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Bruekers JPJ, Hellinghuizen MA, Vanthuyne N, Tinnemans P, Gilissen PJ, Buma WJ, Naubron J, Crassous J, Elemans JAAW, Nolte RJM. Allosteric Guest Binding in Chiral Zirconium(IV) Double Decker Porphyrin Cages. European J Org Chem 2021; 2021:607-617. [PMID: 33679232 PMCID: PMC7898692 DOI: 10.1002/ejoc.202001392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/03/2020] [Indexed: 12/11/2022]
Abstract
Chiral zirconium(IV) double cage sandwich complex Zr(1)2 has been synthesized in one step from porphyrin cage H21. Zr(1)2 was obtained as a racemate, which was resolved by HPLC and the enantiomers were isolated in >99.5 % ee. Their absolute configurations were assigned on the basis of X-ray crystallography and circular dichroism spectroscopy. Vibrational circular dichroism (VCD) experiments on the enantiomers of Zr(1)2 revealed that the chirality around the zirconium center is propagated throughout the whole cage structure. The axial conformational chirality of the double cage complex displayed a VCD fingerprint similar to the one observed previously for a related chiral cage compound with planar and point chirality. Zr(1)2 shows fluorescence, which is quenched when viologen guests bind in its cavities. The binding of viologen and dihydroxybenzene derivatives in the two cavities of Zr(1)2 occurs with negative allostery, the cooperativity factors α (=4 K2/K1) being as low as 0.0076 for the binding of N,N'-dimethylviologen. These allosteric effects are attributed to a pinching of the second cavity as a result of guest binding in the first cavity.
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Affiliation(s)
- Jeroen P. J. Bruekers
- Radboud UniversityInstitute for Molecules and MaterialsHeyendaalseweg 1356525AJNijmegenThe Netherlands
| | - Matthijs A. Hellinghuizen
- Radboud UniversityInstitute for Molecules and MaterialsHeyendaalseweg 1356525AJNijmegenThe Netherlands
| | | | - Paul Tinnemans
- Radboud UniversityInstitute for Molecules and MaterialsHeyendaalseweg 1356525AJNijmegenThe Netherlands
| | - Pieter J. Gilissen
- Radboud UniversityInstitute for Molecules and MaterialsHeyendaalseweg 1356525AJNijmegenThe Netherlands
| | - Wybren Jan Buma
- University of AmsterdamVan ‘t Hoff Institute for Molecular SciencesScience Park 9041098XHAmsterdamThe Netherlands
- Radboud UniversityInstitute for Molecules and MaterialsFELIX LaboratoryToernooiveld 7c6525EDNijmegenThe Netherlands
| | | | - Jeanne Crassous
- Univ RennesCNRSInstitut des Sciences Chimiques de RennesISCR-UMR 622635000RennesFrance
| | - Johannes A. A. W. Elemans
- Radboud UniversityInstitute for Molecules and MaterialsHeyendaalseweg 1356525AJNijmegenThe Netherlands
| | - Roeland J. M. Nolte
- Radboud UniversityInstitute for Molecules and MaterialsHeyendaalseweg 1356525AJNijmegenThe Netherlands
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2
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Effective synthetic strategy towards highly selective macrocyclic anion receptors based on static combinatorial chemistry. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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3
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Design a synthetic glucose receptor using computational intelligence approach. J Mol Graph Model 2020; 103:107797. [PMID: 33246193 DOI: 10.1016/j.jmgm.2020.107797] [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: 07/31/2020] [Revised: 11/01/2020] [Accepted: 11/02/2020] [Indexed: 11/24/2022]
Abstract
The synthetic glucose receptors help to develop glucose sensors and alternative insulin therapies. Designing a glucose recognition molecule in an aqueous system remains a considerable challenge. Therefore, In-silico molecular screening hypothesis is proposed to overcome the difficulties found during the modeling of a molecule. The small organic compounds from compound databases are screened for glucose receptor modeling. Thereafter, the different computational models are designed that mimic natural glucose receptors based on screened compounds. The orientation and binding of glucose molecules within the developed receptor are predicted through the molecular interaction approach. The modeled receptors and receptor-glucose complex structures are used for geometry optimization and molecular dynamics computation. The docking results reveal that ZINC82047919, ZINC238094340, and ZINC238519600 compounds-based models provide better interactions with glucose and its orientation within the receptor cavity. The molecular dynamics simulation results showed that the receptor designed using compound ZINC238094340 is unable to hold the glucose and undergo significant conformation changes during simulation process. The receptor designed from ZINC238094340 and ZINC238519600 compounds is utilized as a reference glucose binding receptor in this study. The proposed computational approach is able to develop a novel glucose receptor and other glucose relative sugar molecules.
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Ishizuka T, Tanaka S, Uchida S, Wei L, Kojima T. Selective Convergence to Atropisomers of a Porphyrin Derivative Having Bulky Substituents at the Periphery. J Org Chem 2020; 85:12856-12869. [PMID: 32990441 DOI: 10.1021/acs.joc.0c01876] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Four kinds of possible atropisomers of a porphyrin derivative (1), having mesityl groups at one of the o-positions of each meso-aryl group, can be selectively converged to targeted atropisomers among the four isomers (αααα, αααβ, αβαβ, and ααββ) under appropriate conditions for each atropisomer. For example, protonation and subsequent neutralization of a free base porphyrin (H2-1) induces a convergence reaction to the αβαβ atropisomer, H2-1-αβαβ, from an atropisomeric mixture. The αααα isomer, H2-1-αααα, was also obtained by heating a solution of H2-1 in CHCl3 in 60% isolated yield, probably owing to a template effect of the solvent molecule. Remarkably, when an atropisomeric mixture of its zinc complex, Zn-1, was heated at 70 °C in a ClCH2CH2Cl/MeOH mixed solvent, crystals composed of only Zn-1-αααα were formed. The hydrophobic space formed by the four mesityl groups in the αααα isomer can be used for repeatable molecular encapsulation of benzene, and the encapsulation structure was elucidated by powder X-ray diffraction analysis. Heating the solid of an atropisomeric mixture of Zn-1 to 400 °C afforded the ααββ isomer almost quantitatively. On the other hand, the solid of H2-1-αααα can be converted by heating, successively to H2-1-αααβ at 286 °C and then to H2-1-ααββ at 350 °C.
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Affiliation(s)
- Tomoya Ishizuka
- Department of Chemistry, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan.,PRESTO, Japan Science and Technology Agency (JST), Kawaguchi 332-0012, Japan
| | - Shogo Tanaka
- Department of Chemistry, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan
| | - Sayaka Uchida
- Department of Basic Science, School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Lianyu Wei
- Department of Chemistry, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan
| | - Takahiko Kojima
- Department of Chemistry, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan
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Elemans JAAW, Nolte RJM. Porphyrin cage compounds based on glycoluril – from enzyme mimics to functional molecular machines. Chem Commun (Camb) 2019; 55:9590-9605. [DOI: 10.1039/c9cc04372a] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This Feature Article gives an overview of the application of glycoluril-based porphyrin cage compounds in host–guest chemistry, allosterically controlled self-assembly, biomimetic catalysis, and polymer encoding.
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Affiliation(s)
| | - Roeland J. M. Nolte
- Radboud University
- Institute for Molecules and Materials
- 6525 AJ Nijmegen
- The Netherlands
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Leben L, Näther C, Herges R. Crystal structure of (methanol-κ O)[5,10,15,20-tetra-kis-(2-amino-phen-yl)porphyrinato-κ 4N]zinc(II)-chloro-form-methanol (1/1/1). Acta Crystallogr E Crystallogr Commun 2018; 74:1285-1289. [PMID: 30225118 PMCID: PMC6127699 DOI: 10.1107/s205698901801099x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 08/01/2018] [Indexed: 11/11/2022]
Abstract
In the crystal structure of the title compound, [Zn(C44H32N8)(CH3OH)]·CHCl3·CH3OH, the ZnII cation is coordinated by four porphyrin N and one methanol O atom within a slightly distorted square-pyramidal environment and is shifted out of the porphyrin plane towards the direction of the methanol mol-ecule. The methyl group of the coordinating methanol mol-ecule is disordered over two sets of sites. The porphyrin backbone is nearly planar and the phenyl rings are almost perpendicular to the porphyrin plane. As is typical for picket-fence porphyrins, all four ortho substituents of the meso-phenyl groups (here the amino groups) are facing to the same side of the porphyrin mol-ecule. In the crystal structure, two neighbouring porphyrin complexes form centrosymmetric dimers that are connected via O-H⋯N hydrogen bonding. With the aid of additional N-H⋯N and C-H⋯N hydrogen bonding, these dimers are stacked into columns parallel to [010] that are finally arranged into layers parallel to (001). Between these layers channels are formed where chloro-form solvent mol-ecules are located that are connected to the porphyrin complexes by weak C-H⋯Cl hydrogen bonding. There are additional cavities in the structure where some small residual electron density is found, indicating the presence of disordered methanol mol-ecules, but a reasonable model could not be refined. Therefore the contribution of the electron density associated with the methanol solvent mol-ecule was removed with the SQUEEZE procedure [Spek (2015 ▸). Acta Cryst. C71, 9-18] in PLATON. Nevertheless, the given chemical formula and other crystal data take into account the methanol solvent mol-ecule.
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Affiliation(s)
- Lisa Leben
- Institut für Organische Chemie, Universität Kiel, Otto-Hahn-Platz 4, 24118, Kiel, Germany
| | - Christian Näther
- Institut für Anorganische Chemie, Universität Kiel, Otto-Hahn-Platz 6/7, 24118, Kiel, Germany
| | - Rainer Herges
- Institut für Organische Chemie, Universität Kiel, Otto-Hahn-Platz 4, 24118, Kiel, Germany
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Ohishi Y, Abe H, Inouye M. Native Mannose‐Dominant Extraction by Pyridine–Phenol Alternating Oligomers Having an Extremely Efficient Repeating Motif of Hydrogen‐Bonding Acceptors and Donors. Chemistry 2015; 21:16504-11. [DOI: 10.1002/chem.201503149] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Yuki Ohishi
- Graduate School of Pharmaceutical Sciences, University of Toyama, Toyama 930‐0194 (Japan)
| | - Hajime Abe
- Graduate School of Pharmaceutical Sciences, University of Toyama, Toyama 930‐0194 (Japan)
| | - Masahiko Inouye
- Graduate School of Pharmaceutical Sciences, University of Toyama, Toyama 930‐0194 (Japan)
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Mukosera GT, Adams TP, Rothbarth RF, Langat H, Akanda S, Barkley RG, Dolewski RD, Ruppel JV, Snyder NL. Synthesis of glycosylated zinc (II) 5,15-diphenylporphyrin and zinc (II) 5,10,15,20-tetraphenylporphyrin analogs using Cu-catalyzed azide-alkyne 1,3-dipolar cycloaddition reactions. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2014.10.117] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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9
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Yoon H, Lee CH, Jang WD. Absolute Stereochemical Determination of Chiral Carboxylates Using an Achiral Molecular Tweezer. Chemistry 2012; 18:12479-86. [DOI: 10.1002/chem.201200371] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 06/04/2012] [Indexed: 11/10/2022]
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Wu X, Starnes SD. l-Nipecotic Acid-Porphyrin Derivative: A Chiral Host with Introverted Functionality for Chiral Recognition. Org Lett 2012; 14:3652-5. [DOI: 10.1021/ol301499w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaowen Wu
- Department of Chemistry, Texas A&M University-Commerce, Commerce, Texas 75429, United States
| | - Stephen D. Starnes
- Department of Chemistry, Texas A&M University-Commerce, Commerce, Texas 75429, United States
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11
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Mazik M. Recent developments in the molecular recognition of carbohydrates by artificial receptors. RSC Adv 2012. [DOI: 10.1039/c2ra01138g] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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12
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Lee CH, Lee S, Yoon H, Jang WD. Strong Binding Affinity of a Zinc-Porphyrin-Based Receptor for Halides through the Cooperative Effects of Quadruple CH Hydrogen Bonds and Axial Ligation. Chemistry 2011; 17:13898-903. [DOI: 10.1002/chem.201101884] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 08/25/2011] [Indexed: 01/13/2023]
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Abe H, Chida Y, Kurokawa H, Inouye M. Selective binding of D2h-symmetrical, acetylene-linked pyridine/pyridone macrocycles to maltoside. J Org Chem 2011; 76:3366-71. [PMID: 21410290 DOI: 10.1021/jo2003055] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A macrocyclic host molecule having pyridine-pyridone-pyridine modules for saccharide recognition was prepared by Cu(II)-mediated oxidative homocoupling of a tandem diethynyl precursor. In CH(2)Cl(2), the host molecule associated with dodecyl β-maltoside much more strongly (K(a) = 1.4 × 10(6) M(-1)) than with octyl monohexosides (K(a) = ca. 2 × 10(3) to 1 × 10(4) M(-1)), accompanied with induced CDs. An all-pyridine macrocyclic host was also studied, and its binding strength with saccharides was weaker than that for the pyridine-pyridone-pyridine host.
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Affiliation(s)
- Hajime Abe
- Graduate School of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan.
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