Thermochemical properties from ab initio calculations: π- and σ-Free radicals of importance in soot formation: •C3H3 (propargyl), •C4H3, •C13H9 (phenalenyl), •C6H5 (phenyl), •C10H7 (naphthyl), •C14H9 (anthryl), •C14H9 (phenanthryl), •C16H9 (pyrenyl), •C12H7 (acenaphthyl), and •C12H9 (biphenylyl)

The calculated difference in the standard heat of formation Δ Δ_fH°(298.15) of n- and i-C₄H₃^• free radicals is 37.9 kJ mol⁻¹ for G3MP2B3 and 45.0 kJ mol⁻¹ for CCSD(T)-CBS (W1U) calculations, which seems to preclude the direct even-carbon radical pathway to benzene and higher PAH (polycyclic aromatic hydrocarbon) formation including soot in a hydrocarbon flame. For the phenyl-type σ-radicals listed in the title, absolute values of Δ_fH°(298.15) have been calculated using G3MP2B3-computed values of bond dissociation energies D°(298.15) and combined with experimental values of Δ_fH° (298.15) for the parent hydrocarbon because of a slight systematic overprediction of the thermodynamic stability of large PAHs by the applied computational G3MP2B3 method. Standard enthalpies of formation Δ_fH°(298.15) as well as absolute entropies S° and heat capacities C°_p are given for a series of π- and σ-free radicals important to combustion as a function of temperature. A spread of roughly 40 kJ mol⁻¹ in the average C H bond strength of PAH leading to σ-radicals has been calculated, the lowest leading to 4-phenanthryl (463.6 kJ mol⁻¹), the highest leading to 2-biphenylyl radical (502.5 kJ mol⁻¹). © 2008 Wiley Periodicals, Inc. Int J Chem Kinet 40: 395–415, 2008     

An ab initio study of intermolecular interactions of nitromethane dimer and nitromethane trimer

Different geometries of nitromethane dimer and nitromethane trimer have been fully optimized employing the density functional theory B3LYP method and the 6-31++G** basis set. Three-body interaction energy has been obtained with the ab initio supermolecular approach at the levels of MP2/6-31++G**//B3LYP/6-31++G** and MP2/aug-cc-pVDZ//B3LYP/6-31++G**. The internal rotation of methyl group induced by intermolecular interaction has been observed theoretically. For the optimized structures of nitromethane dimer, the strength of C--H...O--N H-bond ranges from -9.0 to -12.4 kJ mol(-1) at the MP2/aug-cc-pVDZ//B3LYP/6-31++G** level, and the B3LYP method underestimates the interaction strength compared with the MP2 method, while MP2/6-31++G**//B3LYP/6-31++G** calculated DeltaE(C) is within 2.5 kJ mol(-1) of the corresponding value at the MP4(SDTQ)/6-31G**//B3LYP/6-31++G** level. The analytic atom-atom intermolecular potential has been successfully regressed by using the MP2/6-31++G**//B3LYP/6-31++G** calculated interaction energies of nitromethane dimer. For the optimized structures of nitromethane trimer the three-body interaction energies occupy small percentage of corresponding total binding energies, but become important for the compressed nitromethane explosive. In addition, it has been discovered that the three-body interaction energy in the cyclic nitromethane trimer is more and more negative as intermolecular distances decrease from 2.2 to 1.7 A.     

The Molecular Composition of Soot

Soot (sometimes referred to as black carbon) is produced when hydrocarbon fuels are burned. Our hypothesis is that polynuclear aromatic hydrocarbon (PAH) molecules are the dominant component of soot, with individual PAH molecules forming ordered stacks that agglomerate into primary particles (PP). Here we show that the PAH composition of soot can be exactly determined and spatially resolved by low-fluence laser desorption ionization, coupled with high-resolution mass spectrometry imaging. This analysis revealed that PAHs of 239–838 Da, containing few oxygenated species, comprise the soot observed in an ethylene diffusion flame. As informed by chemical graph theory (CGT), the vast majority of species observed in the sampled particulate matter may be described as benzenoids, consisting of only fused 6-membered rings. Within that limit, there is clear evidence for the presence of radical PAH in the particulate samples. Further, for benzenoid structures the observed empirical formulae limit the observed isomers to those which are nearly circular with high aromatic conjugation lengths for a given aromatic ring count. These results stand in contrast to recent reports that suggest higher aliphatic composition of primary particles.     

The Molecular Composition of Soot

Soot (sometimes referred to as black carbon) is produced when hydrocarbon fuels are burned. Our hypothesis is that polynuclear aromatic hydrocarbon (PAH) molecules are the dominant component of soot, with individual PAH molecules forming ordered stacks that agglomerate into primary particles (PP). Here we show that the PAH composition of soot can be exactly determined and spatially resolved by low‐fluence laser desorption ionization, coupled with high‐resolution mass spectrometry imaging. This analysis revealed that PAHs of 239–838 Da, containing few oxygenated species, comprise the soot observed in an ethylene diffusion flame. As informed by chemical graph theory (CGT), the vast majority of species observed in the sampled particulate matter may be described as benzenoids, consisting of only fused 6‐membered rings. Within that limit, there is clear evidence for the presence of radical PAH in the particulate samples. Further, for benzenoid structures the observed empirical formulae limit the observed isomers to those which are nearly circular with high aromatic conjugation lengths for a given aromatic ring count. These results stand in contrast to recent reports that suggest higher aliphatic composition of primary particles.     

掺混含氧燃料的柴油替代物部分预混火焰中多环芳香烃的荧光光谱和碳烟浓度

为研究不同含氧燃料与柴油掺混后碳烟降低机理, 本文在自行设计的燃烧器上构建部分预混层流火焰, 采用甲苯和正庚烷混合物(T20, 20%(体积分数)甲苯、80%正庚烷)作为柴油替代物,并分别添加甲醇、乙醇、正丁醇、丁酸甲酯和2,5-二甲基呋喃(DMF), 且保证混合燃料的含氧量均为4%. 进而应用激光诱导荧光法和激光诱导炽光法分别测量不同混合燃料的火焰中多环芳香烃(PAHs)的荧光光谱和碳烟浓度. 结果表明: 通过PAHs的荧光光谱可测量不同燃料火焰中PAHs的生成和增长历程. 四环芳香烃(A4)的生成氧化规律和碳烟基本一致, 说明通过分析A4变化可以预测碳烟变化. 添加含氧燃料后, T20燃料中甲苯含量降低是导致PAHs的荧光光谱强度降低和碳烟生成量减少的主要原因; 同时不同含氧燃料本身对多环芳香烃的生成贡献能力也是影响PAHs的荧光强度和碳烟生成的重要原因. 含氧量相当时, 掺混正丁醇后PAHs的荧光光谱强度和碳烟浓度比添加甲醇、乙醇、丁酸甲酯和DMF这四种含氧燃料的更低. 因此从含氧燃料结构来讲, 正丁醇掺混入T20燃料中降低PAHs和碳烟作用最显著.     

On the aromatic character of the heterocyclic bases of DNA and RNA

Studies based on ab initio optimized geometries (at B3LYP/6-311+G** and MP2/6-311+G** levels) and on experimental structures retrieved from the Cambridge Structural Database (CSD) reveal that the nucleobases constituting DNA and RNA differ significantly in their aromatic character, as shown by the geometry-based index of aromaticity HOMA that ranges from 0.466 for thymine to 0.917 for adenine, based on B3LYP/6-311+G** calculations, and 0.495-0.926, respectively, if based on the MP2/6-311+G** level. Aromaticity of the bases decreases markedly with an increase of the number of double-bond C=X (X = N, O) substituents at the rings. H-bonds involving C=O groups in Watson-Crick pairs cause an increase of the aromatic character of the rings.     

Theoretical study on tetrazole and its derivatives (3) MP2 and thermodynamic calculations of amino derivatives of tetrazole

Fully optimized geometries and electronic structures of amino derivatives of tetrazole are obtained at MP2/6-31G* level. The tetrazole rings are planar and aromatic for all the amino derivatives of tetrazole. The amino group is not co-planar with the ring and its conformation is mainly determined by the lone pair electronic repulsion between the substituent and the ring. N(4) atom is more negatively charged and is the most probable coordination site. The energy gaps between LUMOs and HOMOs of 2H-aminotetrazoles and C-aminotetrazole neutrals are smaller than those of the corresponding 1H-isomers and N-aminotetrazole neutrals respectively. The IR frequencies, thermodynamic properties and temperature-dependent functions for heat capacities in the form (a bT cT2) in the 300-1000K range are reported.     

Theoretical study for the reaction of CH3OCl with Cl atom

A direct dynamics method is employed to study the kinetics of the multiple channel reaction CH(3)OCl + Cl. The potential energy surface (PES) information is explored from ab initio calculations. Two reaction channels, Cl- and H-abstractions, have been identified. The optimized geometries and frequencies of the stationary points and the minimum-energy paths (MEPs) are calculated at the MP2 level of theory using the 6-311G(d, p) and cc-pVTZ basis sets, respectively. The single-point energies along the MEPs are further refined at the G3(MP2)//MP2/6-311G(d, p), G3//MP2/6-311G(d, p), as well as by the multicoefficient correlation method based on QCISD (MC-QCISD) using the MP2/cc-pVTZ geometries. The enthalpies of formation for the species CH(3)OCl and CH(2)OCl are calculated via isodesmic reactions. The rate constants of the two reaction channels are evaluated by using the variational transition-state theory over a wide range of temperature, 220-2200 K. The calculated rate constants exhibit the slightly negative temperature dependence and show good agreement with the available experimental data at room temperature at the G3(MP2)//MP2/6-311G(d, p) level. The present calculations indicate that the two channels are competitive at low temperatures while H-abstraction plays a more important role with the increase of temperature. The calculated k(1a)/k(1) ratio of 0.5 at 298 K is in general agreement with the experimental one, 0.8 +/- 0.2. The high rate constant for CH(3)OCl + Cl shows that removal by reaction with Cl atom is a potentially important loss process for CH(3)OCl in the polar stratosphere.     

Theoretical study of the formation of naphthalene from the radical/π-bond addition between single-ring aromatic hydrocarbons

The experimental investigations performed in the 1960s on the o-benzyne + benzene reaction as well as the more recent studies on reactions involving π-electrons highlight the importance of π-bonding for different combustion processes related to PAH's and soot formation. In the present investigation radical/π-bond addition reactions between single-ring aromatic compounds have been proposed and computationally investigated as possible pathways for the formation of two-ring fused compounds, such as naphthalene, which serve as precursors to soot formation. The computationally generated optimized structures for the stationary points were obtained with uB3LYP/6-311+G(d,p) calculations, while the energies of the optimized complexes were refined using the uCCSD(T) method and the cc-pVDZ basis set. The computations have addressed the relevance of a number of radical/π-bond addition reactions including the singlet benzene + o-benzyne reaction, which leads to formation of naphthalene and acetylene through fragmentation of the benzobicyclo[2,2,2]octatriene intermediate. For this reaction, the high-pressure limit rate constants for the individual elementary reactions involved in the overall process were evaluated using transition state theory analysis. Other radical/π-bond addition reactions studied were between benzene and triplet o-benzyne, between benzene and phenyl radical, and between phenyl radicals, for all of which potential energy surfaces were produced. On the basis of the results of these reaction studies, it was found necessary to propose and subsequently confirm additional, alternative pathways for the formation of the types of PAH compounds found in combustion systems. The potential energy surface for one reaction in particular, the phenyl + phenyl addition, is shown to contain a low-energy channel leading to formation of naphthalene that is energetically comparable to the other examined conventional pathways leading to formation of biphenyl compounds. This channel is the first evidence of a reaction which involves an aromatic radical adding to the nonradical π-bond site of another aromatic radical which leads directly to a fused ring structure.     

Reaction of phenyl radicals with propyne

The potential energy surface (PES) for the phenyl + propyne reaction, which might contribute to the growth of polycyclic aromatic hydrocarbons (PAHs) under a wide variety of reaction conditions, is described. The PES was characterized at the B3LYP-DFT/6-31G(d) and B3LYP-DFT/6-311+G(d,p) levels of theory. The energies of the entrance transition states, a direct hydrogen-transfer channel and two addition reactions leading to chemically activated C(9)H(9) intermediates, were also evaluated at the QCISD(T)/ 6-311G(d,p) and CCSD(T)/6-311G(d,p) levels of theory. An extensive set of unimolecular reactions was examined for these activated C(9)H(9)(dagger) intermediates, comprising 70 equilibrium structures and over 150 transition states, and product formation channels leading to substituted acetylenes and allenes such as PhCCH, PhCCCH(3), and PhCHCCH(2) were identified. The lowest energy pathway leads to indene, a prototype PAH molecule containing a five-membered ring. The title reaction thus is an example of possible direct formation of a PAH containing a five-membered ring, necessary to explain formation of nonplanar PAH structures, from an aromatic radical unit and an unsaturated hydrocarbon bearing an odd number of carbons. Extensive Supporting Information is available.     

基于不同燃料PAH特性改进的适用于多组分燃料的碳烟模型

将多环芳烃(PAH)骨架模型与甲苯参比燃料(TRF)氧化模型耦合,构建了一个新的TRF-PAH骨架模型.以新的TRF-PAH骨架模型作为燃料燃烧的气相化学反应模型,基于不同分子结构的燃料氧化过程中生成PAHs和碳烟的路径也不同的研究结论,本文进一步优化了以PAHs为碳烟前驱生成物的碳烟半经验模型.通过甲苯在流动反应器、搅拌反应器和激波管中的氧化/裂解实验验证发现,新的TRF-PAH骨架模型可以相对准确地预测小分子PAHs和重要中间组分的浓度.通过对比烷烃和芳香烃氧化过程中生成苯的计算值可以发现,燃料的分子结构对PAHs的生成路径影响很大.另外,改进后的碳烟模型利用甲苯、正庚烷/甲苯及异辛烷/甲苯混合物为燃料的激波管中裂解和氧化实验验证,结果表明在较宽的工况内碳烟模拟值与实验值吻合较好.最后,将新的碳烟模型应用于KIVA程序,模拟以TRF20为燃料的柴油机碳烟排放,结果表明TRF-PAH骨架模型和碳烟模型能重现缸内燃烧和排放的特性.     

Conformational study of the structure of free 18-crown-6

A conformational search was performed for 18-crown-6 using the CONLEX method at the MM3 level. To have a more accurate energy order of the predicted conformations, the predicted conformations were geometry optimized at the HF/STO-3G level and the 198 lowest energy conformations, according to the HF/STO-3G energy order, were geometry optimized at the HF/6-31+G level. In addition, the 47 nonredundant lowest energy conformations, according to the MP2/6-31+G energy order at the HF/6-31+G optimized geometry, hereafter the MP2/6-31+G//HF/6-31+G energy order, were geometry optimized at the B3LYP/6-31+G level. According to the MP2/6-31+G//B3LYP/6-31+G energy order, three conformations had energies lower than the experimentally known Ci conformation of 18c6. At the MP2/6-31+G//B3LYP/6-31+G level, the S6 lowest energy conformation is more stable by 1.96 kcal/mol than this Ci conformation. This was confirmed by results at the MP2/6-31+G level with an energy difference of 1.84 kcal/mol. Comparison between the structure of the S6 conformation of 18c6 and the S4 lowest energy conformation of 12-crown-4, as well as other important conformations of both molecules, is made. It is concluded that the correlation energy is necessary to have an accurate energy order of the predicted conformations. A rationalization of the conformational energy order in terms of the hydrogen bonding and conformational dihedral angles is given. It is also suggested that to have a better energy order of the predicted conformations at the MM3 level, better empirical force fields corresponding to the hydrogen bond interactions are needed.     

Enthalpy of formation and bond energies on unsaturated oxygenated hydrocarbons using G3MP2B3 calculation methods

Enthalpies of unsaturated oxygenated hydrocarbons and radicals corresponding to the loss of hydrogen atoms from the parent molecules are intermediates and decomposition products in the oxidation and combustion of aromatic and polyaromatic species. Enthalpies (Δ_fH⁰₂₉₈) are calculated for a set of 27 oxygenated and nonoxygenated, unsaturated hydrocarbons and 12 radicals at the G3MP2B3 level of theory and with the commonly used B3LYP/6‐311g(d,p) density functional theory (DFT) method. Standard enthalpies of formation (Δ_fH⁰₂₉₈) are determined from the calculated enthalpy of reaction (ΔH⁰_rxn,298) using isodesmic work reactions with reference species that have accurately known Δ_fH⁰₂₉₈ values. The deviation between G3MP2B3 and B3LYP methods is under ±0.5 kcal mol^?1 for 9 species, 18 other species differs by less than ±1 kcal mol^?1 , and 11 species differ by about 1.5 kcal mol^?1. Under them are 11 radicals derived from the above‐oxygenated hydrocarbons that show good agreement between G3MP2B3 and B3LYP methods. G3 calculations have been performed to further validate enthalpy values, where a discrepancy of more than 2.5 kcal mol^?1 exists between the G3MP3B3 and density functional results. Surprisingly the G3 calculations support the density functional calculations in these several nonagreement cases. © 2005 Wiley Periodicals, Inc. Int J Chem Kinet 37: 633–648, 2005     

Reduction of PAH and soot precursors in benzene flames by addition of ethanol

A one-dimensional premixed flame model (PREMIX) and schemes resulting from the merging of validated kinetic schemes for the oxidation of the components of the present mixtures (benzene and ethanol) were used to investigate the effect of oxygenated additives on aromatic species, which are known to be soot precursors, in fuel-rich benzene combustion. The specific flames were low-pressure (45 mbar), laminar, premixed flames at an equivalence ratio of 2.0. The blended fuels were formed by incrementally adding 4% wt of oxygen (ethanol) to the neat benzene flame and by keeping the inert mole fraction (argon) and the equivalence ratio constants. Special emphasis was directed toward the causes for the concentration-dependent influence of the blends on the amount of polycyclic aromatic hydrocarbons (PAHs) formed. The effects of oxygenate addition to the benzene base flame were seen to result in interesting differences, especially regarding trends to form PAH. The modeling results indicated that the concentration of acetylene and propargyl radicals, the main PAH precursors, as well as the PAH amounts were lower in the flame of the ethanol-benzene fuel mixture than in the pure benzene flame and that all of the formed PAHs were issued from the phenyl radical. Finally, the modeling results provided evidence that the PAH reduction was a result of simply replacing "sooting" benzene with "nonsooting" ethanol without influencing the combustion chemistry of the benzene.     

Computational study of the reactions of SiH3X (X=H, Cl, Br, I) with HCN

Ab initio calculations were carried out for the reactions of silane and halosilanes (SiH3X, X=H, Cl, Br, I) with HCN. Geometries of the reactants, transition states, intermediates and products were optimized at HF, MP2, and B3LYP levels of theory using the 6-31G(d) and 6-31G(d,p) basis sets. Energies were also obtained using G3MP2 and G3B3 levels of theory. Intrinsic reaction coordinate (IRC) calculations were performed to characterize the transition states on the potential energy surface. It was found that HCN can react with silane and halosilanes via three different mechanisms. One involves HX elimination by a one-step pathway producing SiH3CN. The second mechanism consists of H2 elimination, producing SiH2XCN via a one-step pathway or three multiple-step pathways. The third mechanism involves dissociation of SiH3X to various products, which can then react with HCN. Activation energies, enthalpies, and free energies of activation along with the thermodynamic properties (DeltaE, DeltaH, and DeltaG) of each reaction pathway were calculated. The reaction of SiH3X with HCN produce different products depending on substituent X. We have found that the standard 6-31G(d) bromine basis set gave results which were in better agreement with the G3MP2 results than for the Binning-Curtiss basis set. Computed heats of formation (DeltaHf) for SiH3CN, SiH3NC, SiH2ClCN, SiH2BrCN, SiH2ICN, SiHCl, SiHBr, and SiHI were found to be 133.5, 150.8, -34.4, 23.6, 102.4, 48.7, 127.1, and 179.8 kJ mol-1, respectively. From enthalpies calculated at G3MP2, we predict that the DeltaHf for SiH2 to be 262.8 kJ mol-1 compared to the experimental value of 273.8+/-4.2 kJ mol-1.     

Geometry prediction of hafnocenes by quantum chemical methods

The performance of quantum chemical methods for geometry prediction of hafnocenes was evaluated. HF, B3LYP and MP2 in combination with nonrelativistic (MHF) and relativistic (MWB and LANL2DZ) basis sets for hafnium together with standard basis sets 3-21G*, 6-31G* and 6-311G** for other elements were applied. Five basic structural parameters of the optimized structures of the hafnocenes were compared with experimental crystal structures obtained from the Cambridge structural database. Altogether 80 hafnocenes were included in the analysis. The results show that relativistic corrections are necessary for Hf atom. However, even the Hartree–Fock (HF) method, when combined with relativistic pseudopotentials, reproduces the experimental crystal structures with significant accuracy. The good performance of the HF method can be understood to originate from the absence of significant near-degeneracy correlations for hafnium. On average, the B3LYP and MP2 methods provide structural parameters somewhat closer to the experimental ones.     

Interaction of anions with perfluoro aromatic compounds

The complexes formed by a variety of anions with perfluoro derivatives of benzene, naphthalene, pyridine, thiophene, and furan have been calculated using DFT (B3LYP/6-31++G**) and MP2 (MP2/6-31++G** and MP2/6-311++G**) ab initio methods. The minimum structures show the anion interacting with the pi-cloud of the aromatic compounds. The interaction energies obtained range between -8 and -19 kcal mol(-1). The results obtained at the MP2/6-31++G** and MP2/6-311++G** levels are similar. However, the B3LYP/6-31++G** results provide longer interaction distances and smaller interaction energies than do the MP2 results. The interaction energies have been partitioned using an electrostatic, polarization, and van der Waals scheme. The AIM analysis of the electron density shows a variety of topologies depending on the aromatic system considered.     

Theoretical studies on dynamics and thermochemistry of the reactions CF(3)CHCl(2)+Cl-->CF(3)CCl(2)+HCl and CF(3)CHFCl+Cl-->CF(3)CFCl+HCl

A dual-level direct dynamics study has been carried out for the two hydrogen abstraction reactions CF(3)CHCl(2)+Cl and CF(3)CHFCl+Cl. The geometries and frequencies of the stationary points are optimized at the BHLYP/6-311G(d,p), B3LYP/6-311G(d,p), and MP2/6-31G(d) levels, respectively, with single-point calculations for energy at the BHLYP/6-311++G(3df,2p), G3(MP2), and QCISD(T)/6-311G(d,p) levels. The enthalpies of formation for the species CF(3)CHCl(2), CF(3)CHFCl, CF(3)CCl(2), and CF(3)CFCl are evaluated at higher levels. With the information of the potential energy surface at BHLYP/6-311++G(3df,2p)//6-311G(d,p) level, we employ canonical variational transition-state theory with small-curvature tunneling correction to calculate the rate constants. The agreement between theoretical and experimental rate constants is good in the measured temperature range 276-382 K. The effect of fluorine substitution on reactivity of the C-H bond is discussed.     

A computational study of intramolecular proton transfer in gaseous protonated glycine

The minimum energy paths for intramolecular proton transfer between the amino nitrogen and carbonyl oxygen atoms in gaseous protonated glycine were estimated at the Hartree-Fock (HF) and second-order M?ller-Plesset Perturbation (MP2) levels of theory. Potential energy profiles and their associated reactant, transition state, and product species calculated at the MP2/6-31G* level were shown to differ significantly from those obtained at the HF/6-31G* level. Effects of electron correlation and basis functions on the calculated geometries and energies of relevant species were examined at the HF, MP2, MP4, CCSD, and B3LYP levels using the 6-31G*, 6-31G**, 6-31+G**, 6-311+G**, 6-31+G(2d,2p), 6-311+G(3df,2p), cc-pVDZ, aug-cc-pVDZ, and cc-pVTZ basis sets. The HF and MP2 optimized levels with the 6-31G*, 6-31G**, 6-31+G**, and 6-311+G** bases were used to calculate the thermodynamic and kinetic properties of the proton transfer reaction at 298.15 K and 1 atm, which include enthalpy, entropy, Gibbs free energy, equilibrium constant, potential energy barriers, tunneling transmission coefficients, and rate constants. Results indicate that the proton in a carbonyl O-protonated glycine undergoes a rapid migration to the amino nitrogen atom, while the reverse process is extremely unfavorable. The objective of this work is to develop practical theoretical procedures for studying proton transfer reactions in amino acids and peptides and to assemble physical data from these model calculations for future references.