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Wang M, Garrison N, Nguyen PM, Prasad A, Wang Y, Kwon HK, Kim G, Siegler MA, Lectka T. Can the -CF 3 Group Act as a Tight, Well-Defined Hydrogen Bond Acceptor? A Clear Crystallographic CF 2-F···H-N + Interaction Says Yes. J Org Chem 2024; 89:9681-9685. [PMID: 38965938 DOI: 10.1021/acs.joc.4c00873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
The CF3 group is well noted for being noninteractive with other functional groups. In this Note, we present a highly rigid model system containing a significant hydrogen bonding interaction between a charged N-H donor and a CF3 acceptor that challenges this accepted wisdom. Spectroscopic and single crystal X-ray crystallography data characterize this interaction, consistent with a weak to moderate hydrogen bond that would be difficult to observe in an intermolecular system.
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Affiliation(s)
- Muyuan Wang
- Department of Chemistry, Johns Hopkins University, 3400 North Charles St., Baltimore, Maryland 21218, United States
| | - Nathaniel Garrison
- Department of Chemistry, Johns Hopkins University, 3400 North Charles St., Baltimore, Maryland 21218, United States
| | - Phuong Minh Nguyen
- Department of Chemistry, Johns Hopkins University, 3400 North Charles St., Baltimore, Maryland 21218, United States
| | - Aarush Prasad
- Department of Chemistry, Johns Hopkins University, 3400 North Charles St., Baltimore, Maryland 21218, United States
| | - Yuang Wang
- Department of Chemistry, Johns Hopkins University, 3400 North Charles St., Baltimore, Maryland 21218, United States
| | - Hyeok-Kyu Kwon
- Department of Chemistry, Johns Hopkins University, 3400 North Charles St., Baltimore, Maryland 21218, United States
| | - Gina Kim
- Department of Chemistry, Johns Hopkins University, 3400 North Charles St., Baltimore, Maryland 21218, United States
| | - Maxime A Siegler
- Department of Chemistry, Johns Hopkins University, 3400 North Charles St., Baltimore, Maryland 21218, United States
| | - Thomas Lectka
- Department of Chemistry, Johns Hopkins University, 3400 North Charles St., Baltimore, Maryland 21218, United States
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2
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Li C, Cao Y, Hu B, Li Y. Unraveling the effect of fluorine substitution on the hydrogen bonding interaction in the complexes of fluorosubstituted pyridines and acetic acid. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Chaozheng Li
- School of Mechanical and Electrical Engineering Henan Institute of Science and Technology Xinxiang China
| | - Yonghua Cao
- School of Mechanical and Electrical Engineering Henan Institute of Science and Technology Xinxiang China
| | - Bo Hu
- School of Mechanical and Electrical Engineering Henan Institute of Science and Technology Xinxiang China
| | - Yongfeng Li
- School of Mechanical and Electrical Engineering Henan Institute of Science and Technology Xinxiang China
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3
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Arya N, Mishra SK, Suryaprakash N. Intramolecular hydrogen bond directed distribution of conformational populations in the derivatives of N′-benzylidenebenzohydrazide. NEW J CHEM 2019. [DOI: 10.1039/c9nj03071a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The extensive NMR investigations reveal the presence of E-isomers in the derivative of N′-benzylidenebenzohydrazide. The different conformer populations are controlled by the strength of intramolecular hydrogen bonds.
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Affiliation(s)
- Neeru Arya
- NMR Research Centre and Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560012
- India
| | - Sandeep Kumar Mishra
- NMR Research Centre and Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560012
- India
| | - N. Suryaprakash
- NMR Research Centre and Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560012
- India
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4
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Patel AK, Mishra SK, Krishnamurthy K, Suryaprakash N. Retention of strong intramolecular hydrogen bonds in high polarity solvents in binaphthalene–benzamide derivatives: extensive NMR studies. RSC Adv 2019; 9:32759-32770. [PMID: 35529738 PMCID: PMC9073135 DOI: 10.1039/c9ra07299c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 10/07/2019] [Indexed: 11/21/2022] Open
Abstract
Advanced multidimensional NMR techniques have been employed to investigate the intramolecular hydrogen bonds (HBs) in a series of N,N′-([1,1′-binaphthalene]-2,2′-diyl)bis(benzamide) derivatives, with the site-specific substitution of different functional groups. The existence of intramolecular HBs and the elimination of any molecular aggregation and possible intermolecular HBs are ascertained by various experimental NMR techniques, including solvent polarity dependent modifications of HB strengths. In the fluorine substituted derivative, direct evidence for the engagement of organic fluorine in HB is obtained by the detection of heteronuclear through-space correlation and the coupling between two NMR active nuclei where the transmission of spin polarization is mediated through HBs (1hJFH). The extent of reduction in the strength of 1hJFH on dilution with high polarity solvents directly provided the qualitative measure of HB strength. The HB, although becoming weakened, does not get nullified even in pure high polarity solvent, which is attributed to the structural constraints. The rate of exchange of a labile hydrogen atom with the deuterium of the solvent permitted the measurement of their half-lives, that are correlated to the relative strengths of HBs. The experimental NMR findings are further validated by XRD and DFT-based theoretical computations, such as, NCI and QTAIM. NMR studies reveal very strong hydrogen bond unbreakable even in high polarity solvents.![]()
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Affiliation(s)
- Arun Kumar Patel
- Solid State and Structural Chemistry Unit and NMR Research Centre
- Indian Institute of Science
- Bangalore 560012
- India
- NMR Research Centre
| | | | | | - N. Suryaprakash
- Solid State and Structural Chemistry Unit and NMR Research Centre
- Indian Institute of Science
- Bangalore 560012
- India
- NMR Research Centre
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5
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Peñas-Defrutos MN, Bartolomé C, García-Melchor M, Espinet P. Hidden aryl-exchange processes in stable 16e Rh III [RhCp*Ar 2] complexes, and their unexpected transmetalation mechanism. Chem Commun (Camb) 2018; 54:984-987. [PMID: 29322151 DOI: 10.1039/c7cc09352g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Experiments mixing the stable 16e 5-coordinate complexes [RhCp*Ar2] (Cp* = C5Me5; Ar = C6F5, C6F3Cl2-3,5) uncover fast aryl transmetalations. Unexpectedly, as supported computationally, these exchanges are not spontaneous, but catalyzed by minute amounts of 18e (μ-OH)2[RhCp*Ar]2 as a source of 16e [RhCp*Ar(OH)]. The OH group is an amazingly efficient bridging partner to diminish the activation barrier of transmetalation.
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Affiliation(s)
- M N Peñas-Defrutos
- IU CINQUIMA/Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, 47071-Valladolid, Spain.
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6
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Dhanishta P, Mishra SK, Suryaprakash N. Intramolecular HB Interactions Evidenced in Dibenzoyl Oxalamide Derivatives: NMR, QTAIM, and NCI Studies. J Phys Chem A 2017; 122:199-208. [DOI: 10.1021/acs.jpca.7b10598] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- P. Dhanishta
- NMR Research Centre, Solid
State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sandeep Kumar Mishra
- NMR Research Centre, Solid
State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - N. Suryaprakash
- NMR Research Centre, Solid
State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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7
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Mishra SK, Suryaprakash N. Intramolecular Hydrogen Bonding Involving Organic Fluorine: NMR Investigations Corroborated by DFT-Based Theoretical Calculations. Molecules 2017; 22:E423. [PMID: 28272370 PMCID: PMC6155419 DOI: 10.3390/molecules22030423] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/02/2017] [Indexed: 01/24/2023] Open
Abstract
The combined utility of many one and two dimensional NMR methodologies and DFT-based theoretical calculations have been exploited to detect the intramolecular hydrogen bond (HB) in number of different organic fluorine-containing derivatives of molecules, viz. benzanilides, hydrazides, imides, benzamides, and diphenyloxamides. The existence of two and three centered hydrogen bonds has been convincingly established in the investigated molecules. The NMR spectral parameters, viz., coupling mediated through hydrogen bond, one-bond NH scalar couplings, physical parameter dependent variation of chemical shifts of NH protons have paved the way for understanding the presence of hydrogen bond involving organic fluorine in all the investigated molecules. The experimental NMR findings are further corroborated by DFT-based theoretical calculations including NCI, QTAIM, MD simulations and NBO analysis. The monitoring of H/D exchange with NMR spectroscopy established the effect of intramolecular HB and the influence of electronegativity of various substituents on the chemical kinetics in the number of organic building blocks. The utility of DQ-SQ technique in determining the information about HB in various fluorine substituted molecules has been convincingly established.
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Affiliation(s)
- Sandeep Kumar Mishra
- NMR Research Centre, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India.
| | - N Suryaprakash
- NMR Research Centre, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India.
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8
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Mishra SK, Suryaprakash N. Intramolecular hydrogen bonds involving organic fluorine in the derivatives of hydrazides: an NMR investigation substantiated by DFT based theoretical calculations. Phys Chem Chem Phys 2016; 17:15226-35. [PMID: 25993543 DOI: 10.1039/c5cp01505g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rare examples of intramolecular hydrogen bonds (HB) of the type the N-H∙∙∙F-C, detected in a low polarity solvent in the derivatives of hydrazides, by utilizing one and two-dimensional solution state multinuclear NMR techniques, are reported. The observation of through-space couplings, such as, (1h)JFH, and (1h)JFN, provides direct evidence for the existence of intra-molecular HB. Solvent induced perturbations and the variable temperature NMR experiments unambiguously establish the presence of intramolecular HB. The existence of multiple conformers in some of the investigated molecules is also revealed by two dimensional HOESY and (15)N-(1)H HSQC experiments. The (1)H DOSY experimental results discard any possibility of self or cross dimerization of the molecules. The derived NMR experimental results are further substantiated by Density Function Theory (DFT) based Non Covalent Interaction (NCI), and Quantum Theory of Atom in Molecule (QTAIM) calculations. The NCI calculations served as a very sensitive tool for detection of non-covalent interactions and also confirm the presence of bifurcated HBs.
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Affiliation(s)
- Sandeep Kumar Mishra
- NMR Research Centre, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore-560012, India.
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9
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Mishra SK, Suryaprakash N. Organic fluorine involved intramolecular hydrogen bonds in the derivatives of imides: NMR evidence corroborated by DFT based theoretical calculations. RSC Adv 2015. [DOI: 10.1039/c5ra19537c] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The rare occurrence of intramolecular hydrogen bonds (HBs) of the type N–H⋯F–C is detected in the derivatives of imides in a low polarity solvent by using multi-dimensional and multinuclear NMR experiments.
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Affiliation(s)
- Sandeep Kumar Mishra
- NMR Research Centre
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore-560012
- India
| | - N. Suryaprakash
- NMR Research Centre
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore-560012
- India
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10
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Struble MD, Kelly C, Siegler MA, Lectka T. Search for a Strong, Virtually “No-Shift” Hydrogen Bond: A Cage Molecule with an Exceptional OH⋅⋅⋅F Interaction. Angew Chem Int Ed Engl 2014; 53:8924-8. [DOI: 10.1002/anie.201403599] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 06/02/2014] [Indexed: 11/08/2022]
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11
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Struble MD, Kelly C, Siegler MA, Lectka T. Search for a Strong, Virtually “No-Shift” Hydrogen Bond: A Cage Molecule with an Exceptional OH⋅⋅⋅F Interaction. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403599] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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12
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Bartolomé C, Villafañe F, Martín-Alvarez JM, Martínez-Ilarduya JM, Espinet P. [Pd(Fmes)2(tmeda)]: A Case of Intermittent CH⋅⋅⋅FC Hydrogen-Bond Interaction in Solution. Chemistry 2013; 19:3702-9. [DOI: 10.1002/chem.201203512] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Indexed: 11/08/2022]
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13
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Chaudhari SR, Mogurampelly S, Suryaprakash N. Engagement of CF3 Group in N–H···F–C Hydrogen Bond in the Solution State: NMR Spectroscopy and MD Simulation Studies. J Phys Chem B 2013; 117:1123-9. [DOI: 10.1021/jp310798d] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sachin Rama Chaudhari
- NMR
Research Centre, ‡Solid State and Structural Chemistry Unit, and §Department of Physics, Indian Institute of Science, Bangalore
560012, India
| | - Santosh Mogurampelly
- NMR
Research Centre, ‡Solid State and Structural Chemistry Unit, and §Department of Physics, Indian Institute of Science, Bangalore
560012, India
| | - N. Suryaprakash
- NMR
Research Centre, ‡Solid State and Structural Chemistry Unit, and §Department of Physics, Indian Institute of Science, Bangalore
560012, India
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14
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Wang SMJ, Zhao L, Mak TCW. Coordination networks constructed with the multinuclear silver–ethynide supramolecular synthon 4-nitrophenyl–CC⊃Agn(n = 3, 4, 5). Dalton Trans 2010; 39:2108-21. [DOI: 10.1039/b917789b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Garnett JA, Liu Y, Leon E, Allman SA, Friedrich N, Saouros S, Curry S, Soldati-Favre D, Davis BG, Feizi T, Matthews S. Detailed insights from microarray and crystallographic studies into carbohydrate recognition by microneme protein 1 (MIC1) of Toxoplasma gondii. Protein Sci 2009; 18:1935-47. [PMID: 19593815 DOI: 10.1002/pro.204] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The intracellular protozoan Toxoplasma gondii is among the most widespread parasites. The broad host cell range of the parasite can be explained by carbohydrate microarray screening analyses that have demonstrated the ability of the T. gondii adhesive protein, TgMIC1, to bind to a wide spectrum of sialyl oligosaccharide ligands. Here, we investigate by further microarray analyses in a dose-response format the differential binding of TgMIC1 to 2-3- and 2-6-linked sialyl carbohydrates. Interestingly, two novel synthetic fluorinated analogs of 3'SiaLacNAc(1-4) and 3'SiaLacNAc(1-3) were identified as highly potent ligands. To understand the structural basis of the carbohydrate binding specificity of TgMIC1, we have determined the crystal structures of TgMIC1 micronemal adhesive repeat (MAR)-region (TgMIC1-MARR) in complex with five sialyl-N-acetyllactosamine analogs. These crystal structures have revealed a specific, water-mediated hydrogen bond network that accounts for the preferential binding of TgMIC1-MARR to arrayed 2-3-linked sialyl oligosaccharides and the high potency of the fluorinated analogs. Furthermore, we provide strong evidence for the first observation of a C--F...H--O hydrogen bond within a lectin-carbohydrate complex. Finally, detailed comparison with other oligosaccharide-protein complexes in the Protein Data Bank (PDB) reveals a new family of sialic-acid binding sites from lectins in parasites, bacteria, and viruses.
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Affiliation(s)
- James A Garnett
- Division of Molecular Biosciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW72AZ, United Kingdom
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Marchetti F, Marchetti F, Masi F, Pampaloni G, Passarelli V, Sommazzi A, Spera S. Synthesis, variable temperature NMR investigations and solid state characterization of novel octafluorofluorene compounds. J Fluor Chem 2009. [DOI: 10.1016/j.jfluchem.2008.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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17
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Takemura H, Kaneko M, Sako K, Iwanaga T. The intramolecular C–F⋯HO hydrogen bond of 2-fluorophenyldiphenylmethanol. NEW J CHEM 2009. [DOI: 10.1039/b902203a] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Ribeiro JP, Bacchi S, Dell'Anna G, Morando M, Cañada FJ, Cozzi F, Jiménez-Barbero J. A Combined NMR, Computational, and HPLC Study of the Inclusion of Aromatic and Fluoroaromatic Compounds in Cyclodextrins as a Model for Studying Carbohydrate-Aromatic Interactions. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800585] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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