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Kabanda MM, Bahadur I. A DFT and MP2 mechanistic and kinetic study on hypohalogenation reaction of cysteine and N-acetylcysteine in aqueous solution. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Chow R, Mok DKW. A theoretical study of the addition of CH 2OO to hydroxymethyl hydroperoxide and its implications on SO 3 formation in the atmosphere. Phys Chem Chem Phys 2020; 22:14130-14141. [PMID: 32542295 DOI: 10.1039/d0cp00961j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reaction of hydroxymethyl hydroperoxide (HMHP, HOCH2OOH) with the simplest Criegee intermediate, CH2OO, has been examined using quantum chemical methods with transition state theory. Geometry optimization and IRC calculations were performed using the M06-2X, MN15-L, and B2PLYP-D3 functionals in conjunction with the aug-cc-pVTZ basis set. Single point energy calculations using QCISD(T) and BD(T) with the same basis set have been performed to determine the energy of reactants, reactive complexes, transition states, and products. Rate coefficients have been obtained using variational transition state theory. The addition of CH2OO on the three different oxygen atoms in HMHP has been considered and the ether oxide forming channel, CH2OO + HOCH2OOH → HOCH2O(O)CH2OOH (channel 2), is the most favorable. The best computed standard enthalpy of reaction (ΔH) and zero-point corrected barrier height are -20.02 and -6.33 kcal mol-1, respectively. The reaction barrier is negative and our results suggest that both the inner and outer transition states contribute to the corresponding overall reactive flux in the tropospheric temperature range (220 K to 320 K). A two-transition state model has been used to obtain reliable rate coefficients at the high-pressure limit. The pressure-dependent rate coefficient calculations using the SS-QRRK theory have shown that this channel is pressure-dependent. Moreover, our investigation has shown that the ether oxide formed may rapidly react with SO2 at 298 K to form SO3, which can, in turn, react with water to form atmospheric H2SO4. A similar calculation has been conducted for the reaction of HMHP with OH, suggesting that the titled reaction may be a significant sink of HMHP. Therefore, the reaction between CH2OO and HOCH2OOH could be an indirect source for generating atmospheric H2SO4, which is crucial to the formation of clouds, and it might relieve global warming.
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Affiliation(s)
- Ronald Chow
- Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hung Hom, Hong Kong.
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Purushothaman A, Sheeja AA, Janardanan D. Hydroxyl radical scavenging activity of melatonin and its related indolamines. Free Radic Res 2020; 54:373-383. [PMID: 32567401 DOI: 10.1080/10715762.2020.1774575] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The hydroxyl radical (•OH) scavenging activities of Melatonin, an endogenously produced neurohormone and its related indolamines like N-acetyl tryptophan (NAT) and N-acetyl serotonin (NAS) have been investigated using density functional theory. The mechanism involves 4 steps: initial radical addition to position-3 of the indole ring, keto-amine to enol-imine tautomerization, cyclisation, and finally, addition of a second •OH leading to a cyclic end product. Incorporation of an explicit water molecule in tautomerization step leads to a significant reduction in the barrier of this step, so that the subsequent cyclisation step becomes rate-limiting. In agreement with the very high reactivity of •OH, the initial and final addition of •OH to indolamine are found to be barrierless. Radical adduct formed in the initial step was found to be very stable due to the extensive conjugation present in the substrate. Our calculations show that melatonin is the most effective radical scavenger among the three molecules chosen. NAS was found to exhibit antiradical property comparable to that of melatonin. In contrast to the general observation of reduced antioxidant activity of tryptophan, a non-natural derivative of tryptophan used here (NAT) is found to have good radical scavenging activity. This work further implies that non-natural derivatives of indolamines might as well be useful in the detoxification of free radicals as they exhibit almost comparable antioxidant efficiency as that of melatonin.
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Affiliation(s)
- Aiswarya Purushothaman
- Department of Chemistry, School of Physical Sciences, Central University of Kerala, Kasaragod, Kerala, India
| | - Achutha Anil Sheeja
- PG and Research Department of Chemistry, Sree Narayana College Kollam, Kollam, Kerala, India
| | - Deepa Janardanan
- Department of Chemistry, School of Physical Sciences, Central University of Kerala, Kasaragod, Kerala, India
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Manonmani G, Sandhiya L, Senthilkumar K. Mechanism and kinetics of diuron oxidation by hydroxyl radical addition reaction. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:12080-12095. [PMID: 31983006 DOI: 10.1007/s11356-020-07806-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
Diuron is a phenyl urea herbicide used to control weeds in agricultural lands. The degradation of diuron in the atmosphere takes place dominantly via reaction with OH radicals. In this work, the OH addition reaction of diuron has been studied by using density functional theory methods M06-2X, ωB97X-D and MPWB1K with 6-31G(d,p) basis set. The calculated thermochemical parameters show that OH addition reaction occurs favourably at C2 position of diuron. The rate constant is calculated for the favourable initial reaction pathway by using canonical variational transition state theory with small curvature tunnelling (SCT) correction over the temperature range of 200-1000 K. The reaction of initially formed diuron-OH adduct intermediate with O2 leads to the formation of peroxy radical intermediate. The reaction of peroxy radical intermediate with HO2 and NOx (x = 1, 2) radicals is studied in detail. The results obtained from time-dependent density functional theory (TDDFT) calculations show that the intermediates and products formed from oxidation of diuron can be easily photolyzed in the sunlight. This study provides thermodynamical and kinetic data for the atmospheric oxidation of diuron by OH radical addition reaction and demonstrates the atmospheric chemistry of diuron and its derivatives.
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Affiliation(s)
| | - Lakshmanan Sandhiya
- National Institute of Science, Technology, and Development Studies, CSIR, New Delhi, 110012, India
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Manonmani G, Sandhiya L, Senthilkumar K. Mechanism and Kinetics of Diuron Oxidation Initiated by Hydroxyl Radical: Hydrogen and Chlorine Atom Abstraction Reactions. J Phys Chem A 2019; 123:8954-8967. [DOI: 10.1021/acs.jpca.9b04800] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- G. Manonmani
- Department of Physics, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
| | - L. Sandhiya
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - K. Senthilkumar
- Department of Physics, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
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Otukile KP, Kabanda MM. A DFT mechanistic, thermodynamic and kinetic study on the reaction of 1, 3, 5-trihydroxybenzene and 2, 4, 6-trihydroxyacetophenone with •OOH in different media. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2019. [DOI: 10.1142/s0219633619500238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A theoretical investigation on the reactions of 1, 3, 5-trihydroxybenzene (PG) and 2, 4, 6-trihydroxyacetophenone (ACPG) with •OOH has been performed with the aim of elucidating the peroxyl radical scavenging properties of PG and its acylated derivative. The study has considered the hydrogen atom transfer (HAT), the single electron transfer-proton transfer and the sequential proton loss-electron transfer mechanisms and determined the geometric, energetic and electronic properties of the reaction species as well as the kinetic parameters for the HAT mechanism. DFT/M06-2X, DFT/MPW1K and DFT/BHHLYP calculation methods have been utilized in combination with the 6-311++G(3df, 2p) basis set. The DFT methods were benchmarked using the CBS-QB3 method. Thermodynamic parameters such as bond dissociation enthalpy (BDE) and ionization energy suggest that the thermodynamically preferred mechanism is the HAT mechanism. The geometric, electronic and energetic parameters suggest that the preferred site for the abstraction of the free phenolic H atom in ACPG is the ortho position. Spin density and branching ratio values indicate that the most stable and preferable product formed is for the reaction of ACPG [Formula: see text] •OOH at the ortho position. The estimated rate constants obtained indicate that the reaction of ACPG [Formula: see text] •OOH is kinetically preferred to the reaction of PG [Formula: see text] •OOH, which is in agreement with experimental findings.
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Affiliation(s)
- Kgalaletso P. Otukile
- Department of Chemistry, Faculty of Natural and Agriculture Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
- Material Science Innovation and Modelling (MaSIM), Research Focus Area, Faculty of Natural and Agriculture Sciences, North-West University, Private Bag X 2046, Mmabatho 2735, South Africa
| | - Mwadham M. Kabanda
- Department of Chemistry, Faculty of Natural and Agriculture Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
- Material Science Innovation and Modelling (MaSIM), Research Focus Area, Faculty of Natural and Agriculture Sciences, North-West University, Private Bag X 2046, Mmabatho 2735, South Africa
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Otukile KP, Kabanda MM. A DFT mechanistic and kinetic study on the reaction of phloroglucinol with •OH in different media: Hydrogen atom transfer versus oxidation. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2019. [DOI: 10.1142/s0219633619500172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A theoretical study on the reaction of phloroglucinol with •OH has been performed with the aim of elucidating the geometric, energetic and kinetic properties of the reaction as well as identifying the preferred reaction pathway. Three reaction mechanisms have been considered, namely, direct hydrogen atom abstraction, addition–elimination mechanism in the absence and in the presence of a base catalyst and oxidation mechanism in the absence and in the presence of O2. The study has been performed using the DFT/M06[Formula: see text]2X, DFT/BHHLYP and DFT/MPW1K methods in conjunction with either the 6-31++G(d,p) or the 6-311++G(3df,2p) basis set. The energetic parameters are influenced by the type of function utilized and the media in which the calculation is done. The direct hydrogen abstraction mechanism provides the smallest branching ratio with respect to the •OH addition mechanisms. The PG + •OH reaction under atmospheric conditions saturated with O2 would predominantly form tetrahydroxybenzene; the predominant product within the biological system would largely depend on physiological conditions; under pH [Formula: see text] 7 and with oxygen dissolved within the biological system, the preferred product would be tetrahydroxybenzene; however, if the reaction takes place in some part of the biological system where the pH [Formula: see text] 7, the preferred product would be the phenoxyl radical.
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Affiliation(s)
- Kgalaletso P. Otukile
- Department of Chemistry, Faculty of Natural and Agriculture Sciences, North–West University, Private Bag X2046, Mmabatho 2735, South Africa
- Material Science Innovation and Modelling (MaSIM) Research Focus Area, Faculty of Natural and Agriculture Sciences, North–West University, Private Bag X 2046, Mmabatho 2735, South Africa
| | - Mwadham M. Kabanda
- Department of Chemistry, Faculty of Natural and Agriculture Sciences, North–West University, Private Bag X2046, Mmabatho 2735, South Africa
- Material Science Innovation and Modelling (MaSIM) Research Focus Area, Faculty of Natural and Agriculture Sciences, North–West University, Private Bag X 2046, Mmabatho 2735, South Africa
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New catalytic effect of thiourea on the oxidative cyanation of N-aryltetrahydroisoquinolines. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2018.12.050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Ranjbari MA, Tavakol H. Theoretical study of the possible mechanisms for the synthesis of dialkyl thiourea from dithiocarbamate. HETEROATOM CHEMISTRY 2018. [DOI: 10.1002/hc.21421] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Hossein Tavakol
- Department of Chemistry; Isfahan University of Technology; Isfahan Iran
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Otukile KP, Mammino L, Kabanda MM. A Theoretical study on the degradation of 2-mercaptobenzothiazole and 2-mercaptobenzimidazole by OH in vacuo and aqueous media. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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