Kinetic Analysis for Reaction of Cyclopentadiene with Hydroperoxyl Radical under Low- and Medium-Temperature Combustion.

The kinetic data of cyclopentadiene C5H6 oxidation reactions are significant for the construction of aromatics oxidation mechanism because cyclopentadiene C5H6 has been proved to be an important intermediate in the aromatics combustion. Kinetics for the elementary reactions on the potential energy surface (PES) relevant for the C5H6 + HO2 reaction are studied in this work. Stationary points on the PES are calculated by employing the CCSD(T)/cc-pVTZ//B3LYP/6-311G(d,p) level of theory. High-pressure limit and pressure-dependent rate constants for elementary reactions on this PES are calculated using conventional transition state theory (TST), variational transition-state theory (VTST) and Rice-Ramsberger-Kassel-Marcus/master equation (RRKM/ME) theory. In this work, the reaction channels for the C5H6 + HO2 reaction, which include H-abstraction channels from C5H6 by HO2 to form the C5H5 + H2O2 and the addition channels through well-skipping pathways to form the bimolecular products C5H7 + O2 or C5H6O + OH, or through C5H7O2 stabilization and its unimolecular decomposition to form the bimolecular products C5H7 + O2 or C5H6O + OH, namely sequential pathways, are studied. Also, the consuming reaction channels for the compounds C5H6O and C5H7 in the addition products are studied. The dominant reaction channels for these reactions are unraveled through comparing the energy barriers and rate constants of all elementary reactions and it is found: (1) HO2 addition to cyclopentadiene C5H6 is more important than direct H-abstraction. (2) in the HO2 addition channels, the well-skipping pathways and sequential pathways are competing and the well-skipping pathways will be favor in the higher pressures and the sequential pathways will be favor in the higher temperature. (3) The major consumption reaction channel for the five-member-ring compound C5H6O is the reaction channel to form C4H6 + CO and the major consumption reaction channel for the five-member-ring compound C5H7 is the reaction channel to form C3H5 + C2H2. High-pressure limit rate constants and pressure-dependent rate constants for elementary reactions on the PES are calculated, which will be useful in modeling the oxidation of aromatic compounds at low- and medium-temperatures.

Potential Energy Surface for Large Barrierless Reaction Systems: Application to the Kinetic Calculations of the Dissociation of Alkanes and the Reverse Recombination Reactions.

The isodesmic reaction method is applied to calculate the potential energy surface (PES) along the reaction coordinates and the rate constants of the barrierless reactions for unimolecular dissociation reactions of alkanes to form two alkyl radicals and their reverse recombination reactions. The reaction class is divided into 10 subclasses depending upon the type of carbon atoms in the reaction centers. A correction scheme based on isodesmic reaction theory is proposed to correct the PESs at UB3LYP/6-31+G(d,p) level. To validate the accuracy of this scheme, a comparison of the PESs at B3LYP level and the corrected PESs with the PESs at CASPT2/aug-cc-pVTZ level is performed for 13 representative reactions, and it is found that the deviations of the PESs at B3LYP level are up to 35.18 kcal/mol and are reduced to within 2 kcal/mol after correction, indicating that the PESs for barrierless reactions in a subclass can be calculated meaningfully accurately at a low level of ab initio method using our correction scheme. High-pressure limit rate constants and pressure dependent rate constants of these reactions are calculated based on their corrected PESs and the results show the pressure dependence of the rate constants cannot be ignored, especially at high temperatures. Furthermore, the impact of molecular size on the pressure-dependent rate constants of decomposition reactions of alkanes and their reverse reactions has been studied. The present work provides an effective method to generate meaningfully accurate PESs for large molecular system.

Pressure-Dependent Rate Rules for Intramolecular H-Migration Reactions of Hydroperoxyalkylperoxy Radicals in Low Temperature.

Intramolecular H-migration reaction of hydroperoxyalkylperoxy radicals (•O2QOOH) is one of the most important reaction families in the low-temperature oxidation of hydrocarbon fuels. This reaction family is first divided into classes depending upon H atom transfer from -OOH bonded carbon or non-OOH bonded carbon, and then the two classes are further divided depending upon the ring size of the transition states and the types of the carbons from which the H atom is transferred. High pressure limit rate rules and pressure-dependent rate rules for each class are derived from the rate constants of a representative set of reactions within each class using electronic structure calculations performed at the CBS-QB3 level of theory. For the intramolecular H-migration reactions of •O2QOOH radicals for abstraction from an -OOH substituted carbon atom (-OOH bonded case), the result shows that it is acceptable to derive the rate rules by taking the average of the rate constants from a representative set of reactions with different sizes of the substitutes. For the abstraction from a non-OOH substituted carbon atom (non-OOH bonded case), rate rules for each class are also derived and it is shown that the difference between the rate constants calculated by CBS-QB3 method and rate constants estimated from the rate rules may be large; therefore, to get more reliable results for the low-temperature combustion modeling of alkanes, it is better to assign each reaction its CBS-QB3 calculated rate constants, instead of assigning the same values for the same reaction class according to rate rules. The intramolecular H-migration reactions of •O2QOOH radicals (a thermally equilibrated system) are pressure-dependent, and the pressure-dependent rate constants of these reactions are calculated by using the Rice-Ramsberger-Kassel-Marcus/master-equation theory at pressures varying from 0.01 to 100 atm. The impact of molecular size on the pressure-dependent rate constants of the intramolecular H-migration reactions of •O2QOOH radicals has been studied, and it is shown that the pressure dependence of the rate constants of intramolecular H-migration reactions of •O2QOOH radicals decreases with the molecular size at low temperatures and the impact of molecular size on the pressure-dependent rate constants decreases as temperature increases. It is shown that it is acceptable to derive the pressure-dependent rate rules by taking the average of the rate constants from a representative set of reactions with different sizes of the substitutes. The barrier heights follow the Evans-Polanyi relationship for each type of intramolecular hydrogen-migration reaction studied. All calculated rate constants are fitted by a nonlinear least-squares method to the form of a modified Arrhenius rate expression at pressures varying from 0.01 to 100 atm and at the high-pressure limit. Furthermore, thermodynamic parameters for all species involved in these reactions are calculated by the composite CBS-QB3 method and are given in NASA format.

Interpretation and application of reaction class transition state theory for accurate calculation of thermokinetic parameters using isodesmic reaction method.

We present a further interpretation of reaction class transition state theory (RC-TST) proposed by Truong et al. for the accurate calculation of rate coefficients for reactions in a class. It is found that the RC-TST can be interpreted through the isodesmic reaction method, which is usually used to calculate reaction enthalpy or enthalpy of formation for a species, and the theory can also be used for the calculation of the reaction barriers and reaction enthalpies for reactions in a class. A correction scheme based on this theory is proposed for the calculation of the reaction barriers and reaction enthalpies for reactions in a class. To validate the scheme, 16 combinations of various ab initio levels with various basis sets are used as the approximate methods and CCSD(T)/CBS method is used as the benchmarking method in this study to calculate the reaction energies and energy barriers for a representative set of five reactions from the reaction class: R(c)CH(R(b))CR(a)CH2 + OH(•) → R(c)C(•)(R(b))CR(a)CH2 + H2O (R(a), R(b), and R(c) in the reaction formula represent the alkyl or hydrogen). Then the results of the approximate methods are corrected by the theory. The maximum values of the average deviations of the energy barrier and the reaction enthalpy are 99.97 kJ/mol and 70.35 kJ/mol, respectively, before correction and are reduced to 4.02 kJ/mol and 8.19 kJ/mol, respectively, after correction, indicating that after correction the results are not sensitive to the level of the ab initio method and the size of the basis set, as they are in the case before correction. Therefore, reaction energies and energy barriers for reactions in a class can be calculated accurately at a relatively low level of ab initio method using our scheme. It is also shown that the rate coefficients for the five representative reactions calculated at the BHandHLYP/6-31G(d,p) level of theory via our scheme are very close to the values calculated at CCSD(T)/CBS level. Finally, reaction barriers and reaction enthalpies and rate coefficients of all the target reactions calculated at the BHandHLYP/6-31G(d,p) level of theory via the same scheme are provided.

Effect of training data size and noise level on support vector machines virtual screening of genotoxic compounds from large compound libraries.

Various in vitro and in-silico methods have been used for drug genotoxicity tests, which show limited genotoxicity (GT+) and non-genotoxicity (GT-) identification rates. New methods and combinatorial approaches have been explored for enhanced collective identification capability. The rates of in-silco methods may be further improved by significantly diversified training data enriched by the large number of recently reported GT+ and GT- compounds, but a major concern is the increased noise levels arising from high false-positive rates of in vitro data. In this work, we evaluated the effect of training data size and noise level on the performance of support vector machines (SVM) method known to tolerate high noise levels in training data. Two SVMs of different diversity/noise levels were developed and tested. H-SVM trained by higher diversity higher noise data (GT+ in any in vivo or in vitro test) outperforms L-SVM trained by lower noise lower diversity data (GT+ in in vivo or Ames test only). H-SVM trained by 4,763 GT+ compounds reported before 2008 and 8,232 GT- compounds excluding clinical trial drugs correctly identified 81.6% of the 38 GT+ compounds reported since 2008, predicted 83.1% of the 2,008 clinical trial drugs as GT-, and 23.96% of 168 K MDDR and 27.23% of 17.86M PubChem compounds as GT+. These are comparable to the 43.1-51.9% GT+ and 75-93% GT- rates of existing in-silico methods, 58.8% GT+ and 79% GT- rates of Ames method, and the estimated percentages of 23% in vivo and 31-33% in vitro GT+ compounds in the "universe of chemicals". There is a substantial level of agreement between H-SVM and L-SVM predicted GT+ and GT- MDDR compounds and the prediction from TOPKAT. SVM showed good potential in identifying GT+ compounds from large compound libraries based on higher diversity and higher noise training data.

Theoretical investigations on removal reactions of ethenol by H atom.

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 "CH(2)═". 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-CH(2)═CHOH + H ↔ CH(3)·CHOH, are consistent with the available literature values. Finally, the Fukui functions are calculated to analyze the site reactivity.

Accurate prediction of enthalpies of formation for a large set of organic compounds.

This article describes a multiparameter calibration model, which improves the accuracy of density functional theory (DFT) for the prediction of standard enthalpies of formation for a large set of organic compounds. The model applies atom based, bond based, electronic, and radical environmental correction terms to calibrate the calculated enthalpies of formation at B3LYP/6-31G(d,p) level by a least-square method. A diverse data set of 771 closed-shell compounds and radicals is used to train the model. The leave-one-out cross validation squared correlation coefficient q(2) of 0.84 and squared correlation coefficient r(2) of 0.86 for the final model are obtained. The mean absolute error in enthalpies of formation for the dataset is reduced from 4.9 kcal/mol before calibration to 2.1 kcal/mol after calibration. Five-fold cross validation is also used to estimate the performance of the calibration model and similar results are obtained.

Accurate prediction of thermodynamic properties of alkyl peroxides by combining density functional theory calculation with least-square calibration.

Owing to the significance in kinetic modeling of the oxidation and combustion mechanisms of hydrocarbons, a fast and relatively accurate method was developed for the prediction of Delta(f)H(298)(o) of alkyl peroxides. By this method, a raw Delta(f)H(298)(o) value was calculated from the optimized geometry and vibration frequencies at B3LYP/6-31G(d,p) level and then an accurate Delta(f)H(298)(o) value was obtained by a least-square procedure. The least-square procedure is a six-parameter linear equation and is validated by a leave-one out technique, giving a cross-validation squared correlation coefficient q(2) of 0.97 and a squared correlation coefficient of 0.98 for the final model. Calculated results demonstrated that the least-square calibration leads to a remarkable reduction of error and to the accurate Delta(f)H(298)(o) values within the chemical accuracy of 8 kJ mol(-1) except (CH(3))(2)CHCH(2)CH(2)CH(2)OOH which has an error of 8.69 kJ mol(-1). Comparison of the results by CBS-Q, CBS-QB3, G2, and G3 revealed that B3LYP/6-31G(d,p) in combination with a least-square calibration is reliable in the accurate prediction of the standard enthalpies of formation for alkyl peroxides. Standard entropies at 298 K and heat capacities in the temperature range of 300-1500 K for alkyl peroxides were also calculated using the rigid rotor-harmonic oscillator approximation.

Kinetics and mechanism for formation of enols in reaction of hydroxide radical with propene.

Recently, enols have been found to be the common intermediates in hydrocarbon combustion flames (Taatjes et al. Science 2005, 308, 1887), but the knowledge of kinetic properties for such species in combustion flames is rare. Therefore in this work, particular attention is paid to the formation of enols in combustion flames. Starting with HO and propene (CH(3)CH=CH(2)), the reaction mechanism involving eight product channels has been investigated systematically. It is revealed that the electrophilic addition of OH to the double bond of CH(3)CH=CH(2) is unselective and the chemically activated adducts, CH(3)CHOH=CH(2) and CH(3)CH=CH(2)OH, may undergo dissociation in competition with H-abstractions. The kinetics and product branching ratios of the HO and propene reaction have been evaluated in the temperature range of 200-3000 K by Variflex code, based on the weak collision master equation/microcanonical variational RRKM theory. Available experimental kinetic data can be quantitatively reproduced by this study, with a minor adjustment (1.0 kcal/mol) of the OH central addition barrier. From the theoretical calculations with multiple reflection correction included, the total rate constant is fitted to k(t) = 6.07 x 10(-5)T(-2.54) exp(108/T) cm(3) x molecule(-1) x s(-1) in the range of 200-800 K and k(t) = 7.11 x 10(-23)T(3.38) exp(-1097/T) cm(3) x molecule(-1) x s(-1) in the range of 800-3000 K, which are in close agreement with experimental data. The branching ratios of enol channels are consistent with the observation in low-pressure flames and hence the reaction mechanisms presented here provide valuable descriptions of enol formations in hydrocarbon combustion chemistry.

An ab initio/Rice-Ramsperger-Kassel-Marcus prediction of rate constant and product branching ratios for unimolecular decomposition of propen-2-ol and related H + CH2COHCH2 reaction.

Enols have been found to be important intermediates in the combustion flames of hydrocarbon [C. A. Taatjes et al., Science 308, 1887 (2005)]. The removal mechanism of enols in combustion flame has not been established yet. In this work, the potential energy surface for the unimolecular decomposition of syn-propen-2-ol and H + CH(2)COHCH(2) recombination reactions have been first investigated by CCSD(T) method. The barrier heights, reaction energies, and geometrical parameters of the reactants, products, intermediates, and transition states have been investigated theoretically. The results show that the formation of CH(3)CO + CH(3) via the CH(3)COCH(3) intermediate is dominant for the unimolecular decomposition of syn-propen-2-ol and its branching ratio is over 99% in the whole temperature range from 700 to 3000 K, and its rate constant can be expressed as an analytical form in the range of T=700-3000 K at atmospheric pressure. This can be attributed to the lower energy barrier of this channel compared to the other channels. The association reaction of H with CH(2)COHCH(2) is shown to be a little more complicated than the unimolecular decomposition of syn-propen-2-ol. The channel leading to CH(3)CO + CH(3) takes a key role in the whole temperature range at atmospheric pressure. However at the higher pressure of 100 atm, the recombination by direct formation of syn-propen-2-ol through H addition is important at T<1000 K. In the range of T>1400 K, the recombination channel leading to CH(3)CO + CH(3) turns out to be significant.

Efficacy of different protein descriptors in predicting protein functional families.

BACKGROUND: Sequence-derived structural and physicochemical descriptors have frequently been used in machine learning prediction of protein functional families, thus there is a need to comparatively evaluate the effectiveness of these descriptor-sets by using the same method and parameter optimization algorithm, and to examine whether the combined use of these descriptor-sets help to improve predictive performance. Six individual descriptor-sets and four combination-sets were evaluated in support vector machines (SVM) prediction of six protein functional families. RESULTS: The performance of these descriptor-sets were ranked by Matthews correlation coefficient (MCC), and categorized into two groups based on their performance. While there is no overwhelmingly favourable choice of descriptor-sets, certain trends were found. The combination-sets tend to give slightly but consistently higher MCC values and thus overall best performance such that three out of four combination-sets show slightly better performance compared to one out of six individual descriptor-sets. CONCLUSION: Our study suggests that currently used descriptor-sets are generally useful for classifying proteins and the prediction performance may be enhanced by exploring combinations of descriptors.

Interrelationships between HIV/AIDS and risk behavior prejudice among medical students in Southern China.

Stigma within health care settings poses a considerable barrier to the provision of treatment and care for patients with HIV/AIDS (PLWHA). Southern China is located in a region with one of the world's fastest growing HIV/AIDS epidemics. Attitudes towards PLWHA amongst health workers are currently under-researched in this region. This paper examines the inter-relationships between prejudicial attitudes among Chinese medical students towards HIV/AIDS and attitudes towards three risk behaviors: injecting drug use (IDU), commercial sex (CS) and commercial blood donation (CBD). Medical students (N = 352) in Guangzhou were presented with two random vignettes; each describing a hypothetical male that was identical, except for the disease diagnosis (AIDS/leukemia) and the co-characteristic (IDU/CS/CBD/blood transfusion/no co-characteristic). After reading each vignette, participants completed a standard prejudicial scale. Univariate and multivariable analyses revealed significant levels of prejudice associated with AIDS, IDU and CS. Regardless of the disease, patients with IDU or CS were judged significantly worse than patients who had received a blood transfusion. No significant interactions were found between AIDS and the stigmatized co-characteristics. The findings suggest that prejudice towards PLWHA needs to be understood within the larger context of the stigma towards risk behaviors. Although non-significant interactions were found between AIDS and the stigmatized risk behaviors, the overlap between the local HIV/AIDS, IDU and CS populations suggests that addressing risk behavior-related prejudices could be critical for improving care and treatment for PLWHA.

Advances in machine learning prediction of toxicological properties and adverse drug reactions of pharmaceutical agents.

As part of the intensive efforts in facilitating drug discovery, computational methods have been explored as low-cost and efficient tools for predicting various toxicological properties and adverse drug reactions (ADR) of pharmaceutical agents. More recently, machine learning methods have been applied for developing tools capable of predicting diverse spectrum of compounds of different toxicological properties and ADR profiles. Based on the results of a number of studies, these methods have shown promising potential in predicting a variety of toxicological properties and ADR profiles. This article reviews the strategies, current progresses, underlying difficulties and future prospects in using machine learning methods for predicting compounds of specific toxicological property or ADR profile.

Advances in modeling of biomolecular interactions.

Modeling of molecular interactions is increasingly used in life science research and biotechnology development. Examples are computer aided drug design, prediction of protein interactions with other molecules, and simulation of networks of biomolecules in a particular process in human body. This article reviews recent progress in the related fields and provides a brief overview on the methods used in molecular modeling of biological systems.

Investigation of photoinduced electron transfer in model system of vitamin E-duroquinone by time-dependent density functional theory.

Photoinduced electron transfer of the model system composed of vitamin E and duroquinone has been investigated using time-dependent density functional theory. Calculations for the excited states tell that the photoexcitation of the model system can directly yield the charge transfer states in which the vitamin E moiety is positively charged but the duroquinone moiety is negatively charged. Our theoretical investigations indicate that the second charge transfer state of the model system can also be produced through the decay of higher locally excited state S(4). Since S(4) state in the model system corresponds to S(1) state of the isolated duroquinone used as a model for peroxyl radical, and S(2) state has the character of electron transfer from the tertiary amine group of the vitamin E moiety to the duroquinone moiety, the decay from S(4) to S(2) corresponds to the dynamic process following the photoexcitation of the duroquinone moiety of the model system, i.e., the initial stage of antioxidant reaction of vitamin E. Calculations of the kinetic parameters for the electron transfer have been carried out in the framework of the Marcus-Jortner-Levich formalism. Our calculations confirm that the electron transfer from S(4) to S(2) possesses the character of the inverted regime and the barrier is negligibly small.

[Study on the epidemiology and measures for control on severe acute respiratory syndrome in Guangzhou city].

OBJECTIVE: To analyze the epidemiological characteristics, related risk factors, measures for its control of severe acute respiratory syndrome (SARS). METHODS: Data on epidemiological features, pathogens and measures for control were collected and analyzed. RESULTS: Since Jan 2003, infectious atypical pneumonia (AP) has become epidemic in Guangzhou city. The first autochthonous case was identified on Jan 2nd. Number of cases started to increase since February and reached peak in the early 10 days of February. Hereafter the epidemic tended to decline in March and since early April, the average number of new cases began to decrease, less than 10 per day. Epidemiological studies revealed that the number of cases aged between 20 and 50 was higher than that below the age of 20. Of the total 966 cases, 429 were males versus 537 females. Geographically, the epidemics covered all 13 districts of Guangzhou, but 95% of the cases concentrated in 7 urban districts. As for professional distribution, health care workers accounted for 28.67% of the total cases. There were 36 deaths, aged from 5 to 89, with half of them older than 60. Out of the victims, 38.9% of them had complications as hypertension, diabetes, heart diseases and COPD etc. Data regarding the clustering features of cases showed that there were 42 families having 2 or more cases in one family, while 277 health workers suffered from SARS were concentrated in 28 hospitals. Only one outbreak took place in a public setting but no outbreak was reported in schools. Relevant research also indicated that SARS could be classified as an air-borne infectious disease, transmitted through aerosol and droplets, but close contact also played an important role in the mode of transmission. The disease was highly infectious, suggesting that people who had close contact with patients in the place with poor ventilation was in greater risk of getting infection. The incubation period ranged from 1 to 11 days (mainly from 3 to 8 days), with an average of 5 days. According to our observation, the following measures might be effective such as: early diagnosis, isolation and treatment provided to the patients, and suspected cases under medical observation should also be put in separate places. Improving ventilation and regular disinfection over air and stuff in hospital wards were also recommended. In order to prevent iatrogenic infection, sense on self-protection among health care workers must be strengthened. Patients were not allowed to be visited by any one other than hospital staff. CONCLUSION: SARS is a preventable disease and can be under control. It is of great importance to prevent clustered SARS cases and the prevention of iatrogenic infection is essential.