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López-Coll R, Álvarez-Yebra R, Feixas F, Lledó A. Comprehensive Characterization of the Self-Folding Cavitand Dynamics. Chemistry 2021; 27:10099-10106. [PMID: 33881199 PMCID: PMC8361935 DOI: 10.1002/chem.202100563] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Indexed: 12/21/2022]
Abstract
The conformational equilibria and guest exchange process of a resorcin[4]arene derived self-folding cavitand receptor have been characterized in detail by molecular dynamics simulations (MD) and 1 H EXSY NMR experiments. A multi-timescale strategy for exploring the fluxional behaviour of this system has been constructed, exploiting conventional MD and accelerated MD (aMD) techniques. The use of aMD allows the reconstruction of the folding/unfolding process of the receptor by sampling high-energy barrier processes unattainable by conventional MD simulations. We obtained MD trajectories sampling events occurring at different timescales from ns to s: 1) rearrangement of the directional hydrogen bond seam stabilizing the receptor, 2) folding/unfolding of the structure transiting partially open intermediates, and 3) guest departure from different folding stages. Most remarkably, reweighing of the biased aMD simulations provided kinetic barriers that are in very good agreement with those determined experimentally by 1 H NMR. These results constitute the first comprehensive characterization of the complex dynamic features of cavitand receptors. Our approach emerges as a valuable rational design tool for synthetic host-guest systems.
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Affiliation(s)
- Ricard López-Coll
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, 17003, Girona
| | - Rubén Álvarez-Yebra
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, 17003, Girona
| | - Ferran Feixas
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, 17003, Girona
| | - Agustí Lledó
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, 17003, Girona
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2
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Petroselli M, Chen YQ, Rebek J, Yu Y. Binding and reactivity in deep cavitands based on resorcin[ ]arene. GREEN SYNTHESIS AND CATALYSIS 2021. [DOI: 10.1016/j.gresc.2021.03.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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3
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Natarajan N, Brenner E, Sémeril D, Matt D, Harrowfield J. The Use of Resorcinarene Cavitands in Metal-Based Catalysis. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700725] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Nallusamy Natarajan
- Université de Strasbourg; Laboratoire de Chimie Inorganique Moléculaire et Catalyse, UMR 7177 CNRS; 4 rue Blaise Pascal 67008 Strasbourg France
| | - Eric Brenner
- Université de Strasbourg; Laboratoire de Chimie Inorganique Moléculaire et Catalyse, UMR 7177 CNRS; 4 rue Blaise Pascal 67008 Strasbourg France
| | - David Sémeril
- Université de Strasbourg; Laboratoire de Chimie Inorganique Moléculaire et Catalyse, UMR 7177 CNRS; 4 rue Blaise Pascal 67008 Strasbourg France
| | - Dominique Matt
- Université de Strasbourg; Laboratoire de Chimie Inorganique Moléculaire et Catalyse, UMR 7177 CNRS; 4 rue Blaise Pascal 67008 Strasbourg France
| | - Jack Harrowfield
- Université de Strasbourg; ISIS, UMR 7006 CNRS; 8 allée Gaspard Monge, BP 70028 67083 Strasbourg France
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4
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Boerth DW, Arvanites AC. Nucleophilic aromatic substitution in chlorinated aromatic systems with a glutathione thiolate model. J PHYS ORG CHEM 2016. [DOI: 10.1002/poc.3640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Donald W. Boerth
- Department of Chemistry and Biochemistry; University of Massachusetts Dartmouth; North Dartmouth MA USA
| | - Anthony C. Arvanites
- Department of Chemistry and Biochemistry; University of Massachusetts Dartmouth; North Dartmouth MA USA
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5
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Galan A, Ballester P. Stabilization of reactive species by supramolecular encapsulation. Chem Soc Rev 2016; 45:1720-37. [DOI: 10.1039/c5cs00861a] [Citation(s) in RCA: 224] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This review describes and updated overview of the stabilization of reactive species and reaction intermediates by inclusion in nanocavities provided by covalent- and supra-molecular containers.
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Affiliation(s)
- Albano Galan
- Institute of Chemical Research of Catalonia (ICIQ)
- The Barcelona Institute of Science and Technology
- 43007 Tarragona
- Spain
| | - Pablo Ballester
- Institute of Chemical Research of Catalonia (ICIQ)
- The Barcelona Institute of Science and Technology
- 43007 Tarragona
- Spain
- Catalan Institution for Research and Advanced Studies (ICREA)
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6
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López-Vidal EM, Fernández-Mato A, García MD, Pérez-Lorenzo M, Peinador C, Quintela JM. Metallacycle-Catalyzed SNAr Reaction in Water: Supramolecular Inhibition by Means of Host–Guest Complexation. J Org Chem 2014; 79:1265-70. [DOI: 10.1021/jo402689p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Eva M. López-Vidal
- Departamento
de Química Fundamental and Centro de Investigaciones Científicas
Avanzadas (CICA), Facultad de Ciencias, Universidade da Coruña, A Zapateira
s/n, 15008 A Coruña, Spain
| | - Antonio Fernández-Mato
- Departamento
de Química Fundamental and Centro de Investigaciones Científicas
Avanzadas (CICA), Facultad de Ciencias, Universidade da Coruña, A Zapateira
s/n, 15008 A Coruña, Spain
| | - Marcos D. García
- Departamento
de Química Fundamental and Centro de Investigaciones Científicas
Avanzadas (CICA), Facultad de Ciencias, Universidade da Coruña, A Zapateira
s/n, 15008 A Coruña, Spain
| | | | - Carlos Peinador
- Departamento
de Química Fundamental and Centro de Investigaciones Científicas
Avanzadas (CICA), Facultad de Ciencias, Universidade da Coruña, A Zapateira
s/n, 15008 A Coruña, Spain
| | - José M. Quintela
- Departamento
de Química Fundamental and Centro de Investigaciones Científicas
Avanzadas (CICA), Facultad de Ciencias, Universidade da Coruña, A Zapateira
s/n, 15008 A Coruña, Spain
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7
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Raynal M, Ballester P, Vidal-Ferran A, van Leeuwen PWNM. Supramolecular catalysis. Part 2: artificial enzyme mimics. Chem Soc Rev 2013; 43:1734-87. [PMID: 24365792 DOI: 10.1039/c3cs60037h] [Citation(s) in RCA: 665] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The design of artificial catalysts able to compete with the catalytic proficiency of enzymes is an intense subject of research. Non-covalent interactions are thought to be involved in several properties of enzymatic catalysis, notably (i) the confinement of the substrates and the active site within a catalytic pocket, (ii) the creation of a hydrophobic pocket in water, (iii) self-replication properties and (iv) allosteric properties. The origins of the enhanced rates and high catalytic selectivities associated with these properties are still a matter of debate. Stabilisation of the transition state and favourable conformations of the active site and the product(s) are probably part of the answer. We present here artificial catalysts and biomacromolecule hybrid catalysts which constitute good models towards the development of truly competitive artificial enzymes.
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Affiliation(s)
- Matthieu Raynal
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, 43007 Tarragona, Spain.
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8
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Mechanistic Assessment of SNAr Displacement of Halides from 1-Halo-2,4-dinitrobenzenes by Selected Primary and Secondary Amines: Brønsted and Mayr Analyses. J Org Chem 2012; 77:9738-46. [DOI: 10.1021/jo301862b] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Terrier F, Dust JM, Buncel E. Dual super-electrophilic and Diels–Alder reactivity of neutral 10π heteroaromatic substrates. Tetrahedron 2012. [DOI: 10.1016/j.tet.2011.12.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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10
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Degardin M, Busseron E, Kim DA, Ajami D, Rebek J. Deep cavitands featuring functional acetal-based walls. Chem Commun (Camb) 2012; 48:11850-2. [DOI: 10.1039/c2cc36517k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Affiliation(s)
- Louis Marchetti
- Department of Chemistry, University of Rhode Island, 51 Lower College Road, Kingston, Rhode Island 02881, United States
| | - Mindy Levine
- Department of Chemistry, University of Rhode Island, 51 Lower College Road, Kingston, Rhode Island 02881, United States
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12
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Dawn S, Dewal MB, Sobransingh D, Paderes MC, Wibowo AC, Smith MD, Krause JA, Pellechia PJ, Shimizu LS. Self-Assembled Phenylethynylene Bis-urea Macrocycles Facilitate the Selective Photodimerization of Coumarin. J Am Chem Soc 2011; 133:7025-32. [DOI: 10.1021/ja110779h] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sandipan Dawn
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Mahender B. Dewal
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - David Sobransingh
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Monissa C. Paderes
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Arief C. Wibowo
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Mark D. Smith
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Jeanette A. Krause
- The Richard C. Elder X-ray Crystallographic Facility, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Perry J. Pellechia
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Linda S. Shimizu
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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13
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Laughrey Z, Gibb BC. Water-soluble, self-assembling container molecules: an update. Chem Soc Rev 2011; 40:363-86. [DOI: 10.1039/c0cs00030b] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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14
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Consiglio G, Cosimelli B, Guernelli S, Lanza CZ, Sancassan F, Spinelli D, Stenta M. A Novel Approach to the Evaluation of the Importance of Steric and Electronic Effects in SNAr Reactions: A Computational, Thermodynamic and 1H and 13C NMR Study of “Meisenheimer-Type” Adducts in the Benzo[b]thiophene Series. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000725] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Lledó A, Rebek J. Self-folding cavitands: structural characterization of the induced-fit model. Chem Commun (Camb) 2010; 46:1637-9. [PMID: 20177600 DOI: 10.1039/b927031k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Deletion of structural elements in cavitand receptors is used to evaluate the thermodynamic and kinetic parameters of binding in these hosts. The use of a bulky guest showcases the importance of host-guest shape adaptations in the molecular recognition process.
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Affiliation(s)
- Agustí Lledó
- The Skaggs Institute for Chemical Biology and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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16
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Sinclair AJ, del Amo V, Philp D. Structure-reactivity relationships in a recognition mediated [3+2] dipolar cycloaddition reaction. Org Biomol Chem 2009; 7:3308-18. [PMID: 19641790 DOI: 10.1039/b908072d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The [3+2] dipolar cycloaddition between an azide and maleimide can be accelerated by a factor of more than 100 simply by attaching complementary recognition sites to the reactive partners. This rate acceleration derives from the formation of a reactive binary complex between the azide and the maleimide. The variation of the observed rate acceleration with simple structural changes, such as adding additional rotors, should be relatively predictable. However, the application of a simple, rotor-based increment in the systems reported here is insufficient to predict reactivity correctly. Computational studies suggest that the nature of the available reaction pathways within the binary complex formed by the reactants is important in determining the reactivity of a given complex.
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Affiliation(s)
- Andrew J Sinclair
- Centre for Biomolecular Sciences, School of Chemistry, University of St Andrews, North Haugh, St Andrews, United KingdomKY16 9ST
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17
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Restorp P, Rebek J. Reaction of isonitriles with carboxylic acids in a cavitand: observation of elusive isoimide intermediates. J Am Chem Soc 2008; 130:11850-1. [PMID: 18698780 PMCID: PMC2642476 DOI: 10.1021/ja803854r] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A deep cavitand with an inwardly directed carboxylic acid function reacts with small aliphatic isonitriles to form N-acyl formamides inside the cavity. The unique isolation and stabilization of covalently bound guests within the structured environment of the cavitand allows for observation of the labile O-acyl isoimide intermediate using conventional spectroscopic methods.
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Affiliation(s)
- Per Restorp
- The Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, California, 92037, USA
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18
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Zuidema E, Sarmentero M, Bo C, Ballester P. A Combined Experimental and Theoretical Study of the Molecular Inclusion of Organometallic Sandwich Complexes in a Cavitand Receptor. Chemistry 2008; 14:7285-95. [DOI: 10.1002/chem.200800628] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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19
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Hooley RJ, Rebek J. A deep cavitand catalyzes the Diels-Alder reaction of bound maleimides. Org Biomol Chem 2007; 5:3631-6. [PMID: 17971992 DOI: 10.1039/b713104f] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A deep cavitand catalyzes Diels-Alder reactions of bound maleimides via activation of the dienophile by interaction with the organized hydrogen bonding network at the cavitand rim. Rapid in-out exchange of reactant and product allows efficient turnover. The increase in steric bulk of the reaction product lessens its binding affinity, reducing (and in some cases completely eliminating) product inhibition.
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Affiliation(s)
- Richard J Hooley
- The Skaggs Institute for Chemical Biology, and the Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
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