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Shi R, Zhang L, Ma D, Cao Z. Elucidating the degradation mechanism of the nerve agent A-234 using various detergents: a theoretical investigation. Phys Chem Chem Phys 2024; 26:15292-15300. [PMID: 38767519 DOI: 10.1039/d4cp00881b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
A-234 (ethyl N-[1-(diethylamino)ethylidene]phosphoramidofluoridate) is one of the highly toxic Novichok nerve agents, and its efficient degradation is of significant importance. The possible degradation mechanisms of A-234 by H2O, H2O2, NH3, and their combinations have been extensively investigated by using density functional theory (DFT) calculations. According to the initial intermolecular interaction and the proton transfer patterns between the detergent and the substrate A-234, the A-234 degradation reaction is classified into three categories, denoted as A, B, and C. In modes A and B, the degradation of A-234 by H2O2, H2O, and NH3 is initiated by the nucleophilic attack of the O or N atom of the detergent on the P atom of A-234, coupled with the proton transfer from the detergent to the O or N atom of A-234, whereas in mode C, the direct interaction of H2N-H with the F-P bond of A-234 triggers ammonolysis through a one-step mechanism with the formation of H-F and N-P bonds. Perhydrolysis and hydrolysis of A-234 can be remarkably promoted by introducing the auxiliary NH3, and the timely formed hydrogen bond network among detergent, auxiliary, and substrate molecules is responsible for the enhancement of degradation efficiency.
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Affiliation(s)
- Rongxin Shi
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Lin Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Denghui Ma
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
- School of New Energy, Ningbo University of Technology, Ningbo, 315336, China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
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2
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Elias S, Columbus I, Shoshanim O, Mizrahi D, Chen R, Yehezkel L, Ghindes‐Azaria L, Ashkenazi N, Zafrani Y. The Prominent Motif of the Leaving Group in Chemical and Biological Processes of Phosphonoesters: Understanding the Behavior of V‐type Nerve Agents. ChemistrySelect 2022. [DOI: 10.1002/slct.202201363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shlomi Elias
- Department of Organic Chemistry Israel Institute for Biological Research Ness-Ziona 7410019 Israel
| | - Ishay Columbus
- Department of Organic Chemistry Israel Institute for Biological Research Ness-Ziona 7410019 Israel
| | - Ofir Shoshanim
- Department of Environmental Physics Israel Institute for Biological Research Ness-Ziona 7410019 Israel
| | - Dana Mizrahi
- Department of Organic Chemistry Israel Institute for Biological Research Ness-Ziona 7410019 Israel
| | - Ravit Chen
- Department of Organic Chemistry Israel Institute for Biological Research Ness-Ziona 7410019 Israel
| | - Lea Yehezkel
- Department of Organic Chemistry Israel Institute for Biological Research Ness-Ziona 7410019 Israel
| | - Lee Ghindes‐Azaria
- Department of Organic Chemistry Israel Institute for Biological Research Ness-Ziona 7410019 Israel
| | - Nissan Ashkenazi
- Department of Organic Chemistry Israel Institute for Biological Research Ness-Ziona 7410019 Israel
| | - Yossi Zafrani
- Department of Organic Chemistry Israel Institute for Biological Research Ness-Ziona 7410019 Israel
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3
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Sahu C, Das AK. Solvolysis of organophosphorus pesticide parathion with simple and $$\upalpha $$ α nucleophiles: a theoretical study. J CHEM SCI 2017. [DOI: 10.1007/s12039-017-1322-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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4
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Marciano D, Columbus I, Elias S, Goldvaser M, Shoshanim O, Ashkenazi N, Zafrani Y. Role of the P–F Bond in Fluoride-Promoted Aqueous VX Hydrolysis: An Experimental and Theoretical Study. J Org Chem 2012; 77:10042-9. [DOI: 10.1021/jo301549z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Daniele Marciano
- Department
of Organic Chemistry and ‡Department of Environmental Physics, Israel Institute for Biological Research, Ness-Ziona,
74100, Israel
| | - Ishay Columbus
- Department
of Organic Chemistry and ‡Department of Environmental Physics, Israel Institute for Biological Research, Ness-Ziona,
74100, Israel
| | - Shlomi Elias
- Department
of Organic Chemistry and ‡Department of Environmental Physics, Israel Institute for Biological Research, Ness-Ziona,
74100, Israel
| | - Michael Goldvaser
- Department
of Organic Chemistry and ‡Department of Environmental Physics, Israel Institute for Biological Research, Ness-Ziona,
74100, Israel
| | - Ofir Shoshanim
- Department
of Organic Chemistry and ‡Department of Environmental Physics, Israel Institute for Biological Research, Ness-Ziona,
74100, Israel
| | - Nissan Ashkenazi
- Department
of Organic Chemistry and ‡Department of Environmental Physics, Israel Institute for Biological Research, Ness-Ziona,
74100, Israel
| | - Yossi Zafrani
- Department
of Organic Chemistry and ‡Department of Environmental Physics, Israel Institute for Biological Research, Ness-Ziona,
74100, Israel
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Khan MAS, Bandyopadhyay T, Ganguly B. Probing the simulant behavior of PNPDPP toward parathion and paraoxon: A computational study. J Mol Graph Model 2012; 34:10-7. [DOI: 10.1016/j.jmgm.2011.12.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 12/22/2011] [Accepted: 12/26/2011] [Indexed: 10/14/2022]
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6
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Mandal D, Mondal B, Das AK. Nucleophilic degradation of fenitrothion insecticide and performance of nucleophiles: a computational study. J Phys Chem A 2012; 116:2536-46. [PMID: 22339374 DOI: 10.1021/jp2100057] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ab initio and density functional theory (DFT) calculations have been performed to understand the destruction chemistry of an important organophosphorus insecticide O,O-dimethyl O-(3-methyl-4-nitrophenyl) phosphorothioate, fenitrothion (FN), toward nucleophilic attack. Breaking of the P-OAr linkages through nucleophilic attack is considered to be the major degradation pathway for FN. One simple nucleophile, hydroxide (OH(-)), and two different α-nucleophiles, hydroperoxide (OOH(-)) and hydroxylamine anion (NH(2)O(-)), have been considered for this study. Nucleophilic attack at the two different centers, S(N)2@P and S(N)2@C, has been monitored, and the computed reaction energetics confirms that the S(N)2@P reactions are favorable over the S(N)2@C reactions for all the nucleophiles. All electronic structure calculations for the reaction are performed at DFT-B3LYP/6-31+G(d) level of theory followed by a refinement of energy at ab initio MP2/6-311++G(2d,2p) level. The effect of aqueous polarization on both the S(N)2 reactions is taken into account employing the conductor-like screening model (COSMO) as well as polarization continuum model (PCM) at B3LYP/6-31+G(d) level of theory. Relative performance of the two α-nucleophiles, OOH(-) and NH(2)O(-), at the P center has further been clarified using natural bond orbital (NBO), conceptual DFT, and atoms in molecules (AIM) approaches. The strength of the intermolecular hydrogen bonding in the transition states and topological properties of the electron density distribution for -X-H···S (X = O, N) intermolecular hydrogen bonds are the subject of NBO and AIM analysis, respectively. Our calculated reaction energetics and electronic properties suggest that the relative order of nucleophilicity for the nucleophiles is OOH(-) > NH(2)O(-) > OH(-) for the S(N)2@P, whereas for the S(N)2@C the order, which gets little altered, is NH(2)O(-) > OOH(-) > OH(-).
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Affiliation(s)
- Debasish Mandal
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
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7
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Assessing the reactivation efficacy of hydroxylamine anion towards VX-inhibited AChE: a computational study. J Mol Model 2011; 18:1801-8. [DOI: 10.1007/s00894-011-1209-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 08/01/2011] [Indexed: 11/25/2022]
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8
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Probing the reactivation process of sarin-inhibited acetylcholinesterase with α-nucleophiles: Hydroxylamine anion is predicted to be a better antidote with DFT calculations. J Mol Graph Model 2011; 29:1039-46. [DOI: 10.1016/j.jmgm.2011.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 04/22/2011] [Accepted: 04/27/2011] [Indexed: 11/19/2022]
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9
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Bera NC, Maeda S, Morokuma K, Viggiano AA. Theoretical Proton Affinity and Fluoride Affinity of Nerve Agent VX. J Phys Chem A 2010; 114:13189-97. [DOI: 10.1021/jp107718w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Narayan C. Bera
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States, and Air Force Research Laboratory, Space Vehicles Directorate, 29 Randolph Road, Hanscom AFB, Massachusetts 01731-3010, United States
| | - Satoshi Maeda
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States, and Air Force Research Laboratory, Space Vehicles Directorate, 29 Randolph Road, Hanscom AFB, Massachusetts 01731-3010, United States
| | - Keiji Morokuma
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States, and Air Force Research Laboratory, Space Vehicles Directorate, 29 Randolph Road, Hanscom AFB, Massachusetts 01731-3010, United States
| | - Al A. Viggiano
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States, and Air Force Research Laboratory, Space Vehicles Directorate, 29 Randolph Road, Hanscom AFB, Massachusetts 01731-3010, United States
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10
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Khan MAS, Kesharwani MK, Bandyopadhyay T, Ganguly B. Remarkable effect of hydroxylamine anion towards the solvolysis of sarin: A DFT study. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.12.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Ashkenazi N, Segall Y, Chen R, Sod-Moriah G, Fattal E. The Mechanism of Nucleophilic Displacements at Phosphorus in Chloro-Substituted Methylphosphonate Esters: P−O vs P−C Bond Cleavage: A DFT Study. J Org Chem 2010; 75:1917-26. [DOI: 10.1021/jo9026325] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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12
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Solvolysis process of organophosphorus compound P-[2-(dimethylamino)ethyl]-N,N-dimethylphosphonamidic fluoride with simple and α-nucleophiles: a DFT study. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0701-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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van Bochove MA, Swart M, Bickelhaupt FM. Stepwise walden inversion in nucleophilic substitution at phosphorus. Phys Chem Chem Phys 2008; 11:259-67. [PMID: 19088981 DOI: 10.1039/b813152j] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have studied the mechanism of S(N)2@P reactions in the model systems X(-) + PMe(2)Y and X(-) + POR(2)Y (with R=Me, OH, OMe; and X, Y=Cl, OH, MeO) using density functional theory at OLYP/TZ2P. Our main purpose is to analyze the nature of the Walden inversion in our model nucleophilic substitution reactions. Walden inversion is well-known to proceed, in general, as a concerted umbrella motion of the substituents at the central atom. Interestingly, we find here that, in certain model reactions, Walden inversion can also proceed in a stepwise fashion in which the individual substituents of the umbrella flip, consecutively, from the educt to the product conformation via separate barriers on the reaction profile. We also examine how variation in nucleophile and leaving group may tune the pentavalent transition structure between labile transition state (TS) and stable transition complex (TC). Furthermore, we explore the various competing multistep pathways in the symmetric (X=Y) and asymmetric (X not equal Y) substitution reactions in our model reaction systems.
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Affiliation(s)
- Marc A van Bochove
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, Netherlands
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14
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McAnoy AM, Paine MRL, Blanksby SJ. Reactions of the hydroperoxide anion with dimethyl methylphosphonate in an ion trap mass spectrometer: evidence for a gas phase alpha-effect. Org Biomol Chem 2008; 6:2316-26. [PMID: 18563264 DOI: 10.1039/b803734e] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The gas phase degradation reactions of the chemical warfare agent (CWA) simulant, dimethyl methylphosphonate (DMMP), with the hydroperoxide anion (HOO(-)) were investigated using a modified quadrupole ion trap mass spectrometer. The HOO(-) anion reacts readily with neutral DMMP forming two significant product ions at m/z 109 and m/z 123. The major reaction pathways correspond to (i) the nucleophilic substitution at carbon to form [CH(3)P(O)(OCH(3))O](-) (m/z 109) in a highly exothermic process and (ii) exothermic proton transfer. The branching ratios of the two reaction pathways, 89% and 11% respectively, indicate that the former reaction is significantly faster than the latter. This is in contrast to the trend for the methoxide anion with DMMP, where proton transfer dominates. The difference in the observed reactivities of the HOO(-) and CH(3)O(-) anions can be considered as evidence for an alpha-effect in the gas phase and is supported by electronic structure calculations at the B3LYP/aug-cc-pVTZ//B3LYP/6-31+G(d) level of theory that indicate the S(N)2(carbon) process has an activation energy 7.8 kJ mol(-1) lower for HOO(-) as compared to CH(3)O(-). A similar alpha-effect was calculated for nucleophilic addition-elimination at phosphorus, but this process--an important step in the perhydrolysis degradation of CWAs in solution--was not observed to occur with DMMP in the gas phase. A theoretical investigation revealed that all processes are energetically accessible with negative activation energies. However, comparison of the relative Arrhenius pre-exponential factors indicate that substitution at phosphorus is not kinetically competitive with respect to the S(N)2(carbon) and deprotonation processes.
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Affiliation(s)
- Andrew Michael McAnoy
- Human Protection and Performance Division, Defence Science and Technology Organisation, 506 Lorimer St, Fishermans Bend, Victoria, 3207, Australia.
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15
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Seckute J, Menke JL, Emnett RJ, Patterson EV, Cramer CJ. Ab initio molecular orbital and density functional studies on the solvolysis of sarin and O,S-dimethyl methylphosphonothiolate, a VX-like compound. J Org Chem 2006; 70:8649-60. [PMID: 16238293 DOI: 10.1021/jo0502706] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction: see text] Potential energy surfaces for the alkaline hydrolysis of sarin and O,S-dimethyl methylphosphonothiolate, a VX model compound, and the perhydrolysis of the latter have been computed at the MP2/6-31+G(d)//mPW1K/MIDI! level of theory. The effect of aqueous solvation was accounted for via the integral equation formalism polarizable continuum model (IEF-PCM) at the HF/6-31+G(d) level. Excellent agreement with the experimental enthalpy of activation for alkaline hydrolysis of sarin was found. For the alkaline hydrolysis of O,S-dimethyl methylphosphonothiolate, it was found that the P-O and P-S bond cleavage processes are kinetically competitive but that the products of P-S bond cleavage are thermodynamically favored. For the perhydrolysis of O,S-dimethyl methylphosphonothiolate, it was found that P-O bond cleavage is not kinetically competitive with P-S bond cleavage. In both cases, the data support initial formation of trigonal bipyramidal intermediates and demonstrate kinetic selectivity for nucleophilic attack on the face opposite the more apicophilic methoxide ligand.
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Affiliation(s)
- Jolita Seckute
- Truman State University, Division of Science, Kirksville, Missouri 63501-4221, USA
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16
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Bandyopadhyay I, Kim MJ, Lee YS, Churchill DG. Favorable Pendant-Amino Metal Chelation in VX Nerve Agent Model Systems. J Phys Chem A 2006; 110:3655-61. [PMID: 16526648 DOI: 10.1021/jp055112x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have performed DFT computational studies [B3LYP, 6-31+G] to obtain metal ion coordination isomers of VX-Me [MeP(O)(OMe)(SCH2CH2NMe2)], a model of two of the most lethal nerve agents: VX [MeP(O)(OEt)(SCH2CH2N(iPr)2)] and Russian-VX [MeP(O)(OCH2CHMe2)(SCH2CH2N(Et)2)]. Our calculations involved geometry optimizations of the neutral VX-Me model as well as complexes with H+, Li+, Na+, K+, Be2+, Mg2+, and Ca2+ that yielded 2-8 different stable chelation modes for each ion that involved mainly mono- and bidentate binding. Importantly, our studies revealed that the [O(P),N] bidentate binding mode, long thought to be the active mode in differentiating the hydrolytic path of VX from other nerve agents, was the most stable for all ions studied here. Binding energy depended mainly on ionic size as well as charge, with binding energies ranging from 364 kcal mol(-1) for Be2+ to 33 kcal mol(-1) for K+. Furthermore, calculated NMR shifts for VX-Me correlate to experimental values of VX.
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Affiliation(s)
- Indrajit Bandyopadhyay
- Department of Chemistry and School of Molecular Science (BK 21), Korea Advanced Institute of Science and Technology, Daejeon, 305-701 Republic of Korea
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Jackson C, Kim HK, Carr PD, Liu JW, Ollis DL. The structure of an enzyme-product complex reveals the critical role of a terminal hydroxide nucleophile in the bacterial phosphotriesterase mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1752:56-64. [PMID: 16054447 DOI: 10.1016/j.bbapap.2005.06.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2005] [Revised: 06/08/2005] [Accepted: 06/09/2005] [Indexed: 11/26/2022]
Abstract
A detailed understanding of the catalytic mechanism of enzymes is an important step toward improving their activity for use in biotechnology. In this paper, crystal soaking experiments and X-ray crystallography were used to analyse the mechanism of the Agrobacterium radiobacter phosphotriesterase, OpdA, an enzyme capable of detoxifying a broad range of organophosphate pesticides. The structures of OpdA complexed with ethylene glycol and the product of dimethoate hydrolysis, dimethyl thiophosphate, provide new details of the catalytic mechanism. These structures suggest that the attacking nucleophile is a terminally bound hydroxide, consistent with the catalytic mechanism of other binuclear metallophosphoesterases. In addition, a crystal structure with the potential substrate trimethyl phosphate bound non-productively demonstrates the importance of the active site cavity in orienting the substrate into an approximation of the transition state.
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Affiliation(s)
- Colin Jackson
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia
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18
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Zuo GM, Cheng ZX, Li GW, Wang LY, Chen H. Photoassisted Reaction of Chemical Warfare Agent VX Droplets under UV Light Irradiation. J Phys Chem A 2005; 109:6912-8. [PMID: 16834048 DOI: 10.1021/jp051904f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A photoassisted reaction of O-ethyl S-[2-(diisopropylamino) ethyl] methylphosphonothioate (VX) droplets in air was carried out. The experimental results indicated that VX droplets could be easily and chemically transformed into other compounds under irradiation of a germicidal lamp over sufficient time. Quantum chemical calculation results demonstrated that UV light less than 278 nm wavelength could possibly initiate photoreaction of VX and that both P-S and P=O bonds in the VX molecule were lengthened. The identification of reaction products by gas and liquid chromatography mass spectroscopy and NMR revealed that the VX molecule in air under UV light irradiation could undergo isomerization of S-esters to O-esters, cleavage of P-S, S-C, and C-N bonds, and ozonation of tertiary amines.
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Affiliation(s)
- Guo-Min Zuo
- The No. 3 Department, Institute of Chemical Defence, P.O. Box 1048, Beijing, 102205, China
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19
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Jackson CJ, Liu JW, Coote ML, Ollis DL. The effects of substrate orientation on the mechanism of a phosphotriesterase. Org Biomol Chem 2005; 3:4343-50. [PMID: 16327895 DOI: 10.1039/b512399b] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
While the underlying chemistry of enzyme-catalyzed reactions may be almost identical, the actual turnover rates of different substrates can vary significantly. This is seen in the turnover rates for the catalyzed hydrolysis of organophosphates by the bacterial phosphotriesterase OpdA. We investigate the variation in turnover rates by examining the hydrolysis of three classes of substrates: phosphotriesters, phosphothionates, and phosphorothiolates. Theoretical calculations were used to analyze the reactivity of these substrates and the energy barriers to their hydrolysis. This information was then compared to information derived from enzyme kinetics and crystallographic studies, providing new insights into the mechanism of this enzyme. We demonstrate that the enzyme catalyzes the hydrolysis of organophosphates through steric constraint of the reactants, and that the equilibrium between productively and unproductively bound substrates makes a significant contribution to the turnover rate of highly reactive substrates. These results highlight the importance of correct orientation of reactants within the active sites of enzymes to enable efficient catalysis.
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Affiliation(s)
- Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
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20
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Morales-Rojas H, Moss RA. Phosphorolytic reactivity of o-iodosylcarboxylates and related nucleophiles. Chem Rev 2002; 102:2497-521. [PMID: 12105934 DOI: 10.1021/cr9405462] [Citation(s) in RCA: 173] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hugo Morales-Rojas
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903, USA
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Cramer CJ, Truhlar DG. Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics. Chem Rev 1999; 99:2161-2200. [PMID: 11849023 DOI: 10.1021/cr960149m] [Citation(s) in RCA: 1722] [Impact Index Per Article: 68.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher J. Cramer
- Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
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Affiliation(s)
- Yu-Chu Yang
- U.S. Army Edgewood Research, Development and Engineering Center (ERDEC), Aberdeen Proving Ground, Maryland 21010-5423
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