Kinetics and mechanism of the β-alanine + OH gas phase reaction: A quantum mechanical approach

Cruz-Torres, Armando; Galano, Annia; Álvarez-Idaboy, J. Raúl

doi:10.1039/b507101a

Cited by 16 publications

(26 citation statements)

References 61 publications

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“…κ( T ) is then calculated ,, by the Eckart formula using both the imaginary frequency of TS 0 and the energetics determined from the respective intrinsic reaction coordinate (IRC) path ending at the PRC and PC end points. This approach has been widely used in atmospheric chemistry studies. ,,,,,,,,− In all our investigations concerning reaction , the calculated point group symmetry associated with the HFPE j and TS i conformers was always C 1 , so in this context we can simplify eq to …”

Section: Theory and Computational Methodsmentioning

confidence: 99%

“…Multidimensional tunneling approximations ,− although more accurate, are complex and extremely time-consuming, requiring energies, gradients, and Hessians along the reaction path. Because of its cost-effectiveness, the Eckart tunneling correction has been and still is widely, pragmatically, and successfully used in the literature, particularly in studies involving atmospheric chemistry reactions. ,,,,,− This is by no means an exhaustive list of references.…”

Section: Theory and Computational Methodsmentioning

confidence: 99%

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Simplified Protocol for the Calculation of Multiconformer Transition State Theory Rate Constants Applied to Tropospheric OH-Initiated Oxidation Reactions

Viegas

2021

J. Phys. Chem. A

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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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Section: Theory and Computational Methodsmentioning

confidence: 99%

Section: Theory and Computational Methodsmentioning

confidence: 99%

Simplified Protocol for the Calculation of Multiconformer Transition State Theory Rate Constants Applied to Tropospheric OH-Initiated Oxidation Reactions

Viegas

2021

J. Phys. Chem. A

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“…The third part of the protocol involves the calculation of the

κ (T)

tunneling correction, obtained through the Eckart method, which is widely used in atmospheric chemistry studies . To calculate this correction, we started by selecting the TS conformer with the lowest ZPE‐corrected energy and calculating the IRC in both reactants and products direction at the M08‐HX/pcseg‐1 level of theory.…”

Section: Methodsmentioning

confidence: 99%

Multiconformer transition state theory rate constants for the reaction between OH and ‐dimethoxyfluoropolyethers

Viegas

2019

Int J of Chemical Kinetics

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In this work, we have calculated rate constants for the tropospheric reaction between the OH radical and α,ω‐dimethoxyfluoropolyethers. The latter are a specific class of the hydrofluoropolyethers family with the general formula CH 3( OCF 2 CF 2)italicp( OCF 2)italicq OCH 3, from which we have selected three case studies: p0q2, p0q3, and p2q0. The calculations were performed by applying a cost‐effective protocol developed for bimolecular hydrogen‐abstraction reactions and based on multiconformer transition state theory relying on computationally accessible M08‐HX/apcseg‐2//M08‐HX/pcseg‐1 calculations. Within the protocol's uncertainties and approximations, the results show that (1) the calculated rate constants have the same order of magnitude and (2) if observed together with previous experimental and theoretical investigations, the chain length (that varies with q and p) is seen to have a small effect on the rate constant, which is consistent with the “no discernible effect” reported in the experimental work.

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“…The latter one was also previously detected. 67 Interestingly, both species have been identified from spectral lines in the interstellar medium 68 and reactions between them can produce glycol aldehyde, acetic acid and methyl formate. 69 On the other hand, the hydroxymethyl cation (m/z = 31 amu) was previously observed only in the single ionisation process after direct side chain bond breaking of serine.…”

mentioning

confidence: 99%

Unusual hydroxyl migration in the fragmentation of β-alanine dication in the gas phase

Piekarski

Delaunay

Maclot

et al. 2015

Phys. Chem. Chem. Phys.

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We present a combined experimental and theoretical study of the fragmentation of doubly positively charged β-alanine molecules in the gas phase. The dissociation of the produced dicationic molecules, induced by low-energy ion collisions, is analysed by coincidence mass spectrometric techniques; the coupling with ab initio molecular dynamics simulations allows rationalisation of the experimental observations. The present strategy gives deeper insights into the chemical mechanisms of multiply charged amino acids in the gas phase. In the case of the β-alanine dication, in addition to the expected Coulomb explosion and hydrogen migration processes, we have found evidence of hydroxyl-group migration, which leads to unusual fragmentation products, such as hydroxymethyl cation, and is necessary to explain some of the observed dominant channels.

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Kinetics and mechanism of the β-alanine + OH gas phase reaction: A quantum mechanical approach

Cited by 16 publications

References 61 publications

Simplified Protocol for the Calculation of Multiconformer Transition State Theory Rate Constants Applied to Tropospheric OH-Initiated Oxidation Reactions

Simplified Protocol for the Calculation of Multiconformer Transition State Theory Rate Constants Applied to Tropospheric OH-Initiated Oxidation Reactions

Multiconformer transition state theory rate constants for the reaction between OH and ‐dimethoxyfluoropolyethers

Unusual hydroxyl migration in the fragmentation of β-alanine dication in the gas phase

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