1
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Bąk KM, Patrick SC, Li X, Beer PD, Davis JJ. Engineered Binding Microenvironments in Halogen Bonding Polymers for Enhanced Anion Sensing. Angew Chem Int Ed Engl 2023; 62:e202300867. [PMID: 36749115 PMCID: PMC10946961 DOI: 10.1002/anie.202300867] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 02/08/2023]
Abstract
Mimicking Nature's polymeric protein architectures by designing hosts with binding cavities screened from bulk solvent is a promising approach to achieving anion recognition in competitive media. Accomplishing this, however, can be synthetically demanding. Herein we present a synthetically tractable approach, by directly incorporating potent supramolecular anion-receptive motifs into a polymeric scaffold, tuneable through a judicious selection of the co-monomer. A comprehensive analysis of anion recognition and sensing is demonstrated with redox-active, halogen bonding polymeric hosts. Notably, the polymeric hosts consistently outperform their monomeric analogues, with especially large halide binding enhancements of ca. 50-fold observed in aqueous-organic solvent mixtures. These binding enhancements are rationalised by the generation and presentation of low dielectric constant binding microenvironments from which there is appreciable solvent exclusion.
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Affiliation(s)
- Krzysztof M. Bąk
- Department of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QZUK
| | - Sophie C. Patrick
- Department of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QZUK
| | - Xiaoxiong Li
- Department of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QZUK
| | - Paul D. Beer
- Department of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QZUK
| | - Jason J. Davis
- Department of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QZUK
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2
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Li MS, Dong YW, Pang XY, Chai H, Wang X, Jiang W. The Influence of Small Biomolecules, Salts and Buffers on the Molecular Recognition of Amide Naphthotube in Aqueous Solutions. Chemistry 2023; 29:e202202972. [PMID: 36196913 DOI: 10.1002/chem.202202972] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Indexed: 11/18/2022]
Abstract
We found the binding affinities of amide naphthotube to neutral organic molecules in water are not influenced by most of small biomolecules, inorganic salts, and PBS and Tris buffers but are reduced in HEPES buffer through competitive binding. Nevertheless, salts do change the binding affinities of amide naphthotube to charged molecules through a screening effect.
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Affiliation(s)
- Ming-Shuang Li
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology (SUSTech), Xueyuan Blvd 1088, Shenzhen, 518055, P. R. China
| | - Yi-Wei Dong
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology (SUSTech), Xueyuan Blvd 1088, Shenzhen, 518055, P. R. China
| | - Xin-Yu Pang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology (SUSTech), Xueyuan Blvd 1088, Shenzhen, 518055, P. R. China
| | - Hongxin Chai
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology (SUSTech), Xueyuan Blvd 1088, Shenzhen, 518055, P. R. China.,Shenzhen Xinhua Middle School, Shenzhen, 518109, P. R. China
| | - Xiaoping Wang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology (SUSTech), Xueyuan Blvd 1088, Shenzhen, 518055, P. R. China
| | - Wei Jiang
- Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, and Department of Chemistry, Southern University of Science and Technology (SUSTech), Xueyuan Blvd 1088, Shenzhen, 518055, P. R. China
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3
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Kubik S. When Molecules Meet in Water-Recent Contributions of Supramolecular Chemistry to the Understanding of Molecular Recognition Processes in Water. ChemistryOpen 2022; 11:e202200028. [PMID: 35373466 PMCID: PMC8977507 DOI: 10.1002/open.202200028] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/17/2022] [Indexed: 12/19/2022] Open
Abstract
Molecular recognition processes in water differ from those in organic solvents in that they are mediated to a much greater extent by solvent effects. The hydrophobic effect, for example, causes molecules that only weakly interact in organic solvents to stay together in water. Such water-mediated interactions can be very efficient as demonstrated by many of the synthetic receptors discussed in this review, some of which have substrate affinities matching or even surpassing those of natural binders. However, in spite of considerable success in designing such receptors, not all factors determining their binding properties in water are fully understood. Existing concepts still provide plausible explanations why the reorganization of water molecules often causes receptor-substrate interactions in water to be strongly exothermic rather than entropically favored as predicted by the classical view of the hydrophobic effect.
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Affiliation(s)
- Stefan Kubik
- Technische Universität KaiserslauternFachbereich Chemie – Organische ChemieErwin-Schrödinger-Straße 5467663KaiserslauternGermany
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4
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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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5
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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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6
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Amezcua M, El Khoury L, Mobley DL. SAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations. J Comput Aided Mol Des 2021; 35:1-35. [PMID: 33392951 PMCID: PMC8121194 DOI: 10.1007/s10822-020-00363-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/24/2020] [Indexed: 12/15/2022]
Abstract
The SAMPL challenges focus on testing and driving progress of computational methods to help guide pharmaceutical drug discovery. However, assessment of methods for predicting binding affinities is often hampered by computational challenges such as conformational sampling, protonation state uncertainties, variation in test sets selected, and even lack of high quality experimental data. SAMPL blind challenges have thus frequently included a component focusing on host-guest binding, which removes some of these challenges while still focusing on molecular recognition. Here, we report on the results of the SAMPL7 blind prediction challenge for host-guest affinity prediction. In this study, we focused on three different host-guest categories-a familiar deep cavity cavitand series which has been featured in several prior challenges (where we examine binding of a series of guests to two hosts), a new series of cyclodextrin derivatives which are monofunctionalized around the rim to add amino acid-like functionality (where we examine binding of two guests to a series of hosts), and binding of a series of guests to a new acyclic TrimerTrip host which is related to previous cucurbituril hosts. Many predictions used methods based on molecular simulations, and overall success was mixed, though several methods stood out. As in SAMPL6, we find that one strategy for achieving reasonable accuracy here was to make empirical corrections to binding predictions based on previous data for host categories which have been studied well before, though this can be of limited value when new systems are included. Additionally, we found that alchemical free energy methods using the AMOEBA polarizable force field had considerable success for the two host categories in which they participated. The new TrimerTrip system was also found to introduce some sampling problems, because multiple conformations may be relevant to binding and interconvert only slowly. Overall, results in this challenge tentatively suggest that further investigation of polarizable force fields for these challenges may be warranted.
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Affiliation(s)
- Martin Amezcua
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
| | - Léa El Khoury
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA.
- Department of Chemistry, University of California, Irvine, CA, 92697, USA.
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7
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Mittal N, Benselfelt T, Ansari F, Gordeyeva K, Roth SV, Wågberg L, Söderberg LD. Ion-Specific Assembly of Strong, Tough, and Stiff Biofibers. Angew Chem Int Ed Engl 2019; 58:18562-18569. [PMID: 31600016 PMCID: PMC6916401 DOI: 10.1002/anie.201910603] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/01/2019] [Indexed: 11/29/2022]
Abstract
Designing engineering materials with high stiffness and high toughness is challenging as stiff materials tend to be brittle. Many biological materials realize this objective through multiscale (i.e., atomic- to macroscale) mechanisms that are extremely difficult to replicate in synthetic materials. Inspired from the architecture of such biological structures, we here present flow-assisted organization and assembly of renewable native cellulose nanofibrils (CNFs), which yields highly anisotropic biofibers characterized by a unique combination of high strength (1010 MPa), high toughness (62 MJ m-3 ) and high stiffness (57 GPa). We observed that properties of the fibers are primarily governed by specific ion characteristics such as hydration enthalpy and polarizability. A fundamental facet of this study is thus to elucidate the role of specific anion binding following the Hofmeister series on the mechanical properties of wet fibrillar networks, and link this to the differences in properties of dry nanostructured fibers. This knowledge is useful for rational design of nanomaterials and is critical for validation of specific ion effect theories. The bioinspired assembly demonstrated here is relevant example for designing high-performance materials with absolute structural control.
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Affiliation(s)
- Nitesh Mittal
- Linné FLOW CentreDepartment of MechanicsKTH Royal Institute of TechnologyStockholmSE-100 44Sweden
- Wallenberg Wood Science CenterKTH Royal Institute of TechnologyStockholmSE-100 44Sweden
- Department of Chemical EngineeringMassachusetts Institute of TechnologyCambridgeMA02142USA
| | - Tobias Benselfelt
- Wallenberg Wood Science CenterKTH Royal Institute of TechnologyStockholmSE-100 44Sweden
- Department of Fibre and Polymer TechnologyKTH Royal Institute of TechnologyStockholmSE-100 44Sweden
| | - Farhan Ansari
- Department of Materials Science and EngineeringStanford UniversityStanfordCA94305-2205USA
| | - Korneliya Gordeyeva
- Linné FLOW CentreDepartment of MechanicsKTH Royal Institute of TechnologyStockholmSE-100 44Sweden
| | - Stephan V. Roth
- Department of Fibre and Polymer TechnologyKTH Royal Institute of TechnologyStockholmSE-100 44Sweden
- Deutsches Elektronen-Synchrotron (DESY)22607HamburgGermany
| | - Lars Wågberg
- Wallenberg Wood Science CenterKTH Royal Institute of TechnologyStockholmSE-100 44Sweden
- Department of Fibre and Polymer TechnologyKTH Royal Institute of TechnologyStockholmSE-100 44Sweden
| | - L. Daniel Söderberg
- Linné FLOW CentreDepartment of MechanicsKTH Royal Institute of TechnologyStockholmSE-100 44Sweden
- Wallenberg Wood Science CenterKTH Royal Institute of TechnologyStockholmSE-100 44Sweden
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8
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Mittal N, Benselfelt T, Ansari F, Gordeyeva K, Roth SV, Wågberg L, Söderberg LD. Ion‐Specific Assembly of Strong, Tough, and Stiff Biofibers. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Nitesh Mittal
- Linné FLOW CentreDepartment of MechanicsKTH Royal Institute of Technology Stockholm SE-100 44 Sweden
- Wallenberg Wood Science CenterKTH Royal Institute of Technology Stockholm SE-100 44 Sweden
- Department of Chemical EngineeringMassachusetts Institute of Technology Cambridge MA 02142 USA
| | - Tobias Benselfelt
- Wallenberg Wood Science CenterKTH Royal Institute of Technology Stockholm SE-100 44 Sweden
- Department of Fibre and Polymer TechnologyKTH Royal Institute of Technology Stockholm SE-100 44 Sweden
| | - Farhan Ansari
- Department of Materials Science and EngineeringStanford University Stanford CA 94305-2205 USA
| | - Korneliya Gordeyeva
- Linné FLOW CentreDepartment of MechanicsKTH Royal Institute of Technology Stockholm SE-100 44 Sweden
| | - Stephan V. Roth
- Department of Fibre and Polymer TechnologyKTH Royal Institute of Technology Stockholm SE-100 44 Sweden
- Deutsches Elektronen-Synchrotron (DESY) 22607 Hamburg Germany
| | - Lars Wågberg
- Wallenberg Wood Science CenterKTH Royal Institute of Technology Stockholm SE-100 44 Sweden
- Department of Fibre and Polymer TechnologyKTH Royal Institute of Technology Stockholm SE-100 44 Sweden
| | - L. Daniel Söderberg
- Linné FLOW CentreDepartment of MechanicsKTH Royal Institute of Technology Stockholm SE-100 44 Sweden
- Wallenberg Wood Science CenterKTH Royal Institute of Technology Stockholm SE-100 44 Sweden
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9
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Assaf KI, Nau WM. The Chaotropic Effect as an Assembly Motif in Chemistry. Angew Chem Int Ed Engl 2018; 57:13968-13981. [PMID: 29992706 PMCID: PMC6220808 DOI: 10.1002/anie.201804597] [Citation(s) in RCA: 199] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/01/2018] [Indexed: 11/26/2022]
Abstract
Following up on scattered reports on interactions of conventional chaotropic ions (for example, I- , SCN- , ClO4- ) with macrocyclic host molecules, biomolecules, and hydrophobic neutral surfaces in aqueous solution, the chaotropic effect has recently emerged as a generic driving force for supramolecular assembly, orthogonal to the hydrophobic effect. The chaotropic effect becomes most effective for very large ions that extend beyond the classical Hofmeister scale and that can be referred to as superchaotropic ions (for example, borate clusters and polyoxometalates). In this Minireview, we present a continuous scale of water-solute interactions that includes the solvation of kosmotropic, chaotropic, and hydrophobic solutes, as well as the creation of void space (cavitation). Recent examples for the association of chaotropic anions to hydrophobic synthetic and biological binding sites, lipid bilayers, and surfaces are discussed.
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Affiliation(s)
- Khaleel I. Assaf
- Department of Life Sciences and ChemistryJacobs University BremenCampus Ring 128759BremenGermany
| | - Werner M. Nau
- Department of Life Sciences and ChemistryJacobs University BremenCampus Ring 128759BremenGermany
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10
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Affiliation(s)
- Khaleel I. Assaf
- Department of Life Sciences and Chemistry; Jacobs University Bremen; Campus Ring 1 28759 Bremen Deutschland
| | - Werner M. Nau
- Department of Life Sciences and Chemistry; Jacobs University Bremen; Campus Ring 1 28759 Bremen Deutschland
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11
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Qi Z, Chiappisi L, Gong H, Pan R, Cui N, Ge Y, Böttcher C, Dong S. Ion Selectivity in Nonpolymeric Thermosensitive Systems Induced by Water-Attenuated Supramolecular Recognition. Chemistry 2018; 24:3854-3861. [DOI: 10.1002/chem.201705838] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Zhenhui Qi
- Sino-German Joint Research Lab for Space Biomaterials and Translational Technology; School of Life Sciences; Northwestern Polytechnical University; 127 Youyi Xilu, Xi'an Shaanxi 710072 P. R. China
| | - Leonardo Chiappisi
- Stranski Laboratorium für Physikalische Chemie und Theoretische Chemie; Institut für Chemie; Technische Universität Berlin; Strasse des 17. Juni 124, Sekr. TC7 D-10623 Berlin Germany
- Institut Max von Laue-Paul Langevin; 71 Avenue des Martyrs 38042 Grenoble Cedex 9 France
| | - Hanlin Gong
- Sino-German Joint Research Lab for Space Biomaterials and Translational Technology; School of Life Sciences; Northwestern Polytechnical University; 127 Youyi Xilu, Xi'an Shaanxi 710072 P. R. China
| | - Ren Pan
- Sino-German Joint Research Lab for Space Biomaterials and Translational Technology; School of Life Sciences; Northwestern Polytechnical University; 127 Youyi Xilu, Xi'an Shaanxi 710072 P. R. China
| | - Ning Cui
- Sino-German Joint Research Lab for Space Biomaterials and Translational Technology; School of Life Sciences; Northwestern Polytechnical University; 127 Youyi Xilu, Xi'an Shaanxi 710072 P. R. China
| | - Yan Ge
- Sino-German Joint Research Lab for Space Biomaterials and Translational Technology; School of Life Sciences; Northwestern Polytechnical University; 127 Youyi Xilu, Xi'an Shaanxi 710072 P. R. China
| | - Christoph Böttcher
- Research Center for Electron Microscopy, BioSupraMol; Institut für Chemie und Biochemie; Freie Universität Berlin; Fabeckstr. 36a 14195 Berlin Germany
| | - Shengyi Dong
- College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 Hunan P. R. China
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12
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Avram L, Wishard AD, Gibb BC, Bar‐Shir A. Quantifying Guest Exchange in Supramolecular Systems. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708726] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Liat Avram
- Department of Chemical Research Support The Weizmann Institute of Science 7610001 Rehovot Israel
| | | | - Bruce C. Gibb
- Department of Chemistry Tulane University New Orleans LA 70118 USA
| | - Amnon Bar‐Shir
- Department of Organic Chemistry The Weizmann Institute of Science 7610001 Rehovot Israel
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13
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Avram L, Wishard AD, Gibb BC, Bar-Shir A. Quantifying Guest Exchange in Supramolecular Systems. Angew Chem Int Ed Engl 2017; 56:15314-15318. [PMID: 28972281 DOI: 10.1002/anie.201708726] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Indexed: 11/08/2022]
Abstract
The ability to accurately determine and quantitatively evaluate kinetic phenomena associated with supramolecular assemblies, in real time, is key to a better understanding of their defined architectures and diverse functionalities. Therefore, analytical tools that can precisely assess a wide range of exchange rates within such systems are of considerable importance. This study demonstrates the ability to use an NMR approach based on saturation transfer for the determination of rates of guest exchange from molecular capsules. By using cavitands that assemble into distinct dimeric assemblies, we show that this approach, which we term guest exchange saturation transfer (GEST), allows the use of a conventional NMR setup to study and quantitatively assess a wide range of exchange rates, from 35 to more than 5000 s-1 .
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Affiliation(s)
- Liat Avram
- Department of Chemical Research Support, The Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Anthony D Wishard
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA
| | - Bruce C Gibb
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA
| | - Amnon Bar-Shir
- Department of Organic Chemistry, The Weizmann Institute of Science, 7610001, Rehovot, Israel
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14
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Havel V, Babiak M, Sindelar V. Modulation of Bambusuril Anion Affinity in Water. Chemistry 2017; 23:8963-8968. [DOI: 10.1002/chem.201701316] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Vaclav Havel
- Department of Chemistry; Masaryk University, Faculty of Science; Kamenice 5 625 00 Brno Czech Republic
- RECETOX-Research Centre for Toxic Compounds in the Environment; Masaryk University, Faculty of Science; Kamenice 5 625 00 Brno Czech Republic
| | - Michal Babiak
- Department of Chemistry; Masaryk University, Faculty of Science; Kamenice 5 625 00 Brno Czech Republic
- CEITEC-Central European Institute of Technology and National Centre for Biomolecular Research; Masaryk University; Kamenice 5 625 00 Brno Czech Republic
| | - Vladimir Sindelar
- Department of Chemistry; Masaryk University, Faculty of Science; Kamenice 5 625 00 Brno Czech Republic
- RECETOX-Research Centre for Toxic Compounds in the Environment; Masaryk University, Faculty of Science; Kamenice 5 625 00 Brno Czech Republic
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15
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Abstract
Binding free energy calculations based on molecular simulations provide predicted affinities for biomolecular complexes. These calculations begin with a detailed description of a system, including its chemical composition and the interactions among its components. Simulations of the system are then used to compute thermodynamic information, such as binding affinities. Because of their promise for guiding molecular design, these calculations have recently begun to see widespread applications in early-stage drug discovery. However, many hurdles remain in making them a robust and reliable tool. In this review, we highlight key challenges of these calculations, discuss some examples of these challenges, and call for the designation of standard community benchmark test systems that will help the research community generate and evaluate progress. In our view, progress will require careful assessment and evaluation of new methods, force fields, and modeling innovations on well-characterized benchmark systems, and we lay out our vision for how this can be achieved.
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Affiliation(s)
- David L Mobley
- Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, California 92697;
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences and Center for Drug Discovery Innovation, University of California, San Diego, La Jolla, California 92093;
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16
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Hartle MD, Hansen RJ, Tresca BW, Prakel SS, Zakharov LN, Haley MM, Pluth MD, Johnson DW. A Synthetic Supramolecular Receptor for the Hydrosulfide Anion. Angew Chem Int Ed Engl 2016; 55:11480-4. [PMID: 27510286 DOI: 10.1002/anie.201605757] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Indexed: 12/11/2022]
Abstract
Hydrogen sulfide (H2 S) has emerged as a crucial biomolecule in physiology and cellular signaling. Key challenges associated with developing new chemical tools for understanding the biological roles of H2 S include developing platforms that enable reversible binding of this important biomolecule. The first synthetic small molecule receptor for the hydrosulfide anion, HS(-) , using only reversible, hydrogen-bonding interactions in a series of bis(ethynylaniline) derivatives, is reported. Binding constants of up to 90 300±8700 m(-1) were obtained in MeCN. The fundamental science of reversible sulfide binding, in this case featuring a key CH⋅⋅⋅S hydrogen bond, will expand the possibility for discovery of sulfide protein targets and molecular recognition agents.
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Affiliation(s)
- Matthew D Hartle
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403-1253, USA
| | - Ryan J Hansen
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403-1253, USA
| | - Blakely W Tresca
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403-1253, USA
| | - Samuel S Prakel
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403-1253, USA
| | - Lev N Zakharov
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403-1253, USA.,CAMCOR-Center for Advanced Materials Characterization in Oregon, University of Oregon, Eugene, OR, 97403-1443, USA
| | - Michael M Haley
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403-1253, USA.
| | - Michael D Pluth
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403-1253, USA.
| | - Darren W Johnson
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403-1253, USA.
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17
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Hartle MD, Hansen RJ, Tresca BW, Prakel SS, Zakharov LN, Haley MM, Pluth MD, Johnson DW. A Synthetic Supramolecular Receptor for the Hydrosulfide Anion. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605757] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Matthew D. Hartle
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology University of Oregon Eugene OR 97403-1253 USA
| | - Ryan J. Hansen
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology University of Oregon Eugene OR 97403-1253 USA
| | - Blakely W. Tresca
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology University of Oregon Eugene OR 97403-1253 USA
| | - Samuel S. Prakel
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology University of Oregon Eugene OR 97403-1253 USA
| | - Lev N. Zakharov
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology University of Oregon Eugene OR 97403-1253 USA
- CAMCOR—Center for Advanced Materials Characterization in Oregon University of Oregon Eugene OR 97403-1443 USA
| | - Michael M. Haley
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology University of Oregon Eugene OR 97403-1253 USA
| | - Michael D. Pluth
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology University of Oregon Eugene OR 97403-1253 USA
| | - Darren W. Johnson
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology University of Oregon Eugene OR 97403-1253 USA
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Langton MJ, Serpell CJ, Beer PD. Anion Recognition in Water: Recent Advances from a Supramolecular and Macromolecular Perspective. Angew Chem Int Ed Engl 2016; 55:1974-87. [PMID: 26612067 PMCID: PMC4755225 DOI: 10.1002/anie.201506589] [Citation(s) in RCA: 315] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Indexed: 12/22/2022]
Abstract
The recognition of anions in water remains a key challenge in modern supramolecular chemistry, and is essential if proposed applications in biological, medical, and environmental arenas that typically require aqueous conditions are to be achieved. However, synthetic anion receptors that operate in water have, in general, been the exception rather than the norm to date. Nevertheless, a significant step change towards routinely conducting anion recognition in water has been achieved in the past few years, and this Review highlights these approaches, with particular focus on controlling and using the hydrophobic effect, as well as more exotic interactions such as C-H hydrogen bonding and halogen bonding. We also look beyond the field of small-molecule recognition into the macromolecular domain, covering recent advances in anion recognition based on biomolecules, polymers, and nanoparticles.
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Affiliation(s)
- Matthew J Langton
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Christopher J Serpell
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.
- School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH, UK.
| | - Paul D Beer
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.
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Langton MJ, Serpell CJ, Beer PD. Anionenerkennung in Wasser: aktuelle Fortschritte aus supramolekularer und makromolarer Sicht. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506589] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Matthew J. Langton
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; Mansfield Road Oxford OX1 3TA Vereinigtes Königreich
| | - Christopher J. Serpell
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; Mansfield Road Oxford OX1 3TA Vereinigtes Königreich
- School of Physical Sciences, Ingram Building; University of Kent; Canterbury Kent CT2 7NH Vereinigtes Königreich
| | - Paul D. Beer
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; Mansfield Road Oxford OX1 3TA Vereinigtes Königreich
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Assaf KI, Ural MS, Pan F, Georgiev T, Simova S, Rissanen K, Gabel D, Nau WM. Water Structure Recovery in Chaotropic Anion Recognition: High-Affinity Binding of Dodecaborate Clusters to γ-Cyclodextrin. Angew Chem Int Ed Engl 2015; 54:6852-6. [PMID: 25951349 PMCID: PMC4510780 DOI: 10.1002/anie.201412485] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 03/18/2015] [Indexed: 12/29/2022]
Abstract
Dodecaborate anions of the type B12X12(2-) and B12X11Y(2-) (X=H, Cl, Br, I and Y=OH, SH, NH3(+), NR3(+)) form strong (K(a) up to 10(6) L mol(-1), for B12Br12(2-)) inclusion complexes with γ-cyclodextrin (γ-CD). The micromolar affinities reached are the highest known for this native CD. The complexation exhibits highly negative enthalpies (up to -25 kcal mol(-1)) and entropies (TΔS up to -18.4 kcal mol(-1), both for B12I12(2-)), which position these guests at the bottom end of the well-known enthalpy-entropy correlation for CDs. The high driving force can be traced back to a chaotropic effect, according to which chaotropic anions have an intrinsic affinity to hydrophobic cavities in aqueous solution. In line with this argument, salting-in effects revealed dodecaborates as superchaotropic dianions.
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Affiliation(s)
- Khaleel I Assaf
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen (Germany)
| | - Merve S Ural
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen (Germany)
| | - Fangfang Pan
- University of Jyvaskyla, Department of Chemistry, Nanoscience Center, P.O. Box. 35, 40014 University of Jyvaskyla (Finland)
| | - Tony Georgiev
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen (Germany)
| | - Svetlana Simova
- Institute of Organic Chemistry with Center of Phytochemistry, Bulgarian Academy of Science, 1113 Sofia (Bulgaria)
| | - Kari Rissanen
- University of Jyvaskyla, Department of Chemistry, Nanoscience Center, P.O. Box. 35, 40014 University of Jyvaskyla (Finland).
| | - Detlef Gabel
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen (Germany).
| | - Werner M Nau
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen (Germany).
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Assaf KI, Ural MS, Pan F, Georgiev T, Simova S, Rissanen K, Gabel D, Nau WM. Water Structure Recovery in Chaotropic Anion Recognition: High-Affinity Binding of Dodecaborate Clusters to γ-Cyclodextrin. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412485] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Yawer MA, Havel V, Sindelar V. A bambusuril macrocycle that binds anions in water with high affinity and selectivity. Angew Chem Int Ed Engl 2014; 54:276-9. [PMID: 25385515 DOI: 10.1002/anie.201409895] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Indexed: 11/12/2022]
Abstract
Synthetic receptors that function in water are important for the qualitative and quantitative detection of anions, which may act as pollutants in the environment or play important roles in biological processes. Neutral receptors are particularly appealing because they are often more selective than positively charged receptors; however, their affinity towards anions in pure water is only in range of 1-10(3) L mol(-1) . The anion-templated synthesis of a water-soluble bambusuril derivative is shown to be an outstanding receptor for various inorganic anions in pure water, with association constants of up to 10(7) L mol(-1) . Furthermore, the macrocycle discriminates between anions with unprecedented selectivity (up to 500 000-fold). We anticipate that the combination of remarkable affinity and selectivity of this macrocycle will enable the efficient detection and isolation of diverse anions in aqueous solutions, which is not possible with current supramolecular systems.
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Affiliation(s)
- Mirza Arfan Yawer
- Department of Chemistry and RECETOX, Masaryk University, Kamenice 5, 625 00 Brno (Czech Republic)
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Yawer MA, Havel V, Sindelar V. A Bambusuril Macrocycle that Binds Anions in Water with High Affinity and Selectivity. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409895] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Mirza Arfan Yawer
- Department of Chemistry and RECETOX, Masaryk University, Kamenice 5, 625 00 Brno (Czech Republic)
| | - Vaclav Havel
- Department of Chemistry and RECETOX, Masaryk University, Kamenice 5, 625 00 Brno (Czech Republic)
| | - Vladimir Sindelar
- Department of Chemistry and RECETOX, Masaryk University, Kamenice 5, 625 00 Brno (Czech Republic)
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