consejo Superior de Investigaciones Científicas (UPV-CSIC) , Avda. de los Naranjos s/n , 46022 Valencia , Spain
| | - Marta Mon
- Departamento de Química Inorgánica, Instituto de Ciencia Molecular (ICMol), Catedrático José Beltrán Martínez, 2 , Universidad de Valencia , 46980 Paterna , Valencia , Spain
| | - Rossella Greco
- Instituto de Tecnología Química , Universidad Politècnica de València-Consejo Superior de Investigaciones Científicas (UPV-CSIC) , Avda. de los Naranjos s/n , 46022 Valencia , Spain
| | - Lucas H G Kalinke
- Departamento de Química Inorgánica, Instituto de Ciencia Molecular (ICMol), Catedrático José Beltrán Martínez, 2 , Universidad de Valencia , 46980 Paterna , Valencia , Spain.,Instituto Federal de Goiás-IFG , 75131-457 , Anápolis , Goiás , Brazil
| | - Alejandro Vidal-Moya
- Instituto de Tecnología Química , Universidad Politècnica de València-Consejo Superior de Investigaciones Científicas (UPV-CSIC) , Avda. de los Naranjos s/n , 46022 Valencia , Spain
| | - Antonio Fernandez
- Chemistry Department , Sir David Davies Building, Loughborough University , Loughborough LE11 3TU , United Kingdom
| | - Richard E P Winpenny
- School of Chemistry and Photon Science Institute , The University of Manchester , Oxford Road , Manchester M13 9PL , United Kingdom
| | - Antonio Doménech-Carbó
- Departament de Química Analítica , Universitat de València , Dr. Moliner, 50 , 46100 Burjassot , València , Spain
| | - Antonio Leyva-Pérez
- Instituto de Tecnología Química , Universidad Politècnica de València-Consejo Superior de Investigaciones Científicas (UPV-CSIC) , Avda. de los Naranjos s/n , 46022 Valencia , Spain
| | - Donatella Armentano
- Dipartimento di Chimica e Tecnologie Chimiche (CTC) , Università della Calabria , via P. Bucci, 12 , Rende 87036 , Cosenza , Italy
| | - Emilio Pardo
- Departamento de Química Inorgánica, Instituto de Ciencia Molecular (ICMol), Catedrático José Beltrán Martínez, 2 , Universidad de Valencia , 46980 Paterna , Valencia , Spain
| | - Jesús Ferrando-Soria
- Departamento de Química Inorgánica, Instituto de Ciencia Molecular (ICMol), Catedrático José Beltrán Martínez, 2 , Universidad de Valencia , 46980 Paterna , Valencia , Spain
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40
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Qiu QF, Chen CX, Wei ZW, Cao CC, Zhu NX, Wang HP, Wang D, Jiang JJ, Su CY. A Flexible Cu-MOF as Crystalline Sponge for Guests Determination. Inorg Chem 2018; 58:61-64. [DOI: 10.1021/acs.inorgchem.8b02993] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Qian-feng Qiu
- Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, P. R. China
| | - Cheng-Xia Chen
- Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, P. R. China
| | - Zhang-Wen Wei
- Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, P. R. China
| | - Chen-Chen Cao
- Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, P. R. China
| | - Neng-Xiu Zhu
- Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, P. R. China
| | - Hai-Ping Wang
- Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, P. R. China
| | - Dawei Wang
- Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, P. R. China
| | - Ji-Jun Jiang
- Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, P. R. China
| | - Cheng-Yong Su
- Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, P. R. China
- Shanghai Institute of Organic Chemistry, Shanghai, 200032, P. R. China
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41
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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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42
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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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43
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Christ B, Pluskal T, Aubry S, Weng JK. Contribution of Untargeted Metabolomics for Future Assessment of Biotech Crops. TRENDS IN PLANT SCIENCE 2018; 23:1047-1056. [PMID: 30361071 DOI: 10.1016/j.tplants.2018.09.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/14/2018] [Accepted: 09/24/2018] [Indexed: 05/20/2023]
Abstract
The nutritional value and safety of food crops are ultimately determined by their chemical composition. Recent developments in the field of metabolomics have made it possible to characterize the metabolic profile of crops in a comprehensive and high-throughput manner. Here, we propose that state-of-the-art untargeted metabolomics technology should be leveraged for safety assessment of new crop products. We suggest generally applicable experimental design principles that facilitate the efficient and rigorous identification of both intended and unintended metabolic alterations associated with a newly engineered trait. Our proposition could contribute to increased transparency of the safety assessment process for new biotech crops.
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Affiliation(s)
- Bastien Christ
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Tomáš Pluskal
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Sylvain Aubry
- Federal Office for Agriculture, 3003 Bern, Switzerland; Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland.
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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44
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Mitsuhashi T, Kikuchi T, Hoshino S, Ozeki M, Awakawa T, Shi SP, Fujita M, Abe I. Crystalline Sponge Method Enabled the Investigation of a Prenyltransferase-terpene Synthase Chimeric Enzyme, Whose Product Exhibits Broadened NMR Signals. Org Lett 2018; 20:5606-5609. [PMID: 30179018 DOI: 10.1021/acs.orglett.8b02284] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
By the genome-mining approach, a chimeric enzyme of prenyltransferase-diterpene synthase was discovered from Penicillium chrysogenum MT-12. Since its product exhibited broadened NMR signals, the structural determination by only the NMR analysis was difficult, but the crystalline sponge method successfully revealed the structure with a 6-5-5-5 fused ring system. This demonstrated that the collaboration between the genome-mining and crystalline sponge method has the potential to facilitate rapid inquiries into the unexplored chemical space of small molecules.
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Affiliation(s)
- Takaaki Mitsuhashi
- Graduate School of Pharmaceutical Sciences , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-0033 , Japan
| | - Takashi Kikuchi
- Rigaku Corporation , 3-9-12 Matsubara-cho, Akishima-shi , Tokyo 196-8666 , Japan
| | - Shotaro Hoshino
- Graduate School of Pharmaceutical Sciences , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-0033 , Japan
| | - Masahiro Ozeki
- Graduate School of Pharmaceutical Sciences , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-0033 , Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-0033 , Japan.,Collaborative Research Institute for Innovative Microbiology , The University of Tokyo , Yayoi 1-1-1, Bunkyo-ku , Tokyo 113-8657 , Japan
| | - She-Po Shi
- Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica , Beijing University of Chinese Medicine , Beijing 100029 , People's Republic of China
| | - Makoto Fujita
- Department of Applied Chemistry, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-0033 , Japan.,Collaborative Research Institute for Innovative Microbiology , The University of Tokyo , Yayoi 1-1-1, Bunkyo-ku , Tokyo 113-8657 , Japan
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