1
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Nardi AN, Olivieri A, D'Abramo M, Amadei A. A Theoretical-Computational Study of Phosphodiester Bond Cleavage Kinetics as a Function of the Temperature. Chemphyschem 2024; 25:e202300952. [PMID: 38372713 DOI: 10.1002/cphc.202300952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 02/20/2024]
Abstract
The hydrolysis of the phosphodiester bond is an important chemical reaction involved in several biological processes. Here, we study the cleavage of this bond by means of a theoretical-computational method in a model system, the dineopentyl phosphate. By such an approach, we reconstructed the kinetics and related thermodynamics of this chemical reaction along an isochore. In particular, we evaluated the kinetic constants of all the reaction steps within a wide range of temperatures, mostly corresponding to conditions where no experimental measures are available due to the extremely slow kinetics. Our results, in good agreement with the experimental data, show the robustness of our theoretical-computational methodology which can be easily extended to more complex systems.
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Affiliation(s)
| | - Alessio Olivieri
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | - Marco D'Abramo
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | - Andrea Amadei
- Department of Technological and Chemical Sciences, Tor Vergata University of Rome, Italy
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2
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de Andrade KN, Peixoto BP, Carneiro JWDM, Fiorot RG. Exploring borderline S N1-S N2 mechanisms: the role of explicit solvation protocols in the DFT investigation of isopropyl chloride. RSC Adv 2024; 14:4692-4701. [PMID: 38318615 PMCID: PMC10841197 DOI: 10.1039/d4ra00066h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 01/30/2024] [Indexed: 02/07/2024] Open
Abstract
Nucleophilic substitution at saturated carbon is a crucial class of organic reactions, playing a pivotal role in various chemical transformations that yield valuable compounds for society. Despite the well-established SN1 and SN2 mechanisms, secondary substrates, particularly in solvolysis reactions, often exhibit a borderline pathway. A molecular-level understanding of these processes is fundamental for developing more efficient chemical transformations. Typically, quantum-chemical simulations of the solvent medium combine explicit and implicit solvation methods. The configuration of explicit molecules can be defined through top-down approaches, such as Monte Carlo (MC) calculations for generating initial configurations, and bottom-up methods that involve user-dependent protocols to add solvent molecules around the substrate. Herein, we investigated the borderline mechanism of the hydrolysis of a secondary substrate, isopropyl chloride (iPrCl), at DFT-M06-2X/aug-cc-pVDZ level, employing explicit and explicit + implicit protocols. Top-down and bottom-up approaches were employed to generate substrate-solvent complexes of varying number (n = 1, 3, 5, 7, 9, and 12) and configurations of H2O molecules. Our findings consistently reveal that regardless of the solvation approach, the hydrolysis of iPrCl follows a loose-SN2-like mechanism with nucleophilic solvent assistance. Increasing the water cluster around the substrate in most cases led to reaction barriers of ΔH‡ ≈ 21 kcal mol-1, with nine water molecules from MC configurations sufficient to describe the reaction. The More O'Ferrall-Jencks plot demonstrates an SN1-like character for all transition state structures, showing a clear merged profile. The fragmentation activation strain analyses indicate that energy barriers are predominantly controlled by solvent-substrate interactions, supported by the leaving group stabilization assessed through CHELPG atomic charges.
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Affiliation(s)
- Karine Nascimento de Andrade
- Department of Organic Chemistry, Chemistry Institute, Universidade Federal Fluminense (UFF) Outeiro de São João Batista 24020-141 Niterói RJ Brazil
| | - Bárbara Pereira Peixoto
- Department of Organic Chemistry, Chemistry Institute, Universidade Federal Fluminense (UFF) Outeiro de São João Batista 24020-141 Niterói RJ Brazil
| | - José Walkimar de Mesquita Carneiro
- Department of Inorganic Chemistry, Chemistry Institute, Universidade Federal Fluminense (UFF) Outeiro de São João Batista 24020-141 Niterói RJ Brazil
| | - Rodolfo Goetze Fiorot
- Department of Organic Chemistry, Chemistry Institute, Universidade Federal Fluminense (UFF) Outeiro de São João Batista 24020-141 Niterói RJ Brazil
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3
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Modelling Complex Bimolecular Reactions in a Condensed Phase: The Case of Phosphodiester Hydrolysis. Molecules 2023; 28:molecules28052152. [PMID: 36903398 PMCID: PMC10004441 DOI: 10.3390/molecules28052152] [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: 01/31/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
(1) Background: the theoretical modelling of reactions occurring in liquid phase is a research line of primary importance both in theoretical-computational chemistry and in the context of organic and biological chemistry. Here we present the modelling of the kinetics of the hydroxide-promoted hydrolysis of phosphoric diesters. (2) Method: the theoretical-computational procedure involves a hybrid quantum/classical approach based on the perturbed matrix method (PMM) in conjunction with molecular mechanics. (3) Results: the presented study reproduces the experimental data both in the rate constants and in the mechanistic aspects (C-O bond vs. O-P bond reactivity). The study suggests that the basic hydrolysis of phosphodiesters occurs through a concerted ANDN mechanism, with no formation of penta-coordinated species as reaction intermediates. (4) Conclusions: the presented approach, despite the approximations, is potentially applicable to a large number of bimolecular transformations in solution and therefore leads the way to a fast and general method to predict the rate constants and reactivities/selectivities in complex environments.
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4
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De Souza LA, Da Silva Ferreira L, Gomes EM, P. O. Silva J, Belchior JC, Marques LF. Structure and stability of Eu3+ complexes derivatives from non-steroidal anti-inflammatory drug ibuprofen through a DFT study. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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5
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Yang X, Wei R, Shi Y, Liu LL, Wu Y, Zhao Y, Stephan DW. Oxyphosphoranes as precursors to bridging phosphate-catecholate ligands. Chem Commun (Camb) 2021; 57:1194-1197. [PMID: 33439178 DOI: 10.1039/d0cc07736d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Examples of chelating ligands that incorporate P-O donors are seldom encountered. Herein, a series of novel bridging diphosphate ligand supported bimetallic Zr(iv), V(iii) and Ni(ii) complexes have been derived from reactions of the oxyphosphorane (C6Cl4O2)P(OEt)3 with the corresponding metal halides. The mechanism is probed and shown to involve elimination of ethyl halide, and ring opening affording the chelating phosphate-catecholate ligands.
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Affiliation(s)
- Xin Yang
- Institute of Drug Discovery Technology, Ningbo University, Zhejiang, China.
| | - Rui Wei
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yaping Shi
- Institute of Drug Discovery Technology, Ningbo University, Zhejiang, China.
| | - Liu Leo Liu
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yile Wu
- Institute of Drug Discovery Technology, Ningbo University, Zhejiang, China. and Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Zhejiang, China. and Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Douglas W Stephan
- Institute of Drug Discovery Technology, Ningbo University, Zhejiang, China. and Department of Chemistry, University of Toronto, 80 St. George St, Toronto, ON M5S3H6, Canada.
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6
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Mironov VF, Dimukhametov MN, Blinova YS, Karataeva FK. Simultaneous Formation of Cage and Spirane Pentaalkoxyphosphoranes in Reaction of 5,5-Dimethyl-2-(2-oxo-1,2-diphenylethoxy)-1,3,2-dioxaphosphorinane with Hexafluoroacetone. RUSS J GEN CHEM+ 2020. [DOI: 10.1134/s1070363220110109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Segreto GE, Alba J, Salvio R, D’Abramo M. DNA cleavage by endonuclease I-DmoI: a QM/MM study and comparison with experimental data provide indications on the environmental effects. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-2585-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Sharma G, Jayasinghe-Arachchige VM, Hu Q, Schenk G, Prabhakar R. Effect of Chemically Distinct Substrates on the Mechanism and Reactivity of a Highly Promiscuous Metallohydrolase. ACS Catal 2020. [DOI: 10.1021/acscatal.9b04847] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Gaurav Sharma
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | | | - Qiaoyu Hu
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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9
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Mattioli EJ, Bottoni A, Calvaresi M. DNAzymes at Work: A DFT Computational Investigation on the Mechanism of 9DB1. J Chem Inf Model 2019; 59:1547-1553. [DOI: 10.1021/acs.jcim.8b00815] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Edoardo Jun Mattioli
- Dipartimento di Chimica “G. Ciamician”, Alma Mater Studiorum - Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy
| | - Andrea Bottoni
- Dipartimento di Chimica “G. Ciamician”, Alma Mater Studiorum - Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy
| | - Matteo Calvaresi
- Dipartimento di Chimica “G. Ciamician”, Alma Mater Studiorum - Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy
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10
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De Freitas LV, Dos Santos ALDS, Da Costa FC, Calixto JB, Miranda PVP, Silva TJ, Pereira ES, Rocha WR, De Almeida WB, De Souza LA, Freitas MC. Synthesis and structural characterization of a 8-hydroxyquinoline derivative coordinated to Zn(II). J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.05.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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11
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Chagas MA, Pereira ES, Da Silva JCS, Rocha WR. Theoretical investigation of the neutral hydrolysis of diethyl 4-nitrophenyl phosphate (paraoxon) in aqueous solution. J Mol Model 2018; 24:259. [DOI: 10.1007/s00894-018-3798-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 08/15/2018] [Indexed: 10/28/2022]
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12
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Lima MF, da Cruz PAU, Fernandes MEC, Polaquini C, Miguel ELM, Pliego JR, Scorsin L, Oliveira BS, Nome F. Cleaving paraoxon with hydroxylamine: Ammonium oxide isomer favors a Frontside attack mechanism. J PHYS ORG CHEM 2018. [DOI: 10.1002/poc.3866] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Marcelo F. Lima
- Departamento de Química e Ciências Ambientais, Laboratório de Química Bio-orgânica Ambiental; Instituto de Biociências, Letras e Ciências Exatas, UNESP - Univ Estadual Paulista, Câmpus São José do Rio Preto; São José do Rio Preto SP Brazil
| | - Priscilla Amanda Urbano da Cruz
- Laboratório de Química Bio-orgânica do Araguaia; Câmpus Universitário do Araguaia, UFMT-Universidade Federal de Mato Grosso, Instituto de Ciências Exatas e da Terra; Barra do Garças MT Brazil
| | - Maria Eduarda Camilo Fernandes
- Departamento de Química e Ciências Ambientais, Laboratório de Química Bio-orgânica Ambiental; Instituto de Biociências, Letras e Ciências Exatas, UNESP - Univ Estadual Paulista, Câmpus São José do Rio Preto; São José do Rio Preto SP Brazil
| | - Carlos Polaquini
- Departamento de Química e Ciências Ambientais, Laboratório de Química Bio-orgânica Ambiental; Instituto de Biociências, Letras e Ciências Exatas, UNESP - Univ Estadual Paulista, Câmpus São José do Rio Preto; São José do Rio Preto SP Brazil
| | - Elizabeth L. M. Miguel
- Departamento de Ciências Naturais; Universidade Federal de São João del-Rei; São João del-Rei MG Brazil
| | - Josefredo R. Pliego
- Departamento de Ciências Naturais; Universidade Federal de São João del-Rei; São João del-Rei MG Brazil
| | - Leandro Scorsin
- Departamento de Química, Laboratório de Catálise e Fenômenos Interfaciais; Universidade Federal de Santa Catarina; Florianópolis SC Brazil
| | - Bruno Surdi Oliveira
- Departamento de Química, Laboratório de Catálise e Fenômenos Interfaciais; Universidade Federal de Santa Catarina; Florianópolis SC Brazil
| | - Faruk Nome
- Departamento de Química, Laboratório de Catálise e Fenômenos Interfaciais; Universidade Federal de Santa Catarina; Florianópolis SC Brazil
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13
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Chagas MA, Pereira ES, Godinho MPB, Da Silva JCS, Rocha WR. Base Mechanism to the Hydrolysis of Phosphate Triester Promoted by the Cd2+/Cd2+ Active site of Phosphotriesterase: A Computational Study. Inorg Chem 2018; 57:5888-5902. [DOI: 10.1021/acs.inorgchem.8b00361] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Marcelo A. Chagas
- LQC-MM: Laboratório de Química Computacional e Modelagem Molecular Departamento de Química, ICEx, Universidade Federal de Minas Gerais 31270-901 Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Eufrásia S. Pereira
- LQC-MM: Laboratório de Química Computacional e Modelagem Molecular Departamento de Química, ICEx, Universidade Federal de Minas Gerais 31270-901 Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Marina P. B. Godinho
- LQC-MM: Laboratório de Química Computacional e Modelagem Molecular Departamento de Química, ICEx, Universidade Federal de Minas Gerais 31270-901 Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Júlio Cosme S. Da Silva
- LQC-MM: Laboratório de Química Computacional e Modelagem Molecular Departamento de Química, ICEx, Universidade Federal de Minas Gerais 31270-901 Pampulha, Belo Horizonte, Minas Gerais, Brazil
- GQC: Grupo de Química Computacional Instituto de Química e Biotecnologia, IQB, Universidade Federal de Alagoas Campus A. C. Simões, 57072-900 Maceió, Alagoas, Brazil
| | - Willian R. Rocha
- LQC-MM: Laboratório de Química Computacional e Modelagem Molecular Departamento de Química, ICEx, Universidade Federal de Minas Gerais 31270-901 Pampulha, Belo Horizonte, Minas Gerais, Brazil
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14
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Mikkola S, Lönnberg T, Lönnberg H. Phosphodiester models for cleavage of nucleic acids. Beilstein J Org Chem 2018; 14:803-837. [PMID: 29719577 PMCID: PMC5905247 DOI: 10.3762/bjoc.14.68] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/12/2018] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids that store and transfer biological information are polymeric diesters of phosphoric acid. Cleavage of the phosphodiester linkages by protein enzymes, nucleases, is one of the underlying biological processes. The remarkable catalytic efficiency of nucleases, together with the ability of ribonucleic acids to serve sometimes as nucleases, has made the cleavage of phosphodiesters a subject of intensive mechanistic studies. In addition to studies of nucleases by pH-rate dependency, X-ray crystallography, amino acid/nucleotide substitution and computational approaches, experimental and theoretical studies with small molecular model compounds still play a role. With small molecules, the importance of various elementary processes, such as proton transfer and metal ion binding, for stabilization of transition states may be elucidated and systematic variation of the basicity of the entering or departing nucleophile enables determination of the position of the transition state on the reaction coordinate. Such data is important on analyzing enzyme mechanisms based on synergistic participation of several catalytic entities. Many nucleases are metalloenzymes and small molecular models offer an excellent tool to construct models for their catalytic centers. The present review tends to be an up to date summary of what has been achieved by mechanistic studies with small molecular phosphodiesters.
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Affiliation(s)
- Satu Mikkola
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Harri Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
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15
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Salvio R, Casnati A. Guanidinium Promoted Cleavage of Phosphoric Diesters: Kinetic Investigations and Calculations Provide Indications on the Operating Mechanism. J Org Chem 2017; 82:10461-10469. [DOI: 10.1021/acs.joc.7b01925] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Riccardo Salvio
- Dipartimento
di Chimica and IMC - CNR Sezione Meccanismi di Reazione, Università La Sapienza, 00185 Roma, Italy
| | - Alessandro Casnati
- Dipartimento
di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Viale delle Scienze 17/A, 43124 Parma, Italy
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16
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Shin YH, Koh HJ, Um IH. Kinetic Study on Alkaline Hydrolysis of 2-Pyridyl and 4-Pyridyl X-substituted-Benzoates: Effects of Benzoyl Substituent X and Leaving-Group Basicity on Reactivity and Reaction Mechanism. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Young-Hee Shin
- Department of Chemistry; Seoul National University; Seoul 08826 Korea
| | - Han-Joong Koh
- Department of Science Education; Jeonju National University of Education; Jeonju 55101 Korea
| | - Ik-Hwan Um
- Department of Chemistry; Ewha Womans University; Seoul 03760 Korea
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17
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Shin YH, Kang JS, Um IH. Alkaline Hydrolysis of 4-Nitrophenyl X-Substituted-Benzoates Revisited: New Insights from Yukawa-Tsuno Equation. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.11000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Young-Hee Shin
- Department of Chemistry; Seoul National University; Seoul 08826 Korea
| | - Ji-Sun Kang
- Engineering Plastic R&T Solvey; Seoul 153-023 Korea
| | - Ik-Hwan Um
- Department of Chemistry; Ewha Womans University; Seoul 120-750 Korea
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