On the formation of resonantly stabilized C5H3 radicals--a crossed beam and ab initio study of the reaction of ground state carbon atoms with vinylacetylene

The formation of polycyclic aromatic hydrocarbons in combustion environments is linked to resonance stabilized free radicals. Here, we investigated the reaction dynamics of ground state carbon atoms, C((3)P(j)), with vinylacetylene at two collision energies of 18.8 kJ mol(-1) and 26.4 kJ mol(-1) employing the crossed molecular beam technique leading to two resonantly stabilized free radicals. The reaction was found to be governed by indirect scattering dynamics and to proceed without an entrance barrier through a long-lived collision complex to reach the products, n- and i-C(5)H(3) isomers via tight exit transition states. The reaction pathway taken is dependent on whether the carbon atom attacks the π electron density of the double or triple bond, both routes have been compared to the reactions of atomic carbon with ethylene and acetylene. Electronic structure/statistical theory calculations determined the product branching ratio to be 2:3 between the n- and i-C(5)H(3) isomers.     

A combined crossed molecular beam and ab initio investigation of C2 and C3 elementary reactions with unsaturated hydrocarbons--pathways to hydrogen deficient hydrocarbon radicals in combustion flames

Crossed molecular beam experiments on dicarbon and tricarbon reactions with unsaturated hydrocarbons acetylene, methylacetylene, and ethylene were performed to investigate the dynamics of channels leading to hydrogen-deficient hydrocarbon radicals. In the light of the results of new ab initio calculations, the experimental data suggest that these reactions are governed by an initial addition of C2/C3 to the pi molecular orbitals forming highly unsaturated cyclic structures. These intermediates are connected via various transition states and are suggested to ring open to chain isomers which decompose predominantly by displacement of atomic hydrogen, forming C4H, C5H, HCCCCCH2, HCCCCCCH3, H2CCCCH and H2CCCCCH. The C2(1 sigma g+) + C2H4 reaction has no entrance barrier and the channel leading to the H2CCCCH product is strongly exothermic. This is in strong contrast with the C3(1 sigma g+) + C2H4 reaction as this is characterized by a 26.4 kJ mol-1 threshold to form a HCCCCCH2 isomer. Analogous to the behavior with ethylene, preliminary results on the reactions of C2 and C3 with C2H2 and CH3CCH showed the H-displacement channels of these systems to share many similarities such as the absence/presence of an entrance barrier and the reaction mechanism. The explicit identification of the C2/C3 vs. hydrogen displacement demonstrates that hydrogen-deficient hydrocarbon radicals can be formed easily in environments like those of combustion processes. Our work is a first step towards a systematic database of the intermediates and the reaction products which are involved in this important class of reactions. These findings should be included in future models of PAH and soot formation in combustion flames.     

Short-time Fourier transform analysis of ab initio molecular dynamics simulation: collision reaction between CN and C4H6

Collision reactions between cyano radical (CN) and dimethylacetylene (C4H6) are thought to occur in the atmosphere of Saturn's moon Titan. However, it is difficult to reproduce reactions occurring in unique environments to study their dynamical processes. In this study, collision reactions between CN and C4H6 were investigated using ab initio molecular dynamics (AIMD) simulations. The simulation results were categorized into three kinds: nonreactive collision, incorporation, and substitution. Short-time Fourier transform analysis of velocity autocorrelation functions obtained by the AIMD simulations, which has been recently developed by our research group, was performed to examine the nonequilibrium condition of the vibrational states. Spectrograms, which correspond to the time evolution of power spectra, clarify the relationship between the three reaction channels and the dynamical changes of the vibrational states.     

An ab initio SCF + CI study of the SH3 and SF3 radicals

The symmetric sulfuranyl radicals SH₃ and SF₃ are studied by means of ab initio SCF + CI calculations. All geometries are optimized at the UHF level using analytical gradients. SH₃ is found to be a transition state corresponding to a hydrogen exchange reaction, whereas SF₃ is stable with respect to decomposition to SF₂ + F.     

Comparative study between ab initio and semiempirical electrostatic potentials on molecular surfaces

The electrostatic potentials of 21 molecules containing different functional groups has been computed at the ab initio RHF/6-31G* level on a series of solvent accessible surfaces and compared with MNDO, AM1, and PM3-derived pontentials. We analyzed in detail the distribution of electrostatic potentials on the surfaces around their maximum and minimum values and found out that consistently MNDO gives results similar to ab initio potentials. The actual values of the MNDO electrostatic potentials show a systematic deviation from the “correct” results, but the pattern of the MEP distribution on the surface is similar to that of the ab initio results. In contrast, PM3 fails in some cases to give even the correct number or distribution of “hot spots” of potential (low MEP) on the surface. AM1 behaves somewhere between these two semiempirical methods. As a conclusion, MNDO would be suggested as the best approach to analyses requiring a fast and efficient mapping of electrostatic potentials on simplified models of molecular surfaces. © 1993 John Wiley & Sons, Inc.     

A crossed beam and ab initio study of the reaction of atomic boron with ethylene

The reaction of atomic boron, B(2P), with the simplest alkene, C2H4, has been investigated under single collision conditions in crossed beam experiments with mass spectrometric detection. Our experimental data clearly showed that the atomic boron versus hydrogen exchange reaction led to molecule(s) of gross formula C2H3B via bound intermediate(s). According to the experimentally derived fraction of the available energy released as product translational energy, we propose that an important reaction pathways is the one leading to the borirene plus atomic hydrogen and/or the one leading to ethynylborane plus atomic hydrogen. The experimental results are accompanied by electronic structure calculations of the relevant potential energy surface and RRKM estimates of the product branching ratio. According to RRKM calculations, within the limit of complete energy randomization, the three isomers borirene, BH=C=CH2 and BH2-CCH, are all formed, with BH2-CCH being the dominant one. The discrepancies between the trend of the product translational energy distributions and the picture emerging from RRKM estimates are a symptom that a statistical treatment is not warranted for this system.     

Reaction dynamics on the formation of 1- and 3-cyanopropylene in the crossed beams reaction of ground-state cyano radicals (CN) with propylene (C3H6) and its deuterated isotopologues

Crossed molecular beams experiments were utilized to explore the chemical reaction dynamics of ground-state cyano radicals, CN(X(2)Sigma(+)), with propylene (CH3CHCH2) together with two d3-isotopologues (CD3CHCH2, CH3CDCD2) as potential pathways to form organic nitriles under single collision conditions in the atmosphere of Saturn's moon Titan and in the interstellar medium. On the basis of the center-of-mass translational and angular distributions, the reaction dynamics were deduced to be indirect and commenced via an addition of the electrophilic cyano radical with its radical center to the alpha-carbon atom of the propylene molecule yielding a doublet radical intermediate: CH3CHCH2CN. Crossed beam experiments with propylene-1,1,2-d3 (CH3CDCD2) and propylene-3,3,3-d3 (CD3CHCH2) indicated that the reaction intermediates CH3CDCD2CN (from propylene-1,1,2-d3) and CD3CHCH2CN (from propylene-3,3,3-d3) eject both atomic hydrogen through tight exit transition states located about 40-50 kJ mol(-1) above the separated products: 3-butenenitrile [H2CCDCD2CN] (25%), and cis/trans-2-butenenitrile [CD3CHCHCN] (75%), respectively, plus atomic hydrogen. Applications of our results to the chemical processing of cold molecular clouds like TMC-1 and OMC-1 are also presented.     

The single-electron hydrogen, lithium, and halogen bonds with HBe, H2B, and H3C radicals as the electron donor: an ab initio study

Quantum chemical calculations have been performed for the complexes with HBe, H₂B, and H₃C radicals as the electron donors and with HF, LiF, and ClF as the electron acceptors. For HBe, H₂B, and H₃C radicals, the ability of donating electrons is dependent on the nature of the electron donor atom. In addition, it is also affected by the nature of the electron acceptor atom. A partially covalent bond is formed in HBe–Cl···F and H₂B–Cl···F complexes, which exhibits a large interaction energy, short binding distance, large bond elongation, and big frequency shift. The complexes have also been analyzed with natural bond orbital and atoms in molecules.     

Energy-flow dynamics in the molecular channel of propanal photodissociation, C2H5CHO --> C2H6 + CO: direct ab initio molecular dynamics study

Direct ab initio molecular dynamics calculations have been carried out for the molecular channel of the photodissociation of propanal, C2H5CHO --> C2H6 + CO, at the RMP2(full)/cc-pVDZ level of ab initio molecular orbital theory. The initial conditions were generated using the microcanonical sampling to put the excess energy randomly into all vibrational modes of the TS. Starting from the TS, a total of approximately 700 trajectories were numerically integrated for 100 fs. The obtained final energy distributions for the C2H6 and CO fragments and their relative translational motion were found to be quite similar to those obtained for the acetaldehyde reaction, CH3CHO --> CH4 + CO, in our previous study (Chem. Phys. Lett. 2006, 421, 549) despite the fact that the number of degree of freedom for C2H6 is larger than that for CH4. The coupling between the intrinsic reaction coordinate and one of the generalized normal modes orthogonal to it was predicted substantially strong around s = 1.4 amu(1/2) bohr, and it is expected that the energy flow out of C2H6 proceeds through this coupling. However, the obtained energy distributions strongly suggest that the coupling among the modes in C2H6 is quite small and the intramolecular energy redistribution does not occur efficiently in this molecule.     

Hydrogen bonded structure and dynamics of liquid-vapor interface of water-ammonia mixture: an ab initio molecular dynamics study

We have carried out ab initio molecular dynamics simulations of a liquid-vapor interfacial system consisting of a mixture of water and ammonia molecules. We have made a detailed analysis of the structural and dynamical properties of the bulk and interfacial regions of the mixture. Among structural properties, we have looked at the inhomogeneous density profiles of water and ammonia molecules, hydrogen bond distributions, orientational profiles, and also vibrational frequency distributions of bulk and interfacial molecules. It is found that the interfacial molecules show preference for specific orientations so as to form water-ammonia hydrogen bonds at the interface with ammonia as the acceptor. The structure of the system is also investigated in terms of inter-atomic voids present in the system. Among the dynamical properties, we have calculated the diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational spectral diffusion in bulk and interfacial regions. It is found that the diffusion and orientation relaxation of the interfacial molecules are faster than those of the bulk. However, the hydrogen bond lifetimes are longer at the interface which can be correlated with the time scales found from the decay of frequency time correlations.     

Accurate ab initio predictions of ionization energies of hydrocarbon radicals: CH2, CH3, C2H, C2H3, C2H5, C3H3, and C3H5

The ionization energies for methylene (CH2), methyl (CH3), ethynyl (C2H), vinyl (C2H3), ethyl (C2H5), propargyl (C3H3), and allyl (C3H5) radicals have been calculated by the wave-function-based ab initio CCSD(T)/CBS approach, which involves the approximation to the complete basis set (CBS) limit at the coupled-cluster level with single and double excitations plus a quasiperturbative triple excitation [CCSD(T)]. When it is appropriate, the zero-point vibrational energy correction, the core-valence electronic correction, the scalar relativistic effect correction, the diagonal Born-Oppenheimer correction, and the high-order correlation correction have also been made in these calculations. The comparison between the computed ionization energy (IE) values and the highly precise experimental IE values determined in previous pulsed field ionization-photoelectron (PFI-PE) studies indicates that the CCSD(T)/CBS method is capable of providing accurate IE predictions for these hydrocarbon radicals achieving error limits well within +/-10 meV. The benchmarking of the CCSD(T)/CBS IE predictions by the PFI-PE experimental results also lends strong support for the conclusion that the CCSD(T)/CBS approach with high-level energy corrections can serve as a valuable alternative for reliable IE determination of radicals, particularly for those radicals with very unfavorable Franck-Condon factors for photoionization transitions near their ionization thresholds.     

A crossed beams study of the reaction of carbon atoms, C(3Pj), with vinyl cyanide, C2H3CN(X 1A')--investigating the formation of cyano propargyl radicals

The chemical dynamics of the reaction of ground state carbon atoms, C(3Pj), with vinyl cyanide, C2H3CN(X 1A'), were examined under single collision conditions at collision energies of 29.9 and 43.9 kJ mol(-1) using the crossed molecular beams approach. The experimental studies were combined with electronic structure calculations on the triplet C4H3N potential energy surface (H. F. Su, R. I. Kaiser, A. H. H. Chang, J. Chem. Phys., 2005, 122, 074320). Our investigations suggest that the reaction follows indirect scattering dynamics via addition of the carbon atom to the carbon-carbon double bond of the vinyl cyanide molecule yielding a cyano cyclopropylidene collision complex. The latter undergoes ring opening to form cis/trans triplet cyano allene which fragments predominantly to the 1-cyano propargyl radical via tight exit transition states; the 3-cyano propargyl isomer was inferred to be formed at least a factor of two less; also, no molecular hydrogen elimination channel was observed experimentally. These results are in agreement with the computational studies predicting solely the existence of a carbon versus hydrogen atom exchange pathway and the dominance of the 1-cyano propargyl radical product. The discovery of the cyano propargyl radical in the reaction of atomic carbon with vinyl cyanide under single collision conditions implies that this molecule can be an important reaction intermediate in combustion flames and also in extraterrestrial environments (cold molecular clouds, circumstellar envelopes of carbon stars) which could lead to the formation of cyano benzene (C6H5CN) upon reaction with a propargyl radical.     

C2BH3稳定性与芳香性的从头算研究

在密度泛函理论B3LYP/6-311 G(2df)水平上,对C2BH3异构体进行结构优化和简谐振动频率计算。结果表明C2BH3基态为平面环状结构(1A1,C2V)。分子轨道分析显示基态有一个垂直于分子平面、双电子占据的π分子轨道;其三元环几何中心核独立化学位移(NICS)为较大负值,这些表明基态分子具有较强的芳香性。在相同的理论水平上,本文最后详细地分析了基态的红外振动光谱。     

A data mining and ab initio study of the interaction between the aromatic and backbone amide groups in proteins

Interactions between aromatic groups and backbone amide groups in protein environments are characterized both through data mining analyses of X‐ray protein structures and through ab initio molecular orbital calculations on a model complex. The data mining analyses of 1029 X‐ray protein structures elucidate the configurational characteristics of the interaction as well as the positions of the interacting moieties involved. On a statistical average, more than seven such interactions occur in a typical protein structure. The configurations of these interactions are restricted with the face‐to‐face orientation as the preferred arrangement. The interaction occurs mainly within a single peptide chain. Both α‐helix and β‐strand secondary structures provide an almost equal number of backbone amides to participate within this interaction. The interaction energy was evaluated with the supermolecular ab initio method at the MP2 level. It is shown that aromatic–amide(backbone) interactions identified in proteins can achieve a stabilization energy of 3.3 kcal/mol. The interaction involves the entirety of the backbone amide rather than only its amine portion. This study concludes that the interaction between aromatic and backbone amide groups is of general significance to protein structure due to its strength and common occurrence. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 80: 44–60, 2000     

Heavy atom nitroxyl radicals. V. An experimental and ab initio study of the previously unknown H2PS free radical

The B?(2)A(')-X?(2)A(') transition of the prototypical thiophosphoryl radical, H(2)PS, was observed for the first time using laser-induced fluorescence and single vibronic level emission spectroscopy. H(2)PS and its deuterated isotopologues, D(2)PS and HDPS, were produced in a pulsed supersonic discharge jet from a precursor mixture of Cl(3)PS and H(2) or D(2) or an H(2)/D(2) mixture in high-pressure argon. High level ab initio calculations of the lowest three doublet electronic states helped in the definitive assignment of the B?-X? transition, which involves electron promotion from the π to the π? orbital. Vibrational frequencies were determined for several modes of each isotopologue in the X? and B? states and found to be in accord with theoretical predictions. Although a line-by-line rotational analysis was not possible, the observed band contours are consistent with the geometries obtained from our ab initio calculations. Theory indicates that PS bond length increases upon electronic excitation, while the pyramidalization of the radical does not change significantly.     

A molecular mechanics and ab initio prediction of the 1H chemical shifts of pinanes

Molecular mechanics calculations plus the application of a refined Karplus equation gave the conformations of 19 pinanes. These range from a Y‐shaped geometry in the apopinene and α‐pinene series to a pseudo chair conformation in β‐pinene, nopinone and verbanone, a flattened chair in pinocarvone and the pinocarveols and a distorted Y shape for iso‐verbanone. These structures were then used as input to predict the ¹H chemical shifts of these compounds by semi‐empirical (¹H‐NMR spectra (HSPEC)) and ab initio gauge‐invariant atomic orbital (GIAO) calculations, the latter at the B3LYP hybrid density functional theory level using 6‐31++G** basis set. The two methods gave generally good agreement with the 184 observed shifts with root mean square (RMS) errors 0.07 ppm (HSPEC) and 0.10 ppm (GIAO), but the GIAO calculations gave several significant (>0.25 ppm) errors. One was for the H₃ proton in apopinenone and other α,β unsaturated ketones; the others occurred for protons in close proximity to hydroxyl groups. To provide more information, smaller analogues of known geometry and chemical shifts were subject to the same analysis. In cyclopentenone, the Gaussian geometry gave good agreement with the observed shifts, but the MMFF94, MMX and MM3 geometries all gave errors for different protons. These results show clearly that the molecular geometries of the α,β unsaturated ketones are responsible for the errors. The errors for the alcohols were examined using ethanol as model and were shown to be due to the different possible conformations of the OH group. Similar GIAO calculations on substituted methanes gave good agreement for the methyl compounds but poor agreement for di and tri halosubstituted methanes. The aforementioned method of molecular mechanics plus GIAO calculations is shown to be a very useful tool for the investigation of molecular geometries and conformations. However, multihalogen compounds may require different basis sets for accurate calculations. Copyright © 2017 John Wiley & Sons, Ltd.     

Hyperfine interactions in aqueous solution of Cr3+: an ab initio molecular dynamics study

We performed an ab initio molecular dynamics simulation of the paramagnetic transition metal ion Cr³⁺ in aqueous solution. Isotropic hyperfine coupling constants between the electron spin of the chromium ion and nuclear spins of all water molecules have been determined for instantaneous snapshots extracted from the trajectory. The coupling constant of first sphere oxygen, A _iso(¹⁷O_I)=1.9±0.3 MHz, is independent on Cr–O_I distance but increases with the tilt angle for the water molecule approaching 180°. First sphere hydrogen spins have A _iso(¹ H_I)=2.1±0.2 MHz which decreases with increasing tilt angle and shows a Cr–H_I distance dependence. The hyperfine coupling constants for second sphere ¹⁷O is negative and an order of magnitude smaller (−0.20±0.02 MHz) compared to first sphere.     

Reactions between rubidium atoms and C6F6, C2Cl4, C2HCl3, CH2=CCl2 or trans-C2H2Cl2 in crossed molecular beams

Molecular and fragment negative ions are produced from the collisions between rubidium atoms and several kinds of halogenated unsaturated organic molecules in crossed supersonic beams. Their apparent electron affinities and the bond dissociation energies are measured.     

A spectroscopic and ab initio study on Bi(III) complex formation with 3-mercaptopropanesulfonic acid

This article deals with complex formation of Bi(III) with 3-mercaptopropanesulfonic acid (H₂MPS) in aqueous perchloric acid solutions, with synthesis and characterization of a solid 3-mercaptopropanesulfonate complex of bismuth(III). The stoichiometry and structures of Bi-MPS species in aqueous solution and of a solid complex have been studied by UV–Vis, ¹H-NMR, ICP-AES, Raman, and EXAFS spectroscopic methods; the structures have also been simulated with DFT/PBE0 calculations. The Bi(III) L_III-edge EXAFS oscillation for a solid compound with the empirical formula [Bi(HMPS)₂(ClO₄)]⁰ was simulated with two Bi–S interatomic distances at 2.50 ± 0.01 Å, two Bi–O distances at 2.56 ± 0.02 Å and two Bi–O distances at 2.75 ± 0.02 Å. Implementation of the same approach for aqueous solutions on the assumption of S₃BiO₃ coordination at the H₂MPS?:?Bi(III) mole ratio ≥ 3.0 revealed three Bi–S bonds at 2.53 ± 0.02 Å and three Bi–O bonds at 2.68 ± 0.02 Å, respectively. Optimized geometries, electronic structures of Bi(HMPS)₃ and [Bi(HMPS)₂ClO₄]⁰, vibrational properties of [Bi(HMPS)₂ClO₄]⁰, and electronic absorption spectrum of Bi(HMPS)₃ species obtained by DFT and TD–DFT modeling are consistent with empirical parameters. In the UV–Vis spectrum of Bi(HMPS)₃ the LMCT and MLCT S^2? ? Bi³⁺ band appears at 268 nm.     

Electron super-rich radicals in the gas phase. A neutralization-reionization mass spectrometric and ab initio/RRKM study of diaminohydroxymethyl and triaminomethyl radicals

Diaminohydroxymethyl (1) and triaminomethyl (2) radicals were generated by femtosecond collisional electron transfer to their corresponding cations (1+ and 2+, respectively) and characterized by neutralization-reionization mass spectrometry and ab initio/RRKM calculations at correlated levels of theory up to CCSD(T)/aug-cc-pVTZ. Ion 1+ was generated by gas-phase protonation of urea which was predicted to occur preferentially at the carbonyl oxygen with the 298 K proton affinity that was calculated as PA = 875 kJ mol-1. Upon formation, radical 1 gains vibrational excitation through Franck-Condon effects and rapidly dissociates by loss of a hydrogen atom, so that no survivor ions are observed after reionization. Two conformers of 1, syn-1 and anti-1, were found computationally as local energy minima that interconverted rapidly by inversion at one of the amine groups with a <7 kJ mol-1 barrier. The lowest energy dissociation of radical 1 was loss of the hydroxyl hydrogen atom from anti-1 with ETS = 65 kJ mol-1. The other dissociation pathways of 1 were a hydroxyl hydrogen migration to an amine group followed by dissociation to H2N-C=O* and NH3. Ion 2+ was generated by protonation of gas-phase guanidine with a PA = 985 kJ mol-1. Electron transfer to 2+ was accompanied by large Franck-Condon effects that caused complete dissociation of radical 2 by loss of an H atom on the experimental time scale of 4 mus. Radicals 1 and 2 were calculated to have extremely low ionization energies, 4.75 and 4.29 eV, respectively, which belong to the lowest among organic molecules and bracket the ionization energy of atomic potassium (4.34 eV). The stabilities of amino group containing methyl radicals, *CH2NH2, *CH(NH2)2, and 2, were calculated from isodesmic hydrogen atom exchange with methane. The pi-donating NH2 groups were found to increase the stability of the substituted methyl radicals, but the stabilities did not correlate with the radical ionization energies.