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Viegas LP. A Multiconformational Transition State Theory Approach to OH Tropospheric Degradation of Fluorotelomer Aldehydes. Chemphyschem 2023; 24:e202300259. [PMID: 37326576 DOI: 10.1002/cphc.202300259] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/17/2023]
Abstract
Experimental work on the OH-initiated oxidation reactions of fluorotelomer aldehydes (FTALs) strongly suggests that the respective rate coefficients do not depend on the size of the Cx F2x+1 fluoroalkyl chain. FTALs hence represent a challenging test to our multiconformer transition state theory (MC-TST) protocol based on constrained transition state randomization (CTSR), since the calculated rate coefficients should not show significant variations with increasing values of x ${x}$ . In this work we apply the MC-TST/CTSR protocol to thex = 2 , 3 ${x={\rm 2,3}}$ cases and calculate both rate coefficients at 298.15 K with a value ofk = ( 2 . 4 ± 1 . 4 ) × 10 - 12 ${k=(2.4\pm 1.4)\times {10}^{-12}}$ cm3 molecule-1 s-1 , practically coincident with the recommended experimental value of kexp =( 2 . 8 ± 1 . 4 ) × 10 - 12 ${(2.8\pm 1.4)\times {10}^{-12}}$ cm3 molecule-1 s-1 . We also show that the use of tunneling corrections based on improved semiclassical TST is critical in obtaining Arrhenius-Kooij curves with a correct behavior at lower temperatures.
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Affiliation(s)
- Luís P Viegas
- Coimbra Chemistry Centre-Institute of Molecular Sciences (CQC-IMS), Department of Chemistry, University of Coimbra, 3004-535, Coimbra, Portugal
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2
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Lan X, Dai Y, Jing W, Meng X, Liu F, Wang S, He A, Li N. DFT investigation on the carbonate radical formation in the system containing carbon dioxide and hydroxyl free radical. J Mol Graph Model 2022; 114:108182. [DOI: 10.1016/j.jmgm.2022.108182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/23/2022] [Accepted: 03/24/2022] [Indexed: 10/18/2022]
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3
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Viegas LP. Simplified Protocol for the Calculation of Multiconformer Transition State Theory Rate Constants Applied to Tropospheric OH-Initiated Oxidation Reactions. J Phys Chem A 2021; 125:4499-4512. [PMID: 33902279 DOI: 10.1021/acs.jpca.1c00683] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemical kinetics plays a fundamental role in the understanding and modeling of tropospheric chemical processes, one of the most important being the atmospheric degradation of volatile organic compounds. These potentially harmful molecules are emitted into the troposphere by natural and anthropogenic sources and are chemically removed by undergoing oxidation processes, most frequently initiated by reaction with OH radicals, the atmosphere's "detergent". Obtaining the respective rate constants is therefore of critical importance, with calculations based on transition state theory (TST) often being the preferred choice. However, for molecules with rich conformational variety, a single-conformer method such as lowest-conformer TST is unsuitable while state-of-the-art TST-based methodologies easily become unmanageable. In this Feature Article, the author reviews his own cost-effective protocol for the calculation of bimolecular rate constants of OH-initiated reactions in the high-pressure limit based on multiconformer transition state theory. The protocol, which is easily extendable to other oxidation reactions involving saturated organic molecules, is based on a variety of freeware and open-source software and tested against a series of oxidation reactions of hydrofluoropolyethers, computationally very challenging molecules with potential environmental relevance. The main features, advantages and disadvantages of the protocol are presented, along with an assessment of its predictive utility based on a comparison with experimental rate constants.
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Affiliation(s)
- Luís P Viegas
- Aarhus Institute of Advanced Studies, Aarhus University, Høegh-Guldbergs Gade 6B, Buildings 1630-1632, Aarhus 8000, Denmark
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Viegas LSP, Jensen F. Reactivity of α,ω-Dihydrofluoropolyethers toward OH Predicted by Multiconformer Transition State Theory and the Interacting Quantum Atoms Approach. J Phys Chem A 2020; 124:3460-3470. [PMID: 32242667 DOI: 10.1021/acs.jpca.0c02911] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report rate constants for the tropospheric reaction between the OH radical and α,ω-dihydrofluoropolyethers, which represent a specific class of the hydrofluoropolyethers family with the formula HF2C(OCF2CF2)p(OCF2)qOCF2H. Four cases were considered: p0q2, p0q3, p1q0, and p1q1 (pxqy denoting p = x and q = y) with the calculations performed by a cost-effective protocol developed for bimolecular hydrogen-abstraction reactions. This protocol is based on multiconformer transition state theory and relies on computationally accessible M08-HX/apcseg-2//M08-HX/pcseg-1 calculations. Within the protocol's approximations, the results show that (1) the calculated rate constants are within a factor of five of the experimental results (p1q0 and p1q1) and (2) the chain length and composition have a negligible effect on the rate constants, which is consistent with the experimental work. The interacting quantum atoms energy decomposition scheme is used to analyze the observed trends and extract chemical information related to the imaginary frequencies and barrier heights that are key parameters controlling the reactivity of the reaction. The intramolecular exchange-correlation contributions in the reactants and transition states were found to be the dominating factor.
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Affiliation(s)
- Luı S P Viegas
- Aarhus Institute of Advanced Studies, Aarhus University, Høegh-Guldbergs Gade 6B, Buildings 1630-1632, Aarhus 8000, Denmark
| | - Frank Jensen
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
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Viegas LP. Theoretical determination of the OH-initiated oxidation rate constants of $${\alpha ,\omega }$$-dialkoxyfluoropolyethers. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2436-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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6
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Viegas LP. Multiconformer transition state theory rate constants for the reaction between OH and ‐dimethoxyfluoropolyethers. INT J CHEM KINET 2019. [DOI: 10.1002/kin.21259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Luís P. Viegas
- Aarhus Institute of Advanced StudiesAarhus UniversityAarhus Denmark
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Keshavarz F, Mazarei E. From Kinetics of OH Reaction with Glutamic Acid to Oxidative Damage to Proteins. J Phys Chem A 2019; 123:429-442. [DOI: 10.1021/acs.jpca.8b08664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fatemeh Keshavarz
- Department of Chemistry, College of Science, Shiraz University, Shiraz, Iran
| | - Elham Mazarei
- Department of Chemistry, College of Science, Shiraz University, Shiraz, Iran
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Piekarski DG, Delaunay R, Maclot S, Adoui L, Martín F, Alcamí M, Huber BA, Rousseau P, Domaracka A, Díaz-Tendero S. Unusual hydroxyl migration in the fragmentation of β-alanine dication in the gas phase. Phys Chem Chem Phys 2015; 17:16767-78. [DOI: 10.1039/c5cp01628b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Experimental and theoretical investigations show that hydroxyl migration leads to unexpected fragmentation dynamics of β-alanine dication in the gas phase.
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Affiliation(s)
| | - Rudy Delaunay
- CIMAP (UMR 6252) - CEA
- CNRS
- ENSICAEN
- Unicaen
- 14070 Caen Cedex 5
| | - Sylvain Maclot
- CIMAP (UMR 6252) - CEA
- CNRS
- ENSICAEN
- Unicaen
- 14070 Caen Cedex 5
| | - Lamri Adoui
- CIMAP (UMR 6252) - CEA
- CNRS
- ENSICAEN
- Unicaen
- 14070 Caen Cedex 5
| | - Fernando Martín
- Departamento de Química
- Módulo 13
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
| | - Manuel Alcamí
- Departamento de Química
- Módulo 13
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
| | - Bernd A. Huber
- CIMAP (UMR 6252) - CEA
- CNRS
- ENSICAEN
- Unicaen
- 14070 Caen Cedex 5
| | | | | | - Sergio Díaz-Tendero
- Departamento de Química
- Módulo 13
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
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Signorelli S, Coitiño EL, Borsani O, Monza J. Molecular mechanisms for the reaction between (˙)OH radicals and proline: insights on the role as reactive oxygen species scavenger in plant stress. J Phys Chem B 2013; 118:37-47. [PMID: 24328335 DOI: 10.1021/jp407773u] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The accumulation of proline (Pro) and overproduction of reactive oxygen species (ROS) by plants exposed to stress is well-documented. In vitro assays show that enzyme inactivation by hydroxyl radicals ((•)OH) can be avoided in the presence of Pro, suggesting this amino acid might act as a (•)OH scavenger. Although production of hydroxyproline (Hyp) has been hypothesized in connection with such antioxidant activity, no evidence on the detailed mechanism of scavenging has been reported. To elucidate whether and how Hyp might be produced, we used density functional theory calculations coupled to a polarizable continuum model to explore 27 reaction channels including H-abstraction by (•)OH and (•)OH/H2O addition. The structure and energetics of stable species and transition states for each reaction channel were characterized at the PCM-(U)M06/6-31G(d,p) level in aqueous solution. Evidence is found for a main pathway in which Pro scavenges (•)OH by successive H-abstractions (ΔG(‡,298) = 4.1 and 7.5 kcal mol(-1)) to yield 3,4-Δ-Pro. A companion pathway with low barriers yielding Δ(1)-pyrroline-5-carboxylate (P5C) is also supported, linking with 5-Hyp through hydration. However, this connection remains unlikely in stressed plants because P5C would be efficiently recycled to Pro (contributing to its accumulation) by P5C reductase, hypothesis coined here as the "Pro-Pro cycle".
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Affiliation(s)
- Santiago Signorelli
- Laboratorio de Bioquímica, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República , Av. E. Garzón 780, CP 12900 Montevideo, Uruguay
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Mishra BK, Chakrabartty AK, Deka RC. A computational perspective on the kinetics and thermochemistry of the gas phase reactions of 1, 1-dichlorodimethylether (DCDME) with OH radical at 298 K. Mol Phys 2013. [DOI: 10.1080/00268976.2013.842008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
| | | | - Ramesh Chandra Deka
- Department of Chemical Sciences, Tezpur University, Tezpur Napaam, Assam, India
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Liessmann M, Hansmann B, Blachly PG, Francisco JS, Abel B. Primary Steps in the Reaction of OH Radicals with Amino Acids at Low Temperatures in Laval Nozzle Expansions: Perspectives from Experiment and Theory. J Phys Chem A 2009; 113:7570-5. [DOI: 10.1021/jp9015596] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Matthias Liessmann
- Institut für Physikalische Chemie der Universität Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany, Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, and W.-Ostwald-Institut für Physikalische und Theoretische Chemie der Universität Leipzig, Linné-Strasse 2, D-04103 Leipzig, Germany
| | - Björn Hansmann
- Institut für Physikalische Chemie der Universität Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany, Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, and W.-Ostwald-Institut für Physikalische und Theoretische Chemie der Universität Leipzig, Linné-Strasse 2, D-04103 Leipzig, Germany
| | - Patrick G. Blachly
- Institut für Physikalische Chemie der Universität Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany, Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, and W.-Ostwald-Institut für Physikalische und Theoretische Chemie der Universität Leipzig, Linné-Strasse 2, D-04103 Leipzig, Germany
| | - Joseph S. Francisco
- Institut für Physikalische Chemie der Universität Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany, Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, and W.-Ostwald-Institut für Physikalische und Theoretische Chemie der Universität Leipzig, Linné-Strasse 2, D-04103 Leipzig, Germany
| | - Bernd Abel
- Institut für Physikalische Chemie der Universität Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany, Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, and W.-Ostwald-Institut für Physikalische und Theoretische Chemie der Universität Leipzig, Linné-Strasse 2, D-04103 Leipzig, Germany
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Sun Q, Nelson H, Ly T, Stoltz BM, Julian RR. Side chain chemistry mediates backbone fragmentation in hydrogen deficient peptide radicals. J Proteome Res 2009; 8:958-66. [PMID: 19113886 DOI: 10.1021/pr800592t] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A crown ether based, photolabile radical precursor which forms noncovalent complexes with peptides has been prepared. The peptide/precursor complexes can be electrosprayed, isolated in an ion trap, and then subjected to laser photolysis and collision induced dissociation to generate hydrogen deficient peptide radicals. It is demonstrated that these peptide radicals behave very differently from the hydrogen rich peptide radicals generated by electron capture methods. In fact, it is shown that side chain chemistry dictates both the occurrence and relative abundance of backbone fragments that are observed. Fragmentation at aromatic residues occurs preferentially over most other amino acids. The origin of this selectivity relates to the mechanism by which backbone dissociation is initiated. The first step is abstraction of a beta-hydrogen from the side chain, followed by beta-elimination to yield primarily a-type fragment ions. Calculations reveal that those side chains which can easily lose a beta-hydrogen correlate well with experimentally favored sites for backbone fragmentation. In addition, radical mediated side chain losses from the parent peptide are frequently observed. Eleven amino acids exhibit unique mass losses from side chains which positively identify that particular amino acid as part of the parent peptide. Therefore, side chain losses allow one to unambiguously narrow the possible sequences for a parent peptide, which when combined with predictable backbone fragmentation should lead to greatly increased confidence in peptide identification.
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Affiliation(s)
- Qingyu Sun
- Department of Chemistry, University of California, Riverside, California 92521, USA
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13
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Francisco-Marquez M, Galano A. Role of the Sulfur Atom on the Reactivity of Methionine toward OH Radicals: Comparison with Norleucine. J Phys Chem B 2009; 113:4947-52. [DOI: 10.1021/jp900118f] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Misaela Francisco-Marquez
- Departamento de Química, Universidad Autónoma Metropolitana—Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, C. P. 09340 Iztapalapa, México D. F., Mexico, and Laboratorio de Química Computacional, FES-Zaragoza, Universidad Nacional Autónoma de México (UNAM), C. P. 09230 Iztapalapa, México, D. F., Mexico
| | - Annia Galano
- Departamento de Química, Universidad Autónoma Metropolitana—Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, C. P. 09340 Iztapalapa, México D. F., Mexico, and Laboratorio de Química Computacional, FES-Zaragoza, Universidad Nacional Autónoma de México (UNAM), C. P. 09230 Iztapalapa, México, D. F., Mexico
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