Hydroperoxyl-alkyl-peroxyl radicals (O2QOOH) are an important radical intermediate in low-temperature combustion, and its concerted elimination reaction to produce Q″OOH and HO2 is an important reaction class in low-temperature combustion modeling of hydrocarbons. In this paper, isodesmic reaction method is used for the accurate calculation of rate constants for a representative set of 45 reactions in the class. All geometries of the reactants, the transition states and the products are optimized under the B3LYP/6-311 + G(d, p) level. It is shown that the geometries at the reaction center of the transition states in this reaction class are conserved, and hence, the minus of any two reactions for the formation of transition states can be considered as an isodesmic reaction. One reaction is called reference reaction and as is usually done in reaction class-transition state theory, the reaction in the class with the minimum size is chosen as the reference reaction, and other reactions are called target reactions. According to isodesmic reaction theory, it can be derived that the energy difference between the high-level ab initio result and the low-level result for the reference reaction can be used to correct the low-level energy barriers for the target reactions. In this study, B3LYP/6-311 + G(d, p) method is used as the low-level ab initio method and the composite Gaussian-4 (G4) method is used as the high-level ab initio method. CCSD(T)/cc-PVTZ method is chosen as the benchmarking method to validate the accuracy of G4 method through a comparison of the energy barriers for three selected small molecular reactions calculated by G4 method with the results by CCSD(T)/cc-PVTZ method, and it is found that the difference of the energy barriers by these two methods are between 0.35 and 2.11 kJ/mol, indicating that the accuracy of G4 method is close to that of the benchmarking method. Meanwhile, ten representative target reactions in this class from the O2QOOH to Q″OOH + HO2 are selected to validate the correction scheme through a comparison of the energy barriers before and after correction with the energy barriers by G4 method. It is found that the deviations of the energy barriers calculated by direct DFT method are between 16.58 and 24.95 kJ/mol, and after correction, the deviations of the energy barriers are reduced to −3.28 to 5.09 kJ/mol, indicating that the results of the energy barriers corrected by the isodesmic reaction method are close to that of the G4 method. Finally, using this correction scheme, the energy barriers, reaction enthalpies and rate constants of all reactions are calculated and kinetic parameters in the form of (A, n, E) are provided for this important elimination reaction class of hydroperoxyl-alkyl-peroxyl radicals (O2QOOH), which is useful for the simulation of low-temperature combustion for hydrocarbon.

Hydroperoxyl-alkyl-peroxyl radicals (O2QOOH) are an important radical intermediate in low-temperature combustion, and its concerted elimination reaction to produce Q″OOH and HO2 is an important reaction class in low-temperature combustion modeling of hydrocarbons. In this paper, isodesmic reaction method is used for the accurate calculation of rate constants for a representative set of 45 reactions in the class. All geometries of the reactants, the transition states and the products are optimized under the B3LYP/6-311 + G(d, p) level. It is shown that the geometries at the reaction center of the transition states in this reaction class are conserved, and hence, the minus of any two reactions for the formation of transition states can be considered as an isodesmic reaction. One reaction is called reference reaction and as is usually done in reaction class-transition state theory, the reaction in the class with the minimum size is chosen as the reference reaction, and other reactions are called target reactions. According to isodesmic reaction theory, it can be derived that the energy difference between the high-level ab initio result and the low-level result for the reference reaction can be used to correct the low-level energy barriers for the target reactions. In this study, B3LYP/6-311 + G(d, p) method is used as the low-level ab initio method and the composite Gaussian-4 (G4) method is used as the high-level ab initio method. CCSD(T)/cc-PVTZ method is chosen as the benchmarking method to validate the accuracy of G4 method through a comparison of the energy barriers for three selected small molecular reactions calculated by G4 method with the results by CCSD(T)/cc-PVTZ method, and it is found that the difference of the energy barriers by these two methods are between 0.35 and 2.11 kJ/mol, indicating that the accuracy of G4 method is close to that of the benchmarking method. Meanwhile, ten representative target reactions in this class from the O2QOOH to Q″OOH + HO2 are selected to validate the correction scheme through a comparison of the energy barriers before and after correction with the energy barriers by G4 method. It is found that the deviations of the energy barriers calculated by direct DFT method are between 16.58 and 24.95 kJ/mol, and after correction, the deviations of the energy barriers are reduced to −3.28 to 5.09 kJ/mol, indicating that the results of the energy barriers corrected by the isodesmic reaction method are close to that of the G4 method. Finally, using this correction scheme, the energy barriers, reaction enthalpies and rate constants of all reactions are calculated and kinetic parameters in the form of (A, n, E) are provided for this important elimination reaction class of hydroperoxyl-alkyl-peroxyl radicals (O2QOOH), which is useful for the simulation of low-temperature combustion for hydrocarbon.

This study focuses on the studies of the main pressure-dependent reaction types of iso-octane (iso-C8H18) pyrolysis, including initial C–C bond fission of iso-octane, isomerization, and β-scission reactions of the alkyl radicals produced by the C–C bond fission of iso-octane. For the C–C bond fission of iso-octane, the minimum energy potentials are calculated at the CASPT2(2e,2o)/6-31+G(d,p)//CAS(2e,2o)/6-31+G(d,p) level of theory. For the isomerization and the β-scission reactions of the alkyl radicals, the optimization of the geometries and the vibrational frequencies of the reactants, transition states, and products are performed at the B3LYP/CBSB7 level, and their single point energies are calculated by using the composite CBS-QB3 method. Variable reaction coordinate transition state theory (VRC-TST) is used for the high-pressure limit rate constant calculation and Rice–Ramsperger–Kassel–Marcus/master equation (RRKM/ME) is used to calculate the pressure-dependent rate constants of these channels with pressure varying from 0.01–100 atm. The rate constants obtained in this work are in good agreement with those available from literatures. We have updated the rate constants and thermodynamic parameters for species involved in these reactions into a current chemical kinetic mechanism and also have improved the concentration profiles of main products such as C3H6 and C4H6 in the shock tube pyrolysis of iso-octane. The results of this study provide insight into the pyrolysis of iso-octane and will be helpful in the future development of branched paraffin kinetic mechanisms.

The mechanism and substituent effects on the aminolysis reaction of p-substituted phenyl acetates (CH3C(O)OC6H4X, X = Cl, H, and NH2) with dimeric ammonia molecules are studied using the B3LYP/6-31+G(d,p) method in the gas phase. Single-point computations at the MP2/6-311++G(d,p) level are performed for more precise energy predictions. Two pathways are considered: the concerted and the neutral stepwise mechanisms. The results show that the stepwise mechanism is slightly energetically preferred to the concerted one for the three reaction systems in the gas phase. The solvent effect of acetonitrile is also assessed through single-point calculations by use of the conductor-like polarizable continuum model (CPCM) at the MP2/6-311++G(d,p) level on the gas-phase optimized geometries. Our computational results indicate that the reaction of CH3C(O)OC6H4X with ammonia dimer is more favorable for X = Cl than for X = H and NH2 in the gas phase and in acetonitrile. The solvation effect decreases the barrier height. When X = NH2, the stepwise process is also favored in acetonitrile, while the concerted mechanism is favorable in solution when X = H and Cl.Graphical abstractHighlights► The mechanism and substituent effects on the aminolysis reaction are studied. ► Using the B3LYP/6-31+G(d,p) method in the gas phase. ► Using Single-point computations at the MP2/6-311++G(d,p) level. ► Two pathways are considered: the concerted and the neutral stepwise mechanisms.

In the present work, the reaction mechanisms for thermal decomposition of cyclohexane in the gas phase have been investigated using quantum chemical calculations and transition-state theory. Three series of reaction schemes containing 38 elementary reactions are proposed. The geometry optimization and vibrational frequencies of reactants, transition states, and products are determined at the BH&HLYP/cc-pVDZ level, while energies are calculated at the CCSD(T)/cc-pVDZ level. The rate constants for the reactions without transition states, including the initial steps of cyclohexane decomposition (C–C bond scission or C–H bond scission), are obtained by the canonical variational transition-state theory (CVT), while the rate constants for the other reactions with saddle-point transition states are obtained by the conventional transition-state theory (TST) in the temperature range of 300–3000 K. The rate constants are in good agreement with data available from the literature. The kinetic parameters in the modified Arrhenius equation form for all of the reactions studied are given and can be used in chemical kinetic modeling studies.

In the current study, computational models for hPXR activators and hPXR non-activators were developed using support vector machine (SVM), k-nearest neighbor (k-NN), and artificial neural networks (ANN) algorithms. 73 molecular descriptors used for hPXR activator and hPXR non-activator prediction were selected from a pool of 548 descriptors by using a multi-step hybrid feature selection method combining Fischer's score and Monte Carlo simulated annealing method. The y-scrambling method was used to test if there is a chance correlation in the developed SVM model. In the meantime, five-fold cross validation of these machine learning methods results in the prediction accuracies of 87.2–92.5% for hPXR activators and 73.8–87.8% for hPXR non-activators, and the prediction accuracies for external test set are 93.8–95.8% for hPXR activators and 86.7–92.8% for hPXR non-activators. Our study suggested that the tested machine learning methods are potentially useful for hPXR activators identification.

Polycyclic aromatic hydrocarbons (PAHs) play important roles in the formation of combustion generated particles such as soot, but many details of the formation and growth of the PAHs are not yet completely understood. A novel phenyl addition/cyclization (PAC) mechanism has been suggested for the PAHs growth by Koshi et al. based on their experimental result and this PAC mechanism is theoretically investigated in the present work. B3LYP/6-311G(d,p) calculations are used to optimize the geometries of equilibrium and transition state structures as well as to obtain kinetic parameters with the single-point energies being calculated at BMK/6-311+G(3df,2p) level. Conventional transition state theory (TST) with Eckart tunneling correction is employed to calculate the rate coefficients in a temperature range from 300 to 2000 K for all the elementary reactions involved in the formation of triphenylene from C6H5 addition to C12H10. Our calculated rate coefficient of the phenylation reaction of biphenyl is consistent with available literature value.Graphical abstractHighlights► The formation of triphenylene from C6H5 + C12H10 via the PAC mechanism. ► Two channels of phenyl radical addition to biphenyl have been found for the first time. ► The H-elimination of the phenyl radical-biphenyl adducts is the rate-determining step. ► The agreement between experimental and calculated rate coefficients of the phenylation reaction of biphenyl.

Ethenol is a recently identified combustion intermediate. However, its chemistry remains unclear. In present work, the removal reactions of ethenol by H atom are investigated. The geometries of all species involved in the reaction are optimized at B3LYP/6-311++G(d,p), and their single point energies are extrapolated to the infinite-basis-set limit at the level CCSD(T). Energies are also calculated at G3B3, CBS-APNO, and CCSD(T)/6-311++G(3df, 2p) for comparison. A total of six elementary reactions, including four abstractions and two additions, with explicit transition states are investigated. The results show that the reactions are selective: for abstractions, the hydrogen atom, linked to the oxygen atom, is the most reactive; while for additions, the preferred carbon site is the head “CH2═”. The rate constants are estimated in the temperature range 300−3000 K according to the conventional transition state theory with the Eckart tunneling model. The dominant channels are the two additions in the whole temperature range. The abstractions can be competitive at high temperature but still do not dominate. The calculated rate constants for the reverse reaction of (R6), syn-CH2═CHOH + H ↔ CH3·CHOH, are consistent with the available literature values. Finally, the Fukui functions are calculated to analyze the site reactivity.

Support vector machines (SVM) and artificial neural networks (ANN) are applied for prediction of the acute toxicity of compounds to fathead minnow from molecular structure. A diverse set of 611 compounds, including 442 fathead minnow toxicity (FMT) agents and 169 non-FMT agents, are adopted to develop the classification models. A hybrid feature selection method, which combines Fischer's score and Monte Carlo simulated annealing embedded in the SVM approach, is used to select the relevant descriptors from 1559 molecular descriptors. Five-fold cross-validation method is used to optimize the model parameters and select the relevant descriptors. Using the 60 selected descriptors, SVM model gives an averaged prediction accuracy of 95.5% for FMT, 79.3% for non-FMT and 91.0% for all samples, while the corresponding values of the ANN model are 92.5%, 75.2% and 87.7%, respectively. The study indicates that the hybrid feature selection method is very efficient and the selected descriptors from the SVM approach have also a good performance for the ANN approach. A hold-out method is used to build the final classification models by using the selected descriptors and optimized model parameters from the 5-fold cross-validation. The SVM model gives an excellent prediction accuracy of 96.6% for FMT, 93.0% for non-FMT and 95.1% for all samples, while the corresponding values of the ANN model are 91.4%, 90.7% and 91.1%, respectively.

•It computes the currently most comprehensive (up to 329) network descriptors.•It supports five network types with different biological representations.•It is user-friendly with simple input/output and easy operation.•This paper discussed the applications of network descriptors in systems biology.•PROFEAT could facilitate the functional investigations of biological networks.The studies of biological, disease, and pharmacological networks are facilitated by the systems-level investigations using computational tools. In particular, the network descriptors developed in other disciplines have found increasing applications in the study of the protein, gene regulatory, metabolic, disease, and drug-targeted networks. Facilities are provided by the public web servers for computing network descriptors, but many descriptors are not covered, including those used or useful for biological studies. We upgraded the PROFEAT web server http://bidd2.nus.edu.sg/cgi-bin/profeat2016/main.cgi for computing up to 329 network descriptors and protein–protein interaction descriptors. PROFEAT network descriptors comprehensively describe the topological and connectivity characteristics of unweighted (uniform binding constants and molecular levels), edge-weighted (varying binding constants), node-weighted (varying molecular levels), edge-node-weighted (varying binding constants and molecular levels), and directed (oriented processes) networks. The usefulness of the network descriptors is illustrated by the literature-reported studies of the biological networks derived from the genome, interactome, transcriptome, metabolome, and diseasome profiles.Download high-res image (141KB)Download full-size image