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Liu P, Wang D, Xu Y. A new, double-inversion mechanism of the F - + CH 3Cl S N2 reaction in aqueous solution. Phys Chem Chem Phys 2018; 18:31895-31903. [PMID: 27844085 DOI: 10.1039/c6cp06195h] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Atomic-level, bimolecular nucleophilic substitution reaction mechanisms have been studied mostly in the gas phase, but the gas-phase results cannot be expected to reliably describe condensed-phase chemistry. As a novel, double-inversion mechanism has just been found for the F- + CH3Cl SN2 reaction in the gas phase [Nat. Commun., 2015, 6, 5972], here, using multi-level quantum mechanics methods combined with the molecular mechanics method, we discovered a new, double-inversion mechanism for this reaction in aqueous solution. However, the structures of the stationary points along the reaction path show significant differences from those in the gas phase due to the strong influence of solvent and solute interactions, especially due to the hydrogen bonds formed between the solute and the solvent. More importantly, the relationship between the two double-inversion transition states is not clear in the gas phase, but, here we revealed a novel intermediate complex serving as a "connecting link" between the two transition states of the abstraction-induced inversion and the Walden-inversion mechanisms. A detailed reaction path was constructed to show the atomic-level evolution of this novel double reaction mechanism in aqueous solution. The potentials of mean force were calculated and the obtained Walden-inversion barrier height agrees well with the available experimental value.
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Affiliation(s)
- Peng Liu
- College of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
| | - Dunyou Wang
- College of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
| | - Yulong Xu
- School of Science, Qilu University of Technology, Jinan, 250353, China
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2
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Tratnyek PG, Bylaska EJ, Weber EJ. In silico environmental chemical science: properties and processes from statistical and computational modelling. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2017; 19:188-202. [PMID: 28262894 DOI: 10.1039/c7em00053g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Quantitative structure-activity relationships (QSARs) have long been used in the environmental sciences. More recently, molecular modeling and chemoinformatic methods have become widespread. These methods have the potential to expand and accelerate advances in environmental chemistry because they complement observational and experimental data with "in silico" results and analysis. The opportunities and challenges that arise at the intersection between statistical and theoretical in silico methods are most apparent in the context of properties that determine the environmental fate and effects of chemical contaminants (degradation rate constants, partition coefficients, toxicities, etc.). The main example of this is the calibration of QSARs using descriptor variable data calculated from molecular modeling, which can make QSARs more useful for predicting property data that are unavailable, but also can make them more powerful tools for diagnosis of fate determining pathways and mechanisms. Emerging opportunities for "in silico environmental chemical science" are to move beyond the calculation of specific chemical properties using statistical models and toward more fully in silico models, prediction of transformation pathways and products, incorporation of environmental factors into model predictions, integration of databases and predictive models into more comprehensive and efficient tools for exposure assessment, and extending the applicability of all the above from chemicals to biologicals and materials.
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Affiliation(s)
- Paul G Tratnyek
- Institute of Environmental Health, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.
| | - Eric J Bylaska
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
| | - Eric J Weber
- National Exposure Assessment Laboratory, U.S. Environmental Protection Agency, 960 College Station Road, Athens, GA 30605, USA
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Lv J, Zhang J, Wang D. A multi-level quantum mechanics and molecular mechanics study of SN2 reaction at nitrogen: NH2Cl + OH(-) in aqueous solution. Phys Chem Chem Phys 2016; 18:6146-52. [PMID: 26847380 DOI: 10.1039/c5cp07370g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We employed a multi-level quantum mechanics and molecular mechanics approach to study the reaction NH2Cl + OH(-) in aqueous solution. The multi-level quantum method (including the DFT method with both the B3LYP and M06-2X exchange-correlation functionals and the CCSD(T) method, and both methods with the aug-cc-pVDZ basis set) was used to treat the quantum reaction region in different stages of the calculation in order to obtain an accurate potential of mean force. The obtained free energy activation barriers at the DFT/MM level of theory yielded a big difference of 21.8 kcal mol(-1) with the B3LYP functional and 27.4 kcal mol(-1) with the M06-2X functional respectively. Nonetheless, the barrier heights become very close when shifted from DFT to CCSD(T): 22.4 kcal mol(-1) and 22.9 kcal mol(-1) at CCSD(T)(B3LYP)/MM and CCSD(T)(M06-2X)/MM levels of theory, respectively. The free reaction energy obtained using CCSD(T)(M06-2X)/MM shows an excellent agreement with the one calculated using the available gas-phase data. Aqueous solution plays a significant role in shaping the reaction profile. In total, the water solution contributes 13.3 kcal mol(-1) and 14.6 kcal mol(-1) to the free energy barrier heights at CCSD(T)(B3LYP)/MM and CCSD(T)(M06-2X)/MM respectively. The title reaction at nitrogen is a faster reaction than the corresponding reaction at carbon, CH3Cl + OH(-).
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Affiliation(s)
- Jing Lv
- College of Physics and Electronics, Shandong Normal University, Jinan 250014, Shandong, China.
| | - Jingxue Zhang
- School of Physics, Nankai University, Tianjin 300071, China
| | - Dunyou Wang
- College of Physics and Electronics, Shandong Normal University, Jinan 250014, Shandong, China.
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Zhang J, Xu Y, Chen J, Wang D. A multilayered-representation, quantum mechanical/molecular mechanics study of the CH3Cl + F− reaction in aqueous solution: the reaction mechanism, solvent effects and potential of mean force. Phys Chem Chem Phys 2014; 16:7611-7. [DOI: 10.1039/c3cp55401e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A multi-layered representation, hybrid quantum mechanical and molecular mechanics method study of the CH3Cl + F− → CH3F + Cl− reaction in water.
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Affiliation(s)
- Jingxue Zhang
- College of Physics and Electronics
- Shandong Normal University
- Jinan, 250014 China
| | - Yulong Xu
- College of Physics and Electronics
- Shandong Normal University
- Jinan, 250014 China
- School of Science
- Qilu University of Technology
| | - Jie Chen
- College of Physics and Electronics
- Shandong Normal University
- Jinan, 250014 China
| | - Dunyou Wang
- College of Physics and Electronics
- Shandong Normal University
- Jinan, 250014 China
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Brudnik K, Twarda M, Sarzyński D, Jodkowski JT. Theoretical study of the kinetics of chlorine atom abstraction from chloromethanes by atomic chlorine. J Mol Model 2013; 19:4181-93. [PMID: 23455925 PMCID: PMC3778224 DOI: 10.1007/s00894-013-1779-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 01/21/2013] [Indexed: 11/25/2022]
Abstract
Ab initio calculations at the G3 level were used in a theoretical description of the kinetics and mechanism of the chlorine abstraction reactions from mono-, di-, tri- and tetra-chloromethane by chlorine atoms. The calculated profiles of the potential energy surface of the reaction systems show that the mechanism of the studied reactions is complex and the Cl-abstraction proceeds via the formation of intermediate complexes. The multi-step reaction mechanism consists of two elementary steps in the case of CCl4 + Cl, and three for the other reactions. Rate constants were calculated using the theoretical method based on the RRKM theory and the simplified version of the statistical adiabatic channel model. The temperature dependencies of the calculated rate constants can be expressed, in temperature range of 200-3,000 K as [Formula: see text]. The rate constants for the reverse reactions CH3/CH2Cl/CHCl2/CCl3 + Cl2 were calculated via the equilibrium constants derived theoretically. The kinetic equations [Formula: see text] allow a very good description of the reaction kinetics. The derived expressions are a substantial supplement to the kinetic data necessary to describe and model the complex gas-phase reactions of importance in combustion and atmospheric chemistry.
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Affiliation(s)
- Katarzyna Brudnik
- Department of Physical Chemistry, Wroclaw Medical University, pl. Nankiera 1, 50-140, Wroclaw, Poland,
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Elsner M, Hofstetter TB. Current Perspectives on the Mechanisms of Chlorohydrocarbon Degradation in Subsurface Environments: Insight from Kinetics, Product Formation, Probe Molecules, and Isotope Fractionation. ACS SYMPOSIUM SERIES 2011. [DOI: 10.1021/bk-2011-1071.ch019] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Martin Elsner
- Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstr. 1 85764 Neuherberg, Germany
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), Überlandstr. 133, 8600 Dübendorf, Switzerland
| | - Thomas B. Hofstetter
- Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstr. 1 85764 Neuherberg, Germany
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), Überlandstr. 133, 8600 Dübendorf, Switzerland
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Bylaska EJ, Glaesemann KR, Felmy AR, Vasiliu M, Dixon DA, Tratnyek PG. Free Energies for Degradation Reactions of 1,2,3-Trichloropropane from ab Initio Electronic Structure Theory. J Phys Chem A 2010; 114:12269-82. [DOI: 10.1021/jp105726u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Andrew R. Felmy
- Fundamental Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | | | | | - Paul G. Tratnyek
- OGI School of Science and Engineering, Oregon Health & Science University, 20000 NW Walker Road, Beaverton, Oregon 97006-8921, United States
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Isse AA, Sandonà G, Durante C, Gennaro A. Voltammetric investigation of the dissociative electron transfer to polychloromethanes at catalytic and non-catalytic electrodes. Electrochim Acta 2009. [DOI: 10.1016/j.electacta.2008.12.034] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Bylaska EJ, Dupuis M, Tratnyek PG. One-Electron-Transfer Reactions of Polychlorinated Ethylenes: Concerted and Stepwise Cleavages. J Phys Chem A 2008; 112:3712-21. [DOI: 10.1021/jp711021d] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eric J. Bylaska
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352
| | - Michel Dupuis
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352
| | - Paul G. Tratnyek
- OGI School of Science & Engineering, Oregon Health & Science University, 20000 NW Walker Road, Beaverton, Oregon 97006-8921
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Valiev M, Bylaska EJ, Dupuis M, Tratnyek PG. Combined Quantum Mechanical and Molecular Mechanics Studies of the Electron-Transfer Reactions Involving Carbon Tetrachloride in Solution. J Phys Chem A 2008; 112:2713-20. [DOI: 10.1021/jp7104709] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marat Valiev
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington, 99352
| | - Eric J. Bylaska
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington, 99352
| | - Michel Dupuis
- Fundamental Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352
| | - Paul G. Tratnyek
- OGI School of Science & Engineering, Oregon Health & Science University, 20000 Northwest Walker Road, Beaverton, Oregon 97006-8921
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Feng J, Lim TT. Iron-mediated reduction rates and pathways of halogenated methanes with nanoscale Pd/Fe: analysis of linear free energy relationship. CHEMOSPHERE 2007; 66:1765-74. [PMID: 16899274 DOI: 10.1016/j.chemosphere.2006.06.068] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Revised: 06/24/2006] [Accepted: 06/26/2006] [Indexed: 05/11/2023]
Abstract
The influence of halogen substitution in chlorinated methanes and brominated methanes on their abiotic reductive dehalogenation with nanoscale Pd/Fe bimetallic particles was investigated in this study. The 0.2% and 1.0% Pd/Fe particles, with particle sizes of less than 100nm, were synthesized in the laboratory. Reduction of the halogenated methanes with the Pd/Fe particles followed pseudo-first-order kinetics. The Pd/Fe bimetallic particles demonstrated at least an order of magnitude higher in reactivity compared to the unpalladized Fe particles of similar particle size. Comparing the 0.2% Pd/Fe and the 1.0% Pd/Fe particles, the latter exhibited higher reduction rates of various halogenated methanes. On the other hand, the reduction rates of chlorinated methanes were consistently lower than those of their brominated counterparts. The compounds with higher number of halogen substitutions were more readily reduced than the lightly halogenated ones. Coupled hydrogenolysis-elimination processes were the important mechanism for complete dehalogenation of the chlorinated and brominated methanes. From the kinetic examination of their transformation rates and mechanistic insight into the associated pathways, an attempt to analyze linear free energy relationship between the observed kinetics and the associated thermodynamic constants was performed. The observed reaction rate constants were analyzed for their correlations with one-electron potential (E(1)), two-electron potential (E(2)), bond dissociation energy (BDE) and the lowest unoccupied molecular orbital (LUMO) energy (E(LUMO)). LUMO energy appeared to be the best descriptor for the kinetic prediction, while E(1) and E(2) might be more suitable for mechanistic analysis.
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Affiliation(s)
- Jing Feng
- Environmental Engineering Research Centre, School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
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Krivenko AG, Kurmaz VA. Thermodynamic and kinetic characteristics of intermediates of electrode reactions. Comparative laser photoemission study of the kinetics of electron transfer for certain alkylaryl and alkylhalide radicals. RUSS J ELECTROCHEM+ 2006. [DOI: 10.1134/s1023193506020017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Bylaska EJ. Estimating the thermodynamics and kinetics of chlorinated hydrocarbon degradation. Theor Chem Acc 2005. [DOI: 10.1007/s00214-005-0042-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Dutton AS, Fukuto JM, Houk KN. Theoretical reduction potentials for nitrogen oxides from CBS-QB3 energetics and (C)PCM solvation calculations. Inorg Chem 2005; 44:4024-8. [PMID: 15907131 DOI: 10.1021/ic048734q] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The complete basis set method, CBS-QB3, is used in combination with two continuum solvation models for aqueous solvation to compute reduction potentials previously determined experimentally for 36 nitrogen oxides and related species of the general formula H(V)C(W)N(X)O(Y)Cl(Z). The PCM model led to the correlation E(o)exp (vs NHE) = 0.84E(o)calc + 0.03 V with an average error of 0.12 V (2.8 kcal/mol) and a maximum error of 0.32 V (7.4 kcal/mol). The CPCM/UAKS model gave E(o)exp (vs NHE) = 0.83E(o)calc + 0.11 V with the same average error. This general method was used to predict reduction potentials (+/-0.3 V) for nitrogen oxides for which reduction potentials are not known with certainty: NO2/NO2- (0.6 V), NO3/NO3- (1.9 V), N2O3-/N2O3(2-) (0.5 V), HN2O3/HN2O3- (0.9 V), HONNO,H+/HONNOH (1.6 V), 2NO,H+/HONNO (0.0 V), 2NO/ONNO- (-0.1 V), ONNO-/ONNO(2-) (-0.4 V), HNO,H+/H2NO (0.6 V), H2NO,H+/H2NOH (0.9 V), HNO,2H+/H2NOH (0.8 V), and HNO/HNO- (-0.7 V).
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Affiliation(s)
- Andrew S Dutton
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, USA
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Bylaska EJ, Dupuis M, Tratnyek PG. Ab Initio Electronic Structure Study of One-Electron Reduction of Polychlorinated Ethylenes. J Phys Chem A 2005; 109:5905-16. [PMID: 16833925 DOI: 10.1021/jp0407526] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Polychlorethylene radicals, anions, and radical anions are potential intermediates in the reduction of polychlorinated ethylenes (C(2)Cl(4), C(2)HCl(3), trans-C(2)H(2)Cl(2), cis-C(2)H(2)Cl(2), 1,1-C(2)H(2)Cl(2), C(2)H(3)Cl). Ab initio electronic structure methods were used to calculate the thermochemical properties, (298.15 K), S degrees (298.15 K,1 bar), and DeltaG(S)(298.15 K, 1 bar) of 37 different polychloroethylenyl radicals, anions, and radical anion complexes, C(2)H(y)Cl(3)(-)(y)(*), C(2)H(y)Cl(3)(-)(y)(-), and C(2)H(y))Cl(4)(-)(y)(*)(-) for y = 0-3, for the purpose of characterizing reduction mechanisms of polychlorinated ethylenes. In this study, 8 radicals, 7 anions, and 22 radical anions were found to have stable structures, i.e., minima on the potential energy surfaces. This multitude of isomers for C(2)H(y)Cl(4)(-)(y)(*)(-) radical anion complexes are pi*, sigma*, and -H...Cl(-) structures. Several stable pi* radical anionic structures were obtained for the first time through the use of restricted open-shell theories. On the basis of the calculated thermochemical estimates, the overall reaction energetics (in the gas phase and aqueous phase) for several mechanisms of the first electron reduction of the polychlorinated ethylenes were determined. In almost all of the gas-phase reactions, the thermodynamically most favorable pathways involve -H...Cl(-) complexes of the C(2)H(y)Cl(4)(-)(y)(*)(-) radical anion, in which a chloride ion is loosely bound to a hydrogen of a C(2)H(x)Cl(2)(-)(x))(*) radical. The exception is for C(2)Cl(4), in which the most favorable anionic structure is a loose sigma* radical anion complex, with a nearly iso-energetic pi* radical anion. Solvation significantly changes the product energetics with the thermodynamically most favorable pathway leading to C(2)H(y)Cl(3)(-)(y)(*) + Cl(-). The results suggest that a higher degree of chlorination favors reduction, and that reduction pathways involving the C(2)H(y)Cl(3)(-)(y)(-) anions are high energy pathways.
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Affiliation(s)
- Eric J Bylaska
- Fundamental Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
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A density functional study of dissociative electron transfer reactions with participation of halogenated methanes. J Electroanal Chem (Lausanne) 2004. [DOI: 10.1016/j.jelechem.2004.07.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Bylaska EJ, Dixon DA, Felmy AR, Aprà E, Windus TL, Zhan CG, Tratnyek PG. The Energetics of the Hydrogenolysis, Dehydrohalogenation, and Hydrolysis of 4,4‘-Dichloro-diphenyl-trichloroethane from ab Initio Electronic Structure Theory. J Phys Chem A 2004. [DOI: 10.1021/jp0312316] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | | | - Chang-Guo Zhan
- Division of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 907 Rose Street, Room 501B, Lexington, Kentucky 40536
| | - Paul G. Tratnyek
- OGI School of Science & Engineering, Oregon Health & Science University, 20000 NW Walker Road, Beaverton, Oregon 97006-8921
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Reaction rates of the hydrated electron with N2O in high temperature water and potential surface of the N2O− anion. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2003.11.050] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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