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

Fluorinated Pharmaceutical and Pesticide Photolysis: Investigating Reactivity and Identifying Fluorinated Products by Combining Computational Chemistry,19F NMR, and Mass Spectrometry

Fluorinated breakdown products from photolysis of pharmaceuticals and pesticides are of environmental concern due to their potential persistence and toxicity. While mass spectrometry workflows have been shown to be useful in identifying products, they fall short for fluorinated products and may miss up to 90% of products. Studies have shown that 19F NMR measurements assist in identifying and quantifying reaction products, but this protocol can be further developed by incorporating computations. Density functional theory was used to compute 19F NMR shifts for parent and product structures in photolysis reactions. Computations predicted NMR spectra of compounds with an R2 of 0.98. Computed shifts for several isolated product structures from LC-HRMS matched the experimental shifts with <0.7 ppm error. Multiple products including products that share the same shift that were not previously reported were identified and quantified using computational shifts, including aliphatic products in the range of -80 to -88 ppm. Thus, photolysis of fluorinated pharmaceuticals and pesticides can result in compounds that are polyfluorinated alkyl substances (PFAS), including aliphatic-CF3 or vinyl-CF2 products derived from heteroaromatic-CF3 groups. C-F bond-breaking enthalpies and electron densities around the fluorine motifs agreed well with the experimentally observed defluorination of CF3 groups. Combining experimental-computational 19F NMR allows quantification of products identified via LC-HRMS without the need for authentic standards. These results have applications for studies of environmental fate and analysis of fluorinated pharmaceuticals and pesticides in development.

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

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.

Experimental and theoretical study on Fe(VI) oxidative degradation of dichlorophen in water: Kinetics and reaction mechanisms

Dichlorophenol (DCP), a commonly used fungicide and insecticide, is widely found in waters and wastewaters. Herein, the degradation of DCP by Ferrate (Fe(VI)) in different matrices was comprehensively investigated. In pure water, a complete removal of DCP was achieved in 300 s at [Fe(VI)]:[DCP] molar ratio of 2:1. The presence of HA (10 mg L^-1) inhibited DCP degradation to a certain extent. A total of twenty degradation products were identified by HPLC/MS analysis. Based on these products, reaction pathways including the cleavage of C-C bridge bond, hydroxylation, and radical coupling were proposed. These reaction mechanisms were further rationalized by theoretical calculations. The analyses of Wiberg bond orders and transition state indicated that C₇-C₈ bond was the most vulnerable site for cleavage, and C₁₂ site was the most likely site for hydroxyl addition. Mulliken atomic spin densities distribution suggested that self-coupling products was easily generated via C-O-C coupling ways. Finally, the feasibility of applying Fe(VI) to degrade DCP (20 μM) in a municipal wastewater effluent and a lake water was evaluated and verified. The findings in this study are of relevance in designing Fe(VI)-based treatment strategy for chlorine-containing persistent pesticides.

Mechanical insight into the formation of H2S from thiophene pyrolysis: The influence of H2O

The thermal utilization of waste rubber is accompanied by the release of sulfur, and the release of H₂S to the gas phase is one of the crucial issues. In this work, density functional theory (DFT) calculations and wave function analysis were employed to explore the possible formation pathways of H₂S and its precursor (·SH radical) during the pyrolysis of thiophene in the presence of H₂O. It indicates that H₂O affects the decomposition of thiophene and the formation of H₂S in two patterns. First, H₂O can participate in the hydrogen transfer process by acting as a catalyst or generating weak hydrogen bonds with thiophene. In this way, the hydrogen transfer reactions are promoted with lower energy barriers, and thus the formation of H₂S is facilitated by H₂O without changing the pyrolysis pathways. Secondly, H₂O can saturate the thiophene ring by addition reactions and alter the generation pathways of H₂S significantly. The energy barriers can be decreased with one or two CC bonds of thiophene being saturated. The completely saturated thiophene results in a greater decline of the overall energy barriers for H₂S formation. H₂O provides the H atom for H₂S in the second pattern. Due to the combination of the two influence patterns, the release of H₂S can be promoted greatly in the presence of H₂O. The present study aims to lay a foundation for the clean thermal utilization of thiophene/rubber and to inspire the advance of desulfurization techniques.