Mechanism of cysteine oxidation by a hydroxyl radical: a theoretical study.

Cysteine oxidation by HO(.) was studied at a high level of ab initio theory in both gas phase and aqueous solution. Potential energy surface scans in the gas phase performed for the model system methanethiol+HO(.) indicate that the reactants can form two intermediate states: a sulfur-oxygen adduct and a hydrogen bound reactant complex. However these states appear to play a minor role in the reaction mechanism as long as they are fast dissociating states. Thus the main reaction channel predicted at the QCISD(T)/6-311+G(2df,2pd) level of theory is the direct hydrogen atom abstraction. The reaction mechanism is not perturbed by solvation which was found to induce only small variations in the Gibbs free energy of different reactant configurations. The larger size reactant system cysteine+HO* was treated by the integrated molecular orbital+molecular orbital (IMOMO) hybrid method mixing the QCISD(T)/6-311+G(2df,2pd) and the UMP2/6-311+G(d,p) levels of theory. The calculated potential energy, enthalpy, and Gibbs free energy barriers are slightly different from those of methanethiol. The method gave a rate constant for cysteine oxidation in aqueous solution, k=2.4 x 10(9) mol(-1) dm(3) s(-1), which is in good agreement with the experimental rate constant. Further analysis showed that the reaction is not very sensitive to hydrogen bonding and electrical polarity of the molecular environment.     

An experimental and theoretical study of the catalytic effect of quaternary ammonium salts on the oxidation of hydrocarbons

The enhancement in the autoxidation of ethylbenzene by molecular oxygen in the presence of quaternary ammonium salts (QAS) was investigated from the experimental and theoretical points of view. The primary effect of the addition of QAS to the reaction medium was an increase in ethylbenzene conversion. Quantum chemical calculations, using B3LYP hybrid functional, revealed a weakening of C-O and O-H bonds of the hydroperoxide. These effects favor the formation of ethylbenzenyl and peroxyl radicals, respectively, both of which are involved in the propagation reaction that leads to the formation of hydroperoxide, the desired final product.     

Mechanism of water oxidation to molecular oxygen with osmocene as photocatalyst: a theoretical study

In the present work, photoinduced O(2) evolution from the [Cp(2)Os-OH](+) complex in aqueous solution has been studied by the DFT, CASSCF, and CASPT2 methods. The CASPT2//CASSCF calculations predict that the S(3) state is initially populated and the subsequent deprotonation of [Cp(2)Os-OH](+) proceeds very easily along the T(1) pathway as a result of the efficient S(3) → T(1) intersystem crossing. It is found that the O-O bond is formed via the acid-base mechanism, which is different from the direct oxo-oxo coupling mechanism suggested in the experimental study. Formation of the O-O bond is the rate-determining step and has an activation energy and activation free energy of 81.3 and 90.4 kcal/mol, respectively. This is consistent with the low quantum yield observed for generating molecular oxygen upon irradiation at 350 nm (~ 82 kcal/mol). The O(2) release from an intermediate complex has to overcome a small barrier on the triplet pathway first and then pass through the triplet-singlet intersection, generating the O(2) molecules in either the lowest singlet or triplet state. The formed (3)O(2) molecule can be converted into the (1)O(2) molecule by the heavy atom effect in the Os complexes, which is probably the reason only the (1)O(2) molecule was detected experimentally.     

Mechanism of the Pechmann reaction: a theoretical study

One of the most widespread synthetic routes to coumarins is the condensation of esters and phenols via the Pechmann reaction. Despite the industrial and technological importance of the reaction, its mechanism is still poorly understood. We have explored several possible reaction paths by DFT calculations at the M05-2X/6-31+G* level. Amphoteric groups and the solvent have a crucial role in the frequent proton-transfer steps of the mechanisms; therefore, we have employed a mixed solvent model, where we combined the implicit PCM model together with an explicit water molecule placed at the actual proton transfer region. The Gibbs free-energy profiles of the possible routes suggest that three parallel channels (featuring water elimination, trans-esterification, and electrophilic attack) operate simultaneously. Enolic routes have prohibitively high activation barriers rendering these paths untenable. The calculated profiles indicate that in each feasible route the first elementary step has the highest activation energy. Reaction intermediates identified on the free-energy profiles can explain several experimental observations.     

Selective organocatalytic oxygenation of hydrocarbons by dioxygen using anthraquinones and N-hydroxyphthalimide

[Reaction: see text] Purely organic and catalytic systems of anthraquinones and N-hydroxyphthalimide efficiently promote oxygenation of hydrocarbons with dioxygen under mild conditions, e.g., fluorene can be converted completely to fluorenone with 85% yield at 80 degrees C.     

Noble metal loaded zeolites for the catalytic oxidation of chlorinated hydrocarbons

Summary A series of metal loaded zeolite catalysts (Pd/H-ZSM-5, Pd/H-BETA, Pt/H-ZSM-5, and Pt/H-BETA) were investigated for their activity and selectivity during oxidation of different chlorinated hydrocarbons, namely dichloromethane and trichloroethylene, at constant gas space velocity (15,000 h^-1) and constant chlorohydrocarbon concentration (1,000 ppm in dry air). It was observed that the two noble metals played a major role in influencing the catalytic performance for complete oxidation of both chlorinated compounds. The acidic properties of the zeolite support in combination with increased oxygen activation owing to the noble metal were responsible for the high chlorocarbon destruction activity exhibited by this type of catalysts.     

A theoretical study of alcohol oxidation by ferrate

The conversion of methanol to formaldehyde mediated by ferrate (FeO(4)2-), monoprotonated ferrate (HFeO4-), and diprotonated ferrate (H2FeO4) is discussed with the hybrid B3LYP density functional theory (DFT) method. Diprotonated ferrate is the best mediator for the activation of the O-H and C-H bonds of methanol via two entrance reaction channels: (1) an addition-elimination mechanism that involves coordination of methanol to diprotonated ferrate; (2) a direct abstraction mechanism that involves H atom abstraction from the O-H or C-H bond of methanol. Within the framework of the polarizable continuum model (PCM), the energetic profiles of these reaction mechanisms in aqueous solution are calculated and investigated. In the addition-elimination mechanism, the O-H and C-H bonds of ligating methanol are cleaved by an oxo or hydroxo ligand, and therefore the way to the formation of formaldehyde is branched into four reaction pathways. The most favorable reaction pathway in the addition-elimination mechanism is initiated by an O-H cleavage via a four-centered transition state that leads to intermediate containing an Fe-O bond, followed by a C-H cleavage via a five-centered transition state to lead to formaldehyde complex. In the direct abstraction mechanism, the oxidation reaction can be initiated by a direct H atom abstraction from either the O-H or C-H bond, and it is branched into three pathways for the formation of formaldehyde. The most favorable reaction pathway in the direct abstraction mechanism is initiated by C-H activation that leads to organometallic intermediate containing an Fe-C bond, followed by a concerted H atom transfer from the OH group of methanol to an oxo ligand of ferrate. The first steps in both mechanisms are all competitive in energy, but due to the significant energetical stability of the organometallic intermediate, the most likely initial reaction in methanol oxidation by ferrate is the direct C-H bond cleavage.     

Selenocysteine versus cysteine reactivity: a theoretical study of their oxidation by hydrogen peroxide

The cysteine and selenocysteine oxidation by H2O2 in vacuo and in aqueous solution was studied using the integrated molecular orbital + molecular orbital (IMOMO) method combining the quadratic configuration method QCISD(T) and the spin projection of second-order perturbation theory PMP2. It is shown that including in the model system of cysteine (selenocysteine) residue up to 20 atoms has significant consequences upon the calculated reaction energy barrier. On the other hand, it is demonstrated that free cysteine and selenocysteine have very similar reaction energy barriers, 77-79 kJ mol(-1) in aqueous solution. It is thus concluded that the high experimental reaction rate constant reported for the oxidation of the selenocysteine residue in the glutathione peroxidase (GPx) active center is due to an important interaction between selenocysteine and its molecular environment. The sensitivity of the calculated energy barrier to the dielectric constant of the molecular environment observed for both cysteine and selenocysteine as well as the catalytic effect of the NH group emphasized in the case of cysteine supports this hypothesis.     

Mechanism of catalytic oxidation of water-lipid substrate

The processes of ethyl oleate water-emulsion oxidation in the presence of copper (II) complexes with α-alanine as a catalyst were investigated spectroscopically. UV spectra of the samples revealed the competitive nature of the formation and decomposition of hydroperoxides in the course of oxidation. Vis spectra of the aqueous phase revealed the constant presence of copper (II) complex with α-alanine and the formation of a similar complex with copper (I) in organic phase. The involvement of these complexes in the reactions of chain nucleation and decay of hydroperoxides is suggested.     

One-electron oxidation and reduction potentials of nitroxide antioxidants: a theoretical study

High-level ab initio calculations have been used to determine the oxidation and reduction potentials of a large number of nitroxides including derivatives of piperidine, pyrrolidine, isoindoline, and azaphenalene, substituted with COOH, NH2, NH3+, OCH3, OH, and NO2 groups, with a view to (a) identifying a low-cost theoretical procedures for the determination of electrode potentials of nitroxides and (b) studying the effect of substituents on these systems. Accurate oxidation and reduction potentials to within 40 mV (3.9 kJ mol(-1)) of experimental values were found using G3(MP2)-RAD//B3-LYP/6-31G(d) gas-phase energies and PCM solvation calculations at the B3-LYP/6-31G(d) level. For larger systems, an ONIOM method in which G3(MP2)-RAD calculations for the core are combined with lower-cost RMP2/6-311+G(3df,2p) calculations for the full system, was able to approximate G3(MP2)-RAD values (to within 1.6 kJ mol(-1)) at a fraction of the computational cost. The overall ring structure has more effect on the electrode potentials than the inclusion of substituents. Azaphenalene derivatives display the lowest oxidation potentials and least negative reduction potentials and are thus the most promising target to function as antioxidants in biological systems. Piperidine and pyrrolidine derivatives have intermediate oxidation potentials but on average pyrrolidine derivatives display more negative reduction potentials. Isoindoline derivatives show higher oxidation potentials and more negative reduction potentials. Within a ring, the substituents have a relatively small effect with electron donating groups such as amino and hydroxy groups stabilizing the oxidized species and electron withdrawing groups such as carboxy groups stabilizing the reduced species, as expected.     

Catalytic oxidation of p-xylene with molecular oxygen in the presence of N-hydroxyphthalimide

Relationships of p-xylene oxidation in the presence of N-hydroxyphthalimide and Co(II) and Mn(II) salts were studied. The activity of the catalytic system strongly depends on the volume of the ligand incorporated in the salt. The synergism in combined use of Co(II) and Mn(II) salts is observed only in the step of p-toluic acid oxidation, whereas replacement of a half of the Co(II) salt by the Mn(II) salt in p-xylene oxidation leads to additive increase in the reaction rate.     

Size-modulated catalytic activity of enzyme-nanoparticle conjugates: a combined kinetic and theoretical study

A series of experiments were performed to systematically analyze the effect of nanoparticle (NP) size on the catalytic behavior of enzyme-NP conjugates, and a shielding model based on diffusion-collision theory was developed to explain the correlation between the size effects and the kinetic responses.     

Mechanism and kinetics of the selective catalytic oxidation of acetone

The kinetics of the heterogeneous catalytic vapor-phase oxidation of acetone on vanadium pentoxide was studied under gradientless conditions at the temperature 413–453 K. The degree of conversion of acetone did not exceed 20%. The main carbon-containing oxidation products were acetic acid and carbon dioxide. Methanol and small quantities of formaldehyde and acetaldehyde were also formed. Possible mechanisms of the reaction are discussed.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 22, No. 2, pp. 252–254, March–April, 1986.     

Mechanism and kinetics of the atmospheric degradation of perfluoropolymethylisopropyl ether by OH radical: a theoretical study

In the present work, the mechanism and kinetics of the reaction of perfluoropolymethylisopropyl ether (PFPMIE) with OH radical are studied. The reaction between PFPMIE and OH radical is initiated through breaking of C–C or C–O bond of PFPMIE. These reactions lead to the formation of COF₂ molecules and alkyl radical. The pathways corresponding to the reaction between PFPMIE and OH radical have been modelled using density functional theory methods M06-2X and MPW1K with 6-31G(d,p) basis set. It is found that the C–C bond breaking reaction is most favourable than the C–O bond breaking reaction. The subsequent reactions of the alkyl radicals, formed from the C–C bond breaking reactions, are studied in detail. The rate constant for the initial oxidation reactions is calculated using canonical variational transition state theory with small curvature tunnelling corrections over the temperature range of 278–350 K. From the calculated reaction, potential energy surface and rate constant, the lifetime and global warming potential of PFPMIE are studied.     

Role of Asp102 in the catalytic relay system of serine proteases: a theoretical study

The role of Asp102 in the catalytic relay system of serine proteases is studied theoretically by calculating the free energy profiles of the single proton-transfer reaction by the Asn102 mutant trypsin and the concerted double proton-transfer reaction (so-called the charge-relay mechanism) of the wild-type trypsin. For each reaction, the reaction free energy profile of the rate-determining step (the tetrahedral intermediate formation step) is calculated by using ab initio QM/MM electronic structure calculations combined with molecular dynamics-free energy perturbation method. In the mutant reaction, the free energy monotonically increases along the reaction path. The rate-determining step of the mutant reaction is the formation of tetrahedral intermediate complex, not the base (His57) abstraction of the proton from Ser195. In contrast to the single proton-transfer reaction of the wild-type, MD simulations of the enzyme-substrate complex show that the catalytically favorable alignment of the relay system (the hydrogen bonding network between the mutant triad, His57, Asn102, and Ser195) is rarely observed even in the presence of a substrate at the active site. In the double proton-transfer reaction, the energy barrier is observed at the proton abstraction step, which corresponds to the rate-determining step of the single proton-transfer reaction of the wild-type. Although both reaction profiles show an increase of the activation barrier by several kcals/mol, these increases have different energetic origins: a large energetic loss of the electrostatic stabilization between His57 and Asn102 in the mutant reaction, while the lack of stabilization by the protein environment in the double proton-transfer reaction. Comparing the present results with the single proton transfer of the wild-type, Asp102 is proven to play two important roles in the catalytic process. One is to stabilize the protonated His57, or ionic intermediate, formed during the acylation, and the other is to fix the configuration around the active site, which is favorable to promote the catalytic process. These two factors are closely related to each other and are indispensable for the efficient catalysis. Also the present calculations suggest the importance of the remote site interaction between His57 and Val213-Ser214 at the catalytic transition state.