Quantum chemistry and TST study of the mechanisms and branching ratios for the reactions of OH with unsaturated aldehydes

Theoretical studies on the aqueous phase and graphene heterogeneous degradation of acrylamide and acrylonitrile by HO, ClO, and BrO radicals

The newly discovered ClO• and BrO• contribute to pollutant degradation in advanced oxidation processes, while acrylamide (AM) and acrylonitrile (ACN) are always the focus of scientists concerned due to their continuous production and highly toxic effects. Moreover, various particles with a graphene-like structure are the companions of AM/ACN in dry/wet sedimentation or aqueous phase existence, which play an important role in heterogeneous oxidation. Thus, this work focuses on the reaction mechanism and environmental effect of AM/ACN with ClO•/BrO•/HO• in the water environment under the influence of graphene (GP). The results show that although the reactivity sequence of AM and ACN takes the order of with HO• > with BrO• > with ClO•, the easiest channel always occurs at the same C-position of the two reactants. The reaction rate constants (k) of AM with three radicals are 2 times larger than that with ACN, and amide groups have a better ability to activate CC bonds than cyanide groups. The existence of GP can accelerate the target reaction, and the k increased by 9-13 orders of magnitude. The toxicity assessment results show that the toxic effect of most products is lower than that of parent compounds, but the environmental risk of products from ClO•/BrO•-adducts is higher than those from HO•-adducts. The oxidative degradation process based on ClO• and BrO• deserves special attention, and the catalytic effect of GP and its derivatives on the oxidation process is non-negligible.

Exploring the Multitarget Activity of Wedelolactone against Alzheimer's Disease: Insights from In Silico Study

In this study, Wedelolactone's multitarget activity against Alzheimer's disease was examined using density functional theory and molecular docking techniques. At physiological pH, the pK _a and molar fractions have been estimated. The most likely relative rate constants of two radical scavenger mechanisms are formal hydrogen transfer in a lipid environment and single-electron transfer in a water solvent. Compared to Trolox (k _overall = 8.96 × 10⁴ M^-1 s^-1), Wedelolactone (k _overall = 4.26 × 10⁹ M^-1 s^-1) is more efficient in scavenging the HOO^• radical in an aqueous environment. The chelation capacity of metals was investigated by examining the complexation of the Cu(II) ion at various coordination positions and calculating the complexation kinetic constants. Furthermore, molecular docking simulations showed that the known forms of Wedelolactone at physiological pH effectively inhibited the AChE and BChE enzymes by comparing their activity to that of tacrine (control). Wedelolactone is a promising drug candidate for Alzheimer's disease therapy in light of these findings.

Theoretical Study of Radical-Molecule Reactions with Negative Activation Energies in Combustion: Hydroxyl Radical Addition to Alkenes

Many of the radical-molecule reactions are nonelementary reactions with negative activation energies, which usually proceed through two steps. They exist extensively in the atmospheric chemistry and hydrocarbon fuel combustion, so they are extensively studied both theoretically and experimentally. At the same time, various models, such as a two transition state model, a steady-state model, an equilibrium-state model, and a direct elementary dynamics model are proposed to get the kinetic parameters for the overall reaction. In this paper, a conversion temperature T _C1 is defined as the temperature at which the standard molar Gibbs free energy change of the formation of the reaction complex is equal to zero, and it is found that when T ≫ T _C1, the direct elementary dynamics model with an inclusion of the tunneling correction of the second step reaction is applicable to calculate the overall reaction rate constants for this kind of reaction system. The reaction class of hydroxyl radical addition to alkenes is chosen as the objects of this study, five reactions are chosen as the representative for the reaction class, and their single-point energies are calculated using the method of CCSD(T)/CBS, and it is shown that the highest conversion temperature for the five reactions is 139.89 K, far below the usual initial low-temperature (550 K) oxidation chemistry of hydrocarbon fuels; therefore, the steady-state approximation method is applicable. All geometry optimizations are performed at the BH&HLYP/6-311+G(d,p) level, and the result shows that the geometric parameters in the reaction centers are conserved; hence, the isodesmic reaction method is applicable to this reaction class. To validate the accuracy of this scheme, a comparison of electronic energy difference at the BH&HLYP/6-311+G(d,p) level and the corrected electronic energy difference with the electronic energy difference at the CCSD(T)/CBS level is performed for the five representative reactions, and it is shown that the maximum absolute deviation of electronic energy difference can be reduced from 2.54 kcal·mol^-1 before correction to 0.58 kcal·mol^-1 after correction, indicating that the isodesmic reaction method is applicable for the accurate calculation of the kinetic parameters for large-size molecular systems with a negative activation energy reaction. The overall rate constants for 44 reactions of the reaction class of hydroxyl radical addition to alkenes are calculated using the transition-state theory in combination with the isodesmic correction scheme, and high-pressure limit rate rules for the reaction class are developed. In addition, the thermodynamic parameter is calculated and the results indicate that our dynamics model is applicable for our studied reaction class. A chemical kinetic modeling and sensitivity analysis using the calculated kinetic data is performed for the combustion of ethene, and the results indicate the studied reaction is important for the low-to-medium temperature combustion modeling of ethene.

A Combined Experimental and Theoretical Study on the Gas Phase Reaction of OH Radicals with Ethyl Propyl Ether

The reaction of ethyl propyl ether (EnPE) with OH radicals was studied using proton-transfer-reaction mass spectrum (PTR-MS), and the rate constant was measured at 298 K and atmospheric pressure using the relative rate method: k_exp(OH+EnPE) = (1.13 ± 0.09) × 10^-11 cm³ molecules^-1 s^-1. In addition, a parallel theoretical study was performed using the traditional transition state theory (TST) with a tunnelling effect correction in combination at M05-2X method with two basis sets, 6-311++G(d,p) and aug-cc-pVTZ. According to these calculations, H atom abstraction occurs more favorably from the methylene group adjacent to the -O- bond than from the other groups. The theoretical calculation of the total rate constant of the reaction of EnPE with OH radicals was consistent with the experimental values. The gas-phase products indicated that the major products observed were ethyl formate, ethyl propionate, propionic acid. Combined with the experimental and theoretical results, the possible reaction mechanisms were proposed and discussed. The atmospheric implications of the studied reaction are presented, and the lifetime of EnPE in the presence of OH radicals was evaluated to be approximately 1 day.

Gas-Phase Reactions of Isoprene and Its Major Oxidation Products

Isoprene carries approximately half of the flux of non-methane volatile organic carbon emitted to the atmosphere by the biosphere. Accurate representation of its oxidation rate and products is essential for quantifying its influence on the abundance of the hydroxyl radical (OH), nitrogen oxide free radicals (NO _x), ozone (O₃), and, via the formation of highly oxygenated compounds, aerosol. We present a review of recent laboratory and theoretical studies of the oxidation pathways of isoprene initiated by addition of OH, O₃, the nitrate radical (NO₃), and the chlorine atom. From this review, a recommendation for a nearly complete gas-phase oxidation mechanism of isoprene and its major products is developed. The mechanism is compiled with the aims of providing an accurate representation of the flow of carbon while allowing quantification of the impact of isoprene emissions on HO _x and NO _x free radical concentrations and of the yields of products known to be involved in condensed-phase processes. Finally, a simplified (reduced) mechanism is developed for use in chemical transport models that retains the essential chemistry required to accurately simulate isoprene oxidation under conditions where it occurs in the atmosphere-above forested regions remote from large NO _x emissions.

Theoretical Insights on the Inefficiency of RNA Oxidative Damage under Aerobic Conditions

Oxidative damage to RNA has been linked to change or loss of RNA function and development of many human age-related diseases. However, knowledge on the nature of RNA oxidative damage is relatively limited. In this study, oxidative damage to RNA is investigated under anaerobic and aerobic conditions by exploring the properties and reactions of 5-hydroxyl-2'-uridin-6-yl and its peroxyl diastereoisomers in the RNA strand, respectively. Selective addition of OH to the nucleic base from the 5'-end is studied at the molecular level for the first time, explaining the large number of the 5S-isomer available for further reactions. Our results provide clear evidence that the efficiency of C2'-H2' bond activation in the peroxyl isomers is lower than in the carbon radical species. An exception is observed for the isomer cis-(5S,6R)-A1, whose internucleotidyl H2'-abstraction barrier is far smaller than that in the corresponding C6-yl radical. However, analysis of the equilibrium species distribution reveals that the amount of cis-(5S,6R)-A1 is very small among the peroxyl diastereoisomers, and hence the resulting products from direct strand scission should be a less important component in RNA oxidative damage. The species with maximum distribution is the cis-(5S,6R)-B1 isomer, which is derived from cis-(5S,6R)-A1 and has a moderate intranucleotidyl H2'-abstraction barrier. More importantly, the reaction is mildly exothermic. These results show that the main fraction of the intranucleotidyl H2'-abstraction intermediates can be formed from the cis-(5S,6R)-B1 isomer. The absolute reduction potentials, the hydrogen atom binding energies, and the key structural parameters of the C6-peroxyl species are used to understand the diverse reactivity of the cis-(5S,6R) diastereoisomers toward the C2'-H2' bonds activation. The present study shows that in addition to the selectivity of the OH radical addition, there is a strong correlation between the conformation of the modified uracil base and its reactivity in RNA oxidative damage.

DLPNO-CCSD(T) scaled methods for the accurate treatment of large supramolecular complexes

In this work, we present scaled variants of the DLPNO-CCSD(T) method, dubbed as (LS)DLPNO-CCSD(T) and (NS)DLPNO-CCSD(T), to obtain accurate interaction energies in supramolecular complexes governed by noncovalent interactions. The novel scaled schemes are based on the linear combination of the DLPNO-CCSD(T) correlation energies calculated with the standard (LoosePNO and NormalPNO) and modified (Loose2PNO and Normal2PNO) DLPNO-CCSD(T) accuracy levels. The scaled DLPNO-CCSD(T) variants provide nearly TightPNO accuracy, which is essential for the quantification of weak noncovalent interactions, with a noticeable saving in computational cost. Importantly, the accuracy of the proposed schemes is preserved irrespective of the nature and strength of the supramolecular interaction. The (LS)DLPNO-CCSD(T) and (NS)DLPNO-CCSD(T) protocols have been used to study in depth the role of the CH-π versus π-π interactions in the supramolecular complex formed by the electron-donor truxene-tetrathiafulvalene (truxTTF) and the electron-acceptor hemifullerene (C₃₀ H₁₂ ). (NS)DLPNO-CCSD(T)/CBS calculations clearly reveal the higher stability of staggered (dominated by CH-π interactions) versus bowl-in-bowl (dominated by π-π interactions) arrangements in the truxTTF•C₃₀ H₁₂ heterodimer. Hemifullerene and similar carbon-based buckybowls are therefore expected to self-assemble with donor compounds in a richer way other than the typical concave-convex π-π arrangement found in fullerene-based aggregates. © 2017 Wiley Periodicals, Inc.

Mechanism and kinetics for the reactions of methacrolein and methyl vinyl ketone with HO2 radical

The mechanism and kinetics for the reactions of unsaturated aldehyde and ketone with HO₂ radical were investigated.

A quantum chemical study on ˙Cl-initiated atmospheric degradation of acrylonitrile

Degradation of acrylonitrile (CH₂CHCN) by reaction with atomic chlorine was studied using quantum chemical methods.

Benchmarking the DFT methodology for assessing antioxidant-related properties: quercetin and edaravone as case studies

The overall objective was to identify an accurate computational electronic method to virtually screen phenolic compounds through their antioxidant and free-radical scavenging activity. The impact of a key parameter of the density functional theory (DFT) approach was studied. Performances of the 21 most commonly used exchange-correlation functionals are thus detailed in the evaluation of the main energetic parameters related to the activities of two prototype antioxidants, namely quercetin and edaravone, is reported. These functionals have been chosen among those belonging to three different families of hybrid functionals, namely global, range separated, and double hybrids. Other computational parameters have also been considered, such as basis set and solvent effects. The selected parameters, namely bond dissociation enthalpy (BDE), ionization potential (IP), and proton dissociation enthalpy (PDE) allow a mechanistic evaluation of the antioxidant activities of free radical scavengers. Our results show that all the selected functionals provide a coherent picture of these properties, predicting the same order of BDEs and PDEs. However, with respect to the reference values, the errors found at CBS-Q3 level significantly vary with the functional. Although it is difficult to evidence a global trend from the reported data, it clearly appears that LC-ωPBE, M05-2X, and M06-2X are the most suitable approaches for the considered properties, giving the lowest cumulative mean absolute errors. These methods are therefore suggested for an accurate and fast evaluation of energetic parameters related to an antioxidant activity via free radical scavenging.

Kinetic Reaction Mechanism of Sinapic Acid Scavenging NO2 and OH Radicals: A Theoretical Study

The mechanism and kinetics underlying reactions between the naturally-occurring antioxidant sinapic acid (SA) and the very damaging ·NO2 and ·OH were investigated through the density functional theory (DFT). Two most possible reaction mechanisms were studied: hydrogen atom transfer (HAT) and radical adduct formation (RAF). Different reaction channels of neutral and anionic sinapic acid (SA-) scavenging radicals in both atmosphere and water medium were traced independently, and the thermodynamic and kinetic parameters were calculated. We find the most active site of SA/SA- scavenging ·NO2 and ·OH is the -OH group in benzene ring by HAT mechanism, while the RAF mechanism for SA/SA- scavenging ·NO2 seems thermodynamically unfavorable. In water phase, at 298 K, the total rate constants of SA eliminating ·NO2 and ·OH are 1.30×108 and 9.20×109 M-1 S-1 respectively, indicating that sinapic acid is an efficient scavenger for both ·NO2 and ·OH.

The formation of high-purity isocyanurate through proazaphosphatrane-catalysed isocyanate cyclo-trimerisation: computational insights

Polyurethane foams are widely used materials and control of their physical properties is a significant challenge. Management of cyclo-trimerisation during the polymerisation process is vital when tailoring the mechanical properties of the foam. Proazaphosphatranes are known to efficiently catalyse the cyclo-trimerisation of organic isocyanates, giving high purity isocyanurate with little uretdione by-product. The mechanism of this catalysis was previously unknown, although some zwitterionic intermediates have been identified spectroscopically. We have investigated a nucleophilic-catalysis reaction pathway involving sequential addition of methyl isocyanate to activated zwitterionic intermediates using density functional theory calculations. Evidence for significant transannulation by the proazaphosphatrane nitrogen was found for all intermediates, offering stabilisation of the phosphonium cation. Steric crowding at the proazaphosphatrane nucleophilic phosphorus gives rise to a preference for direct isocyanurate formation rather than via the uretdione, in sharp contrast to the uncatalysed system which has been found to preferentially proceed via the kinetic uretdione product. The investigations suggest the mechanism of proazaphosphatrane catalysed cyclo-oligomerisation does not proceed via the uretdione product, and hence why little of this impurity is observed experimentally.

On the chemical repair of DNA radicals by glutathione: hydrogen vs electron transfer

The chemical repair of radical-damaged DNA by glutathione in aqueous solution has been studied using density functional theory. Two main mechanisms were investigated: the single electron transfer (SET) and the hydrogen transfer (HT). Glutathione was found to repair radical damaged DNA by HT from the thiol group with rate constants that are close to the diffusion-limited regime, which means that the process is fast enough for repairing the damage before replication and therefore for preventing permanent DNA damage. The SET mechanism was found to be of minor importance for the activity of glutathione. In addition while SET can be essential for other compounds when repairing radical cation species, repairing the C'-centered guanosyl radicals via SET is not a viable mechanism, due to the very low electron affinity of these species. The importance of considering pH-related physiological conditions and using complex enough models, including the ribose moiety and the H bonding between base pairs, to study this kind of systems is discussed.

On the peroxyl scavenging activity of hydroxycinnamic acid derivatives: mechanisms, kinetics, and importance of the acid-base equilibrium

The peroxyl radical scavenging activity of four hydroxycinnamic acid derivatives (HCAD) has been studied in non-polar and aqueous solutions, using the density functional theory. The studied HCAD are: ferulic acid (4-hydroxy-3-methoxycinnamic acid), p-coumaric acid (trans-4-hydroxycinnamic acid), caffeic acid (3,4-dihydroxycinnamic acid), and dihydrocaffeic acid (3-(3,4-dihydroxyphenyl)-2-propionic acid). It was found that the polarity of the environment plays an important role in the relative efficiency of these compounds as peroxyl scavengers. It was also found that in aqueous solution the pH is a key factor for the overall reactivity of HCAD towards peroxyl radicals, for their relative antioxidant capacity, and for the relative importance of the different mechanisms of reaction. The H transfer from the phenolic OH has been identified as the main mechanism of reaction in non-polar media and in aqueous solution at acid pHs. On the other hand, the single electron transfer mechanism from the phenoxide anion is proposed to be the one contributing the most to the overall peroxyl scavenging activity of HCAD in aqueous solution at physiological pH (7.4). This process is also predicted to be a key factor in the reactivity of these compounds towards a large variety of free radicals.

Detailed Investigation of the OH Radical Quenching by Natural Antioxidant Caffeic Acid Studied by Quantum Mechanical Models

The effectiveness of naturally occurring antioxidant caffeic acid in the inactivation of the very damaging hydroxyl radical has been theoretically investigated by means of hybrid density functional theory. Three possible pathways by which caffeic acid may inactivate free radicals were analyzed: hydrogen abstraction from all available hydrogen atoms, hydroxyl radical addition to all carbon atoms in the molecule, and single electron transfer. The reaction paths were traced independently, and the respective thermal rate constants were calculated using variational transition-state theory including the contribution of tunneling. The more reactive sites in caffeic acid are the C4OH phenolic group and the C4 carbon atom, for the hydrogen abstraction and radical addition, respectively. The single electron transfer process seems to be thermodynamically unfavored, in both polar and nonpolar media. Both hydrogen abstraction and radical addition are very feasible, with a slight preference for the latter, with a rate constant of 7.29 × 10(10) M(-1) s(-1) at 300 K. Tunnel effects are found to be quite unimportant in both cases. Results indicate caffeic acid as a potent natural antioxidant in trapping and scavenging hydroxyl radicals.

Role of allyl group in the hydroxyl and peroxyl radical scavenging activity of S-allylcysteine

S-Allylcysteine (SAC) is the most abundant compound in aged garlic extracts, and its antioxidant properties have been demonstrated. It is known that SAC is able to scavenge different reactive species including hydroxyl radical (•OH), although its potential ability to scavenge peroxyl radical (ROO•) has not been explored. In this work the ability of SAC to scavenge ROO• was evaluated, as well as the role of the allyl group (-S-CH(2)-CH═CH(2)) in its free radical scavenging activity. Two derived compounds of SAC were prepared: S-benzylcysteine (SBC) and S-propylcysteine (SPC). Their abilities to scavenge •OH and ROO• were measured. A computational analysis was performed to elucidate the mechanism by which these compounds scavenge •OH and ROO•. SAC was able to scavenge •OH and ROO•, in a concentration-dependent way. Such activity was significantly ameliorated when the allyl group was replaced by benzyl or propyl groups. It was shown for the first time that SAC is able to scavenge ROO•.