1
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Tosolini M, Gianferrara T, Mion G, Dovigo L, Mancin F, Sissi C, Tecilla P. Interaction with plasmid DNA of Hoechst-TACN conjugates. Supramol Chem 2019. [DOI: 10.1080/10610278.2019.1699657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Massimo Tosolini
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Teresa Gianferrara
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Giuliana Mion
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Luca Dovigo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Fabrizio Mancin
- Department of Chemical Sciences, University of Padova, Padova, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Paolo Tecilla
- Department of Mathematic and Geosciences, University of Trieste, Trieste, Italy
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2
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Zhou X, Zhang XP, Li W, Jiang J, Xu H, Ke Z, Phillips DL, Zhao C. Unraveling mechanisms of the uncoordinated nucleophiles: theoretical elucidations of the cleavage of bis( p-nitrophenyl) phosphate mediated by zinc-complexes with apical nucleophiles. RSC Adv 2019; 9:37696-37704. [PMID: 35541823 PMCID: PMC9075727 DOI: 10.1039/c9ra06737j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/01/2019] [Indexed: 02/01/2023] Open
Abstract
A theoretical approach was used to investigate the hydrolytic cleavage mechanisms of the bis(p-nitrophenyl) phosphate (BNPP-) catalyzed by Zn(ii)-complexes featuring uncoordinated nucleophiles. Ligand-based and alternative solvent-based nucleophilic attack reaction models are proposed. The pK a values of the Zn(ii)-bound water molecules or ligands in the [Zn(L n H)(η-H2O)(H2O)]2+ (n = 1, 2 and 3) complexes, as well as the dimerization tendency of the mononuclear Zn(ii)-complexes, were found to significantly influence the reaction mechanisms. The Zn(ii)-L3 complexes were found to be more favorable for the hydrolytic cleavage of the BNPP- via a ligand-based nucleophilic attack pathway. This was due to the lower pK a value for the deprotonation of the oxime ligand, the hard dimerization of the mononuclear Zn(ii)-L3 species, and the presence of an uncoordinated nucleophile. The origins of the uncoordinated reactions were systematically elucidated. The theoretical results reported here are in good agreement with experimental observations and more importantly, help to elucidate the factors that influence intermolecular nucleophilic attack reactions with coordinated/uncoordinated nucleophiles.
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Affiliation(s)
- Xiaoyu Zhou
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Xue-Peng Zhang
- School of Chemisty and Chemical Engineering, Shaanxi Normal University Xi'an 710119 P. R. China
| | - Weikang Li
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Jingxing Jiang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, School of Materials Science and Engineering, Sun Yat-sen University Guangzhou 510275 P. R. China
| | - Huiying Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Zhuofeng Ke
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, School of Materials Science and Engineering, Sun Yat-sen University Guangzhou 510275 P. R. China
| | - David Lee Phillips
- Department of Chemistry, University of Hong Kong Pokfulam Road Hong Kong P. R. China
| | - Cunyuan Zhao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 P. R. China
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3
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Conjugates between minor groove binders and Zn(II)-tach complexes: Synthesis, characterization, and interaction with plasmid DNA. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.04.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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4
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Diez-Castellnou M, Martinez A, Mancin F. Phosphate Ester Hydrolysis: The Path From Mechanistic Investigation to the Realization of Artificial Enzymes. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2017. [DOI: 10.1016/bs.apoc.2017.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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5
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Laine M, Lönnberg T, Helkearo M, Lönnberg H. Cleavage of short oligoribonucleotides by a Zn2+ binding multi-nucleating azacrown conjugate. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2015.12.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Bím D, Svobodová E, Eigner V, Rulíšek L, Hodačová J. Copper(II) and Zinc(II) Complexes of Conformationally Constrained Polyazamacrocycles as Efficient Catalysts for RNA Model Substrate Cleavage in Aqueous Solution at Physiological pH. Chemistry 2016; 22:10426-37. [DOI: 10.1002/chem.201601175] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Daniel Bím
- Department of Organic Chemistry, Faculty of Chemical Technology; University of Chemistry and Technology; Technická 5 166 28 Prague 6 Czech Republic), Fax: (+420) 220-444-288
- Institute of Organic Chemistry and Biochemistry; v.v.i. and Gilead Sciences Research Center, Academy of Sciences of the Czech Republic; Flemingovo náměstí 2 166 10 Prague 6 Czech Republic
| | - Eva Svobodová
- Department of Organic Chemistry, Faculty of Chemical Technology; University of Chemistry and Technology; Technická 5 166 28 Prague 6 Czech Republic), Fax: (+420) 220-444-288
| | - Václav Eigner
- Department of Solid State Chemistry, Faculty of Chemical Technology; University of Chemistry and Technology; Technická 5 166 28 Prague 6 Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry; v.v.i. and Gilead Sciences Research Center, Academy of Sciences of the Czech Republic; Flemingovo náměstí 2 166 10 Prague 6 Czech Republic
| | - Jana Hodačová
- Department of Organic Chemistry, Faculty of Chemical Technology; University of Chemistry and Technology; Technická 5 166 28 Prague 6 Czech Republic), Fax: (+420) 220-444-288
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7
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Zhang X, Liu X, Phillips DL, Zhao C. Hydrolysis mechanisms of BNPP mediated by facial copper(ii) complexes bearing single alkyl guanidine pendants: cooperation between the metal centers and the guanidine pendants. Dalton Trans 2016; 45:1593-603. [DOI: 10.1039/c5dt03949e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The inter-complex and intra-complex nucleophilic attacks by metal-bound hydroxide were investigated by considering the second coordination spheres.
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Affiliation(s)
- Xuepeng Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- P. R. China
| | - Xueping Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- P. R. China
| | | | - Cunyuan Zhao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- P. R. China
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8
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Kang MS, Kim CJ, Kang SJ, Koh HJ. Studies of Solvolyses of Di-n-butyl Phosphorochloridate by Extended Grunwald-Winstein Equation. JOURNAL OF THE KOREAN CHEMICAL SOCIETY-DAEHAN HWAHAK HOE JEE 2015. [DOI: 10.5012/jkcs.2015.59.5.373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Brown RS. Bio-inspired approaches to accelerating metal ion-promoted reactions: enzyme-like rates for metal ion mediated phosphoryl and acyl transfer processes. PURE APPL CHEM 2015. [DOI: 10.1515/pac-2014-1008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Intense efforts by many research groups for more than 50 years have been directed at biomimetic approaches to understand how enzymes achieve their remarkable rate accelerations. Nevertheless, it was noted in 2003 that, despite numerous efforts to design models for catalyzing the cleavage of such species as phosphate diesters, “none of the several models so far described approaches the enormous catalytic efficiency of natural enzymes”. The same could be said for biomimetics of other enzymes promoting acyl or phosphoryl transfer reactions, particularly those mediated by metal ions such as Zn(II). Clearly other important factors were being overlooked or awaiting discovery. In this manuscript we describe two important effects that we have implemented to accelerate metal ion catayzed phosphoryl and acyl transfer reactions. The first of these relates to a medium effect where the polarity of the solution, as measured by dielectric constant, is reduced from that of water (ε = 78) to values of 31.5 and 24.3 when the solvent is changed to methanol or ethanol. Among organic solvents these light alcohols are closest to water in terms of structure and properties as well as retaining important H-bonding properties. The second important effect involves a known but difficult to demonstrate mode of catalysis where the leaving group (LG) in a solvolysis reaction is accelerated as it becomes progressively poorer. In the cases described herein, the LG’s propensity to depart from a substrate during the course of reaction is accelerated by coordination to a metal ion in a process known as leaving group assistance, or LGA. These two effects can each impart accelerations of 109–1017 for certain metal ion catalyzed reactions relative to the corresponding solvent, or base induced reactions.
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10
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Tirel EY, Williams NH. Enhancing Phosphate Diester Cleavage by a Zinc Complex through Controlling Nucleophile Coordination. Chemistry 2015; 21:7053-6. [PMID: 25787696 DOI: 10.1002/chem.201500619] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Indexed: 11/11/2022]
Abstract
Metal-ion complexes are the most effective artificial catalysts capable of cleaving phosphate diesters under mild aqueous conditions. A central strategy for making these complexes highly reactive has been to use ligand-based alcohols that are coordinated to the ion, providing an ionised nucleophile under neutral conditions but at the expense of deactivating it. We have created a highly reactive Zn complex that is 350-fold more reactive than an alcohol analogue by preventing the nucleophile binding to the metal ion. This strategy successfully delivers the benefits of efficient nucleophile delivery without strongly deactivating the metal ion Lewis acidity nor the oxyanion nucleophilicity. Varying the leaving group reveals that the transition state of the reaction is much further advanced than the reaction with hydroxide.
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Affiliation(s)
- Emmanuel Y Tirel
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF (UK)
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11
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Zhang X, Zhu Y, Gao H, Zhao C. Solvolysis Mechanisms of RNA Phosphodiester Analogues Promoted by Mononuclear Zinc(II) Complexes: Mechanisic Determination upon Solvent Medium and Ligand Effects. Inorg Chem 2014; 53:11903-12. [DOI: 10.1021/ic501084a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Xuepeng Zhang
- MOE
Key Laboratory of Bioinorganic and Synthetic Chemistry, School of
Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Yajie Zhu
- MOE
Key Laboratory of Bioinorganic and Synthetic Chemistry, School of
Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Hui Gao
- Key
Laboratory of Renewable Energy and Gas Hydrate, Guangzhou Institute
of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, P. R. China
| | - Cunyuan Zhao
- MOE
Key Laboratory of Bioinorganic and Synthetic Chemistry, School of
Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
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12
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Konstantinova LS, Knyazeva EA, Obruchnikova NV, Vasilieva NV, Irtegova IG, Nelyubina YV, Bagryanskaya IY, Shundrin LA, Sosnovskaya ZY, Zibarev AV, Rakitin OA. 1,2,5-Thiadiazole 2-oxides: selective synthesis, structural characterization, and electrochemical properties. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.06.096] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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13
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Tirel EY, Bellamy Z, Adams H, Lebrun V, Duarte F, Williams NH. Catalytic zinc complexes for phosphate diester hydrolysis. Angew Chem Int Ed Engl 2014; 53:8246-50. [PMID: 24919567 PMCID: PMC4140542 DOI: 10.1002/anie.201400335] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 03/21/2014] [Indexed: 12/19/2022]
Abstract
Creating efficient artificial catalysts that can compete with biocatalysis has been an enduring challenge which has yet to be met. Reported herein is the synthesis and characterization of a series of zinc complexes designed to catalyze the hydrolysis of phosphate diesters. By introducing a hydrated aldehyde into the ligand we achieve turnover for DNA-like substrates which, combined with ligand methylation, increases reactivity by two orders of magnitude. In contrast to current orthodoxy and mechanistic explanations, we propose a mechanism where the nucleophile is not coordinated to the metal ion, but involves a tautomer with a more effective Lewis acid and more reactive nucleophile. This data suggests a new strategy for creating more efficient metal ion based catalysts, and highlights a possible mode of action for metalloenzymes.
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Affiliation(s)
| | - Zoë Bellamy
- Department of Chemistry, Sheffield UniversitySheffield (UK)
| | - Harry Adams
- Department of Chemistry, Sheffield UniversitySheffield (UK)
| | - Vincent Lebrun
- Department of Chemistry, Sheffield UniversitySheffield (UK)
| | - Fernanda Duarte
- Department of Cell and Molecular Biology, Uppsala UniversityUppsala (Sweden)
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14
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Belzile MN, Neverov AA, Brown RS. Cu(II)-Ion-Catalyzed Solvolysis of N,N-Bis(2-picolyl)ureas in Alcohol Solvents: Evidence for Cleavage Involving Nucleophilic Addition and Strong Assistance of Bis(2-picolyl)amine Leaving Group Departure. Inorg Chem 2014; 53:7916-25. [DOI: 10.1021/ic500620k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mei-Ni Belzile
- Department
of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - Alexei. A. Neverov
- Department
of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - R. Stan Brown
- Department
of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
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15
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Tirel EY, Bellamy Z, Adams H, Lebrun V, Duarte F, Williams NH. Catalytic Zinc Complexes for Phosphate Diester Hydrolysis. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400335] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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16
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Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 329] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
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17
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Raycroft MAR, Cimpean L, Neverov AA, Brown RS. Rapid Ni, Zn, and Cu Ion-Promoted Alcoholysis of N,N-Bis(2-picolyl)- and N,N-Bis((1H-benzimidazol-2-yl)methyl)-p-nitrobenzamides in Methanol and Ethanol. Inorg Chem 2014; 53:2211-21. [DOI: 10.1021/ic4028755] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Mark A. R. Raycroft
- Department
of Chemistry, Queen’s University, 90 Bader Lane, Kingston, Ontario, Canada, K7L 3N6
| | - Luana Cimpean
- Department
of Chemistry, Queen’s University, 90 Bader Lane, Kingston, Ontario, Canada, K7L 3N6
| | - Alexei A. Neverov
- Department
of Chemistry, Queen’s University, 90 Bader Lane, Kingston, Ontario, Canada, K7L 3N6
| | - R. Stan Brown
- Department
of Chemistry, Queen’s University, 90 Bader Lane, Kingston, Ontario, Canada, K7L 3N6
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18
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Kim SI, Cho HJ, Um IH. Nucleophilic Substitution Reactions of Y-Substituted-Phenyl Benzoates with Potassium Ethoxide in Anhydrous Ethanol: Reaction Mechanism and Role of K+Ion. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.1.177] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Kim SI, Kim MY, Um IH. Kinetic Study on Nucleophilic Substitution Reactions of 4-Nitrophenyl X-Substituted-Benzoates with Potassium Ethoxide: Reaction Mechanism and Role of K+Ion. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.1.225] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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20
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Diez-Castellnou M, Mancin F, Scrimin P. Efficient Phosphodiester Cleaving Nanozymes Resulting from Multivalency and Local Medium Polarity Control. J Am Chem Soc 2014; 136:1158-61. [DOI: 10.1021/ja411969e] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Marta Diez-Castellnou
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - Fabrizio Mancin
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - Paolo Scrimin
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
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21
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Yan H, Yue P, Li Z, Guo Z, Lu Z. Syntheses of bifunctional molecules containing [12]aneN3 and carbazol moieties as effective DNA condensation agents. Sci China Chem 2013. [DOI: 10.1007/s11426-013-5031-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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22
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Maxwell CI, Mosey NJ, Stan Brown R. DFT Computational Study of the Methanolytic Cleavage of DNA and RNA Phosphodiester Models Promoted by the Dinuclear Zn(II) Complex of 1,3-Bis(1,5,9-triazacyclododec-1-yl)propane. J Am Chem Soc 2013; 135:17209-22. [DOI: 10.1021/ja4088264] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | - Nicholas J. Mosey
- Department
of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - R. Stan Brown
- Department
of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
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23
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Neverov AA, Chen LD, George S, Simon D, Maxwell CI, Brown RS. A mechanistic study of the [La2(OCH3)2]4+- and [(1,5,9-triazacyclodo-decane):Zn:(OCH3)]+-catalyzed methanolysis of carbonates: possible application for the recycling of bisphenol A polycarbonates. CAN J CHEM 2013. [DOI: 10.1139/cjc-2013-0270] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The kinetics of the methanolysis of seven methyl aryl carbonates (3) and two methyl alkyl carbonates (4) promoted by [12[ane]N3:Zn:(OCH3)]+ and [La2(OCH3)2]4+ catalysts (1 and 2, respectively) have been studied at 25.0 °C. Brønsted plots of the [Formula: see text] values for methanolysis versus aryloxy and alkoxy leaving group (LG) [Formula: see text] or [Formula: see text] values (the pKa values of the parent ArOH or ROH in methanol) for substrates 3 and 4 show an apparent downward break at [Formula: see text] ∼16.6 and 15.2 with [12[ane]N3:Zn:(OCH3)]+ and [La2(OCH3)2]4+, respectively. The breakpoint is not due to a change in rate-limiting step in a two-step process involving metal ion delivery of a coordinated methoxide to a transiently associated substrate and the subsequent breakdown of a tetrahedral intermediate to form product. The more satisfactory explanation is that the break arises when one correlates the rate constants for two dissimilar sets of substrates, namely aryloxy- and alkoxy-substituted 3 and 4. DFT calculations for the 1-promoted reactions of methyl 4-nitrophenyl carbonate (3b), which has a good aryloxy leaving group, and methyl isopropyl carbonate (4b), which has a relatively poor alkyl one, indicate that the catalyzed processes involve two steps. Accordingly, the methanolysis of all 3 having [Formula: see text] values for the parent phenols ≤15.3 involves rate-limiting nucleophilic attack and fast breakdown. For the isopropyl alkyl derivative (4b) having a [Formula: see text] > 18.13, the rate-liming step is the metal ion promoted breakdown of a tetrahedral intermediate. The catalytic system employing 2 has utility for the catalytic decomposition of poly(bisphenol A carbonate). In a semi-optimized system where 1000 mg of poly(bisphenol A carbonate), treated at 100 °C for 30 min in 2 mL of 60:40 chloroform−methanol containing La(OTf)3:NaOMe (5:7.5 mmol L−1), the reaction gave an 84% yield of bisphenol A, corresponding to >300 turnovers per catalyst.
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Affiliation(s)
- Alexei A. Neverov
- Department of Chemistry, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Leanne D. Chen
- Department of Chemistry, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Sean George
- Department of Chemistry, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - David Simon
- Department of Chemistry, Queen’s University, Kingston, ON K7L 3N6, Canada
| | | | - R. Stan Brown
- Department of Chemistry, Queen’s University, Kingston, ON K7L 3N6, Canada
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24
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Bonomi R, Saielli G, Scrimin P, Mancin F. An experimental and theoretical study of the mechanism of cleavage of an RNA-model phosphate diester by mononuclear Zn(II) complexes. Supramol Chem 2013. [DOI: 10.1080/10610278.2013.830724] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Renato Bonomi
- Dipartimento di Scienze Chimiche and CNR-ITM, Università di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Giacomo Saielli
- Dipartimento di Scienze Chimiche and CNR-ITM, Università di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Paolo Scrimin
- Dipartimento di Scienze Chimiche and CNR-ITM, Università di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Fabrizio Mancin
- Dipartimento di Scienze Chimiche and CNR-ITM, Università di Padova, Via Marzolo 1, 35131 Padova, Italy
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25
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Um IH, Song YJ, Kim MY, Lee JI. Metal-Ion Catalysis in Alkaline Ethanolysis of 2-Pyridyl Thionobenzoate: Effects of Modification of Electrophilic Center from C=O to C=S. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.5.1525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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Song Y, Zan J, Yan H, Lu ZL, Wang R. Steric effects on the catalytic activities of zinc(II) complexes containing [12]aneN3 ligating units in the cleavage of the RNA and DNA model phosphates. Org Biomol Chem 2013; 10:7714-20. [PMID: 22699360 DOI: 10.1039/c2ob25624j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A series of N-methylated mono- and di-[12]aneN(3) ligands () have been synthesized and characterized. The steric effects on the catalytic activities of their mononuclear and dinuclear zinc(ii) complexes in the cleavage of a RNA model 2-hydroxypropyl 4-nitrophenyl phosphate (HPNPP, ) and a DNA model methyl 4-nitrophenyl phosphates (MPNPP, 4) in methanol have been investigated at 25 °C. In the cleavage of phosphate catalyzed by the mononuclear complexes, derived from the N-methylation in the [12]aneN(3) backbone, the plots of k(obs)versus [Zn(II)] changed from an upward curvature to linearity with increasing level of methylation, indicating that N-methylations led to a reduction of dinuclear association that was responsible for the synergetic effect. Compared to the activities of the complex with non-methylated di-[12]aneN(3) ligand, those of the dinuclear zinc(ii) complex (Zn(2)-8), which has the two N-methyl groups, were reduced by two orders of magnitude as measured by the second-order rate constants and synergetic effect in the cleavage of both model compounds. For reactions catalyzed by the fully N-methylated dinuclear complex (Zn(2)-9), no synergetic effect was observed. Nevertheless, complex Zn(2)-8 still showed the remarkable catalytic efficiency, with rate accelerations of 10(9-10)-fold in the cleavage of each of the two phosphates relative to the background reactions, and the synergetic effects of up to 561 folds. pH jump experiments confirmed that the rate-limiting step in the cleavage of by Zn(2)-8 involved the binding process, while that in the reaction with 4 was the chemical cleavage of the P-O bond. Steric effects in the cleavage reactions were analyzed in detail and were compared with the electronic effect caused by oxy anion bridging group in the di-[12]aneN(3) ligand and also with the hydrophobic effect observed in other systems. The work has further confirmed that the combination of the cooperativity between two metal ions and a medium effect could result in excellent catalytic activities for the cleavage of phosphate diesters.
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Affiliation(s)
- Yang Song
- College of Chemistry, Beijing Normal University, Xinjiekouwai Street 19, Beijing, 100875, China
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Korhonen H, Koivusalo T, Toivola S, Mikkola S. There is no universal mechanism for the cleavage of RNA model compounds in the presence of metal ion catalysts. Org Biomol Chem 2013; 11:8324-39. [DOI: 10.1039/c3ob41554f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Um IH, Kang JS, Shin YH, Buncel E. A kinetic study on nucleophilic displacement reactions of aryl benzenesulfonates with potassium ethoxide: role of K+ ion and reaction mechanism deduced from analyses of LFERs and activation parameters. J Org Chem 2012; 78:490-7. [PMID: 23215678 DOI: 10.1021/jo302373y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pseudofirst-order rate constants (k(obsd)) have been measured spectrophotometrically for the nucleophilic substitution reactions of 2,4-dinitrophenyl X-substituted benzenesulfonates 4a-f and Y-substituted phenyl benzenesulfonates 5a-k with EtOK in anhydrous ethanol. Dissection of k(obsd) into k(EtO(-)) and k(EtOK) (i.e., the second-order rate constants for the reactions with the dissociated EtO(-) and ion-paired EtOK, respectively) shows that the ion-paired EtOK is more reactive than the dissociated EtO(-), indicating that K(+) ion catalyzes the reaction. The catalytic effect exerted by K(+) ion (e.g., the k(EtOK)/k(EtO(-)) ratio) decreases linearly as the substituent X in the benzenesulfonyl moiety changes from an electron-donating group (EDG) to an electron-withdrawing group (EWG), but it is independent of the electronic nature of the substituent Y in the leaving group. The reactions have been concluded to proceed through a concerted mechanism from analyses of the kinetic data through linear free energy relationships (e.g., the Brønsted-type, Hammett, and Yukawa-Tsuno plots). K(+) ion catalyzes the reactions by increasing the electrophilicity of the reaction center through a cyclic transition state (TS) rather than by increasing the nucleofugality of the leaving group. Activation parameters (e.g., ΔH(‡) and ΔS(‡)) determined from the reactions performed at five different temperatures further support the proposed mechanism and TS structures.
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Affiliation(s)
- Ik-Hwan Um
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea.
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Choi HJ, Koh HJ, Ali D, Yang KY, Koo IS. Rate-Product Correlations for the Solvolysis of 5-Nitro-2-Furoyl Chloride. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.10.3293] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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30
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Miyasaka A, Amaya T, Hirao T. Design and synthesis of dinuclear hemisalen complex on hexaarylbenzene scaffold. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.07.127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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31
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Barrozo A, Borstnar R, Marloie G, Kamerlin SCL. Computational protein engineering: bridging the gap between rational design and laboratory evolution. Int J Mol Sci 2012. [PMID: 23202907 PMCID: PMC3497281 DOI: 10.3390/ijms131012428] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Enzymes are tremendously proficient catalysts, which can be used as extracellular catalysts for a whole host of processes, from chemical synthesis to the generation of novel biofuels. For them to be more amenable to the needs of biotechnology, however, it is often necessary to be able to manipulate their physico-chemical properties in an efficient and streamlined manner, and, ideally, to be able to train them to catalyze completely new reactions. Recent years have seen an explosion of interest in different approaches to achieve this, both in the laboratory, and in silico. There remains, however, a gap between current approaches to computational enzyme design, which have primarily focused on the early stages of the design process, and laboratory evolution, which is an extremely powerful tool for enzyme redesign, but will always be limited by the vastness of sequence space combined with the low frequency for desirable mutations. This review discusses different approaches towards computational enzyme design and demonstrates how combining newly developed screening approaches that can rapidly predict potential mutation “hotspots” with approaches that can quantitatively and reliably dissect the catalytic step can bridge the gap that currently exists between computational enzyme design and laboratory evolution studies.
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Affiliation(s)
- Alexandre Barrozo
- Department of Cell and Molecular Biology, Uppsala Biomedical Center (BMC), Uppsala University, Box 596, S-751 24 Uppsala, Sweden; E-Mails: (A.B.); (R.B.); (G.M.)
| | - Rok Borstnar
- Department of Cell and Molecular Biology, Uppsala Biomedical Center (BMC), Uppsala University, Box 596, S-751 24 Uppsala, Sweden; E-Mails: (A.B.); (R.B.); (G.M.)
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Gaël Marloie
- Department of Cell and Molecular Biology, Uppsala Biomedical Center (BMC), Uppsala University, Box 596, S-751 24 Uppsala, Sweden; E-Mails: (A.B.); (R.B.); (G.M.)
| | - Shina Caroline Lynn Kamerlin
- Department of Cell and Molecular Biology, Uppsala Biomedical Center (BMC), Uppsala University, Box 596, S-751 24 Uppsala, Sweden; E-Mails: (A.B.); (R.B.); (G.M.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +46-18-471-4423; Fax: +46-18-530-396
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Um IH, Seo JY, Kang JS, An JS. A Kinetic Study on Nucleophilic Displacement Reactions of Phenyl Y-Substituted-Phenyl Carbonates with Alkali Metal Ethoxides: Metal Ion Effect and Reaction Mechanism. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2012. [DOI: 10.1246/bcsj.20120104] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ik-Hwan Um
- Department of Chemistry and Nano Science, Ewha Womans University
| | - Ji-Yoon Seo
- Department of Chemistry and Nano Science, Ewha Womans University
| | - Ji-Sun Kang
- Department of Chemistry and Nano Science, Ewha Womans University
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Raycroft MAR, Maxwell CI, Oldham RAA, Andrea AS, Neverov AA, Brown RS. Trifunctional metal ion-catalyzed solvolysis: Cu(II)-promoted methanolysis of N,N-bis(2-picolyl) benzamides involves unusual Lewis acid activation of substrate, delivery of coordinated nucleophile, powerful assistance of the leaving group departure. Inorg Chem 2012; 51:10325-33. [PMID: 22971051 DOI: 10.1021/ic301454y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The methanolyses of Cu(II) complexes of a series of N,N-bis(2-picolyl) benzamides (4a-g) bearing substituents X on the aromatic ring were studied under (s)(s)pH-controlled conditions at 25 °C. The active form of the complexes at neutral (s)(s)pH has a stoichiometry of 4:Cu(II):((-)OCH(3))(HOCH(3)) and decomposes unimolecularly with a rate constant k(x). A Hammett plot of log(k(x)) vs σ(x) values has a ρ(x) of 0.80 ± 0.05. Solvent deuterium kinetic isotope effects of 1.12 and 1.20 were determined for decomposition of the 4-nitro and 4-methoxy derivatives, 4b:Cu(II):((-)OCH(3))(HOCH(3)) and 4g:Cu(II):((-)OCH(3))(HOCH(3)), in the plateau region of the (s)(s)pH/log(k(x)) profiles in both CH(3)OH and CH(3)OD. Activation parameters for decomposition of these complexes are ΔH(++) = 19.1 and 21.3 kcal mol(-1) respectively and ΔS(++) = -5.1 and -2 cal K(-1) mol(-1). Density functional theory (DFT) calculations for the reactions of the Cu(II):((-)OCH(3))(HOCH(3)) complexes of 4a,b and g (4a, X = 3,5-dinitro) were conducted to probe the relative transition state energies and geometries of the different states. The experimental and computational data support a mechanism where the metal ion is coordinated to the N,N-bis(2-picolyl) amide unit and positioned so that it permits delivery of a coordinated Cu(II):((-)OCH(3)) nucleophile to the C═O in the rate-limiting transition state (TS) of the reaction. This proceeds to a tetrahedral intermediate INT, occupying a shallow minimum on the free energy surface with the Cu(II) coordinated to both the methoxide and the amidic N. Breakdown of INT is a virtually barrierless process, involving a Cu(II)-assisted departure of the bis(2-picolyl)amide anion. The analysis of the data points to a trifunctional role for the metal ion in the solvolysis mechanism where it activates intramolecular nucleophilic attack on the C═O group by coordination to an amidic N in the first step of the reaction and subsequently assists leaving group departure in the second step. The catalysis is very large; compared with the second order rate constant for methoxide attack on 4b, the computed reaction of CH3O(-) and 4b:Cu(II):(HOCH(3))(2) is accelerated by roughly 2.0 × 10(16) times.
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Affiliation(s)
- Mark A R Raycroft
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6
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Koh HJ, Kang SJ. Correlation of the Rates on Solvolysis of 2,2,2-Trichloroethyl Chloroformate Using the Extended Grunwald-Winstein Equation. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.5.1729] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
The development of synthetic agents able to hydrolytically cleave DNA with high efficiency and selectivity is still a fascinating challenge. Over the years, many examples have been reported reproducing part of the behaviour of the corresponding natural enzymes. Eventually, even the possibility to apply such systems to the manipulation of DNA of higher organisms has been demonstrated. However, efficiency of enzymes is still unrivalled. This feature article discusses the progress reported toward the realization of synthetic nucleases with particular attention to the comprehension of the reaction mechanisms and to the strategies that need to be addressed to obtain more efficient systems.
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Affiliation(s)
- Fabrizio Mancin
- Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, I -35131 Padova, Italy.
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Medina-Molner A, Spingler B. When two metal centres are needed instead of one: exclusive induction of Z-DNA by dinuclear metal complexes. Chem Commun (Camb) 2012; 48:1961-3. [DOI: 10.1039/c2cc16483c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Yan H, Li ZF, Guo ZF, Lu ZL, Wang F, Wu LZ. Effective and reversible DNA condensation induced by bifunctional molecules containing macrocyclic polyamines and naphthyl moieties. Bioorg Med Chem 2012; 20:801-8. [DOI: 10.1016/j.bmc.2011.11.069] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 11/29/2011] [Accepted: 11/30/2011] [Indexed: 10/14/2022]
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Mohamed MF, Sánchez-Lombardo I, Neverov AA, Brown RS. Solvent induced cooperativity of Zn(II) complexes cleaving a phosphate diester RNA analog in methanol. Org Biomol Chem 2011; 10:631-9. [PMID: 22116167 DOI: 10.1039/c1ob06482g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The kinetics of cyclization of 2-hydroxypropyl p-nitrophenyl phosphate (1) promoted by two mononuclear Zn(II) catalytic complexes of bis(2-pyridylmethyl)benzylamine (4) and bis(2-methyl 6-pyridylmethyl)benzylamine (5) in methanol were studied under (s)(s)pH-controlled conditions (where (s)(s)pH refers to [H(+)] activity in methanol). Potentiometric titrations of the ligands in the absence and presence of Zn(2+) and a non-reactive model for 1 (2-hydroxylpropyl isopropyl phosphate (HPIPP, 6)) indicate that the phosphate is bound tightly to the 4:Zn(II) and 5:Zn(II) complexes as L:Zn(II):6(-), and that each of these undergoes an additional ionization to produce L:Zn(II):6(-):((-)OCH(3)) or a bound deprotonated form of the phosphate, L:Zn(II):6(2-). Kinetic studies as a function of [L:Zn(II)] indicate that the rate is linear in [L:Zn(II)] at concentrations well above those required for complete binding of the substrate. Plots of the second order rate constants (defined as the gradient of the rate constant vs. [complex] plot) vs. (s)(s)pH in methanol are bell-shaped with rate maxima of 23 dm mol(-1) s(-1) and 146 dm mol(-1) s(-1) for 4:Zn(II) and 5:Zn(II), respectively, at their (s)(s)pH maxima of 10.5 and 10. A mechanism is proposed that involves binding of one molecule of complex to the phosphate to yield a poorly reactive 1 : 1 complex, which associates with a second molecule of complex to produce a transient cooperative 2 : 1 complex within which the cyclization of 1 is rapid. The observations support an effect of the reduced polarity solvent that encourages the cooperative association of phosphate and two independent mononuclear complexes to give a reactive entity.
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Affiliation(s)
- Mark F Mohamed
- Department of Chemistry, Queen's University Kingston, Ontario, Canada K7L 3N6
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Maxwell CI, Liu CT, Neverov AA, Mosey NJ, Brown RS. Transition from concerted to stepwise processes as a function of leaving group ability: density functional theory and experimental study of lyoxide-promoted cleavages of phosphorothioate and phosphate triesters in water and methanol. J PHYS ORG CHEM 2011. [DOI: 10.1002/poc.1938] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - C. Tony Liu
- Department of Chemistry; Queen's University; Kingston Ontario Canada K7L 3N6
| | - Alexei A. Neverov
- Department of Chemistry; Queen's University; Kingston Ontario Canada K7L 3N6
| | - Nicholas J. Mosey
- Department of Chemistry; Queen's University; Kingston Ontario Canada K7L 3N6
| | - Robert Stan Brown
- Department of Chemistry; Queen's University; Kingston Ontario Canada K7L 3N6
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Amaya T, Miyasaka A, Hirao T. Synthesis of three-dimensionally arranged bis-biphenol ligand on hexaaryl benzene scaffold and its application for cross-pinacol coupling reaction. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.06.113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Edwards DR, Maxwell CI, Harkness RW, Neverov AA, Mosey NJ, Stan Brown R. Experimental and computational determination of Brønsted coefficients for equilibrium transfer of the O
,O
-dimethyl phosphorothioyl group between oxyanion nucleophiles. J PHYS ORG CHEM 2011. [DOI: 10.1002/poc.1903] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- David R. Edwards
- Department of Chemistry; Queen's University; Kingston Ontario K7L 3N6 Canada
| | | | - Robert W. Harkness
- Department of Chemistry; Queen's University; Kingston Ontario K7L 3N6 Canada
| | - Alexei A. Neverov
- Department of Chemistry; Queen's University; Kingston Ontario K7L 3N6 Canada
| | - Nicholas J. Mosey
- Department of Chemistry; Queen's University; Kingston Ontario K7L 3N6 Canada
| | - R. Stan Brown
- Department of Chemistry; Queen's University; Kingston Ontario K7L 3N6 Canada
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An JS, NamKoong G, Kang JS, Um IH. Alkali Metal Ion Catalysis and Inhibition in Nucleophilic Substitution Reactions of 3,4-Dinitrophenyl Diphenylphosphinothioate with Alkali Metal Ethoxides in Anhydrous Ethanol: Effect of Changing Electrophilic Center from P=O to P=S. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.7.2423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Choi SY, Hong YJ, Um IH. Metal Ion Catalysis and Inhibition in Nucleophilic Substitution Reactions of 4-Nitrophenyl Nicotinate and Isonicotinate with Alkali Metal Ethoxides in Anhydrous Ethanol. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.6.1951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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45
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Gao H, Ke Z, DeYonker NJ, Wang J, Xu H, Mao ZW, Phillips DL, Zhao C. Dinuclear Zn(II) Complex Catalyzed Phosphodiester Cleavage Proceeds via a Concerted Mechanism: A Density Functional Theory Study. J Am Chem Soc 2011; 133:2904-15. [DOI: 10.1021/ja106456u] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Hui Gao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Zhuofeng Ke
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Nathan J. DeYonker
- Department of Chemistry, The University of Memphis, Memphis, Tennessee 38152-3550, United States
| | - Juping Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Huiying Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - David Lee Phillips
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | - Cunyuan Zhao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
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Lönnberg H. Cleavage of RNA phosphodiester bonds by small molecular entities: a mechanistic insight. Org Biomol Chem 2011; 9:1687-703. [PMID: 21258754 DOI: 10.1039/c0ob00486c] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
RNA molecules participate in many fundamental cellular processes either as a carrier of genetic information or as a catalyst, and hence, RNA has received increasing interest both as a chemotherapeutic agent and as a target of chemotherapy. In addition the dual nature of RNA has led to the RNA-world concept, i.e. an assumption that the evolution at an early stage of life was based on RNA-like oligomers that were responsible for the storage and transfer of information and as catalysts maintained primitive metabolism. Accordingly, the kinetics and mechanisms of the cleavage of RNA phosphodiester bonds have received interest and it is hoped they will shed light on the mechanisms of enzyme action and on the development of artificial enzymes. The major mechanistic findings concerning the cleavage by small molecules and ions and their significance for the development of efficient and biologically applicable artificial catalysts for RNA hydrolysis are surveyed in the present perspective.
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Affiliation(s)
- Harri Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland.
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Guo ZF, Yan H, Li ZF, Lu ZL. Synthesis of mono- and di-[12]aneN3 ligands and study on the catalytic cleavage of RNA model 2-hydroxypropyl-p-nitrophenyl phosphate with their metal complexes. Org Biomol Chem 2011; 9:6788-96. [DOI: 10.1039/c1ob05942d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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48
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Edwards DR, Tsang WY, Neverov AA, Brown RS. On the question of stepwise vs. concerted cleavage of RNA models promoted by a synthetic dinuclear Zn(ii) complex in methanol: implementation of a noncleavable phosphonate probe. Org Biomol Chem 2010; 8:822-7. [DOI: 10.1039/b918310h] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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49
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Mohamed MF, Neverov AA, Brown RS. Investigation of the Effect of Oxy Bridging Groups in Dinuclear Zn(II) Complexes that Catalyze the Cleavage of a Simple Phosphate Diester RNA Analogue. Inorg Chem 2009; 48:11425-33. [DOI: 10.1021/ic9015965] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mark F. Mohamed
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - Alexei A. Neverov
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - R. Stan Brown
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
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