Ab Initio 6-31G Research Articles

The Role of Methylaryl Radicals in the Growth of Polycyclic Aromatic Hydrocarbons: The Formation of Five-Membered Rings.

The regions of the C13H11 potential energy surface (PES) related to the unimolecular isomerization and decomposition of the 1-methylbiphenylyl radical and accessed by the 1-/2-methylnaphthyl + C2H2 reactions have been explored by ab initio G3(MP2,CC)//B3LYP/6-311G(d,p) calculations. The kinetics of these reactions relevant to the growth of polycyclic aromatic hydrocarbons (PAH) under high-temperature conditions in circumstellar envelopes and in combustion flames has been studied employing the RRKM-Master Equation approach. The unimolecular reaction of 1-methylbiphenylyl proceeding via a five-membered ring closure followed by H elimination is predicted to be very fast, on a submicrosecond scale above 1000 K and to result in the formation of an embedded five-membered ring in the 9H-fluorene product. The 1-/2-methylnaphthyl + C2H2 reaction mechanism involves acetylene addition to the radical on the methylene group followed by a six- or five-membered ring closure and aromatization via an H atom loss. Despite of the complexity of the C13H11 PES, these straightforward pathways are dominant in the high-temperature regime (above ∼1000 K), with the prevailing products being phenalene, with a significant contribution of 1H-cyclopenta(a)naphthalene, for 1-methylnaphthyl + C2H2, and 1H-cyclopenta(b)naphthalene and 3H-cyclopenta(a)naphthalene, for 2-methylnaphthyl + C2H2. The methylnaphthyl reactions with acetylene represent a clean source of the three-ring PAHs, but they are relatively slow owing to the high entrance barriers of ∼10 kcal/mol, with the rate constants of about an order of magnitude lower as compared to those for naphthyl + allene and σ-aryl + C2H2. The 1-methylnaphthyl + C2H2 and 2-methylnaphthyl + C2H2 reactions represent prototypes for PAH growth by an extra six- and five-membered ring on a zigzag edge or a corner of PAH and the generated modified Arrhenius expressions are recommended for kinetic modeling of PAH expansion by the mechanism of acetylene addition to methylaryl radicals.

Formation of phenanthrenyl radicals via the reaction of acenaphthyl with acetylene

Ab initio G3(MP2,CC)/B3LYP/6–31G** calculations of the potential energy surface for the reaction of 3-acenaphthyl radical with acetylene were combined with Rice-Ramsperger-Kassel-Marcus Master Equation calculations of the temperature- and pressure-dependent reaction rate constants and product branching ratios with the goal to examine the transformation of an edge five-membered ring into a six-membered one. The reaction mechanism has been shown to contain two stages: (1) the formation of 3-ethynylacenaphthylene + H in the 3-acenaphthyl + C2H2 reaction via acetylene addition to the radical site and an H loss, (2) the formation of the 1-phenanthrenyl radical in the 3-ethynylacenaphthylene + H reaction via H addition to the five-membered ring followed by the ring flip. The results of kinetic modeling show this pathway being faster than the pathway proposed earlier featuring the CCH chemisorption on the six-membered ring without involvement of the five-membered ring. A kinetic test demonstrated the dominance of the former pathway for the formation of pyrene from naphthalene. It is expected that the new mechanism plays a major role in the transformation of five-membered rings on edges of PAH structures.

The gas-phase pyrolysis of cyclopropylamine. Quantum chemical characterisation of the intermediates involved

A computational study on the molecular structure, harmonic vibrational frequencies and thermochemical parameters of the postulated intermediates and final products involved in the gas-phase pyrolysis of (c-C3H5)NH2 (CPA) has been carried out by ab-initio and DFT methods. Internal rotor potentials were determined employing CAS-MP2 calculations for the singlet ĊH2CH2ĊHNH2 biradical and DFT for singlet CH3CH2C̈NH2, cis- and trans-CH3CH=CHNH2, E- and Z-CH3CH2CH=NH, (c-C3H5)NHCH(NH2)CH2CH3, E- and Z-(c-C3H5)N=CHCH2CH3. The enthalpies of formation at 0 and 298 K for these species were derived from isodesmic reactions using the B3LYP and M06-2X functionals coupled to the 6-311++G(3df,3pd) basis set and ab-initio G3(MP2) and G3(MP2)//B3LYP/6-311++G(3df,3pd) composite models. At the last level, enthalpies of formation at 298 K of 69.94 and 40.37 kcal mol−1 were estimated for the first time for ĊH2CH2ĊHNH2 and CH3CH2C̈NH2, and values of 7.28, 8.12, 5.37 and 6.08 kcal mol−1 were derived for cis-CH3CH=CHNH2, trans-CH3CH=CHNH2, E-CH3CH2CH=NH and Z-CH3CH2CH=NH, respectively. Accordingly, the pyrolysis of CPA to give ĊH2CH2ĊHNH2 and CH3CH2C̈NH2 is predicted to be endothermic by 51.58 and 22.01 kcal mol−1, whereas all other reaction steps are exothermic. For the overall reaction, 2 CPA → (c-C3H5)N=CHCH2CH3 + NH3, a standard change in enthalpy of about −20 kcal mol−1 was obtained.

QSPR Models to Predict Thermodynamic Properties of Cycloalkanes Using Molecular Descriptors and GA-MLR Method.

Aims and Objectives:QSPR models establish relationships between different types of structural information to their observed properties. In the present study the relationship between the molecular de-scriptors and quantum properties of cycloalkanes is represented.Materials and Methods:Genetic Algorithm (GA) and Multiple Linear Regressions (MLR) were successful-ly developed to predict quantum properties of cycloalkanes. A large number of molecular descriptors were calculated with Dragon software and a subset of calculated descriptors was selected with a genetic algorithm as a feature selection technique. The quantum properties consist of the heat capacity (Cv)/ Jmol-1K-1 entropy(S)/ Jmol-1K-1 and thermal energy(Eth)/ kJmol-1 were obtained from quantum-chemistry technique at the Hartree-Fock (HF) level using the ab initio 6-31G* basis sets.Results:The Genetic Algorithm (GA) method was used to select important molecular descriptors and then they were used as inputs for SPSS software package. The predictive powers of the MLR models were dis-cussed using Leave-One-Out (LOO) cross-validation, leave-group (5-fold)-out (LGO) and external predic-tion series. The statistical parameters of the training and test sets for GA–MLR models were calculated.Conclusion:The resulting quantitative GA-MLR models of Cv, S, and Eth were obtained:[r2=0.950, Q2=0.989, r2ext=0.969, MAE(overall,5-flod)=0.6825 Jmol-1K-1], [r2=0.980, Q2=0.947, r2ext=0.943, MAE(overall,5-flod)=0.5891Jmol-1K-1], and [r2=0.980, Q2=0.809, r2ext=0.985, MAE(overall,5-flod)=2.0284 kJmol-1]. The results showed that the predictive ability of the models was satisfactory, and the constitutional, topological indices and ring descriptor could be used to predict the mentioned properties of 103 cycloalkanes.

Синтез и идентификация 3,5-диметиленокситетрагидропиран-4-она

3,5-bis(hydroxymethyl)tetrahydro-4H-pyran-4-one by condensation of acetone with formaldehyde in the ratio of 1:4 in an alkaline medium at a temperature of 30-35°С (product yield 67.4%) was obtained. To determine the composition of obtained compound elemental analysis was used. Functional composition and structural elements were identified using IR spectroscopy. To prove the structure of the synthesized compound, 1H and 13C NMR spectra were taken on a JNN-ECA Jeol 400 spectrometer (at a frequency of 399.78 MHz and 100.53 MHz) with a CDCl3 solvent. Quantum-chemical calculations of stable conformations of 3,5-bis(hydroxymethyl)tetrahydro-4H-pyran-4-one was performed using ab initio DFT B3LYP method and 6-31G (d) and 6-311+G(3df,2p) basis sets. It was found that the stable conformers obtained by calculations are in the "chair" conformation; the hydroxymethyl substituents in conformer I are located equatorially, in conformation II – axially and equatorially, in conformation III – axially. In the conformer III, as a result of spatial proximity, hydroxymethyl substituents form an intramolecular hydrogen bond. The total energies and dipole moments were calculated; a lower value of the dipole moment of the conformation II may indicate its preference over the others.

A thermochemical study on the primary oxidation of sulfur

ABSTRACTSeveral chemical reactions related to the oxidation and combustion of sulfur are investigated using a number of computational chemistry methods with the objective of determining appropriate methods for use in developing an elementary reaction mechanism for oxidation of sulfur. Calculations are focused on thermochemical properties and reaction energetics for reactive species and transition state structures for reactions in the oxidation/combustion of sulfur. Reactions involving several intermediates resulting from the reactions of S2 with oxygen were investigated with the density functional theory B3LYP (with several basis sets) and BB1K/GTLarge. The composite ab-initio methods G2, G3, G3MP2, G3B3, G3MP2B3 and CBS-QB3 were also used. Enthalpies of a series of sulfur compounds and transition state structures are calculated using the ab-initio and DFT calculations. The calculations were combined with isodesmic reaction analysis, whenever possible, in order to cancel error and improve the accuracy of the calculations. Results show that all B3LYP DFT calculations including the 6–311++G(3df,2p) basis set show poor outcome in estimating the enthalpy of reactions involving S2. The six composite methods have all shown consistency with each other and their calculated reaction energies/bond energies are in good agreement with the available literature. Kinetic parameters for calculation of the kinetic parameters on SO3 dissociation to SO2 and O using the canonical transition state theory are reported.

Computational Study on the Unimolecular Decomposition of JP-8 Jet Fuel Surrogates III: Butylbenzene Isomers ( n-, s-, and t-C14H10).

Ab initio G3(CCSD,MP2)//B3LYP/6-311G(d,p) calculations of potential energy surfaces have been carried out to unravel the mechanism of the initial stages of pyrolysis of three C10H14 isomers: n-, s-, and t-butylbenzenes. The computed energy and molecular parameters have been utilized in RRKM-master equation calculations to predict temperature- and pressure-dependent rate constants and product branching ratios for the primary unimolecular decomposition of these molecules and for the secondary decomposition of their radical fragments. The results showed that the primary dissociation of n-butylbenzene produces mostly benzyl (C7H7) + propyl (C3H7) and 1-phenyl-2-ethyl (C6H5C2H4) + ethyl (C2H5), with their relative yields strongly dependent on temperature and pressure, together with a minor amount of 1-phenyl-prop-3-yl (C9H11) + methyl (CH3). Secondary decomposition reactions that are anticipated to occur on a nanosecond scale under typical combustion conditions split propyl (C3H7) into ethylene (C2H4) + methyl (CH3), ethyl (C2H5) into ethylene (C2H4) + hydrogen (H), 1-phenyl-2-ethyl (C6H5C2H4) into mostly styrene (C8H8) + hydrogen (H) and to a lesser extent phenyl (C6H5) + ethylene (C2H4), and 1-phenyl-prop-3-yl (C9H11) into predominantly benzyl (C7H7) + ethylene (C2H4). The primary decomposition of s-butylbenzene is predicted to produce 1-phenyl-1-ethyl (C6H5CHCH3) + ethyl (C2H5) and a minor amount of 1-phenyl-prop-1-yl (C9H11) + methyl (CH3), and then 1-phenyl-1-ethyl (C6H5CHCH3) and 1-phenyl-prop-1-yl (C9H11) rapidly dissociate to styrene (C8H8) + hydrogen (H) and styrene (C8H8) + methyl (CH3), respectively. t-Butylbenzene decomposes nearly exclusively to 2-phenyl-prop-2-yl (C9H11) + methyl (CH3), and further, 2-phenyl-prop-2-yl (C9H11) rapidly eliminates a hydrogen atom to form 2-phenylpropene (C9H10). If hydrogen atoms or other reactive radicals are available to make a direct hydrogen-atom abstraction from butylbenzenes possible, the C10H13 radicals (1-phenyl-but-1-yl, 2-phenyl-but-2-yl, and t-phenyl-isobutyl) can be formed as the primary products from n-, s-, and t-butylbenzene, respectively. The secondary decomposition of 1-phenyl-but-1-yl leads to styrene (C8H8) + ethyl (C2H5), whereas 2-phenyl-but-2-yl and t-phenyl-isobutyl dissociate to 2-phenylpropene (C9H10) + methyl (CH3). Thus, the three butylbenzene isomers produce distinct but overlapping nascent pyrolysis fragments, which likely affect the successive oxidation mechanism and combustion kinetics of these JP-8 fuel components. Temperature- and pressure-dependent rate constants generated for the initial stages of pyrolysis of butylbenzenes are recommended for kinetic modeling.

COMFORMATIONAL ANALYSIS AND ELECTRONIC PROPERTIES OF FLUOROMETHYLFURAN OLIGOMERS: SEMIEMPIRICAL AND DFT STUDY

Structural and electronic properties of oligomers of fluoromethylfurans (FMFs), OC4H4-CHnF3-n with n = 1, 2, 3 and 4 have been studied using ZINDO/AM1 and B3LYP/6-31G(d) basis set. Preliminary study using AM1 and ab initio (HF) 6-31G(d) with medium basis set was carried out on di-, tri- and tetramer FMFs in order to investigate the stability of configuration of the polymer chains and conformation analysis of the dimers. There is noticeable effect of substituents on the geometries of FMFs as compared to polyfuran, polymethylfuran and chloromethylfuran (CMF) analogues [11]as well as improved characteristics as conducting polymers compared polymethylfurans and CMFs. The most stable conformation is the anti-planar conformation except in fluoromethylfuran in which antigauche conformation is most stable. The energy band gaps, electronic spectroscopy and electronic dipole moment vectors of the compounds are presented. Generally FMFs present lower energy band gaps, longer wavelength and higher electric dipole moments and are therefore more suitable as monomer for conducting polymer especially trifluoromethylfuran.

(Invited) Water and Water-Dimer Encapsulations into C70 and C84

Water and water-dimer encapsulations into D5h-C70 and D2(22)-C84 & D2d(23)-C84 fullerenes are evaluated. The water-dimer equilibrium populations are computed using the potential-energy change from the ab initio G3 theory and anharmonic partition functions from the MP2/AUG-cc-pVQZ approach. The encapsulation energetics is treated at the M06-2X/6-31++G** level and it is found, for example, that the water-dimer storage in C84 is attractive, yielding an energy gain of more than 10kcal/mol. This substantial encapsulation energy together with the computed temperature increase of the water-dimer population in the saturated steam suggest that the (H2O)2@Cn endohedrals could also be produced in ahigh-temperature/high-pressure approach similarly to encapsulation of rare gases in fullerenes.

Rate coefficients for hydrogen abstraction reaction of pinonaldehyde (C10H16O2) with Cl atoms between 200 and 400 K: A DFT study

The kinetics of the reaction between pinonaldehyde (C 10 H 16 O 2) and Cl atom were studied using high level ab initio G3(MP2) and DFT based MPWB1K/6-31 + G(d) and MPW1K/6-31 + G(d) levels of theories coupled with Conventional Transition State Theory in the temperature range between 200 and 400 K. The negative temperature dependent rate expression for the title reaction obtained with Wigner’s and Eckart’s symmetrical tunneling corrections are k(T) =(5.1 ± 0.56) × 10 −19 T 2.35exp[(2098 ± 2)/T] cm 3 molecule −1 s −1, and k(T) =(0.92 ± 0.18) × 10 −19 T 2.60exp[(2204 ± 4)/T] cm 3 molecule −1 s −1, respectively, at G3(MP2)//MPWB1K method. The H abstraction reaction from the –CHO group was found to be the most dominant reaction channel among all the possible reaction pathways and its corresponding rate coefficient at 300 K is k(Eckart’s unsymmetrical) = 3.86 ×10−10 cm 3 molecule −1 s −1. Whereas the channel with immediate lower activation energy is the H-abstraction from –CH- group (Tertiary H-abstraction site, C g). The rate coefficient for this channel is k Cg(Eckart’s unsymmetrical) = 1.83 ×10−15 cm 3 molecule −1 s −1 which is smaller than the dominant channel by five orders of magnitude. The atmospherically relevant parameters such as lifetimes were computed in this investigation of its reaction with Cl atom. The kinetics of the reaction between pinonaldehyde (C10H16O2) and Cl atom were studied computationally and computed the rate coefficients in the temperature range between 200 and 400 K. The H abstraction reaction from the –CHO group is found to be the most dominant reaction channel among all the possible reaction pathways.

(Invited) Water-Dimer Encapsulations into C84

The water-dimer formation and its encapsulation into D2(22)-C84 and D2d(23)-C84 fullerenes is computed, following similar evaluations [1] with C60. The water-dimer equilibrium populations are calculated using the potential-energy change from the ab initio G3 theory and anharmonic partition functions from the MP2/AUG-cc-pVQZ approach. The encapsulation energetics is treated at the M06-2X/6-31++G** level and it is found that the water-dimer storage in C84 is attractive, yielding an energy gain of more than 10kcal/mol. This substantial encapsulation energy together with the computed temperature increase of the water-dimer population in the saturated steam suggest that the (H2O)2@C84 endohedrals could be produced in a high-temperature/high-pressure approach similarly to encapsulation of rare gases in fullerenes. [1] F. Uhlik, Z. Slanina, S.-L. Lee, B.-C. Wang, L. Adamowicz, S. Nagase, J. Comput. Theor. Nanosci. 12, 959 (2015); 12, 2622 (2015).

Quantum chemical theory calculations on the mechanism of the homogeneous, unimolecular gas-phase elimination kinetics of selected diazirines

Theoretical calculations on the gas-phase thermal decomposition of dimethyldiazirine, diethyldiazirine and difluorodiazirine have been carried out using ab initio composite methods CBS-QB3 and G3, and DFT CAM-B3LYP, MPW1PW91, PBE1PBE and M062X. Reasonable agreement has been found with the experimental values by the G3 method. Two possible mechanisms were studied: Mechanism A consists the opening of the heterocyclic ring with hydrogen transfer to a nitrogen atom to form prop-1-en-2-yldiazene intermediate which later decomposes to nitrogen gas and the corresponding olefin. Mechanism B involves the extrusion of nitrogen molecule with the formation of carbene intermediate which subsequently yields the corresponding olefin. The results obtained from G3 calculations support the mechanism of a carbene intermediate. Population analysis and Wiberg’s bond order show an interaction between the leaving nitrogen and the electron deficient carbon formed during the first step of the reaction.

Kinetic Study of Di‐Tert‐Butyl Peroxide: Thermal Decomposition and Product Reaction Pathways

ABSTRACTThe major reaction path for oxidation of di‐tert‐butyl peroxide (DTBP) is generally considered to occur via fission of the weak peroxide ROOR bond at temperatures above 393 K. The initial stable intermediates in the thermal decomposition or combustion of DTBP are acetone and ethane, and the overall reaction is accompanied by an important heat release which when mixed with air (oxygen) may exceed the self‐ignition temperatures. A kinetic study on plausible DTBP reaction paths was initiated in this work, and a detailed study of the thermochemistry of new intermediates, transition state structures, and products is reported. The density functional theory (DFT; B3LYP/6‐311g(d,p)), which is practical for large compounds along with the composite ab initio G3MP2B3 and G3 calculations, (when possible), are used. Computational chemistry results from DFT and ab initio calculations are coupled with isodesmic reaction analysis which, as demonstrated in previous studies, results in good accuracy. Over 10 unimolecular decomposition pathways are identified and reported.

Insights into 2-Chloropyrimidine fragmentation through a thermochemical analysis of the ionic fragments

In the present work we have studied the photoinduced ion chemistry of the 2Cl-pyrimidine molecule in the energy region 9−14 eV. The theoretical gas phase enthalpies of formation of the main fragments calculated using the G3B3 and G2 ab initio methods are compared to the experimental values, derived by the measured appearance energy of the fragments. This approach provides new insights into both the geometric structure of the ionic fragments and the basic mechanisms governing the molecular fragmentation.

Reaction dynamics of the 4-methylphenyl radical (p-tolyl) with 1,2-butadiene (1-methylallene): are methyl groups purely spectators?

The reactions of the 4-tolyl radical (C6H4CH3) and of the D7-4-tolyl radical (C6D4CD3) with 1,2-butadiene (C4H6) have been probed in crossed molecular beams under single collision conditions at a collision energy of about 54 kJ mol(-1) and studied theoretically using ab initio G3(MP2,CC)//B3LYP/6-311G** and statistical RRKM calculations. The results show that the reaction proceeds via indirect scattering dynamics through the formation of a van-der-Waals complex followed by the addition of the radical center of the 4-tolyl radical to the C1 or C3 carbon atoms of 1,2-butadiene. The collision complexes then isomerize by migration of the tolyl group from the C1 (C3) to the C2 carbon atom of the 1,2-butadiene moiety. The resulting intermediate undergoes unimolecular decomposition via elimination of a hydrogen atom from the methyl group of the 1,2-butadiene moiety through a rather loose exit transition state leading to 2-para-tolyl-1,3-butadiene (p4), which likely presents the major reaction product. Our observation combined with theoretical calculations suggest that one methyl group (at the phenyl group) acts as a spectator in the reaction, whereas the other one (at the allene moiety) is actively engaged in the underlying chemical dynamics. On the contrary to the reaction of the phenyl radical with allene, which leads to the formation of indene, the substitution of a hydrogen atom by a methyl group in allene essentially eliminates the formation of bicyclic PAHs such as substituted indenes in the 4-tolyl plus 1,2-butadiene reaction.

Theoretical investigations on kinetics, mechanism and thermochemistry of the gas phase reactions of CHF2OCF2CHF2 with OH radicals

Theoretical investigations were carried out on the mechanism, kinetics and thermochemistry of the gas-phase reactions between CHF2CF2OCHF2 and OH radical using the high level ab initio G2(MP2) and hybrid density functional MPWB1K/6-31+G(d,p) methods. Two most stable conformers of CHF2CF2OCHF2 are identified and the energy difference between them is found to be only 0.3kcalmol−1. Both of them are considered for rate coefficient calculations in our study and the contribution from each of the conformers is found to be quite significant in the temperature range of our study. The rate coefficients are determined for the first time in a wide range of temperature 250–1000K. The calculated total rate coefficient value kOH=1.01×10−15cm3molecule−1s−1 is in reasonably good agreement with the experimental value of kOH=2.36×10−15cm3molecule−1s−1 at 298K. The heats of formation for CHF2CF2OCHF2 and CHF2CF2OCF2 and CF2CF2OCHF2 radicals are estimated to be −359.64, −305.43 and −306.88kcalmol−1, respectively. The bond dissociation energies of the two C–H bonds are CHF2CF2OC(–H)F2: 106.3kcalmol−1 and C(–H)F2CF2OCHF2: 104.8kcalmol−1. The atmospheric lifetime of CHF2OCF2CHF2 is estimated to be around 35years.

Formation Mechanism of Polycyclic Aromatic Hydrocarbons beyond the Second Aromatic Ring

The formation mechanism of polycyclic aromatic hydrocarbons (PAH) with three fused aromatic rings starting from naphthalene has been studied using accurate ab initio G3(MP2,CC)//B3LYP/6-311G** calculations followed by the kinetic analysis of various reaction pathways and computations of relative product yields. The results reveal new insights into the classical hydrogen abstraction-C2H2 addition (HACA) scheme of PAH growth. The HACA mechanism has been shown to produce mostly cyclopentafused PAHs instead of PAHs with six-member rings only, in contrast to the generally accepted view on this mechanism. Considering naphthalene as the initial reactant, the HACA-type synthesis of higher PAHs with all six-member rings, anthracene and phenanthrene, accounts only for 3-6% of the total product yield at temperatures relevant to combustion (1000-2000 K), whereas cyclopentafused PAHs, including acenaphthalene (41-48%), 4-ethynylacenaphthalene (∼14%), 3-ethynylacenaphthalene (∼7.5%), 1-methylene-1H-cyclopenta[b]naphthalene (∼6%), and 3-methylene-3H-cyclopenta[a]naphthalene (∼5%), account for another ∼75%. It has been shown that acetylene addition to the radical site adjacent to the bay region in naphthalene (as in 1-naphthyl radical) or other similar PAH with a bay region is highly unlikely to be followed by the addition of a second acetylene molecule; alternatively, the bay region closure with a buildup of a new five-member ring occurs. Acetylene addition to a nonbay carbon atom (as in 2-naphthyl radical) can be followed by the second acetylene addition only at T < 1000 K, producing anthracene and phenanthrene. However, at temperatures relevant to combustion, such pathways give negligible contributions to the total product yield, whereas the dominant reaction product, 2-ethynylnaphthalene, is formed by simple hydrogen atom elimination from the attached ethenyl group. An additional six-member ring buildup may occur only after intermolecular hydrogen abstraction from ethynyl-substituted PAH (2-ethynylnaphthalene), in particular, from the carbon atoms adjacent to the existing ethynyl (C2H) fragment, followed by C2H2 addition producing adducts with two ethynyl C2H and ethenyl C2H2 groups next to each other, which then undergo a fast six-member ring closure. Nevertheless, this process has been shown to be relatively minor (∼25%), whereas the major process is a five-member ring closure involving the same C2H and C2H2 groups and leading to a cyclopentafused PAH molecule. Although the computed product yields show a good agreement with experimentally observed concentrations of acenaphthalene and anthracene in various aliphatic and aromatic flames, the yield of phenanthrene, which exhibits an order of magnitude higher concentration than anthracene both in combustion flames and environmental mixtures, via the considered pathways is significantly underpredicted. This result points at the possible existence of another mechanism responsible for the formation of phenanthrene and other all-six-member-ring PAHs. The overall kinetic scheme for the HACA buildup process leading to various three-ring PAHs (both with six-member rings only and cyclopentafused) from naphthalene, which can be included in flame kinetic models, has been constructed, with rate constants for all individual reaction steps provided.

Determining In Situ Protein Conformation and Orientation from the Amide-I Sum-Frequency Generation Spectrum: Theory and Experiment

Vibrational sum-frequency generation (VSFG) spectra of the amide-I band of proteins can give detailed insight into biomolecular processes near membranes. However, interpreting these spectra in terms of the conformation and orientation of a protein can be difficult, especially in the case of complex proteins. Here we present a formalism to calculate the amide-I infrared (IR), Raman, and VSFG spectra based on the protein conformation and orientation distribution. Based on the protein conformation, we set up the amide-I exciton Hamiltonian for the backbone amide modes that generate the linear and nonlinear spectroscopic responses. In this Hamiltonian, we distinguish between nearest-neighbor and non-nearest-neighbor vibrational couplings. To determine nearest-neighbor couplings we use an ab initio 6-31G+(d) B3LYP-calculated map of the coupling as a function of the dihedral angles. The other couplings are estimated using the transition-dipole coupling model. The local-mode frequencies of hydrogen-bonded peptide bonds and of peptide bonds to proline residues are red-shifted. To obtain realistic hydrogen-bond shifts we perform a molecular dynamics simulation in which the protein is solvated by water. As a first application, we measure and calculate the amide-I IR, Raman, and VSFG spectra of cholera toxin B subunit docked to a model cell membrane. To deduce the orientation of the protein with respect to the membrane from the VSFG spectra, we compare the experimental and calculated spectral shapes of single-polarization results, rather than comparing the relative amplitudes of VSFG spectra recorded for different polarization conditions for infrared, visible, and sum-frequency light. We find that the intrinsic uncertainty in the interfacial refractive index--essential to determine the overall amplitude of the VSFG spectra--prohibits a meaningful comparison of the intensities of the different polarization combinations. In contrast, the spectral shape of most of the VSFG spectra is independent of the details of the interfacial refractive index and provides a reliable way of determining molecular interfacial orientation. Specifically, we find that the symmetry axis of the cholera toxin B subunit is oriented at an angle of 6° ± 17° relative to the surface normal of the lipid monolayer, in agreement with 5-fold binding between the toxin's five subunits and the receptor lipids in the membrane.

Low-Temperature Mechanisms for the Formation of Substituted Azanaphthalenes through Consecutive CN and C2H Additions to Styrene and N-Methylenebenzenamine: A Theoretical Study

Ab initio G3(MP2,CC)/B3LYP/6-311G** calculations of potential energy surfaces (PESs) for the reactions of cyano and ethynyl radicals with styrene and N-methylenebenzenamine have been performed to investigate a possible formation mechanism of the prototype nitrogen-containing polycyclic aromatic compounds: (substituted) 1- and 2-azanaphthalenes. The computed PESs and molecular parameters have been used for RRKM and RRKM-Master Equation calculations of reaction rate constants and product branching ratios under single-collision conditions and at pressures from 3 to 10(-6) mbar and temperatures of 90-200 K relevant to the organic aerosol formation regions in the stratosphere of a Saturn's moon Titan. The results show that ethynyl-substituted 1- and 2-azanaphthalenes can be produced by consecutive CN and C2H additions to styrene or by two C2H additions to N-methylenebenzenamine. All CN and C2H radical addition complexes are formed in the entrance channels without barriers, and the reactions are computed to be exothermic, with all intermediates and transition states along the favorable pathways residing lower in energy than the respective initial reactants. The reactions are completed by dissociation of chemically activated radical intermediates via H losses, so that collisional stabilization of the intermediates is not required to form the final products. These features make the proposed mechanism viable even at very low temperatures and under single-collision conditions and especially significant for astrochemical environments. In Titan's stratosphere, collisional stabilization of the initial CN + styrene reaction adducts may be significant, but substantial amounts of 2-vinylbenzonitrile and 2-ethynyl-N-methylenebenzenamine can still be produced and then react with C2H to form substituted azanaphthalenes.

Conformational Analysis of Some β-Halohydrins via G3 Calculations

The conformational analysis of fifteen β-halohydrins, XCR1R2CR3R4OH, (X=F, Cl and Br) had been studied by ab initio G3 method. The enthalpies of formation values were calculated for nine conformers of each β-halohydrin. The (g , g + ) and (g + , g ) conformers were found to be the most stable due to intramolecular H-bond formation. These H-bonds are weaker than intermolecular H-bonds formed between alkyl halides and alcohols. This trend is more obvious in flouro-species. The rotation of C- X bond of (g , g + ) conformers by 360 ° gives three transition states, this rotation was found to require 6-7 kcal/mol.