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Shiroudi A, Śmiechowski M, Czub J, Abdel-Rahman MA. Computational analysis of substituent effects on proton affinity and gas-phase basicity of TEMPO derivatives and their hydrogen bonding interactions with water molecules. Sci Rep 2024; 14:8434. [PMID: 38600208 PMCID: PMC11006853 DOI: 10.1038/s41598-024-58582-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 04/01/2024] [Indexed: 04/12/2024] Open
Abstract
The study investigates the molecular structure of 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) and its derivatives in the gas phase using B3LYP and M06-2X functional methods. Intermolecular interactions are analyzed using natural bond orbital (NBO) and atoms in molecules (AIM) techniques. NO2-substituted TEMPO displays high reactivity, less stability, and softer properties. The study reveals that the stability of TEMPO derivatives is mainly influenced by LP(e) → σ∗ electronic delocalization effects, with the highest stabilization observed on the oxygen atom of the nitroxide moiety. This work also considers electron density, atomic charges, and energetic and thermodynamic properties of the studied NO radicals, and their relative stability. The proton affinity and gas-phase basicity of the studied compounds were computed at T = 298 K for O-protonation and N-protonation, respectively. The studied DFT method calculations show that O-protonation is more stable than N-protonation, with an energy difference of 16.64-20.77 kcal/mol (22.80-25.68 kcal/mol) at the B3LYP (M06-2X) method. The AIM analysis reveals that the N-O…H interaction in H2O complexes has the most favorable hydrogen bond energy computed at bond critical points (3, - 1), and the planar configurations of TEMPO derivatives exhibit the highest EHB values. This indicates stronger hydrogen bonding interactions between the N-O group and water molecules.
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Affiliation(s)
- Abolfazl Shiroudi
- Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland.
- BioTechMed Center, Gdańsk University of Technology, 80-233, Gdańsk, Poland.
| | - Maciej Śmiechowski
- Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Jacek Czub
- Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
- BioTechMed Center, Gdańsk University of Technology, 80-233, Gdańsk, Poland
| | - Mohamed A Abdel-Rahman
- Department of Chemistry, Faculty of Science, Suez University, P.O. Box: 43221, Suez, Egypt.
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2
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Montà-González G, Sancenón F, Martínez-Máñez R, Martí-Centelles V. Purely Covalent Molecular Cages and Containers for Guest Encapsulation. Chem Rev 2022; 122:13636-13708. [PMID: 35867555 PMCID: PMC9413269 DOI: 10.1021/acs.chemrev.2c00198] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Cage compounds offer unique binding pockets similar to enzyme-binding sites, which can be customized in terms of size, shape, and functional groups to point toward the cavity and many other parameters. Different synthetic strategies have been developed to create a toolkit of methods that allow preparing tailor-made organic cages for a number of distinct applications, such as gas separation, molecular recognition, molecular encapsulation, hosts for catalysis, etc. These examples show the versatility and high selectivity that can be achieved using cages, which is impossible by employing other molecular systems. This review explores the progress made in the field of fully organic molecular cages and containers by focusing on the properties of the cavity and their application to encapsulate guests.
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Affiliation(s)
- Giovanni Montà-González
- 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
| | - Félix Sancenón
- 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,CIBER
de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain,Centro
de Investigación Príncipe Felipe, Unidad Mixta UPV-CIPF
de Investigación de Mecanismos de Enfermedades y Nanomedicina,
Valencia, Universitat Politècnica
de València, 46012 Valencia, Spain,Instituto
de Investigación Sanitaria la Fe, Unidad Mixta de Investigación
en Nanomedicina y Sensores, Universitat
Politènica de València, 46026 València, Spain,Departamento
de Química, Universitat Politècnica
de València, 46022 Valencia, Spain
| | - Ramón Martínez-Máñez
- 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,CIBER
de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain,Centro
de Investigación Príncipe Felipe, Unidad Mixta UPV-CIPF
de Investigación de Mecanismos de Enfermedades y Nanomedicina,
Valencia, Universitat Politècnica
de València, 46012 Valencia, Spain,Instituto
de Investigación Sanitaria la Fe, Unidad Mixta de Investigación
en Nanomedicina y Sensores, Universitat
Politènica de València, 46026 València, Spain,Departamento
de Química, Universitat Politècnica
de València, 46022 Valencia, Spain,R.M.-M.: email,
| | - 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,V.M.-C.:
email,
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3
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Sakowicz AM, Szumna A. Chiral Water-Soluble Molecular Capsules With Amphiphilic Interiors. Front Chem 2022; 10:883093. [PMID: 35494632 PMCID: PMC9047736 DOI: 10.3389/fchem.2022.883093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/17/2022] [Indexed: 11/26/2022] Open
Abstract
We present the synthesis of new chiral water-soluble dimeric capsules by the multicomponent Mannich reaction between charged amino acids (glutamic acid or arginine), resorcinarene, and formaldehyde and by subsequent self-assembly. The zwitterionic character of the backbones enables electrostatic interactions between arms and induces self-assembly of dimeric capsules, namely, (L-ArgR)2 and (L-GluR)2, in water with a wide range of pH, as demonstrated by NMR, diffusion coefficient measurement, and circular dichroism. The assembly/disassembly processes are fast on the NMR timescale. This mode of dimerization leaves side chains available for additional interactions and creates chiral cavities of mixed hydrophobic/hydrophilic character. According to this characteristic, capsules do not bind fully nonpolar or fully polar guests but effectively encapsulate a variety of chiral molecules with mixed polar/apolar characters (aliphatic and aromatic aldehydes, epoxides, alcohols, carboxylic acids, amines, and amino acids) with moderate strength. We also demonstrate the formation of heterocapsules (GluR) (ArgR) (homo- and heterochiral) that utilize additional interactions between charged acidic and basic side chains and have better encapsulation properties than those of the homodimers.
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Zaytseva EV, Mazhukin DG. Spirocyclic Nitroxides as Versatile Tools in Modern Natural Sciences: From Synthesis to Applications. Part I. Old and New Synthetic Approaches to Spirocyclic Nitroxyl Radicals. Molecules 2021; 26:677. [PMID: 33525514 PMCID: PMC7865516 DOI: 10.3390/molecules26030677] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/19/2021] [Accepted: 01/25/2021] [Indexed: 12/19/2022] Open
Abstract
Spirocyclic nitroxyl radicals (SNRs) are stable paramagnetics bearing spiro-junction at a-, b-, or g-carbon atom of the nitroxide fragment, which is part of the heterocyclic system. Despite the fact that the first representatives of SNRs were obtained about 50 years ago, the methodology of their synthesis and their usage in chemistry and biochemical applications have begun to develop rapidly only in the last two decades. Due to the presence of spiro-function in the SNRs molecules, the latter have increased stability to various reducing agents (including biogenic ones), while the structures of the biradicals (SNBRs) comprises a rigid spiro-fused core that fixes mutual position and orientation of nitroxide moieties that favors their use in dynamic nuclear polarization (DNP) experiments. This first review on SNRs will give a glance at various strategies for the synthesis of spiro-substituted, mono-, and bis-nitroxides on the base of six-membered (piperidine, 1,2,3,4-tetrahydroquinoline, 9,9'(10H,10H')-spirobiacridine, piperazine, and morpholine) or five-membered (2,5-dihydro-1H-pyrrole, pyrrolidine, 2,5-dihydro-1H-imidazole, 4,5-dihydro-1H-imidazole, imidazolidine, and oxazolidine) heterocyclic cores.
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Affiliation(s)
| | - Dmitrii G. Mazhukin
- Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences (SB RAS), Academician Lavrentiev Ave. 9, 630090 Novosibirsk, Russia;
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Hunold J, Eisermann J, Brehm M, Hinderberger D. Characterization of Aqueous Lower-Polarity Solvation Shells Around Amphiphilic 2,2,6,6-Tetramethylpiperidine-1-oxyl Radicals in Water. J Phys Chem B 2020; 124:8601-8609. [DOI: 10.1021/acs.jpcb.0c04863] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Johannes Hunold
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Jana Eisermann
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Martin Brehm
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Dariush Hinderberger
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
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6
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Nicholas JD, Chechik V. Characterization of Host-Guest Complexes of Supramolecular Self-Assembled Cages Using EPR Spectroscopy. J Phys Chem B 2020; 124:5646-5653. [PMID: 32520563 DOI: 10.1021/acs.jpcb.0c02599] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Host-guest interactions between nitroxide stable radicals and supramolecular coordination cages were investigated using electron paramagnetic resonance (EPR) spectroscopy in water and acetonitrile. TEMPO showed negligible association with the cages in water, while 4-oxo-TEMPO bound with a strength comparable to that previously reported for related ketones. Carboxylic acid-functionalized nitroxides bound strongly to the acetonitrile-soluble coordination cages. In all cases, host-guest complex formation resulted in significant decreases in the molecular tumbling rate of the guests, with tumbling becoming strongly anisotropic. The polarity of the cage environment in both solvents was found to be intermediate between water and acetonitrile.
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Affiliation(s)
- James D Nicholas
- Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K
| | - Victor Chechik
- Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K
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Petroselli M, Angamuthu V, Rahman FU, Zhao X, Yu Y, Rebek J. Radical Reactions in Cavitands Unveil the Effects of Affinity on Dynamic Supramolecular Systems. J Am Chem Soc 2020; 142:2396-2403. [DOI: 10.1021/jacs.9b11595] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Manuel Petroselli
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, P. R. China
- Department of Physics, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, P. R. China
| | - Venkatachalam Angamuthu
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, P. R. China
| | - Faiz-Ur Rahman
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, P. R. China
| | - Xinluo Zhao
- Department of Physics, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, P. R. China
| | - Yang Yu
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, P. R. China
| | - Julius Rebek
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, P. R. China
- The Skaggs Institute for Chemical Biology and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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8
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Hunold J, Wolf T, Wurm FR, Hinderberger D. Nanoscopic hydrophilic/hydrophilic phase-separation well below the LCST of polyphosphoesters. Chem Commun (Camb) 2019; 55:3414-3417. [DOI: 10.1039/c8cc09788g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The complex phase separation process of thermoresponsive polyphosphoesters (PPEs) with an identical side-group structure but different copolymer compositions is characterized by electron paramagnetic resonance (EPR) spectroscopy.
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Affiliation(s)
- Johannes Hunold
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg
- 06120 Halle (Saale)
- Germany
| | - Thomas Wolf
- Max-Planck-Institut für Polymerforschung
- 55128 Mainz
- Germany
| | | | - Dariush Hinderberger
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg
- 06120 Halle (Saale)
- Germany
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9
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Inthasot A, Le Poul N, Luhmer M, Colasson B, Jabin I, Reinaud O. Selective EPR Detection of Primary Amines in Water with a Calix[6]azacryptand-Based Copper(II) Funnel Complex. Inorg Chem 2018; 57:3646-3655. [DOI: 10.1021/acs.inorgchem.7b02541] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Alex Inthasot
- Laboratoire de Chimie Organique, Université Libre de Bruxelles (U.L.B.), Avenue F.D. Roosevelt 50, CP160/06, B-1050 Brussels, Belgium
- Laboratoire de Résonance Magnétique Nucléaire Haute Résolution, Université Libre de Bruxelles (U.L.B.), Avenue F.D. Roosevelt 50, CP160/08, B-1050 Brussels, Belgium
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (CNRS UMR 8601), Université Paris Descartes Sorbonne Paris Cité, 45 rue des Saints-Pères, 75006 Paris, France
| | - Nicolas Le Poul
- Laboratoire de Chimie, Electrochimie Moléculaires et Chimie Analytique (CNRS UMR 6521), Université de Brest, 6 avenue Le Gorgeu, 29238 Brest Cedex 3, France
| | - Michel Luhmer
- Laboratoire de Résonance Magnétique Nucléaire Haute Résolution, Université Libre de Bruxelles (U.L.B.), Avenue F.D. Roosevelt 50, CP160/08, B-1050 Brussels, Belgium
| | - Benoit Colasson
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (CNRS UMR 8601), Université Paris Descartes Sorbonne Paris Cité, 45 rue des Saints-Pères, 75006 Paris, France
| | - Ivan Jabin
- Laboratoire de Chimie Organique, Université Libre de Bruxelles (U.L.B.), Avenue F.D. Roosevelt 50, CP160/06, B-1050 Brussels, Belgium
| | - Olivia Reinaud
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (CNRS UMR 8601), Université Paris Descartes Sorbonne Paris Cité, 45 rue des Saints-Pères, 75006 Paris, France
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11
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Yin H, Dumur F, Niu Y, Ayhan MM, Grauby O, Liu W, Wang C, Siri D, Rosas R, Tonetto A, Gigmes D, Wang R, Bardelang D, Ouari O. Chameleonic Dye Adapts to Various Environments Shining on Macrocycles or Peptide and Polysaccharide Aggregates. ACS APPLIED MATERIALS & INTERFACES 2017; 9:33220-33228. [PMID: 28857543 DOI: 10.1021/acsami.7b06634] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This work describes latent fluorescence particles (LFPs) based on a new environmentally sensitive carbazole compound aggregated in water and their use as sensors for probing various cavitands and the different stages of aggregating systems. Cyclodextrins (CDs), cucurbit[n]urils (CB[n], n = 6, 7, 8), and a resorcinarene capsule were used to study the dynamic nature of the LFPs. The fluorescence was dramatically enhanced by a proposed disaggregation-induced emission enhancement (DIEE) mechanism with specific features for CB[n]. Then, the aggregated states of the dipeptides Leu-Leu, Phe-Phe, and Fmoc-Leu-Leu (vesicles, crystals, fibers) were studied by fluorescence spectroscopy and confocal fluorescence microscopy thanks to the adaptive and emissive behavior of the LFPs, allowing us to study an interesting polymorphism phenomenon. The LFPs have then been used in the sensing of the aggregation of the polysaccharide alginate, for which distinct fluorescence turn-on is detected upon stepwise biopolymer assembly, and for amylose detection. The carbazole particles not only adapt to various environments but also display multicolor fluorescent signals. They can be used for the fast probing of the aggregation propensity of newly prepared molecules or biologically relevant compounds or to accelerate the discovery of new macrocycles or of self-assembling peptides in water.
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Affiliation(s)
- Hang Yin
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Avenida da Universidade, Taipa, Macau, China
| | | | - Yiming Niu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Avenida da Universidade, Taipa, Macau, China
| | - Mehmet M Ayhan
- Aix Marseille Univ , CNRS, ICR, Marseille, France
- Department of Chemistry, Gebze Technical University , P.K.:141, 41400 Gebze, Kocaeli, Turkey
| | - Olivier Grauby
- Aix Marseille Univ and CINaM , Campus de Luminy, Marseille, France
| | - Wei Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Avenida da Universidade, Taipa, Macau, China
| | - Chunming Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Avenida da Universidade, Taipa, Macau, China
| | - Didier Siri
- Aix Marseille Univ , CNRS, ICR, Marseille, France
| | - Roselyne Rosas
- Aix Marseille Univ , CNRS, Spectropole, FR 1739, Marseille, France
| | - Alain Tonetto
- Aix Marseille Univ , Centrale Marseille, CNRS, Fédération Sciences Chimiques Marseille (FR 1739) - PRATIM, 13331 Marseille, France
| | | | - Ruibing Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Avenida da Universidade, Taipa, Macau, China
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Mosca S, Yu Y, Rebek J. Preparative scale and convenient synthesis of a water-soluble, deep cavitand. Nat Protoc 2016; 11:1371-87. [PMID: 27388554 DOI: 10.1038/nprot.2016.078] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cavitands are established tools of supramolecular chemistry and molecular recognition, and they are finding increasing application in sensing and sequestration of physiologically relevant molecules in aqueous solution. The synthesis of a water-soluble, deep cavitand is described. The route comprises six (linear) steps from commercially available precursors, and it relies on the fourfold oligomeric cyclization reaction of resorcinol with 2,3-dihydrofuran that leads to the formation of a shallow resorcinarene framework; condensation with aromatic panels, which deepens the hydrophobic binding cavity; construction of rigid urea functionalities on the upper rim; and the introduction of the water-solubilizing methylimidazolium groups on the lower rim. Late intermediates of the synthesis can be used in the preparation of congener cavitands with different properties and applications, and a sample of such a synthetic procedure is included in this protocol. Emphasis is placed on scaled-up reactions and on purification procedures that afford materials in high yield and avoid chromatographic purification. This protocol provides improvements over previously described procedures, and it enables the preparation of sizable amounts of deep cavitands: 7 g of a water-soluble cavitand can be prepared from resorcinol in 13 working days.
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Affiliation(s)
- Simone Mosca
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.,Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | - Yang Yu
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.,Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA
| | - Julius Rebek
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.,Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Department of Chemistry, Fudan University, Shanghai, China
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