Accurate Benchmark Calculation of the Reaction Barrier Height for Hydrogen Abstraction by the Hydroperoxyl Radical from Methane. Implications for CnH2n+2 where n = 2 → 4

New insight into molecular mechanism of P450-Catalyzed metabolism of emerging contaminants and its consequence for human health: A case study of preservative methylparaben

Hydroxylated metabolites in the living body are considered as a potential biomarker of exposure to emerging contaminations (ECs) and breast cancer, but their formation mechanism has not received enough attention. Besides, the adverse impacts of metabolites during the metabolic transformation of ECs largely remain unknown. In this study, we employed a density functional calculation combing with in-vitro incubation of human liver microsomes to explore the bio-transformation of preservative methylparaben (MPB) in human bodies. Our results showed that hydroxylated metabolites of MPB (OH-MPB) were observed experimentally, while a formation mechanism was revealed at the molecular level. That is, hydroxylated metabolite was exclusively formed via the hydrogen abstraction from the phenolic hydroxyl group of MPB followed by the OH-rebound pathway, rather than the direct hydroxylation on the benzene ring. The increasing of hydroxyl groups on ECs could improve the metabolisms. This was confirmed in the metabolism of ECs without hydroxyl group and with multiple-hydroxyl groups, respectively. Furthermore, toxicity assessments show that compared to parent MPB, the hydroxylated metabolites have increased negative impacts on the gastrointestinal system and liver. A semiquinone product exhibits potential damage in the cardiovascular system and epoxides are toxic to the blood and gastrointestinal system. The findings deepen our insight into the biotransformation of parabens in human health, especially by providing health warnings about the potential impacts caused by semiquinone and epoxides.

Barrier heights, reaction energies and bond dissociation energies for RH + HO2 reactions with coupled-cluster theory, density functional theory and diffusion quantum Monte Carlo methods

Hydrogen abstraction reactions by the HO₂ radical from hydrocarbon molecules are an important class of reactions in the autoignition of hydrocarbon fuels. Performance of DLPNO-CC and DFT methods using three hybrids and four double hybrids as well as FN-DMC with the single-Slater-Jastrow trial wavefunction on barrier heights and reaction energies of RH + HO₂ reactions as well as bond dissociation energies of the involved X-H molecules is evaluated by comparison with the highly accurate CCSD(T)-F12b/CBS results in this study. Our results show that the DLPNO-CCSD(T)-F12 method can achieve highly accurate barrier heights, reaction energies and X-H bond energies for RH + HO₂ reactions at a relatively low computational cost, and it is applicable to the H-abstraction reactions of larger molecules. Among all DFAs, MN15 and the employed double hybrids can achieve accurate barrier heights and reaction energies with MADs of less than or around 2 kJ mol^-1, but their error on X-H bond energies is more pronounced. Only DSD-BLYP and DSD-PBEB95 can provide X-H bond energies with MADs less than 4 kJ mol^-1. Considering dispersion correction in DFT calculations does not improve these barrier heights and reaction energies. The error of FN-DMC on barrier heights and reaction energies is slightly larger than that of MN15 and those of double hybrids, but it can achieve results within chemical accuracy for these reactions and the X-H bond energies.

On-The-Fly Kinetics of the Hydrogen Abstraction by Hydroperoxyl Radical: An Application of the Reaction Class Transition State Theory

A Reaction Class Transition State Theory (RC-TST) is applied to calculate thermal rate constants for hydrogen abstraction by OOH radical from alkanes in the temperature range of 300–2500 K. The rate constants for the reference reaction C₂H₆ + ∙OOH → ∙C₂H₅ + H₂O₂, is obtained with the Canonical Variational Transition State Theory (CVT) augmented with the Small Curvature Tunneling (SCT) correction. The necessary parameters were obtained from M06-2X/aug-cc-pVTZ data for a training set of 24 reactions. Depending on the approximation employed, only the reaction energy or no additional parameters are needed to predict the RC-TST rates for other class representatives. Although each of the reactions can in principle be investigated at higher levels of theory, the approach provides a nearly equally reliable rate constant at a fraction of the cost needed for larger and higher level calculations. The systematic error is smaller than 50% in comparison with high level computations. Satisfactory agreement with literature data, augmented by the lack of necessity of tedious and time consuming transition state calculations, facilitated the seamless application of the proposed methodology to the Automated Reaction Mechanism Generators (ARMGs) programs.

Insight of UV-vis spectra and atmospheric implication for the reaction of ˙OH radical towards glyphosate herbicide and its hydrates

The rate constant of the reactions of ˙OH radicals with glyphosate (GPS) and its hydrates (GPS(H₂O)_n=1–3) were evaluated using the dual method M06-2X/6-311++G(df,p)//6-31+G(df,p) over the temperature range of 200–400 K. The results served to estimate the atmospheric lifetime along with the photochemical ozone creation potential (POCP). The calculations yielded an atmospheric lifetime of 2.34 hours and a POCP of 24.7 for GPS. Upon addition of water molecules, there is an increase of lifetime and decrease of POCP for water monomer and water dimer. The POCP for water trimer is slightly above the gaseous GPS. However, the POCPs of GPS and its hydrates are comparable to that of alkanes. The GPS and its hydrates were found to be a potential reservoir of CO₂. The acidification potential (AP) of GPS was found to be 0.189 and decreases upon addition of water molecules. This shows negligible contribution to rain acidification as the AP is less than that of SO₂. The UV-vis spectra were attained using the M06-L/6-311++G(3df,3pd) method and cover the range 160–260 nm which fits well with experiment.

The rate constant of the reactions of ˙OH radical with glyphosate (GPS) and its hydrates (GPS(H₂O)_n=1–3) were evaluated using the dual method M06-2X/6-311++G(df,p)//6-31+G(df,p) over the temperature range of 200–400 K.

Kinetic Analysis for Reaction of Cyclopentadiene with Hydroperoxyl Radical under Low- and Medium-Temperature Combustion

The kinetic data of cyclopentadiene C₅H₆ oxidation reactions are significant for the construction of aromatics oxidation mechanism because cyclopentadiene C₅H₆ has been proved to be an important intermediate in the aromatics combustion. Kinetics for the elementary reactions on the potential energy surface (PES) relevant for the C₅H₆ + HO₂ reaction are studied in this work. Stationary points on the PES are calculated by employing the CCSD(T)/cc-pVTZ//B3LYP/6-311G(d,p) level of theory. High-pressure limit and pressure-dependent rate constants for elementary reactions on this PES are calculated using conventional transition state theory (TST), variational transition-state theory (VTST) and Rice-Ramsberger-Kassel-Marcus/master equation (RRKM/ME) theory. In this work, the reaction channels for the C₅H₆ + HO₂ reaction_, which include H-abstraction channels from C₅H₆ by HO₂ to form the C₅H₅ + H₂O₂ and the addition channels through well-skipping pathways to form the bimolecular products C₅H₇ + O₂ or C₅H₆O + OH, or through C₅H₇O₂ stabilization and its unimolecular decomposition to form the bimolecular products C₅H₇ + O₂ or C₅H₆O + OH, namely sequential pathways, are studied. Also, the consuming reaction channels for the compounds C₅H₆O and C₅H₇ in the addition products are studied. The dominant reaction channels for these reactions are unraveled through comparing the energy barriers and rate constants of all elementary reactions and it is found: (1) HO₂ addition to cyclopentadiene C₅H₆ is more important than direct H-abstraction. (2) in the HO₂ addition channels, the well-skipping pathways and sequential pathways are competing and the well-skipping pathways will be favor in the higher pressures and the sequential pathways will be favor in the higher temperature. (3) The major consumption reaction channel for the five-member-ring compound C₅H₆O is the reaction channel to form C₄H₆ + CO and the major consumption reaction channel for the five-member-ring compound C₅H₇ is the reaction channel to form C₃H₅ + C₂H₂. High-pressure limit rate constants and pressure-dependent rate constants for elementary reactions on the PES are calculated, which will be useful in modeling the oxidation of aromatic compounds at low- and medium-temperatures.

Detailed kinetic model for hexyl sulfide pyrolysis and its desulfurization by supercritical water

The automated reaction mechanism generator is used to model the decomposition of hexyl sulfide with and without supercritical water.

Computational Insight into the Activation Mechanism of Carcinogenic N'-Nitrosonornicotine (NNN) Catalyzed by Cytochrome P450

Tobacco-specific N'-nitrosonornicotine (NNN), a genotoxic nitrosamine classified as Group 1 carcinogen, is also present in atmospheric particulate matter and has even been detected as a new disinfection byproduct in wastewaters. NNN generally requires metabolic activation by cytochrome P450 enzymes to exert its genotoxicity, but the respective biotransformation pathways have not been described in detail. In this work, we performed density functional theory (DFT) calculations to unravel possible NNN activation pathways including α-hydroxylation, β-hydroxylation, pyridine N-oxidation, and norcotinine formation. The results reveal an initial rate-determining H_α-atom abstraction step for α-hydroxylation, followed by an unexpected kinetic competition between denitrosation and OH rebound, leading to ( iso-)myosmine as a detoxified product and α-hydroxyNNNs as the precursor of carcinogenic diazohydroxides, respectively. Further detoxification routes are given by β-hydroxylation with relative high reaction barrier and N-oxidation with comparable barrier to the toxifying α-hydroxylation. Moreover, we show for the first time how norcotinine can be generated as a minor NNN metabolite that is formed from iso-myosmine through a unique porphyrin-assisted H atom 1,2-transfer mechanism. These results demonstrate that the carcinogenic potential of NNN is subject to a kinetic competition between activating and deactivating metabolic routes, and identify respective biomarkers to inform about the individual risk associated with NNN exposure.

Barriometry – an enhanced database of accurate barrier heights for gas-phase reactions

The kinetics of many reactions are critically dependent upon the barrier heights for which accurate determination can be difficult. More than 100 accurate barriers are obtained with the high-level W3X-L composite procedure.

Photo-induced β-elimination of 9-fluorenylmethanol leading to dibenzofulvene

An effective photo-induced β-elimination of an alcohol leading to a vinyl compound is introduced for the first time. 9-Fluorenylmethanol was irradiated in a solution using a Xe lamp and was efficiently converted to dibenzofulvene (DBF) (9-methylenefluorene) in the absence of base which is necessary in the corresponding ground-state reaction.

Automatic mechanism generation for pyrolysis of di-tert-butyl sulfide

The automated Reaction Mechanism Generator (RMG), using rate parameters derived from ab initio CCSD(T) calculations, is used to build reaction networks for the thermal decomposition of di-tert-butyl sulfide.

A kinetic and thermochemical database for organic sulfur and oxygen compounds

Potential energy surfaces and reaction kinetics were calculated for reactions involving sulfur and oxygen, which are potentially relevant in combustion and desulfurization chemistry.

Assessment of theoretical methods for the study of hydrogen abstraction kinetics of global warming gas species during their degradation and byproduct formation (IUPAC Technical Report)

Global climate change is a major concern as it leads to an increase in the average temperature of the earth’s atmosphere. The existence and persistence of some gaseous species in the atmosphere contribute to global warming. Experimental techniques are used to study the kinetics and degradation of global warming gases. However, quantum mechanical methods are also useful for the kinetic and radiative forcing study of global warming species and can precede experimental investigations. Research has also been targeted to develop more adapted procedures using ab initio and density functional theory (DFT) methods. This report provides a global perspective, in simplified manner, of the theoretical studies of the degradation of gas species in the atmosphere with an emphasis on the hydrogen abstraction kinetics of global warming gas species during their degradation and byproduct formation. En route, the results obtained from these studies are analysed and compared with experimental data where available. Our analyses indicate that the theoretical predictions are in agreement with experimental findings but the predicted parameters are dependent on the method being used. Theoretical methods are used to predict the thermodynamic parameters of reactions, and, with relevance to this report, the global warming potential (GWP) index can also be calculated. This report can be useful for future investigations involving global warming gaseous species while providing suggestions on how computations can fill in data gaps when experimental data are unavailable.

New pathways for formation of acids and carbonyl products in low-temperature oxidation: the Korcek decomposition of γ-ketohydroperoxides

We present new reaction pathways relevant to low-temperature oxidation in gaseous and condensed phases. The new pathways originate from γ-ketohydroperoxides (KHP), which are well-known products in low-temperature oxidation and are assumed to react only via homolytic O-O dissociation in existing kinetic models. Our ab initio calculations identify new exothermic reactions of KHP forming a cyclic peroxide isomer, which decomposes via novel concerted reactions into carbonyl and carboxylic acid products. Geometries and frequencies of all stationary points are obtained using the M06-2X/MG3S DFT model chemistry, and energies are refined using RCCSD(T)-F12a/cc-pVTZ-F12 single-point calculations. Thermal rate coefficients are computed using variational transition-state theory (VTST) calculations with multidimensional tunneling contributions based on small-curvature tunneling (SCT). These are combined with multistructural partition functions (Q(MS-T)) to obtain direct dynamics multipath (MP-VTST/SCT) gas-phase rate coefficients. For comparison with liquid-phase measurements, solvent effects are included using continuum dielectric solvation models. The predicted rate coefficients are found to be in excellent agreement with experiment when due consideration is made for acid-catalyzed isomerization. This work provides theoretical confirmation of the 30-year-old hypothesis of Korcek and co-workers that KHPs are precursors to carboxylic acid formation, resolving an open problem in the kinetics of liquid-phase autoxidation. The significance of the new pathways in atmospheric chemistry, low-temperature combustion, and oxidation of biological lipids are discussed.

Barrier heights for H-atom abstraction by H*O2 from n-butanol--a simple yet exacting test for model chemistries?

The barrier heights involved in the abstraction of a hydrogen atom from n-butanol by the hydroperoxyl radical have been computed with both compound (CBS-QB3, CBS-APNO, G3) and coupled cluster methods. In particular, the benchmark computations CCSD(T)/cc-pVTZ//MP2/6-311G(d,p) were used to determine that the barrier heights increase in the order alpha < gamma < beta < delta < OH. Two prereaction hydrogen-bonded complexes are formed, one of which connects the TGt conformer of n-butanol to the alpha and beta transition states and the other connects to the gamma and OH channels from the TGg conformer. Four postreaction complexes were also found which link the transition states to the products, hydrogen peroxide + C(4)H(9)O radical. Abstraction from the terminal delta carbon atom does not involve either a pre or postreaction complex. A number of DFT functionals-B3LYP, BMK, MPWB1K, BB1K, MPW1K, and M05-2X-were tested to see whether the correct ranking could be obtained with computationally less expensive methods. Only the later functional predicts the correct order but requires a basis set of 6-311++G(df,pd) to achieve this. However, the absolute values obtained do not agree that well with the benchmarks; the composite G3 method predicts the correct order and comes closest (< or = 2 kJ, mol (-1)) in absolute numerical terms for H-abstraction from carbon.