1
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Piskorz TK, Martí-Centelles V, Spicer RL, Duarte F, Lusby PJ. Picking the lock of coordination cage catalysis. Chem Sci 2023; 14:11300-11331. [PMID: 37886081 PMCID: PMC10599471 DOI: 10.1039/d3sc02586a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/29/2023] [Indexed: 10/28/2023] Open
Abstract
The design principles of metallo-organic assembly reactions have facilitated access to hundreds of coordination cages of varying size and shape. Many of these assemblies possess a well-defined cavity capable of hosting a guest, pictorially mimicking the action of a substrate binding to the active site of an enzyme. While there are now a growing collection of coordination cages that show highly proficient catalysis, exhibiting both excellent activity and efficient turnover, this number is still small compared to the vast library of metal-organic structures that are known. In this review, we will attempt to unpick and discuss the key features that make an effective coordination cage catalyst, linking structure to activity (and selectivity) using lessons learnt from both experimental and computational analysis of the most notable exemplars. We will also provide an outlook for this area, reasoning why coordination cages have the potential to become the gold-standard in (synthetic) non-covalent catalysis.
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Affiliation(s)
- Tomasz K Piskorz
- Chemistry Research Laboratory, University of Oxford Oxford OX1 3TA UK
| | - Vicente Martí-Centelles
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València Camino de Vera, s/n 46022 Valencia Spain
| | - Rebecca L Spicer
- Department of Chemistry, Lancaster University Lancaster LA14YB UK
| | - Fernanda Duarte
- Chemistry Research Laboratory, University of Oxford Oxford OX1 3TA UK
| | - Paul J Lusby
- EaStCHEM School of Chemistry, University of Edinburgh Edinburgh Scotland EH9 3FJ UK
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2
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Ramamurthy V. Photochemistry in a capsule: controlling excited state dynamics via confinement. Chem Commun (Camb) 2022; 58:6571-6585. [PMID: 35611956 DOI: 10.1039/d2cc01758j] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Exerting control on excited state processes has been a long-held goal in photochemistry. One approach to achieve control has been to mimic biological systems in Nature (e.g., photosynthesis) that has perfected it over millions of years by performing the reactions in highly organized assemblies such as membranes and proteins by restricting the freedom of reactants and directing them to pursue a select pathway. The duplication of this concept at a smaller scale in the laboratory involves the use of highly confined and organized assemblies as reaction containers. This article summarizes the studies in the author's laboratory using a synthetic, well-defined reaction container known as octa acid (OA). OA, unlike most commonly known cavitands, forms a capsule in water and remains closed during the lifetime of the excited states of included molecules. Thus, the described excited state chemistry occurs in a small space with hydrophobic characteristics. Examples where the photophysical and photochemical properties are dramatically altered, compared to that in organic solvents wherein the molecules are freely soluble, are presented to illustrate the value of a restricted environment in controlling the dynamics of molecules on an excited state surface. While the ground state complexation of the guest and host is controlled by well-known concepts of tight-fit, lock and key, complementarity, etc., free space around the guest is necessary for it to be able to undergo structural transformations in the excited state, where the time is short. This article highlights the role of free space during the dynamics of molecules within a confined, inflexible reaction cavity.
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3
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Wang Y, Li B, Zhu J, Zhang W, Zheng B, Zhao W, Tang J, Yang X, Wu B. Light‐Triggered High‐Affinity Binding of Tetramethylammonium over Potassium Ions by [18]crown‐6 in a Tetrahedral Anion Cage. Angew Chem Int Ed Engl 2022; 61:e202201789. [DOI: 10.1002/anie.202201789] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Indexed: 01/18/2023]
Affiliation(s)
- Yue Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education College of Chemistry and Materials Science Northwest University Xi'an 710069 China
| | - Boyang Li
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education College of Chemistry and Materials Science Northwest University Xi'an 710069 China
| | - Jiajia Zhu
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering Ministry of Industry and Information Technology School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China
| | - Wenyao Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education College of Chemistry and Materials Science Northwest University Xi'an 710069 China
| | - Bo Zheng
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education College of Chemistry and Materials Science Northwest University Xi'an 710069 China
| | - Wei Zhao
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering Ministry of Industry and Information Technology School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China
| | - Juan Tang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering Ministry of Industry and Information Technology School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China
| | - Xiao‐Juan Yang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering Ministry of Industry and Information Technology School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China
| | - Biao Wu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education College of Chemistry and Materials Science Northwest University Xi'an 710069 China
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering Ministry of Industry and Information Technology School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China
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4
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Wang Y, Li B, Zhu J, Zhang W, Zheng B, Zhao W, Tang J, Yang X, Wu B. Light‐Triggered High‐Affinity Binding of Tetramethylammonium over Potassium Ions by [18]crown‐6 in a Tetrahedral Anion Cage. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201789] [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]
Affiliation(s)
- Yue Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education College of Chemistry and Materials Science Northwest University Xi'an 710069 China
| | - Boyang Li
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education College of Chemistry and Materials Science Northwest University Xi'an 710069 China
| | - Jiajia Zhu
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering Ministry of Industry and Information Technology School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China
| | - Wenyao Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education College of Chemistry and Materials Science Northwest University Xi'an 710069 China
| | - Bo Zheng
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education College of Chemistry and Materials Science Northwest University Xi'an 710069 China
| | - Wei Zhao
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering Ministry of Industry and Information Technology School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China
| | - Juan Tang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering Ministry of Industry and Information Technology School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China
| | - Xiao‐Juan Yang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering Ministry of Industry and Information Technology School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China
| | - Biao Wu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education College of Chemistry and Materials Science Northwest University Xi'an 710069 China
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering Ministry of Industry and Information Technology School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China
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5
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Xie H, Gunawardana VWL, Finnegan TJ, Xie W, Badjić JD. Picking on Carbonate: Kinetic Selectivity in the Encapsulation of Anions. Angew Chem Int Ed Engl 2022; 61:e202116518. [PMID: 35038355 DOI: 10.1002/anie.202116518] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Indexed: 12/21/2022]
Abstract
Supramolecular hosts bind to inorganic anions at a fast rate and select them in proportion with thermodynamic stability of the corresponding [anion⊂host] complexes, forming in a reversible manner. In this study, we describe the action of hexapodal capsule 1 and its remarkable ability to select anions based on a large span of rates by which they enter this host. The thermodynamic affinity of 1 toward eighteen anions extends over eight orders of magnitude (0<Ka <108 M-1 ; 1 H NMR spectroscopy). The capsule would retain CO3 2- (Ka =107 M-1 ) for hours in the presence of eleven competing anions, including stronger binding SO4 2- , HAsO4 2- and HPO4 2- (Ka =107 -108 M-1 ). The observed selection resulted from 1 possessing narrow apertures (ca. 3×6 Å) comparable in size to anions (d=3.5-7.1 Å) slowing down the encapsulation to last from seconds to days. The unorthodox mode of action of 1 sets the stage for creating hosts that pick anions by their ability to access the host.
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Affiliation(s)
- Han Xie
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
| | | | - Tyler J Finnegan
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
| | - William Xie
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
| | - Jovica D Badjić
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
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6
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Pang YP. How neocarcerand Octacid4 self-assembles with guests into irreversible noncovalent complexes and what accelerates the assembly. Commun Chem 2022; 5:9. [PMID: 36697791 PMCID: PMC9814096 DOI: 10.1038/s42004-022-00624-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 12/30/2021] [Indexed: 01/28/2023] Open
Abstract
Cram's supramolecular capsule Octacid4 can irreversibly and noncovalently self-assemble with small-molecule guests at room temperature, but how they self-assemble and what accelerates their assembly remain poorly understood. This article reports 81 distinct Octacid4•guest self-assembly pathways captured in unrestricted, unbiased molecular dynamics simulations. These pathways reveal that the self-assembly was initiated by the guest interaction with the cavity portal exterior of Octacid4 to increase the portal collisions that led to the portal expansion for guest ingress, and completed by the portal contraction caused by the guest docking inside the cavity to impede guest egress. The pathways also reveal that the self-assembly was accelerated by engaging populated host and guest conformations for the exterior interaction to increase the portal collision frequency. These revelations may help explain why the presence of an exterior binding site at the rim of the enzyme active site is a fundamental feature of fast enzymes such as acetylcholinesterase and why small molecules adopt local minimum conformations when binding to proteins. Further, these revelations suggest that irreversible noncovalent complexes with fast assembly rates could be developed-by engaging populated host and guest conformations for the exterior interactions-for materials technology, data storage and processing, molecular sensing and tagging, and drug therapy.
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Affiliation(s)
- Yuan-Ping Pang
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, MN, USA.
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7
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Badjic JD, Xie H, Gunawardana VWL, Finnegan TJ, Xie W, Badjić JD. Picking on Carbonate: Kinetic Selectivity in the Encapsulation of Anions. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jovica D Badjic
- Ohio State University Department of Chemistry 100 W. 18th Avenue 43210 Columbus UNITED STATES
| | - Han Xie
- The Ohio State University Chemistry and Biochemistry UNITED STATES
| | | | | | - William Xie
- The Ohio State University Chemistry and Biochemistry UNITED STATES
| | - Jovica D. Badjić
- The Ohio State University Chemistry and Biochemistry UNITED STATES
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8
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Lalisse RF, Pavlović RZ, Hadad CM, Badjić JD. A computational study of competing conformational selection and induced fit in an abiotic system. Phys Chem Chem Phys 2021; 24:507-511. [PMID: 34904140 DOI: 10.1039/d1cp05253e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Host-guest complexations can be described by two competing mechanisms, conformational selection (CS) and induced fit (IF). In this work, we used a combination of nudged elastic band (NEB), adaptive steered molecular dynamics (ASMD), and density functional theory (DFT, with a correction for dispersion) to study the dynamics of the pathways (IF/CS) by which two conformers of basket B(+) and B(-) interconvert and trap CX4 guests (X = Cl and Br). While the results from NEB/DFT studies disclosed host-guest noncovalent contacts reducing the basket's conformational dynamics, ASMD methodology suggested an associative mechanism for the guest complexation. With theory in excellent agreement with experiments, NEB and ASMD emerge as the methods of choice for studying dynamics of supramolecular systems.
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Affiliation(s)
- Remy F Lalisse
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
| | - Radoslav Z Pavlović
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
| | - Christopher M Hadad
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
| | - Jovica D Badjić
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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9
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Pavlović RZ, Lalisse RF, Hansen AL, Waudby CA, Lei Z, Güney M, Wang X, Hadad CM, Badjić JD. From Selection to Instruction and Back: Competing Conformational Selection and Induced Fit Pathways in Abiotic Hosts. Angew Chem Int Ed Engl 2021; 60:19942-19948. [PMID: 34125989 DOI: 10.1002/anie.202107091] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Indexed: 12/15/2022]
Abstract
Two limiting cases of molecular recognition, induced fit (IF) and conformational selection (CS), play a central role in allosteric regulation of natural systems. The IF paradigm states that a substrate "instructs" the host to change its shape after complexation, while CS asserts that a guest "selects" the optimal fit from an ensemble of preexisting host conformations. With no studies that quantitatively address the interplay of two limiting pathways in abiotic systems, we herein and for the first time describe the way by which twisted capsule M-1, encompassing two conformers M-1(+) and M-1(-), trap CX4 (X=Cl, Br) to give CX4 ⊂M-1(+) and CX4 ⊂M-1(-), with all four states being in thermal equilibrium. With the assistance of 2D EXSY, we found that CBr4 would, at its lower concentrations, bind M-1 via a M-1(+)→M-1(-)→CBr4 ⊂M-1(-) pathway corresponding to conformational selection. For M-1 complexing CCl4 though, data from 2D EXSY measurements and 1D NMR line-shape analysis suggested that lower CCl4 concentrations would favor CS while the IF pathway prevailed at higher proportions of the guest. Since CS and IF are not mutually exclusive, we reason that our work sets the stage for characterizing the dynamics of a wide range of already existing hosts to broaden our fundamental understanding of their action. The objective is to master the way in which encapsulation takes place for designing novel and allosteric sequestering agents, catalysts and chemosensors akin to those found in nature.
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Affiliation(s)
- Radoslav Z Pavlović
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA
| | - Remy F Lalisse
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA
| | - Alexandar L Hansen
- Campus Chemical Instrument Center, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA
| | - Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Zhiquan Lei
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA
| | - Murat Güney
- Agri Ibrahim Çeçen University, Department of Chemistry, 04100, Agri, Turkey
| | - Xiuze Wang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA
| | - Christopher M Hadad
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA
| | - Jovica D Badjić
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA
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10
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Pavlović RZ, Lalisse RF, Hansen AL, Waudby CA, Lei Z, Güney M, Wang X, Hadad CM, Badjić JD. From Selection to Instruction and Back: Competing Conformational Selection and Induced Fit Pathways in Abiotic Hosts. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Radoslav Z. Pavlović
- Department of Chemistry & Biochemistry The Ohio State University 100 West 18th Avenue Columbus OH 43210 USA
| | - Remy F. Lalisse
- Department of Chemistry & Biochemistry The Ohio State University 100 West 18th Avenue Columbus OH 43210 USA
| | - Alexandar L. Hansen
- Campus Chemical Instrument Center The Ohio State University 100 West 18th Avenue Columbus OH 43210 USA
| | - Christopher A. Waudby
- Institute of Structural and Molecular Biology University College London London WC1E 6BT UK
| | - Zhiquan Lei
- Department of Chemistry & Biochemistry The Ohio State University 100 West 18th Avenue Columbus OH 43210 USA
| | - Murat Güney
- Agri Ibrahim Çeçen University Department of Chemistry 04100 Agri Turkey
| | - Xiuze Wang
- Department of Chemistry & Biochemistry The Ohio State University 100 West 18th Avenue Columbus OH 43210 USA
| | - Christopher M. Hadad
- Department of Chemistry & Biochemistry The Ohio State University 100 West 18th Avenue Columbus OH 43210 USA
| | - Jovica D. Badjić
- Department of Chemistry & Biochemistry The Ohio State University 100 West 18th Avenue Columbus OH 43210 USA
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11
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12
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McFerrin KG, Pang YP. How the water-soluble hemicarcerand incarcerates guests at room temperature decoded with modular simulations. Commun Chem 2021; 4:26. [PMID: 36697600 PMCID: PMC9814894 DOI: 10.1038/s42004-021-00469-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/04/2021] [Indexed: 01/28/2023] Open
Abstract
Molecular dynamics simulations of hemicarcerands and related variants allow the study of constrictive binding and offer insight into the rules of molecular complexation, but are limited because three-dimensional models of hemicarcerands are tedious to build and their atomic charges are complicated to derive. There have been no molecular dynamics simulations of the reported water-soluble hemicarcerand (Octacid4) that explain how Octacid4 encapsulates guests at 298 K and keeps them encapsulated at 298 K in NMR experiments. Herein we report a modular approach to hemicarcerand simulations that simplifies the model building and charge derivation in a manner reminiscent of the approach to protein simulations with truncated amino acids as building blocks. We also report that in aqueous molecular dynamics simulations at 298 K apo Octacid4 adopts two clusters of conformations one of which has an equatorial portal open but the guest-bound Octacid4 adopts one cluster of conformations with all portals closed. These results explain how Octacid4 incarcerates guests at room temperature and suggest that the guest-induced host conformational change that impedes decomplexation is a previously unrecognized conformational characteristic that promotes strong molecular complexation.
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Affiliation(s)
| | - Yuan-Ping Pang
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, MN, USA.
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13
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Sakata Y, Okada M, Akine S. Guest Recognition Control Accompanied by Stepwise Gate Closing and Opening of a Macrocyclic Metallohost. Chemistry 2021; 27:2284-2288. [PMID: 33026677 DOI: 10.1002/chem.202004487] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Indexed: 12/12/2022]
Abstract
Host-guest binding behavior of macrocyclic hosts is significantly influenced by the shapes and sizes of the hosts. In particular, closing/opening the apertures of the hosts controls the guest uptake/release. A post-metalation modification method was used to achieve the open/close conversions. The starting open complex, [LCo2 (pip)4 ](OTf)2 , was efficiently converted to the closed complex, [LCo2 (hda)2 ](OTf)2 , which has a doubly bridged structure. The conversion of this closed complex to the open complex [LCo2 (hda)2 (OAc)]+ was too slow to be completed, but this gate-opening was dramatically accelerated by the addition of Na+ . The Na+ binding was also significantly enhanced by the gate-opening, that is, conversion of [LCo2 (hda)2 ]2+ to [LCo2 (hda)2 (OAc)]+ .
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Affiliation(s)
- Yoko Sakata
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan.,Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Masahiro Okada
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Shigehisa Akine
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan.,Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
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14
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Akine S, Sakata Y. Control of Guest Binding Kinetics in Macrocycles and Molecular Cages. CHEM LETT 2020. [DOI: 10.1246/cl.200017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Shigehisa Akine
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Yoko Sakata
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
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15
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Castro AC, Romero-Rivera A, Osuna S, Houk KN, Swart M. Computational NMR Spectra of o-Benzyne and Stable Guests and Their Hemicarceplexes. Chemistry 2020; 26:2626-2634. [PMID: 31765503 DOI: 10.1002/chem.201904756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/20/2019] [Indexed: 12/12/2022]
Abstract
The incarceration of o-benzyne and 27 other guest molecules within hemicarcerand 1, as reported experimentally by Warmuth, and Cram and co-workers, has been studied by density functional theory (DFT). The 1 H NMR chemical shifts, rotational mobility, and conformational preference of the guests within the supramolecular cage were determined, which showed intriguing correlations of the chemical shifts with structural parameters of the host-guest system. Furthermore, based on the computed chemical shifts reassignments of some NMR signals are proposed. This affects, in particular, the putative characterization of the volatile benzyne molecule inside a hemicarcerand, for which our CCSD(T) and KT2 results indicate that the experimentally observed signals are most likely not resulting from an isolated o-benzyne within the supramolecular host. Instead, it is shown that the guest reacted with an aromatic ring of the host, and this adduct is responsible for the experimentally observed signals.
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Affiliation(s)
- Abril C Castro
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus de Montilivi, 17071, Girona, Spain
| | - Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus de Montilivi, 17071, Girona, Spain
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus de Montilivi, 17071, Girona, Spain.,ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095-1569, USA
| | - Marcel Swart
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus de Montilivi, 17071, Girona, Spain.,ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
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16
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Hahn DF, Milić JV, Hünenberger PH. Vase
‐
Kite
Equilibrium of Resorcin[4]arene Cavitands Investigated Using Molecular Dynamics Simulations with Ball‐and‐Stick Local Elevation Umbrella Sampling. Helv Chim Acta 2019. [DOI: 10.1002/hlca.201900060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- David F. Hahn
- Laboratory of Physical Chemistry, Department of Chemistry and Applied BiosciencesETH Zürich Vladimir-Prelog-Weg 2 CH-8093 Zürich Switzerland
| | - Jovana V. Milić
- Laboratory of Photonics and InterfacesÉcole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LPI, Station 6 CH-1015 Lausanne Switzerland
| | - Philippe H. Hünenberger
- Laboratory of Physical Chemistry, Department of Chemistry and Applied BiosciencesETH Zürich Vladimir-Prelog-Weg 2 CH-8093 Zürich Switzerland
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17
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Akine S, Miyashita M, Nabeshima T. A Closed Metallomolecular Cage that can Open its Aperture by Disulfide Exchange. Chemistry 2019; 25:1432-1435. [DOI: 10.1002/chem.201805359] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/27/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Shigehisa Akine
- Graduate School of Natural Science and Technology; Kanazawa University, Kakuma-machi; Kanazawa 920-1192 Japan
- Nano Life Science Institute (WPI-NanoLSI); Kanazawa University, Kakuma-machi; Kanazawa 920-1192 Japan
| | - Masato Miyashita
- Faculty of Pure and Applied Sciences; University of Tsukuba; 1-1-1 Tennodai Tsukuba Ibaraki 305-8571 Japan
| | - Tatsuya Nabeshima
- Faculty of Pure and Applied Sciences; University of Tsukuba; 1-1-1 Tennodai Tsukuba Ibaraki 305-8571 Japan
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18
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Zhiquan L, Xie H, Border SE, Gallucci J, Pavlović RZ, Badjić JD. A Stimuli-Responsive Molecular Capsule with Switchable Dynamics, Chirality, and Encapsulation Characteristics. J Am Chem Soc 2018; 140:11091-11100. [PMID: 30099876 DOI: 10.1021/jacs.8b06190] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Lei Zhiquan
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Han Xie
- 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
| | - Judith Gallucci
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Radoslav Z. Pavlović
- 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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19
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Gropp C, Quigley BL, Diederich F. Molecular Recognition with Resorcin[4]arene Cavitands: Switching, Halogen-Bonded Capsules, and Enantioselective Complexation. J Am Chem Soc 2018; 140:2705-2717. [DOI: 10.1021/jacs.7b12894] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Cornelius Gropp
- Laboratory of Organic Chemistry,
Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg
3, 8093 Zürich, Switzerland
| | - Brendan L. Quigley
- Laboratory of Organic Chemistry,
Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg
3, 8093 Zürich, Switzerland
| | - François Diederich
- Laboratory of Organic Chemistry,
Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg
3, 8093 Zürich, Switzerland
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20
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Gropp C, Husch T, Trapp N, Reiher M, Diederich F. Dispersion and Halogen-Bonding Interactions: Binding of the Axial Conformers of Monohalo- and (±)-trans-1,2-Dihalocyclohexanes in Enantiopure Alleno-Acetylenic Cages. J Am Chem Soc 2017; 139:12190-12200. [DOI: 10.1021/jacs.7b05461] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Cornelius Gropp
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Tamara Husch
- Laboratorium
für Physikalische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Nils Trapp
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Markus Reiher
- Laboratorium
für Physikalische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - François Diederich
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
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21
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Jagadesan P, Samanta SR, Choudhury R, Ramamurthy V. Container Chemistry: Manipulating excited state behavior of organic guests within cavitands that form capsules in water. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3728] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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22
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Akine S, Miyashita M, Nabeshima T. A Metallo-molecular Cage That Can Close the Apertures with Coordination Bonds. J Am Chem Soc 2017; 139:4631-4634. [DOI: 10.1021/jacs.7b00840] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Shigehisa Akine
- Graduate
School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Masato Miyashita
- Faculty
of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
| | - Tatsuya Nabeshima
- Faculty
of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
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23
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Chen HY, Gou M, Wang JB. De novo endo-functionalized organic cages as cooperative multi-hydrogen-bond-donating catalysts. Chem Commun (Camb) 2017; 53:3524-3526. [PMID: 28294247 DOI: 10.1039/c7cc00938k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Two endo-functionalized organic cages as oxyanion hole mimics were achieved via dynamic covalent chemistry, which exhibit good size selectivity, catalytic activity and broad substrate scopes for Friedel-Crafts reactions. The modular character of the synthesis provides an easy way to modify the size, shape and inner function of the molecular cavity.
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Affiliation(s)
- Hong-Yu Chen
- Institute of Organic chemistry & MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
| | - Meng Gou
- School of Life Science, Liaoning Normal University, Dalian 116081, P. R. China. and Lamprey Research Center, Liaoning Normal University, Dalian 116081, P. R. China
| | - Jiao-Bing Wang
- Institute of Organic chemistry & MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
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24
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Zhang D, Martinez A, Dutasta JP. Emergence of Hemicryptophanes: From Synthesis to Applications for Recognition, Molecular Machines, and Supramolecular Catalysis. Chem Rev 2017; 117:4900-4942. [DOI: 10.1021/acs.chemrev.6b00847] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Dawei Zhang
- Shanghai
Key Laboratory of Green Chemistry and Chemical Processes, School of
Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, People’s Republic of China
- Laboratoire
de Chimie, École Normale Supérieure de Lyon, CNRS, UCBL, 46, Allée d’Italie, F-69364 Lyon, France
| | - Alexandre Martinez
- Laboratoire
de Chimie, École Normale Supérieure de Lyon, CNRS, UCBL, 46, Allée d’Italie, F-69364 Lyon, France
- Aix-Marseille University, CNRS, Centrale Marseille, iSm2, Av. Escadrille Normandie-Niemen, F-13397 Marseille, France
| | - Jean-Pierre Dutasta
- Laboratoire
de Chimie, École Normale Supérieure de Lyon, CNRS, UCBL, 46, Allée d’Italie, F-69364 Lyon, France
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25
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Ozores HL, Amorín M, Granja JR. Self-Assembling Molecular Capsules Based on α,γ-Cyclic Peptides. J Am Chem Soc 2017; 139:776-784. [DOI: 10.1021/jacs.6b10456] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Haxel Lionel Ozores
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS),
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Manuel Amorín
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS),
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Juan R. Granja
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS),
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
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26
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Abstract
This review highlights relevant studies of light-controlled molecular containers able to catch and release small molecules.
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Affiliation(s)
- Alejandro Díaz-Moscoso
- Institute of Chemical Research of Catalonia (ICIQ)
- The Barcelona Institute of Science and Technology
- Tarragona
- Spain
| | - Pablo Ballester
- Institute of Chemical Research of Catalonia (ICIQ)
- The Barcelona Institute of Science and Technology
- Tarragona
- Spain
- ICREA
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27
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Zhang D, Jamieson K, Guy L, Gao G, Dutasta JP, Martinez A. Tailored oxido-vanadium(V) cage complexes for selective sulfoxidation in confined spaces. Chem Sci 2017; 8:789-794. [PMID: 28451228 PMCID: PMC5299934 DOI: 10.1039/c6sc03045a] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/04/2016] [Indexed: 01/31/2023] Open
Abstract
Five sets of oxido-vanadium(V) complexes, which include both cages and open structures, were prepared and tested in the catalytic oxidation of sulfides. It was found that the hemicryptophane complexes, which are simultaneously comprised of cyclotriveratrylene (CTV), binaphthol and oxido-vanadium(V) moieties, are the most efficient supramolecular catalysts. The specific shape of the confined hydrophobic space above the metal center leads to a strong improvement in the yield, selectivity and rate of the reaction, compared to the other catalysts investigated herein. A remarkable turnover number (TON) of 10 000 was obtained, which can be attributed to both the high reactivity and stability of the catalyst. Similarly to enzymes, the kinetic analysis shows that the mechanism of oxidation with the supramolecular catalysts obeys the Michaelis-Menten model, in which initial rate saturation occurs upon an increase in substrate concentration. This enzyme-like behavior is also supported by the competitive inhibition and substrate size-selectivity observed, which underline the crucial role played by the cavity.
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Affiliation(s)
- Dawei Zhang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes , School of Chemistry and Molecular Engineering , East China Normal University , 3663 North Zhongshan Road , Shanghai , 200062 , P. R. China
- Laboratoire de Chimie , École Normale Supérieure de Lyon , CNRS , UCBL , 46 allée d'Italie , F-69364 Lyon , France
| | - Kelsey Jamieson
- Laboratoire de Chimie , École Normale Supérieure de Lyon , CNRS , UCBL , 46 allée d'Italie , F-69364 Lyon , France
| | - Laure Guy
- Laboratoire de Chimie , École Normale Supérieure de Lyon , CNRS , UCBL , 46 allée d'Italie , F-69364 Lyon , France
| | - Guohua Gao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes , School of Chemistry and Molecular Engineering , East China Normal University , 3663 North Zhongshan Road , Shanghai , 200062 , P. R. China
| | - Jean-Pierre Dutasta
- Laboratoire de Chimie , École Normale Supérieure de Lyon , CNRS , UCBL , 46 allée d'Italie , F-69364 Lyon , France
| | - Alexandre Martinez
- Laboratoire de Chimie , École Normale Supérieure de Lyon , CNRS , UCBL , 46 allée d'Italie , F-69364 Lyon , France
- Aix Marseille Univ , CNRS , Centrale Marseille , iSm2 , Marseille , France .
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28
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29
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Hu WB, Hu WJ, Liu YA, Li JS, Jiang B, Wen K. Multicavity macrocyclic hosts. Chem Commun (Camb) 2016; 52:12130-12142. [DOI: 10.1039/c6cc03651a] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Multicavity macrocyclic hosts are host molecules comprising more than one macrocyclic guest binding components connected through multipoint linkages.
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Affiliation(s)
- Wei-Bo Hu
- Shanghai Advanced Research Institute
- Chinese Academy of Science
- Shanghai 201210
- China
- University of Chinese Academy of Sciences
| | - Wen-Jing Hu
- Shanghai Advanced Research Institute
- Chinese Academy of Science
- Shanghai 201210
- China
| | - Yahu A. Liu
- Genomics Institute of the Novartis Research Foundation
- San Diego
- USA
| | - Jiu-Sheng Li
- Shanghai Advanced Research Institute
- Chinese Academy of Science
- Shanghai 201210
- China
| | - Biao Jiang
- Shanghai Advanced Research Institute
- Chinese Academy of Science
- Shanghai 201210
- China
| | - Ke Wen
- Shanghai Advanced Research Institute
- Chinese Academy of Science
- Shanghai 201210
- China
- School of Physical Science and Technology
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30
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Hu L, Polen S, Hardin AM, Pratumyot Y, Hadad CM, Badjić JD. On the Transfer of Chirality, Thermodynamic Stability, and Folding Characteristics of Stereoisomeric Gated Baskets. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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31
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Abstract
In this review, we describe the construction of gated molecular baskets, discuss their mechanism of action in regulating the exchange of guests and illustrate the potential of these concave hosts to act as catalysts for controlling chemical reactions. Importantly, a number of computational and experimental studies have suggested that gated baskets ought to unfold their gates at the rim for permitting the passage of guests to/from their inner space. These dynamic hosts are therefore offered as useful models for investigating the process of gating in artificial systems. Furthermore, gated baskets should permit examining the benefit of controlling the rate by which reactants access a gated catalyst for promoting chemical reactions occurring in its confined space.
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Affiliation(s)
- Keith Hermann
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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32
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Kobayashi K, Yamanaka M. Self-assembled capsules based on tetrafunctionalized calix[4]resorcinarene cavitands. Chem Soc Rev 2015; 44:449-66. [DOI: 10.1039/c4cs00153b] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The hemispherical structures of calix[4]resorcinarene cavitands are suitable for forming capsular assemblies with guest encapsulations through various intermolecular interactions.
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Affiliation(s)
- Kenji Kobayashi
- Department of Chemistry
- Graduate School of Science
- Shizuoka University
- Shizuoka 422-8529
- Japan
| | - Masamichi Yamanaka
- Department of Chemistry
- Graduate School of Science
- Shizuoka University
- Shizuoka 422-8529
- Japan
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