Degradation mechanism of tris(2-chloroethyl) phosphate (TCEP) as an emerging contaminant in advanced oxidation processes: A DFT modelling approach

Xia, Hui; Zhang, Wenjing; Yang, Yuesuo; Zhang, Wei; Purchase, Diane; Zhao, Chuanqi; Song, Xiaoming; Wang, Yuanyuan

doi:10.1016/j.chemosphere.2021.129674

Cited by 15 publications

(7 citation statements)

References 82 publications

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“…Reactions described above for DNAN oxidation comprised all possible modes of attack by •OH mentioned in literature including (1) hydrogen abstraction (Buxton et al, 1988; Xia et al, 2021), (2) hydroxylation or addition of •OH (Buxton et al, 1988), particularly by addition to an aromatic ring since it constitutes a negative energetic barrier (Gligorovski et al, 2015), and (3) •OH radical attack resulting in bond cleavage (Xia et al, 2021). Addition of radicals has been reported to be the least energy‐demanding step compared to the cleavage of C–C bonds (Gligorovski et al, 2015).…”

Section: Resultsmentioning

confidence: 99%

“…The high electron density around the DNAN nitro groups and the high negative Mulliken charges increase the probability that -NO2 in DNAN will undergo denitrification with •OH, which likely proceeds, via bond cleavage between C-N atoms (Rayaroth et al, 2022;Zeman et al, 2009). The products of denitrification of DNAN were projected to be 4-nitroanisole and 2-nitroanisole when -NO2 from 2 and (1) hydrogen abstraction (Buxton et al, 1988;Xia et al, 2021),…”

Section: Moranchel Et Al 2019)mentioning

confidence: 99%

“…(2) hydroxylation or addition of •OH (Buxton et al, 1988), particularly by addition to an aromatic ring since it constitutes a negative energetic barrier (Gligorovski et al, 2015), and (3) •OH radical attack resulting in bond cleavage (Xia et al, 2021). Addition of radicals has been reported to be the least energy-demanding step compared to the cleavage of C-C bonds (Gligorovski et al, 2015).…”

Section: Moranchel Et Al 2019)mentioning

confidence: 99%

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2,4‐dinitroanisole transformation during advanced oxidation with ultraviolet light emitting diodes and hydrogen peroxide

Burdsall

Schober

Stubbs

et al. 2022

Water & Environment J

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This study investigated the kinetics and reaction mechanisms associated with advanced oxidation of 2,4-dinitroanisole (DNAN) with light emitting diodes (LEDs) in the UV/H 2 O 2 process. The pseudo first-order reaction rate constants for DNAN oxidation depended on the H 2 O 2 /DNAN molar ratio and were between 0.017 and 0.026 min À1 .Hydroxyl radical scavenging was strongly implicated by the experimental results. High mass spectrophotometric chromatograms showed the presence of several by-products, including three with ecotoxicity that is greater than that of DNAN. Transformation pathways were analysed using Density Functional Theory (DFT), which helped to predict the presence of experimentally detected DNAN by-products by considering Mulliken charges. This study is the first to elucidate DNAN transformation mechanisms using both experimental studies and computational chemistry.

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Section: Resultsmentioning

confidence: 99%

Section: Moranchel Et Al 2019)mentioning

confidence: 99%

Section: Moranchel Et Al 2019)mentioning

confidence: 99%

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2,4‐dinitroanisole transformation during advanced oxidation with ultraviolet light emitting diodes and hydrogen peroxide

Burdsall

Schober

Stubbs

et al. 2022

Water & Environment J

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“…Previous computational studies have examined nucleic acid phosphodiester bond hydrolysis using different DFT approaches, , including the widely used B3LYP − and M06-2X ,, functionals. Although rigorous testing of the accuracy of DFT methods compared to CCSD(T)/CBS energetic data has been performed for the hydrolysis of dimethyl phosphate in the absence of a metal, it is not clear whether the same conclusions will hold for the reaction catalyzed by a single-metal-dependent nuclease.…”

Section: Resultsmentioning

confidence: 99%

“…Importantly, our data supports the use of standard functionals (M06-2X and B3LYP-D3) for these reactions, which have been widely used in literature to study other enzymatic mechanisms. 40,97,98 Regardless, the model used so far is minimal and larger cluster models must be considered to determine the impact of additional amino acids on the reaction mechanism and associated barriers.…”

Section: Different Basis Sets and Density Functional Combinations Yie...mentioning

confidence: 99%

The Impact of DFT Functional, Cluster Model Size, and Implicit Solvation on the Structural Description of Single-Metal-Mediated DNA Phosphodiester Bond Cleavage: The Case Study of APE1

et al. 2022

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Phosphodiester bond hydrolysis in nucleic acids is a ubiquitous reaction that can be facilitated by enzymes called nucleases, which often use metal ions to achieve catalytic function. While a two-metal-mediated pathway has been well established for many enzymes, there is growing support that some enzymes require only one metal for the catalytic step. Using human apurinic/ apyrimidinic endonuclease (APE1) as a prototypical example and cluster models, this study clarifies the impact of DFT functional, cluster model size, and implicit solvation on single-metal-mediated phosphodiester bond cleavage and provides insight into how to efficiently model this chemistry. Initially, a model containing 69 atoms built from a high-resolution X-ray crystal structure is used to explore the reaction pathway mapped by a range of DFT functionals and basis sets, which provides support for the use of standard functionals (M06-2X and B3LYP-D3) to study this reaction. Subsequently, systematically increasing the model size to 185 atoms by including additional amino acids and altering residue truncation points highlights that small models containing only a few amino acids or β carbon truncation points introduce model strains and lead to incorrect metal coordination. Indeed, a model that contains all key residues (general base and acid, residues that stabilize the substrate, and amino acids that maintain the metal coordination) is required for an accurate structural depiction of the one-metal-mediated phosphodiester bond hydrolysis by APE1, which results in 185 atoms. The additional inclusion of the broader enzyme environment through continuum solvation models has negligible effects. The insights gained in the present work can be used to direct future computational studies of other one-metal-dependent nucleases to provide a greater understanding of how nature achieves this difficult chemistry.

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Theoretical insights into the reaction mechanism and kinetics of ampicillin degradation with hydroxyl radical

Aydogdu

Hatipoğlu

2023

J Mol Model

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Degradation mechanism of tris(2-chloroethyl) phosphate (TCEP) as an emerging contaminant in advanced oxidation processes: A DFT modelling approach

Cited by 15 publications

References 82 publications

2,4‐dinitroanisole transformation during advanced oxidation with ultraviolet light emitting diodes and hydrogen peroxide

2,4‐dinitroanisole transformation during advanced oxidation with ultraviolet light emitting diodes and hydrogen peroxide

The Impact of DFT Functional, Cluster Model Size, and Implicit Solvation on the Structural Description of Single-Metal-Mediated DNA Phosphodiester Bond Cleavage: The Case Study of APE1

Theoretical insights into the reaction mechanism and kinetics of ampicillin degradation with hydroxyl radical

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