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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Negro C, Escamilla P, Bruno R, Ferrando‐Soria J, Armentano D, Pardo E. Metal‐Organic Frameworks as Unique Platforms to Gain Insight of σ‐Hole Interactions for the Removal of Organic Dyes from Aquatic Ecosystems. Chemistry 2022; 28:e202200034. [PMID: 35188315 PMCID: PMC9314587 DOI: 10.1002/chem.202200034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Cristina Negro
- Instituto de Ciencia Molecular (ICMOL) Universitat de València Paterna 46980, València Spain
| | - Paula Escamilla
- Instituto de Ciencia Molecular (ICMOL) Universitat de València Paterna 46980, València Spain
| | - Rosaria Bruno
- Dipartimento di Chimica e Tecnologie Chimiche Università della Calabria 87030 Rende, Cosenza Italy
| | - Jesus Ferrando‐Soria
- Instituto de Ciencia Molecular (ICMOL) Universitat de València Paterna 46980, València Spain
| | - Donatella Armentano
- Dipartimento di Chimica e Tecnologie Chimiche Università della Calabria 87030 Rende, Cosenza Italy
| | - Emilio Pardo
- Instituto de Ciencia Molecular (ICMOL) Universitat de València Paterna 46980, València Spain
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3
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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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4
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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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5
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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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6
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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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7
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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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8
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Tominaga M, Hyodo T, Maekawa Y, Kawahata M, Yamaguchi K. One‐Step Synthesis of Cyclophanes as Crystalline Sponge and Their [2]Catenanes through S
N
Ar Reactions. Chemistry 2020; 26:5157-5161. [DOI: 10.1002/chem.201905854] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/24/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Masahide Tominaga
- Faculty of Pharmaceutical Sciences at Kagawa CampusTokushima Bunri University 1314-1 Shido, Sanuki Kagawa 769-2193 Japan
| | - Tadashi Hyodo
- Faculty of Pharmaceutical Sciences at Kagawa CampusTokushima Bunri University 1314-1 Shido, Sanuki Kagawa 769-2193 Japan
| | - Yumi Maekawa
- Faculty of Pharmaceutical Sciences at Kagawa CampusTokushima Bunri University 1314-1 Shido, Sanuki Kagawa 769-2193 Japan
| | - Masatoshi Kawahata
- Showa Pharmaceutical University 3–3165 Higashi-Tamagawagakuen, Machida Tokyo 194-8543 Japan
| | - Kentaro Yamaguchi
- Faculty of Pharmaceutical Sciences at Kagawa CampusTokushima Bunri University 1314-1 Shido, Sanuki Kagawa 769-2193 Japan
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9
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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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10
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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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11
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Kersten RD, Lee S, Fujita D, Pluskal T, Kram S, Smith JE, Iwai T, Noel JP, Fujita M, Weng JK. A Red Algal Bourbonane Sesquiterpene Synthase Defined by Microgram-Scale NMR-Coupled Crystalline Sponge X-ray Diffraction Analysis. J Am Chem Soc 2017; 139:16838-16844. [PMID: 29083151 DOI: 10.1021/jacs.7b09452] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Sesquiterpene scaffolds are the core backbones of many medicinally and industrially important natural products. A plethora of sesquiterpene synthases, widely present in bacteria, fungi, and plants, catalyze the formation of these intricate structures often with multiple stereocenters starting from linear farnesyl diphosphate substrates. Recent advances in next-generation sequencing and metabolomics technologies have greatly facilitated gene discovery for sesquiterpene synthases. However, a major bottleneck limits biochemical characterization of recombinant sesquiterpene synthases: the absolute structural elucidation of the derived sesquiterpene products. Here, we report the identification and biochemical characterization of LphTPS-A, a sesquiterpene synthase from the red macroalga Laurencia pacifica. Using the combination of transcriptomics, sesquiterpene synthase expression in yeast, and microgram-scale nuclear magnetic resonance-coupled crystalline sponge X-ray diffraction analysis, we resolved the absolute stereochemistry of prespatane, the major sesquiterpene product of LphTPS-A, and thereby functionally define LphTPS-A as the first bourbonane-producing sesquiterpene synthase and the first biochemically characterized sesquiterpene synthase from red algae. Our study showcases a workflow integrating multiomics approaches, synthetic biology, and the crystalline sponge method, which is generally applicable for uncovering new terpene chemistry and biochemistry from source-limited living organisms.
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Affiliation(s)
- Roland D Kersten
- Whitehead Institute for Biomedical Research , 455 Main Street, Cambridge, Massachusetts 02142, United States
| | - Shoukou Lee
- Graduate School of Engineering, The University of Tokyo, JST-ACCEL , Tokyo 113-8654, Japan
| | - Daishi Fujita
- Whitehead Institute for Biomedical Research , 455 Main Street, Cambridge, Massachusetts 02142, United States.,Graduate School of Engineering, The University of Tokyo, JST-ACCEL , Tokyo 113-8654, Japan
| | - Tomáš Pluskal
- Whitehead Institute for Biomedical Research , 455 Main Street, Cambridge, Massachusetts 02142, United States
| | - Susan Kram
- Scripps Institution of Oceanography, University of California, San Diego , La Jolla, California 92093, United States
| | - Jennifer E Smith
- Scripps Institution of Oceanography, University of California, San Diego , La Jolla, California 92093, United States
| | - Takahiro Iwai
- Graduate School of Engineering, The University of Tokyo, JST-ACCEL , Tokyo 113-8654, Japan
| | - Joseph P Noel
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies , La Jolla, California 92037, United States
| | - Makoto Fujita
- Graduate School of Engineering, The University of Tokyo, JST-ACCEL , Tokyo 113-8654, Japan
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research , 455 Main Street, Cambridge, Massachusetts 02142, United States.,Department of Biology, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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12
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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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13
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Zigon N, Kikuchi T, Ariyoshi J, Inokuma Y, Fujita M. Structural Elucidation of Trace Amounts of Volatile Compounds Using the Crystalline Sponge Method. Chem Asian J 2017; 12:1057-1061. [DOI: 10.1002/asia.201700515] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Nicolas Zigon
- Department of Applied Chemistry, School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Takashi Kikuchi
- Rigaku Corporation; 3-9-12 Matsubara-cho, Akishima-shi Tokyo 196-8666 Japan
| | - Junko Ariyoshi
- Department of Applied Chemistry, School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Yasuhide Inokuma
- Department of Applied Chemistry, School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
- Present address: Division of Applied Chemistry; Faculty of Engineering; Hokkaido University; Kita 13 Nishi 8 Kita-ku Sapporo Hokkaido 060-8628 Japan
| | - Makoto Fujita
- Department of Applied Chemistry, School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
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14
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Inokuma Y, Matsumura K, Yoshioka S, Fujita M. Finding a New Crystalline Sponge from a Crystallographic Database. Chem Asian J 2016; 12:208-211. [DOI: 10.1002/asia.201601551] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Yasuhide Inokuma
- Department of Applied Chemistry; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
- JST PRESTO; 4-8-1 Honcho Kawaguchi Saitama 332-0012 Japan
- Current address: Division of Applied Chemistry; Faculty of Engineering; Hokkaido University; Kita 13, Nishi 8, Kita-ku Sapporo 060-8628 Japan
| | - Kazuki Matsumura
- Department of Applied Chemistry; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Shota Yoshioka
- Department of Applied Chemistry; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
- Current address: Division of Applied Chemistry; Faculty of Engineering; Hokkaido University; Kita 13, Nishi 8, Kita-ku Sapporo 060-8628 Japan
| | - Makoto Fujita
- Department of Applied Chemistry; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
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15
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Gu XF, Zhao Y, Li K, Su MX, Yan F, Li B, Du YX, Di B. Differentiation of volatile aromatic isomers and structural elucidation of volatile compounds in essential oils by combination of HPLC separation and crystalline sponge method. J Chromatogr A 2016; 1474:130-137. [DOI: 10.1016/j.chroma.2016.10.072] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 10/17/2016] [Accepted: 10/26/2016] [Indexed: 10/20/2022]
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16
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Kikuchi H, Nishimura T, Kwon E, Kawai J, Oshima Y. Development of a Terpenoid Alkaloid-like Compound Library Based on the Humulene Skeleton. Chemistry 2016; 22:15819-15825. [DOI: 10.1002/chem.201603224] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Haruhisa Kikuchi
- Graduate School of Pharmaceutical Sciences; Tohoku University; 6-3, Aza-Aoba, Aoba-ku Sendai 980-8578 Japan
| | - Takehiro Nishimura
- Graduate School of Pharmaceutical Sciences; Tohoku University; 6-3, Aza-Aoba, Aoba-ku Sendai 980-8578 Japan
| | - Eunsang Kwon
- Research and Analytical Center for Giant Molecules, Graduate School of Science; Tohoku University; 6-3, Aza-Aoba, Aoba-ku Sendai 980-8578 Japan
| | - Junya Kawai
- Mushroom Research Laboratory; Hokuto Corporation; Nagano 381-0008 Japan
| | - Yoshiteru Oshima
- Graduate School of Pharmaceutical Sciences; Tohoku University; 6-3, Aza-Aoba, Aoba-ku Sendai 980-8578 Japan
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17
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Lam HC, Spence JTJ, George JH. Biomimetic Total Synthesis of Hyperjapones A–E and Hyperjaponols A and C. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606091] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hiu C. Lam
- Department of Chemistry University of Adelaide Adelaide SA 5005 Australia
| | | | - Jonathan H. George
- Department of Chemistry University of Adelaide Adelaide SA 5005 Australia
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18
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Lam HC, Spence JTJ, George JH. Biomimetic Total Synthesis of Hyperjapones A-E and Hyperjaponols A and C. Angew Chem Int Ed Engl 2016; 55:10368-71. [PMID: 27461748 DOI: 10.1002/anie.201606091] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Indexed: 11/08/2022]
Abstract
Hyperjapones A-E and hyperjaponols A-C are complex natural products of mixed aromatic polyketide and terpene biosynthetic origin that have recently been isolated from Hypericum japonicum. We have synthesized hyperjapones A-E using a biomimetic, oxidative hetero-Diels-Alder reaction to couple together dearomatized acylphloroglucinol and cyclic terpene natural products. Hyperjapone A is proposed to be the biosynthetic precursor of hyperjaponol C through a sequence of: 1) epoxidation; 2) acid-catalyzed epoxide ring-opening; and 3) a concerted, asynchronous alkene cyclization and 1,2-alkyl shift of a tertiary carbocation. Chemical mimicry of this proposed biosynthetic sequence allowed a concise total synthesis of hyperjaponol C to be completed in which six carbon-carbon bonds, six stereocenters, and three rings were constructed in just four steps.
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Affiliation(s)
- Hiu C Lam
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Justin T J Spence
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Jonathan H George
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia.
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19
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Coletta M, McLellan R, Murphy P, Leube BT, Sanz S, Clowes R, Gagnon KJ, Teat SJ, Cooper AI, Paterson MJ, Brechin EK, Dalgarno SJ. Bis-Calix[4]arenes: From Ligand Design to the Directed Assembly of a Metal-Organic Trigonal Antiprism. Chemistry 2016; 22:8791-5. [PMID: 27166930 DOI: 10.1002/chem.201600762] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Indexed: 11/05/2022]
Abstract
Calix[4]arenes (C[4]s) are versatile platforms for the construction of polymetallic clusters containing paramagnetic metal ions. Synthetic modification at the C[4] methylene bridge allows for the design of bis-C[4]s that, depending on the linker employed, can be used to either dictate which clusters can be formed or direct the assembly of a new metal-organic polyhedron (MOP). The assembly resulting from the latter approach displays thermal stability and uptake of N2 or H2 gas, confirming that this is a viable route to the synthesis of new, functional supramolecular architectures.
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Affiliation(s)
- Marco Coletta
- Institute of Chemical Sciences, Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS, UK
| | - Ross McLellan
- Institute of Chemical Sciences, Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS, UK
| | - Paul Murphy
- Institute of Chemical Sciences, Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS, UK
| | - Bernhard T Leube
- Institute of Chemical Sciences, Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS, UK
| | - Sergio Sanz
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Rob Clowes
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, UK
| | - Kevin J Gagnon
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 947240, USA
| | - Simon J Teat
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 947240, USA
| | - Andrew I Cooper
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, UK
| | - Martin J Paterson
- Institute of Chemical Sciences, Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS, UK
| | - Euan K Brechin
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK.
| | - Scott J Dalgarno
- Institute of Chemical Sciences, Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS, UK.
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20
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Matsuda Y, Mitsuhashi T, Lee S, Hoshino M, Mori T, Okada M, Zhang H, Hayashi F, Fujita M, Abe I. Astellifadiene: Structure Determination by NMR Spectroscopy and Crystalline Sponge Method, and Elucidation of its Biosynthesis. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601448] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Yudai Matsuda
- 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
| | - Shoukou Lee
- Graduate School of Engineering; The University of Tokyo; JST-ACCEL; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Manabu Hoshino
- Graduate School of Engineering; The University of Tokyo; JST-ACCEL; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Masahiro Okada
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Huiping Zhang
- RIKEN Center for Life Science Technologies, Yokohama; Kanagawa 230-0045 Japan
| | - Fumiaki Hayashi
- RIKEN Center for Life Science Technologies, Yokohama; Kanagawa 230-0045 Japan
| | - Makoto Fujita
- Graduate School of Engineering; The University of Tokyo; JST-ACCEL; 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
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21
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Matsuda Y, Mitsuhashi T, Lee S, Hoshino M, Mori T, Okada M, Zhang H, Hayashi F, Fujita M, Abe I. Astellifadiene: Structure Determination by NMR Spectroscopy and Crystalline Sponge Method, and Elucidation of its Biosynthesis. Angew Chem Int Ed Engl 2016; 55:5785-8. [DOI: 10.1002/anie.201601448] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Yudai Matsuda
- 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
| | - Shoukou Lee
- Graduate School of Engineering; The University of Tokyo; JST-ACCEL; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Manabu Hoshino
- Graduate School of Engineering; The University of Tokyo; JST-ACCEL; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Masahiro Okada
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Huiping Zhang
- RIKEN Center for Life Science Technologies, Yokohama; Kanagawa 230-0045 Japan
| | - Fumiaki Hayashi
- RIKEN Center for Life Science Technologies, Yokohama; Kanagawa 230-0045 Japan
| | - Makoto Fujita
- Graduate School of Engineering; The University of Tokyo; JST-ACCEL; 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
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22
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In Situ Observation of Thiol Michael Addition to a Reversible Covalent Drug in a Crystalline Sponge. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509801] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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23
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Duplan V, Hoshino M, Li W, Honda T, Fujita M. In Situ Observation of Thiol Michael Addition to a Reversible Covalent Drug in a Crystalline Sponge. Angew Chem Int Ed Engl 2016; 55:4919-23. [PMID: 26970084 DOI: 10.1002/anie.201509801] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/24/2016] [Indexed: 11/10/2022]
Abstract
A reversible Michael addition reaction between thiol nucleophiles and cyanoenones has been previously postulated to be the mechanism-of-action of a new family of reversible covalent drugs. However, the hypothetical Michael adducts in this mechanism have only been detected by spectroscopic methods in solution. Herein, the crystallographic observation of reversible Michael addition with a potent cyanoenone drug candidate by means of the crystalline-sponge method is reported. After inclusion of the cyanoenone substrate, the sponge crystal was treated with a thiol solution. Subsequent crystallographic analysis confirmed the single-crystal-to-single-crystal transformation of the substrate into the impermanent Michael adduct.
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Affiliation(s)
- Vincent Duplan
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Manabu Hoshino
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Wei Li
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Tadashi Honda
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Makoto Fujita
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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24
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Wen Y, Sheng T, Zhu X, Zhang H, Zhuo C, Hu S, Cao W, Wu X. Intercalation of Varied Sulfonates into a Layered MOC: Confinement-Caused Tunable Luminescence and Novel Properties. Chemistry 2016; 22:5327-34. [DOI: 10.1002/chem.201504751] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Yuehong Wen
- State Key Laboratory of Structural Chemistry; Chinese Academy of Sciences; Institution Fujian Institute of Research on the Structure of Matter; Fuzhou 350002 P.R. China
| | - Tianlu Sheng
- State Key Laboratory of Structural Chemistry; Chinese Academy of Sciences; Institution Fujian Institute of Research on the Structure of Matter; Fuzhou 350002 P.R. China
| | - Xiaoquan Zhu
- State Key Laboratory of Structural Chemistry; Chinese Academy of Sciences; Institution Fujian Institute of Research on the Structure of Matter; Fuzhou 350002 P.R. China
| | - Hao Zhang
- State Key Laboratory of Structural Chemistry; Chinese Academy of Sciences; Institution Fujian Institute of Research on the Structure of Matter; Fuzhou 350002 P.R. China
| | - Chao Zhuo
- State Key Laboratory of Structural Chemistry; Chinese Academy of Sciences; Institution Fujian Institute of Research on the Structure of Matter; Fuzhou 350002 P.R. China
| | - Shengmin Hu
- State Key Laboratory of Structural Chemistry; Chinese Academy of Sciences; Institution Fujian Institute of Research on the Structure of Matter; Fuzhou 350002 P.R. China
| | - Wenhai Cao
- State Key Laboratory of Structural Chemistry; Chinese Academy of Sciences; Institution Fujian Institute of Research on the Structure of Matter; Fuzhou 350002 P.R. China
| | - Xintao Wu
- State Key Laboratory of Structural Chemistry; Chinese Academy of Sciences; Institution Fujian Institute of Research on the Structure of Matter; Fuzhou 350002 P.R. China
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25
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Cuenca AB, Zigon N, Duplan V, Hoshino M, Fujita M, Fernández E. Undeniable Confirmation of the syn
-Addition Mechanism for Metal-Free Diboration by Using the Crystalline Sponge Method. Chemistry 2016; 22:4723-6. [DOI: 10.1002/chem.201600392] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Ana B. Cuenca
- Department Quimica Física i Inorgànica; University Rovira i Virgili; C/Marcel⋅lí Domingo s/n 43007 Tarragona Spain
| | - Nicolas Zigon
- Department of Applied Chemistry; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Vincent Duplan
- Department of Applied Chemistry; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Manabu Hoshino
- Department of Applied Chemistry; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Makoto Fujita
- Department of Applied Chemistry; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Elena Fernández
- Department Quimica Física i Inorgànica; University Rovira i Virgili; C/Marcel⋅lí Domingo s/n 43007 Tarragona Spain
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26
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Urban S, Brkljača R, Hoshino M, Lee S, Fujita M. Determination of the Absolute Configuration of the Pseudo‐Symmetric Natural Product Elatenyne by the Crystalline Sponge Method. Angew Chem Int Ed Engl 2016; 55:2678-82. [DOI: 10.1002/anie.201509761] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/26/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Sylvia Urban
- School of Applied Sciences (Discipline of Chemistry) RMIT University GPO Box 2476 Melbourne 3001 Victoria Australia
| | - Robert Brkljača
- School of Applied Sciences (Discipline of Chemistry) RMIT University GPO Box 2476 Melbourne 3001 Victoria Australia
| | - Manabu Hoshino
- Department of Applied Chemistry School of Engineering The University of Tokyo Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Shoukou Lee
- Department of Applied Chemistry School of Engineering The University of Tokyo Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Makoto Fujita
- Department of Applied Chemistry School of Engineering The University of Tokyo Hongo, Bunkyo-ku Tokyo 113-8656 Japan
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27
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Urban S, Brkljača R, Hoshino M, Lee S, Fujita M. Determination of the Absolute Configuration of the Pseudo‐Symmetric Natural Product Elatenyne by the Crystalline Sponge Method. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509761] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sylvia Urban
- School of Applied Sciences (Discipline of Chemistry) RMIT University GPO Box 2476 Melbourne 3001 Victoria Australia
| | - Robert Brkljača
- School of Applied Sciences (Discipline of Chemistry) RMIT University GPO Box 2476 Melbourne 3001 Victoria Australia
| | - Manabu Hoshino
- Department of Applied Chemistry School of Engineering The University of Tokyo Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Shoukou Lee
- Department of Applied Chemistry School of Engineering The University of Tokyo Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Makoto Fujita
- Department of Applied Chemistry School of Engineering The University of Tokyo Hongo, Bunkyo-ku Tokyo 113-8656 Japan
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