Reaction of ethylene with hydroxyl radicals: a theoretical study

Ab initio calculations of portions of the C2H5O potential energy surface critical to the title reaction are presented. These calculations are based on QCISD geometries and frequencies and RQCISD(T) energies extrapolated to the complete-basis-set limit. Rate coefficients for the reaction of C2H4 with OH are calculated using this surface and the two transition-state model of Greenwald and co-workers [J. Phys. Chem. A 2005, 109, 6031] for the association of OH with C2H4. The present calculations reproduce most of the experimental data, including the temperature and pressure dependence of the rate coefficients, with only a small (0.4 kcal/mol) adjustment to the energy barrier for direct hydrogen abstraction. We confirm the importance of this channel above 800 K and find that a significant fraction of the total rate coefficient (approximately 10%) is due to the formation of vinyl alcohol above this temperature. Calculations of the vinyl alcohol channel are consistent with the recent observation of this molecule in low-pressure flames [Taatjes, C. A.; Hansen, N.; McIlroy, A.; Miller, J. A.; Senosiain, J. P.; Klippenstein, S. J.; Qi, F.; Sheng, L.; Zhang, Y.; Cool, T. A.; Wang, J.; Westmoreland, P. R.; Law, M. E.; Kasper, T.; Kohse-H?inghaus, K. Science 2005, 308, 1887] and suggest that this reaction should be included in hydrocarbon oxidation mechanisms.     

Interaction between methyl and hydroxyl radicals: a theoretical study

In this paper, we conduct a computational quantum mechanic study of two molecules interaction between methyl (·CH₃) and hydroxyl (·OH) radicals. The molecular exploration has been focused on the possibility of finding non-bonding interactions (formation of complexes by weak-bond interaction among C–O–H atoms) and the potential energy reaction between those two molecules. It shows that the formed complexes presents in slightly lower potential energy than that of the reactants and/or products. The existence of these complexes could proceed to the further interaction, e.g. reaction of the molecules, as those complexes formed a particular configuration.     

Reaction mechanism of deoxyribonucleotidase: a theoretical study

The reaction mechanism of human deoxyribonucleotidase (dN) is studied using high-level quantum-chemical methods. dN catalyzes the dephosphorylation of deoxyribonucleoside monophosphates (dNMPs) to their nucleoside form in human cells. Large quantum models are employed (99 atoms) based on a recent X-ray crystal structure. The calculations support the proposed mechanism in which Asp41 performs a nucleophilic attack on the phosphate to form a phospho-enzyme intermediate. Asp43 acts in the first step as an acid, protonating the leaving nucleoside, and in the second step as a base, deprotonating the lytic water. No pentacoordinated intermediates could be located.     

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.     

Reaction of hydroxyl radicals with azacytosines: a pulse radiolysis and theoretical study

Pulse radiolysis and density functional theory (DFT) calculations at B3LYP/6-31+G(d,p) level have been carried out to probe the reaction of the water-derived hydroxyl radicals (*OH) with 5-azacytosine (5Ac) and 5-azacytidine (5Acyd) at near neutral and basic pH. A low percentage of nitrogen-centered oxidizing radicals, and a high percentage of non-oxidizing carbon-centered radicals were identified based on the reaction of transient intermediates with 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonate), ABTS2-. Theoretical calculations suggests that the N3 atom in 5Ac is the most reactive center as it is the main contributor of HOMO, whereas C5 atom is the prime donor for the HOMO of cytosine (Cyt) where the major addition site is C5. The order of stability of the adduct species were found to be C6-OH_5Ac*>C4-OH_5Ac*>N3-OH_5Ac*>N5-OH_5Ac* both in the gaseous and solution phase (using the PCM model) respectively due to the additions of *OH at C6, C4, N3, and N5 atoms. These additions occur in direct manner, without the intervention of any precursor complex formation. The possibility of a 1,2-hydrogen shift from the C6 to N5 in the nitrogen-centered C6-OH_5Ac* radical is considered in order to account for the experimental observation of the high yield of non-oxidizing radicals, and found that such a conversion requires activation energy of about 32 kcal/mol, and hence this possibility is ruled out. The hydrogen abstraction reactions were assumed to occur from precursor complexes (hydrogen bonded complexes represented as S1, S2, S3, and S4) resulted from the electrostatic interactions of the lone pairs on the N3, N5, and O8 atoms with the incoming *OH radical. It was found that the conversion of these precursor complexes to their respective transition states has ample barrier heights, and it persists even when the effect of solvent is considered. It was also found that the formation of precursor complexes itself is highly endergonic in solution phase. Hence, the abstraction reactions will not occur in the present case. Finally, the time dependent density functional theory (TDDFT) calculations predicted an absorption maximum of 292 nm for the N3-OH_5Ac* adduct, which is close to the experimentally observed spectral maxima at 290 nm. Hence, it is assumed that the addition to the most reactive center N3, which results the N3-OH_5Ac* radical, occurs via a kinetically driven process.     

Scavenging mechanism of curcumin toward the hydroxyl radical: a theoretical study of reactions producing ferulic acid and vanillin

Curcumin is known to be an antioxidant, as it can scavenge free radicals from biological media. A sequence of H-abstraction and addition reactions involving up to eight OH radicals and curcumin or its degradation products leading to the formation of two other antioxidants, namely, ferulic acid and vanillin, was studied. Single electron transfer from curcumin to an OH radical was also studied. All relevant extrema on the potential energy surfaces were located by optimizing geometries of the reactant and product complexes, as well as those of the transition states, at the BHandHLYP/6-31G(d,p) level of density functional theory in the gas phase. Single-point energy calculations were also performed in the gas phase at the BHandHLYP/aug-cc-pVDZ and B3LYP/aug-cc-pVDZ levels of theory. Solvent effects in aqueous media were treated by performing single-point energy calculations at all of the above-mentioned levels of theory employing the polarizable continuum model and the geometries optimized at the BHandHLYP/6-31G(d,p) level in the gas phase. A few reaction steps were also studied by geometry optimization in aqueous media, and the thus-obtained Gibbs free energy barriers were similar to those obtained by corresponding single-point energy calculations. Our calculations show that the hydrogen atom of the OH group attached to the phenol moiety of curcumin would be most efficiently abstracted by an OH radical, in agreement with experimental observations. Further, our study shows that OH addition would be most favored at the C10 site of the heptadiene chain. It was found that curcumin can serve as an effective antioxidant.     

Formation of cross-linked adducts between guanine and thymine mediated by hydroxyl radical and one-electron oxidation: a theoretical study

The role of local geometric and stereo-electronic effects in tuning the preference for different cross-linked adducts between thymine and purinic bases has been analyzed by a computational approach rooted in density functional theory. Our study points out that G--T and T--G tandem lesions are produced according to the same mechanism as A--T and T--A intrastrand adducts, and in both cases purine--T adducts are preferred rather than the opposite sequences. Moreover, use of conceptual DFT tools allows the rationalization of the preferential occurrence of G--T and T--G tandem lesions in place of their A--T and T--A counterparts.     

IR spectral fingerprints of carbonyl groups in graphite oxide: a theoretical study

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Reaction mechanism studies on isoquinoline with hydroxyl radical in aqueous solutions

The reaction mechanism between isoquinoline and ·OH radical in aqueous dilute solutions under different conditions was studied by pulse radiolysis. The main characteristic peaks in these transient absorption spectra were attributed and the growth-decay trends of several transient species were investigated. Under neutral or alkaline conditions, the reaction of ·OH radical and isoquinoline produces OH-adducts with respective rate constants of 3.4 × 10⁹ and 6.6 × 10⁹ mol⁻¹ · dm³ · s⁻¹ while under acidic conditions, the isoquinoline was firstly protonated and then ·OH added to the benzene ring and produced protonated isoquinoline OH-adducts with a rate constant of 3.9 × 10⁹ mol⁻¹ · dm³ · s⁻¹. With a better understanding on radiolysis of isoquinoline, this study is of help for its degradation and for environmental protection. __________ Translated from Journal of Fudan University (Natural Science), 2006, 45(6): 774–778 [8BD1;81EA: 590D;65E6;5B66;62A5;(自然科学版)]     

Reaction mechanism of the CCN radical with nitric oxide

To investigate the possibility of the carbyne radical CCN in removal of nitric oxide, a detailed computational study is performed at the Gaussian-3//B3LYP/6-31G(d) level on the CCN + NO reaction by constructing the singlet and triplet electronic state [C(2)N(2)O] potential energy surfaces (PESs). The barrierless formation of the chain-like isomers NCCNO (singlet at -106.5, triplet cis at -48.2 and triplet trans at -47.6 kcal/mol) is the most favorable entrance attack on both singlet and triplet PESs. Subsequently, the singlet NCCNO takes an O-transfer to form the branched intermediate singlet NCC(O)N (-85.6), which can lead to the fragments CN + NCO (-51.2) via the intermediate singlet NCOCN (-120.3). The simpler evolution of the triplet NCCNO is the direct N-O rupture to form the weakly bound complex triplet NCCN...O (-56.2) before the final fragmentation to NCCN + (3)O (-53.5). However, the lower lying products (3)NCN + CO (-105.6) and (3)CNN + CO (-74.6) are kinetically much less competitive. All the involved transition states for generation of CN + NCO and NCCN + (3)O lie much lower than the reactants. Thus, the novel reaction CCN + NO can proceed effectively even at low temperatures and is expected to play a role in both combustion and interstellar processes. Significant differences are found on the singlet PES between the CCN + NO and CH + NO reaction mechanisms.     

Reaction of vinyl radical with oxygen: a matrix isolation infrared spectroscopic and theoretical study

The reaction of vinyl radical with molecular oxygen in solid argon has been studied using matrix isolation infrared absorption spectroscopy. The vinyl radical was produced through high frequency discharge of ethylene. The vinyl radical reacted with oxygen spontaneously on annealing to form the vinylperoxy radical C(2)H(3)OO with the O-O bond in a trans position relative to the C-C bond, which is characterized by O-O stretching and out-of-plane CH(2) bending vibrations at 1140.7 and 875.5 cm(-1). The vinylperoxy radical underwent visible photon-induced dissociation to the CH(2)OH(CO) complex or CH(2)OH+CO, which has never been considered in previous studies. The CH(2)OH(CO) product was predicted to be more thermodynamically accessible than the previously reported major HCO+H(2)CO channel, and is most likely produced by hydrogen atom transfer from the first-formed H(2)CO-HCO pair in solid argon.     

A 1:1 complex between a hydroxyl radical and ozone

A hydrogen bonded complex between a hydroxyl radical and ozone has been found in argon matrices at 9 K. The shift of the OH stretch (-12.6 cm-1) indicates that this complex is somewhat weaker than the OH-CO complex (-21.8 cm-1, D0相似文献   

Nitrous oxide as a 1,3-dipole: a theoretical study of its cycloaddition mechanism

The 1,3-dipolar cycloadditions of nitrous oxide and substituted alkynes have been studied at the B3LYP/6-31G(d,p) level. The reaction is controlled by LUMO (dipole)--HOMO (dipolarofile) and involves aromatic transition structures. The shape of the potential energy surface and the regioselectivity are not affected by the polarity of the solvents, except in the case of N2O + HC triple bond CSiH3. Different reactivity criteria including FMO coefficients product C, local softness differences Delta, magnetic susceptibility anisotropy chi(anis), and nucleus-independent chemical shifts NICS were used to predict the regioselectivity in all studied cases; the C, Delta criteria turn out to give the best results among them. The aromaticity of the transition structure is not a factor in determining the regiochemistry of the cycloaddtition reactions.     

Hemibonding between hydroxyl radical and water

The ultraviolet absorption peak commonly used to identify OH radical in liquid water is mainly due to a charge-transfer-from-solvent transition that is prominent when OH is hemibonded, rather than more stable hydrogen bonded, to H(2)O. This work computationally characterizes the hemibonding interaction and the extent of the geometrical region over which it is significant. Hemibonding is found to be associated with an enlarged energy separation between the two lowest-lying electronic states, which are otherwise always quite close to one another. The lower state, wherein the hemibonding occurs, retains an attractive interaction energy between OH and H(2)O that can be as much as one-half as strong as the optimum hydrogen-bonding interaction, while the enlarged separation between the states is mainly due to the upper state becoming repulsive over most of the hemibonding region. Hemibonding also leads to a considerable drop in the energy and a considerable increase in the oscillator strength of the characteristic charge-transfer transition. The region of significant hemibonding is found to lie within a moderate range of O-O azimuthal angles and over quite wide ranges of O-O separation distances and hydroxyl OH tilt angles. In particular, significant hemibonding interactions can extend down to surprisingly short O-O distances, where the oscillator strength for the charge-transfer-from-solvent transition becomes very large.     

Reaction mechanism of ferulic acid scavenging OH and NO2 radicals: a theoretical study

Structural Chemistry - As a derivative of cinnamic acid, ferulic acid (FA) is a bio-active ingredient of many foods and is considered to be a good natural antioxidant. A theoretical study on the...     

Reaction mechanism of HCN+ + C2H4: a theoretical study

The complex doublet potential energy surface for the ion-molecule reaction of HCN(+) with C(2)H(4) is investigated at the B3LYP/6-311G(d,p) and CCSD(T)/6-311++G(3df,2pd) (single-point) levels. The initial association between HCN(+) and C(2)H(4) forms three energy-rich addition intermediates, 1 (HCNCH(2)CH(2)(+)), 2 (HC-cNCH(2)CH(2)(+)), and 3 (N-cCHCH(2)CH(2)(+)), which are predicted to undergo subsequent isomerization and decomposition steps. A total of nine kinds of dissociation products, including P(1) (HCN + C(2)H(4)(+)), P(2) (HCNCHCH(2)(+) + H), P(3) (NCCH(2) + CH(3)(+)), P(4) (CN + C(2)H(5)(+)), P(5) (NCCHCH(2)(+) + H(2)), P(6) (HNCCHCH(2)(+) + H), P(7) (c-CHCCH(2)N(+) + H(2)), P(8) (c-NHCCH(2)C(+) + H(2)), and P(9) (HNCCCH(+) + H(2) + H), are obtained. Among the nine products, P(1) is the most abundant product. P(2) is the second feasible product but is much less competitive than P(1). P(3), P(4), P(5), and P(6) may have the lowest yields observed. Other products, P(7), P(8), and P(9), may become feasible at high temperature. Because the intermediates and transition states involved in the most favorable pathway all lie below the reactant, the HCN(+) + C(2)H(4) reaction is expected to be rapid, which is confirmed by experiment. The present calculation results may provide a useful guide for understanding the mechanism of HCN(+) toward other unsaturated hydrocarbons.     

The gas-phase reaction between O3 and HO radical: a theoretical study.

We report a theoretical study on the reaction of ozone with hydroxyl radical, which is important in the chemistry of the atmosphere and in particular participates in stratospheric ozone destruction. The reaction is a complex process that involves, in the first stage, a pre-reactive hydrogen-bonded complex (C1), which is formed previous to two transition states (TS1 and TS2) involving the addition of the hydroxyl radical to ozone, and leads to the formation of HO4 polyoxide radical before the release of the products HO2 and O2. The reaction is computed to be exothermic by 42.72 kcal mol(-1), which compares quite well with the experimental estimate, and the energy barriers of TS1 and TS2 with respect to C1 are computed to be 1.80 and 2.26 kcal mol(-1) at 0 K. A kinetic study based on the variational transition state theory (VTST) predicts a rate constant, at 298 K, of 7.37 x 10(-14) cm3 molecule(-1) s(-1), compared to the experimentally recommended value of 7.25 x 10(-14) cm3 molecule(-1) s(-1).     

The IR spectra of carbonyl oxide and dioxirane: a theoretical investigation at a correlated level

Harmonic frequencies, IR intensities and ¹⁸O isotopic shifts for carbonyl oxide and dioxirane have been calculated at the MP2/6-31G level of theory. The results are discussed with respect to an experimental distinction between the two peroxide isomers by low-temperature IR spectroscopy.     

Chiral recognition in cyclic alpha-hydroxy carbonyl compounds: a theoretical study

A theoretical study (DFT and MP2) of the self-association of homochiral (RR or SS) and heterochiral (RS or SR) dimers of three series of cyclic alpha-hydroxy-carbonyl derivatives has been carried out. The solvation effect on the parent derivative dimers has been explored, showing nonsignificant changes in the configurations preferred but altering in some cases the homo/heterochiral preference of the dimers. The results in the gas phase of the systems with different substituents show a preference for the heterochiral dimers. The energetic results have been analyzed with the NBO and AIM methodologies. Optical rotatory power calculations of the monomers and homochiral dimers show large variations of this parameter depending on the substituents and the complexation.     

Theoretical study of mechanism and kinetics for the addition of hydroxyl radical to phenol

The reaction mechanism and kinetics for the addition of hydroxyl radical(OH) to phenol have been investigated using the hybrid density functional(B3LYP) method with the 6-311++G(2dp,2df) basis set and the complete basis set(CBS) method using APNO basis sets,respectively.The equilibrium geometries,energies,and thermodynamics properties of all the stationary points along the addition reaction pathway are calculated.The rate constants and the branching ratios of each channel are evaluated using classical transition state theory(TST) in the temperature range of 210 to 360 K,to simulate temperatures in all parts of the troposphere.The ortho addition pathway is dominant and accounts for 99.8% 96.7% of the overall adduct products from 210 to 360 K.The calculated rate constants are in good agreement with existing experimental values.The addition reaction is irreversible.