Mechanism and kinetics of the oxidative damage to ergosterol induced by peroxyl radicals in lipid media: a theoretical quantum chemistry study

In this work, we have studied the mechanisms and kinetics of the initial damage to ergosterol induced by ^?OOH and ^?OOCH₃ peroxyl radicals in a lipid media, using quantum chemistry and computational kinetics methods. The initial damage to ergosterol induced by these radicals occurs predominantly through the hydrogen transfer mechanism (HT) from the allylic position C14 of ergosterol. For the reaction of ergosterol with ^?OOH, the HT‐9 pathway represents ~90.8% of the overall rate constant, while in the case of ^?OOCH₃, the HT‐14 pathway represents more than ~97.2% of the overall rate constant. The calculated overall reaction rates for the initial damage to ergosterol caused by the ^?OOH and ^?OOCH₃ are 2.05 × 10⁶ and 6.26 × 10⁴ M^?1 s^?1, respectively, indicating that the oxidative damage to ergosterol initiated by these radicals, and probably other alkyl‐peroxyl radicals, could be significantly dangerous to their integrity. Taking into account the calculated values of the overall rate coefficients, we can conclude that ergosterol is more susceptible to damage produced by peroxyl radicals than cholesterol and fatty acids. This suggests that fungal cells might be more sensitive to these radicals than animal cells, coinciding with the fact that one of the targets in combating fungi is precisely ergosterol. Finally, theoretical calculations confirm the antioxidant potential of ergosterol and could help explaining the nutraceutical activity of edible and medicinal mushrooms. Copyright © 2015 John Wiley & Sons, Ltd.     

Theoretical studies on the hydrogen abstraction reactions of methyl esters with HO2 radical and the following β‐scission reactions

Unsaturated fatty acid methyl esters are ubiquitous in biodiesel fuels. The C = C double bond greatly affects the combustion characteristics of biodiesel, especially its ignition behavior at low temperatures. In this work, we report detailed theoretical study on the mechanism and kinetics of the hydrogen abstraction reactions of linear unsaturated C6 methyl esters with hydroperoxy radical (HO₂), which play a critical role in the low‐temperature combustion of biodiesel. Reaction profiles are obtained via intrinsic reaction coordinate (IRC) analysis including the formation of reactant complexes and product complexes at the entrance and exit channels, respectively. The potential energy surfaces are explored at the CBS‐QB3 level. The following β‐scission reactions of the forming radicals are also investigated at the same level of theory. The high‐pressure limit rate constants for all the reactions in the temperature range from 500 to 2000 K are calculated via conventional transition‐state theory with quantum tunneling effect and fitted to the modified Arrhenius expression.     

DFT study the interaction of β‐cyclodextrin with benzyl azide and phenyl acetylene in synthesis of 1,2,3‐triazoles

The phenyl acetylene and benzyl azide cycloaddition reaction in water in the presence of β‐cyclodextrin (β‐CD) as a phase transfer catalyst (PTC) can get a better yield in a shorter time. The interaction between β‐CD and phenyl acetylene or benzyl azide plays an important role in this reaction. This paper studies the complexes of β‐CD with phenyl acetylene and benzyl azide using density functional theory (DFT) method. In order to find out the orientations of guests in the cavity of β‐CD, binding energy and deformation energy are investigated, and the calculated results are confirmed by ¹H nuclear magnetic resonance (¹HNMR). The data from single point energy indicate that the inclusion complexes can improve the solubilities of phenyl acetylene and benzyl azide in water. The ¹³C and ¹⁵N spectra show that the most obvious variation concentrates on C₆ and C₈ of phenyl acetylene and N₁₅ of benzyl azide in complexes. Mulliken charge and frontier orbital are employed for revealing the charge distribution. The effect of β‐CD is discussed in terms of the calculated parameters. Copyright © 2014 John Wiley & Sons, Ltd.     

The Raman spectrum of the γ′‐V2O5 polymorph: a combined experimental and DFT study

Structure and vibrational dynamics of γ′‐V₂O₅ synthesized from a pristine γ‐LiV₂O₅ sample via a chemical oxidation route was studied by means of Raman spectroscopy and quantum‐chemical calculations. The calculations based on density functional theory reliably reproduce the experimental structure of the γ′‐V₂O₅ lattice. The calculated Raman spectrum agrees remarkably well with the experimental one. Making use of the agreement, a complete assignment of Raman bands to vibrations of particular structural units is proposed. The comparison of Raman spectra and structural features of α‐V₂O₅ and γ′‐V₂O₅ polymorphs allowed establishing reliable ‘structure–spectrum’ correlations and identifying Raman peaks characteristic for different structural units. Copyright © 2015 John Wiley & Sons, Ltd.     

A comparative study on the gas‐phase and liquid‐phase thermal isomerization reaction of α‐pinene

In this paper, a method of preparation of ocimene is investigated, which is obtained from isomerization reaction of α‐pinene. Two kinds of experimental apparatus are established for the investigation of the thermal isomerization reaction of α‐pinene. The behavior of thermal isomerization reaction of α‐pinene is respectively discussed in the gas phase and in the liquid phase. Under gas phase conditions, the conversion of α‐pinene is 80% and the selectivity of ocimene is 30%–33%. Under liquid phase conditions, the conversion of α‐pinene is 60% and the selectivity of ocimene is 50%–54%. According to the kinetic‐molecular theory of ideal gases, two kinds of reaction models are proposed to visualize the reaction process. In addition, the mechanism and kinetics of thermal isomerization reaction of α‐pinene are respectively discussed. The conclusion is that the gas phase reaction temperature is calculated to be 390–450 °C and the liquid phase reaction temperature is calculated to be 450–550 °C. From a bond dissociation energy point of view, results support the hypothesis that the reaction involves biradical intermediates. Copyright © 2012 John Wiley & Sons, Ltd.     

β‐Elimination of an aziridine to an allylic amine: a mechanistic study

The base‐induced rearrangement of aziridines has been examined using a combination of calculations and experiment. The calculations show that the substituent on nitrogen is a critical feature that greatly affects the favorability of both α‐deprotonation, and β‐elimination to form an allylic amine. Experiments were carried out to determine whether E2‐like rearrangement to the allylic amine with lithium diisopropyl amide (LDA) is possible. N‐tosyl aziridines were found to deprotonate on the tosyl group, preventing further reaction. A variety of N‐benzenesulfonyl aziridines having both α‐ and β‐protons decomposed when treated with LDA in either tetrahydrofuran or hexamethylphosphoramide. However, when α‐protons were not present, allylic amine was formed, presumably via β‐elimination. Copyright © 2011 John Wiley & Sons, Ltd.     

How glucosylation triggers physical–chemical properties of curcumin: an experimental and theoretical study

In the present study, we investigate the structures of glucosylated curcumin derivatives with DFT at B3LYP/6‐31G* level. A conformational analysis is performed in order to determine the conformational minimum (GS) and rotational transition state (TS) of curcumin derivatives and then their electronic features are evaluated. HOMO and LUMO frontier orbitals and maps of electron density potential (MEPs) are plotted and compared. In order to correlate their predicted spectroscopic properties with IR, UV–vis and NMR experimental data we extended the theoretical study on electronic properties to different solvents (H₂O, MeOH, ACN, DMSO). The main finding is that the curcuminic core maintains the same geometrical and electronic structures in all compounds miming the metal coordination capability showed by curcumin. Therefore, we may confirm that the presence of glucose does not affect the electronic properties of the derivatives. Copyright © 2010 John Wiley & Sons, Ltd.     

Acid catalyzed intramolecular attack of β‐phenylthioureido group on amide function. Parallel formation of thiodihydrouracil and 4‐iminothiodihydrouracil. Different pathways in the Edman degradation reaction in the formation of six‐ versus five‐membered cyclic intermediates

Contrary to the cleavage of α‐phenylthioureido peptides 1 proceeding through intermediate 2‐anilinothiazolinone 2 , the b‐analog cis‐2‐(3‐phenylthioureido)cyclopentane‐carboxamide 5 forms transiently 4‐imino‐2‐thioxopyrimidine 6 . Monitoring amide cyclization and hydrolysis of iminopyrimidine 6 in acid by UV showed that an equilibrium between 5 and 6 was reached followed by slower conversion of both compounds into 2‐oxo‐4‐thioxopyrimidine 7 . Both processes were characterized by isosbestic points, the first due to parallel conversion of 5 into 6 and 7 (or 6 into 5 and 7 ) at a constant ratio while the second identical for both reactants – to conversion of equilibrated 5 and 6 into 7 . The special isosbestic points allowed the determination of the individual constants of Scheme 2. Further confirmation was obtained from NMR product analysis and following the cyclization of amide 5 in DMSO:DCl. Product 2‐oxo‐4‐ thioxopyrimidine 7 hydrolyzed reversibly to thioureido acid 8 . The cyclization rate of 8 allowed the participation of 6‐oxothiazine 10 formed by sulfur attack to be excluded. The absence of sulfur attack in the six‐membered case is explained by the longer C? S bond bringing about greater bond angle strain at the tetrahedral ring atoms due to the geometrical characteristics of five‐ and six‐membered rings with planar segments. The cyclizations of amide 5 to iminopyrimidine 6 and to thiodihydrouracil 7 are first order in [H⁺], while the reactions of protonated imine 6 H⁺ are zero order to amide and ?1 to thiodihydrouracil. The reaction orders can be reconciled by assuming a rate determining proton transfer from the tetrahedral intermediate in amide cyclization. Copyright © 2007 John Wiley & Sons, Ltd.     

Mechanistic study on Mo(CO)6‐catalyzed intramolecular [2 + 2] or [2 + 2 + 1] cycloaddition reaction of 5‐allenyl‐1‐ynes

By means of density functional theory, the Mo(CO)₆‐catalyzed intramolecular [2 + 2] or [2 + 2 + 1] cycloaddition reaction of 5‐allenyl‐1‐ynes was investigated. All the intermediates and transition states were optimized completely at B3LYP/6‐311++G(d,p) level (LANL2DZ(f) for Mo). Calculations indicate that the complexation of 5‐allenyl‐1‐ynes with Mo(CO)₆ occurred preferentially at the triple bond to give the complex M1 and then the complexation with the distal double bond of the allenes generates the complex M5 . In this reaction, Mo(CO)₆‐catalyzed intramolecular [2 + 2] cycloaddition is more favorable than [2 + 2 + 1] cycloaddition. The reaction pathway Mo(CO)₆ + R → M5 → T7 → M12 → M13 → T11 → M18 → P4 is the most favorable one, and the most dominant product predicted theoretically is P4 . The solvation effect is remarkable, and it decreases the reaction energy barriers. Copyright © 2011 John Wiley & Sons, Ltd.     

Kinetics and thermochemistry of the unusual [2π + 2σ + 2σ]‐cycloaddition of quadricyclane with some dienophiles

Kinetic parameters of the unusual [2π + 2σ + 2σ]‐cycloaddition reactions of quadricyclane ( 1 ) with tetracyanoethylene ( 2 ), 4‐phenyl‐1,2,4‐triazoline‐3,5‐dione ( 3 ), N‐phenylmaleimide ( 4 ), and diethyl azodicarboxylate ( 5 ) are determined experimentally. Additionally, the enthalpies of 1  +  2 reaction in 1,4‐dioxane solution (?236.6 ± 1.0 kJ mol^?1) and 1  +  3 reaction in toluene (?255.0 ± 2.8 kJ mol^?1) are determined calorimetrically and shown to be the largest in absolute magnitude among all known cycloaddition reactions involving these dienophiles. Solvent effect on the rate of 1 + 3 reaction in 11 solvents is studied and found to be moderate and similar to that of the conventional Diels‐Alder and ene reactions. The difference in the reaction rate constants of 1 with different dienophiles can be up to 9 orders of magnitude and is mainly caused by the difference in activation enthalpies. This difference is not correlated with the standard enthalpies of reactions and is likely the result of high sensitivity of the [2π + 2σ + 2σ] reaction rates to the energy of donor‐acceptor interactions between the reactants.     

Theoretical investigation on H abstraction reaction mechanisms and rate constants of Isoflurane with the OH radical

The mechanism of H abstraction reactions for Isoflurane with the OH radical was investigated using density functional theory and G3(MP2) duel theory methods. The geometrical structures of all the species were fully optimised at B3LYP/6-311++G** level of theory. Thermochemistry data were obtained by utilising the high accurate model chemistry method G3(MP2) combined with the standard statistical thermodynamic calculations. Gibbs free energies were used for the reaction channels analysis. All the reaction channels were confirmed throughout the intrinsic reaction coordinate analysis. The results show that two channels were obtained, which correspond to P(1) and P(2) with the respective activation barriers of 63.03 and 54.82 kJ/mol. The rate constants for the two channels over a wide temperature range of 298.15–2000 K were predicted and the calculated data are in agreement with the experimental one. The results show that P(2) is the dominant reaction channel under 800 K and above 800 K, it can be found that P(1) will be more preferable reaction channel.     

Kinetic study of electrochemically induced Michael reactions of o‐benzoquinones with 2‐acetylcyclohexanone and 2‐acetylcyclopentanone

The reaction of electrochemically generated o‐benzoquinones ( 2a‐f ) as Michael acceptors with 2‐acetylcyclohexanone (ACH) and 2‐acetylcyclopentanone (ACP), as nucleophiles has been studied in various pHs using cyclic voltammetry. The results indicate that the participation of o‐benzoquinones ( 2a‐f ) in the Michael reaction with acetylcyclohexanone (ACH) to form the corresponding catechol derivatives ( 4a‐f ). Based on an EC mechanism, the homogeneous rate constants were estimated by comparing the experimental cyclic voltammetric responses with the digital simulated results. Copyright © 2007 John Wiley & Sons, Ltd.     

Theoretical kinetic study on the decomposition of 1,5‐diaminotetrazole

1,5‐Daminotetrazole (DAT) is of much interest because of the practical significance and the diversity of characteristics. The study on the decomposition pathway and the kinetics of DAT has been performed based on the quantum chemistry theory. The minimum energy path (MEP) calculation has shown that NH₂N₃ and NH₂CN are the initially detected products of DAT. And the structures of reactant, products and transition state were optimized with MP2 methods using 6‐311G** basis sets, and the energies were refined using CCSD(T)/6‐311G** levels of theory. The calculated rate constants were obtained using the conventional transition‐state theory (TST) and the canonical variational transition‐state theory (CVT) methods. The calculation results indicated that the energy barrier of decomposition reaction is 47.98 kcal mol^?1 and the variational effect is small. In addition, the rate constants and the Arrhenius experience formula of DAT decomposition have been obtained between 200 and 2500 K temperature regions. The fitted three‐parameter expressions calculated using the TST and CVT methods are (TST) and (CVT). This work may provide the theoretical support for further experimental synthesis and testing. Copyright © 2015 John Wiley & Sons, Ltd.     

A Combined Experimental and Theoretical Study on the Formation of Ag Filaments on β‐Ag2MoO4 Induced by Electron Irradiation

A combined experimental and theoretical study is presented to understand the novel observed nucleation and early evolution of Ag filaments on β‐Ag₂MoO₄ crystals, driven by an accelerated electron beam from an electronic microscope under high vacuum. The growth process, chemical composition, and the element distribution in these filaments are analyzed in depth at the nanoscale level using field‐emission scanning electron microscopy (FE‐SEM) and transmission electron microscopy (TEM) with energy‐dispersive spectroscopy (EDS) characterization. To complement experimental results, chemical stability, structural and electronic aspects have been studied systematically using first‐principles electronic structure theory within a quantum theory of atoms in molecules (QTAIM) framework. The Ag nucleation and formation on β‐Ag₂MoO₄ are a result of structural and electronic changes of the AgO₄ tetrahedral cluster as a constituent building block of β‐Ag₂MoO₄, consistent with Ag metallic formation. The formation of Ag filament transforms the β‐Ag₂MoO₄ semiconductor from n‐ to p‐type concomitant with the appearance of Ag defects.     

A DFT study on the (2 + 3) cycloaddition reactions of 2‐nitropropene‐1 with Z‐C,N‐diarylnitrones

B3LYP/6‐31G* calculations for competing (2 + 3)‐cycloaddition pathways for 2‐nitropropene‐1 (1) to Z‐C, N‐diarylnitrones ( 2a – e ) suggest a concerted reaction mechanism. However, the results point to the strongly asymmetric nature of transition complexes. Increasing polarity of the reaction environment and presence of electron‐donating substituents in the nitrone phenyl rings contribute to the higher asymmetry of these structures. Copyright © 2009 John Wiley & Sons, Ltd.     

A computational study of the thermolysis of β‐hydroxy ketones in gas phase and in m‐xylene solution

Theoretical calculations at the M05‐2X/6‐31+G(d) level of theory have been carried out in order to explore the nature of the mechanism of the thermal decomposition reactions of the β‐hydroxy ketones, 4‐hydroxy‐2‐butanone, 4‐hydroxy‐2‐pentanone, and 4‐hydroxy‐2‐methyl‐2‐pentanone in gas phase and in m‐xylene solution. The mechanism proposed is a one‐step process proceeding through a six‐membered cyclic transition state. A reasonable agreement between experimental and calculated activation parameters and rate constants has been obtained, the tertiary : secondary : primary alcohol rate constant ratio being calculated, at T = 503.15 K, as 5.9:4.7:1.0 in m‐xylene solution and 44.1:5.0:1.0 in the gas phase, compared with the experimental values, 3.7:1.3:1.0 and 13.5:3.2:1.0, respectively. The progress of the thermal decomposition reactions of β‐hydroxy ketones has been followed by means of the Wiberg bond indices. The lengthening of the O₁–C₂ bond with the initial migration of the H₆ atom from O₅ to O₁ can be seen as the driving force for the studied reactions. Calculated synchronicity values indicate that the mechanisms correspond to concerted and highly synchronous processes. The transition states are “advanced”, nearer to the products than to the reactants. Copyright © 2012 John Wiley & Sons, Ltd.     

Experimental study on the reaction pathway of α‐haloacetophenones with nucleophiles: direct substitution or carbonyl addition?

The reaction of PhCOCH₂Cl with OH^– gave the expected α‐substituted alcohol (PhCOCH₂OH) in addition to three dimer products. To clarify whether the substitution product is formed by direct S_N2 or via carbonyl addition, the reaction of PhCOCH₂Cl and OMe^– was examined. The reaction gave two products, PhCOCH₂OH as the major product after acid hydrolysis and PhCOCH₂OMe as the minor product. An electron‐withdrawing substituent on the phenyl ring enhanced the overall reactivity and gave more alcohol than ether. It was concluded that the alcohol was formed via carbonyl addition‐epoxidation route, whereas the ether was formed by the direct substitution route. Copyright © 2012 John Wiley & Sons, Ltd.     

A computational study of stereospecifity in the thermal elimination reaction of menthyl benzoate in the gas phase

This paper reports a theoretical study, at the B3LYP/6–31 + G(d,p) and M05‐2X/6–31G + (d,p) levels, on the thermal decomposition of menthyl benzoate (2‐isopropyl‐5‐methylcyclohexyl benzoate). It undergoes a unimolecular first‐order elimination to give 3‐menthene (1‐isopropyl‐4‐methylcyclohexene), 2‐menthene (3‐isopropyl‐6‐methylcyclohexene), and benzoic acid. We studied two possible mechanisms trying to explain the formation of 2‐ and 3‐menthene, via six‐membered or four‐membered cyclic transition states. Rate constants were calculated at two temperatures, 587.1 and 598.6 K, and they agree well with the experimentally determined values. We verify that 3‐menthene is the product mainly formed at both temperatures. The progress of the reactions has been followed by means of the Wiberg bond indices. Intrinsic reaction coordinate (IRC) calculations have been carried out to verify that the localized transition state structures connect with the reactants and products and also to verify that the parent compound, menthyl benzoate, is taking the cis‐configuration needed in the reaction. Copyright © 2009 John Wiley & Sons, Ltd.     

Catalysis by hydrogen chloride in the gas‐phase elimination kinetics of 2‐phenyl‐2‐propanol and 3‐methyl‐1‐buten‐3‐ol

A homogeneous, molecular, gas‐phase elimination kinetics of 2‐phenyl‐2‐propanol and 3‐methyl‐1‐ buten‐3‐ol catalyzed by hydrogen chloride in the temperature range 325–386 °C and pressure range 34–149 torr are described. The rate coefficients are given by the following Arrhenius equations: for 2‐phenyl‐2‐propanol log k₁ (s^?1) = (11.01 ± 0.31) ? (109.5 ± 2.8) kJ mol^?1 (2.303 RT)^?1 and for 3‐methyl‐1‐buten‐3‐ol log k₁ (s^?1) = (11.50 ± 0.18) ? (116.5 ± 1.4) kJ mol^?1 (2.303 RT)^?1. Electron delocalization of the CH₂?CH and C₆H₅ appears to be an important effect in the rate enhancement of acid catalyzed tertiary alcohols in the gas phase. A concerted six‐member cyclic transition state type of mechanism appears to be, as described before, a rational interpretation for the dehydration process of these substrates. Copyright © 2007 John Wiley & Sons, Ltd.     

Ab Initio Simulation of Ta2O5: A High Symmetry Ground State Phase with Application to Interface Calculation

It is reported that the recently predicted triclinic γ‐phase ground state Ta₂O₅ by Yang and Kawazoe can be assigned a much more symmetric I4₁/amd space group, and is isomorphic to P‐Nb₂O₅. Interestingly, the well‐known high temperature α‐phase Ta₂O₅ also has the I4₁/amd symmetry, but is unstable at zero temperature according to our phonon dispersion calculation. A thorough energy comparison of the β_AL, δ, λ, Β, L_SR, β_R, Pm, Cmmm, γ, and α phases of Ta₂O₅ is carried out using density functional theory under the generalized gradient approximation (GGA). The GGA‐1/2 method is applied in calculating the electronic structure of various phases, where the tetragonal γ‐phase demonstrates a 4.24 eV indirect band gap, close to experimental value. The high symmetry tetragonal phase together with computationally efficient GGA‐1/2 method greatly facilitates the ab initio simulation of Ta₂O₅‐based devices. As an example, the Ohmic contact nature between metal Ta and Ta₂O₅ by calculating an interface model of b.c.c. Ta and tetragonal γ‐Ta₂O₅, using GGA‐1/2 has been explicitly shown.