Excited state photochemically driven surface formation of benzene from acetylene ices on Pluto and in the outer solar system.

NASA's New Horizons mission unveiled a diverse landscape of Pluto's surface with massive regions being neutral in color, while others like Cthulhu Macula range from golden-yellow to reddish comprising up to half of Pluto's carbon budget. Here, we demonstrate in laboratory experiments merged with electronic structure calculations that the photolysis of solid acetylene - the most abundant precipitate on Pluto's surface - by low energy ultraviolet photons efficiently synthesizes benzene and polycyclic aromatic hydrocarbons via excited state photochemistry thus providing critical molecular building blocks for the colored surface material. Since low energy photons deliver doses to Pluto's surface exceeding those from cosmic rays by six orders of magnitude, these processes may significantly contribute to the coloration of Pluto's surface and of hydrocarbon-covered surfaces of Solar System bodies such as Triton in general. This discovery critically enhances our perception of the distribution of aromatic molecules and carbon throughout our Solar System.

Fragment-Based Ab Initio Molecular Dynamics Simulation for Combustion.

We develop a fragment-based ab initio molecular dynamics (FB-AIMD) method for efficient dynamics simulation of the combustion process. In this method, the intermolecular interactions are treated by a fragment-based many-body expansion in which three- or higher body interactions are neglected, while two-body interactions are computed if the distance between the two fragments is smaller than a cutoff value. The accuracy of the method was verified by comparing FB-AIMD calculated energies and atomic forces of several different systems with those obtained by standard full system quantum calculations. The computational cost of the FB-AIMD method scales linearly with the size of the system, and the calculation is easily parallelizable. The method is applied to methane combustion as a benchmark. Detailed reaction network of methane reaction is analyzed, and important reaction species are tracked in real time. The current result of methane simulation is in excellent agreement with known experimental findings and with prior theoretical studies.

Cyclopentadienyl radical formation from the reaction of excited nitrogen atoms with benzene: a theoretical study.

Ab initio CCSD(T)/CBS//ωB97X-D/6-311+G(d,p) calculations of the C6H6N potential energy surface were performed to investigate the reaction mechanism underlying the reaction of atomic nitrogen (2D) with benzene. Thereafter, Rice-Ramsperger-Kassel-Marcus (RRKM) calculations of reaction rate constants and product branching ratios were performed under single-collision conditions. The results revealed that the N(2D) + C6H6 reaction in the case of statistical behavior is expected to produce hydrogen cyanide plus a cyclopentadienyl radical (91.5-88.9%), acetylene plus a pyrrole radical (5.8-7.5%), 1-cyano-2,4-cyclopentadiene + H (2.3-3.0%) and 1-ethynyl-pyrrole + H (0.4-0.6%), with the most favorable pathways being the initial adduct i1 leading to the formation of a seven-membered cyclic intermediate i12 through an exothermic ring expansion process and a multistep route i12 → i15 → i16 → C5H5 + HCN featuring an intramolecular ring-shrinking process involving a C-C bond fusion elimination channel to yield the bicyclic intermediate i15, followed by hydrogen cyanide elimination, thus forming a cyclopentadienyl radical. The calculated product branching ratios were consistent with the available experimental data; however, some quantitative deviations from the experimental results and the possible reasons are also discussed. The possible effects of the title reaction on the upper atmosphere of Titan, with critical implications for the rapid degradation of nitrogen-bearing polycyclic aromatic hydrocarbons, were compared with the mass growth processes of their polycyclic aromatic hydrocarbon counterparts produced through ring expansion.

ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamics simulations.

Reactive molecular dynamics (MD) simulation makes it possible to study the reaction mechanism of complex reaction systems at the atomic level. However, the analysis of MD trajectories which contain thousands of species and reaction pathways has become a major obstacle to the application of reactive MD simulation in large-scale systems. Here, we report the development and application of the Reaction Network Generator (ReacNetGenerator) method. It can automatically extract the reaction network from the reaction trajectory without any predefined reaction coordinates and elementary reaction steps. Molecular species can be automatically identified from the cartesian coordinates of atoms and the hidden Markov model is used to filter the trajectory noises which makes the analysis process easier and more accurate. The ReacNetGenerator has been successfully used to analyze the reactive MD trajectories of the combustion of methane and 4-component surrogate fuel for rocket propellant 3 (RP-3), and it has great advantages in terms of efficiency and accuracy compared to traditional manual analysis.

Formation mechanism and spectroscopy of C6H radicals in extreme environments: a theoretical study.

This study examined the reaction mechanisms of singlet (rhombic) and triplet (linear) C4 with acetylene by using accurate ab initio CCSD(T)/CBS//B3LYP/6-311G(d,p) calculations followed by a kinetic analysis of various reaction pathways and computations of relative product yields in combustion and planetary atmospheres. These calculations were combined with the Rice-Ramsperger-Kassel-Marcus (RRKM) calculations of reaction rate constants for predicting product-branching ratios, which depend on the collision energy under single-collision conditions. The results demonstrate that the initial reaction begins with the formation of an intermediate 3i2 with an entrance barrier of 3.0 kcal mol-1 and an intermediate 1i1 without entrance barriers. The product-branching ratios obtained by solving kinetic equations with individual rate constants calculated using the RRKM and variational transition-state theories for determining the collision energies between 5 kcal mol-1 and 25 kcal mol-1 demonstrate that l-C6H + H is the dominant reaction product, whereas HC3C3 + H, l-C6 + H2, c-C6H + H, and c-C6 + H2 are minor products. The electronic absorption spectra of solid neon matrices in the range of 17 140-22 200 cm-1 were obtained by Maier et al., and the optimized ground and excited state structures of C6H were used to simulate the absorption spectra by one-photon excitation equations. The displaced harmonic oscillator approximation and the Franck-Condon approximation were used to simulate the absorption spectrum of the B2Π â† X2Π transition of C6H. This indicates that the vibronic structures were dominated by one of the six active completely symmetric modes, with v3 being the most crucial.

Infrared Spectra of the 1-Methylvinoxide Radical and Anion Isolated in Solid Argon.

The 1-methylvinoxy radical (1-MVO) is an important intermediate in the combustion and tropospheric reaction of OH. However, the vibrational structures of this species and its anionic form, 1-methylvinoxide anion (1-MVO-), are not fully known. Thus, in this study, we obtained the infrared (IR) absorption spectra of 1-MVO and 1-MVO- trapped in a solid Ar matrix. 1-MVO- anions were produced by electron bombardment during matrix deposition of Ar containing a small amount of acetone. The anions were destroyed upon irradiation at 675, 365, and 160 nm, although the formation of 1-MVO was only observed upon irradiation at 675 nm. The assignment of the IR bands of 1-MVO- and 1-MVO was based on the expected chemistry upon photoexcitation and comparison of line wavenumbers, relative IR intensities, and D-isotopic shift ratios with those predicted at the B3LYP/aug-cc-pVTZ level of theory.

Direct IR Absorption Spectra of Propargyl Cation Isolated in Solid Argon.

The direct infrared (IR) absorption spectra of propargyl cations were recorded. These cations were generated via the electron bombardment of a propyne/Ar matrix sample during matrix deposition. Secondary photolysis with selected ultraviolet (UV) light was used for grouping the observed bands of various products. The band assignment of the propargyl cation in solid Ar was performed according by referring to the previous infrared photodissociation (IRPD) and velocity-map imaging photoelectron (VMI-PE) data, and via theoretical predictions of the anharmonic vibrational wavenumbers, band intensities, and deuterium-substituted isotopic ratios. Almost all the IR active bands with an observable intensity were recorded and the ν11 mode was reported for the first time.

Formation and identification of borane radical anions isolated in solid argon.

The infrared (IR) spectrum of borane(3) anions (BH3-) isolated in solid Ar was recorded; two vibrational modes were observed at 2259.4 and 606.6 cm-1, which were assigned to the BH2 stretching (ν3) and out-of-plane large-amplitude (ν2) modes, respectively. These anions were produced by the electron bombardment of an Ar matrix sample containing a small proportion of B2H6 and H2 during matrix deposition or by the photolysis of single-bridged-B2H5- in an Ar matrix with the selected ultraviolet light. The band positions, relative intensity ratios, isotopic splitting pattern, and isotopic shift ratios of the observed IR features of BH3- are generally in good agreement with those predicted by the B2PLYP/aug-cc-pVTZ method.

UV absorption spectrum of allene radical cations in solid argon.

Electron bombardment during deposition of an Ar matrix containing a small proportion of allene generated allene cations. Further irradiation of the matrix sample at 385 nm destroyed the allene cations and formed propyne cations in solid Ar. Both cations were identified according to previously reported IR absorption bands. Using a similar technique, we recorded the ultraviolet absorption spectrum of allene cations in solid Ar. The vibrationally resolved progression recorded in the range of 266-237 nm with intervals of about 800 cm-1 was assigned to the A2E ← X2E transition of allene cations, and the broad continuum absorption recorded in the region of 229-214 nm was assigned to their B2A1 ← X2E transition. These assignments were made based on the observed photolytic behavior of the progressions and the vertical excitation energies and oscillator strengths calculated using time-dependent density functional theory.

Direct infrared observation of hydrogen chloride anions in solid argon.

To facilitate direct spectroscopic observation of hydrogen chloride anions (HCl-), electron bombardment of CH3Cl diluted in excess Ar during matrix deposition was used to generate this anion. Subsequent characterization were performed by IR spectroscopy and quantum chemical calculations. Moreover the band intensity of HCl- decays slowly when the matrix sample is maintained in the dark for a prolonged time. High-level ab inito calculation suggested that HCl- is only weakly bound. Atom-in-molecule charge analysis indicated that both atoms of HCl- are negatively charged and the Cl atom is hypervalent.

Parity-dependent hairpin configurations of repetitive DNA sequence promote slippage associated with DNA expansion.

Repetitive DNA sequences are ubiquitous in life, and changes in the number of repeats often have various physiological and pathological implications. DNA repeats are capable of interchanging between different noncanonical and canonical conformations in a dynamic fashion, causing configurational slippage that often leads to repeat expansion associated with neurological diseases. In this report, we used single-molecule spectroscopy together with biophysical analyses to demonstrate the parity-dependent hairpin structural polymorphism of TGGAA repeat DNA. We found that the DNA adopted two configurations depending on the repeat number parity (even or odd). Transitions between these two configurations were also observed for longer repeats. In addition, the ability to modulate this transition was found to be enhanced by divalent ions. Based on the atomic structure, we propose a local seeding model where the kinked GGA motifs in the stem region of TGGAA repeat DNA act as hot spots to facilitate the transition between the two configurations, which may give rise to disease-associated repeat expansion.

Identification of a Simplest Hypervalent Hydrogen Fluoride Anion in Solid Argon.

Hypervalent molecules are one of the exceptions to the octet rule. Bonding in most hypervalent molecules is well rationalized by the Rundle-Pimentel model (three-center four-electron bond), and high ionic bonding between the ligands and the central atom is essential for stabilizing hypervalent molecules. Here, we produced one of the simplest hypervalent anions, HF-, which is known to deviate from the Rundle-Pimentel model, and identified its ro-vibrational features. High-level ab inito calculations reveal that its bond dissociation energy is comparable to that of dihalides, as supported by secondary photolysis experiments with irradiation at various wavelengths. The charge distribution analysis suggested that the F atom of HF- is negative and hypervalent and the bonding is more covalent than ionic.

Photochemistry and infrared spectrum of single-bridged diborane(5) anion isolated in solid argon.

Three-center two-electron bonds are important for understanding electron-deficient molecules. To examine such a molecule, we produced a diborane(5) anion with a single-bridged structure upon electron bombardment during matrix deposition of Ar containing a small proportion of diborane(6). The diborane(5) anion was destroyed upon photolysis at 180, 220, 385, and 450 nm, but not at 532 nm. Moreover, the possible formation of neutral diborane(5) was observed upon photolysis at 385 and 450 nm, whereas neutral diborane(3) was observed upon photolysis at 180 and 220 nm. The observed line wavenumbers, relative intensities, and isotopic ratios of the diborane(5) anion agreed satisfactorily with those predicted by density functional theory calculations at the B3LYP/aug-cc-pVTZ level of theory. Thus, this method produced the boron hydride anion of interest with few other fragments, which enabled us to clearly identify the IR spectrum of the diborane(5) anion.

Theoretical investigations of absorption and fluorescence spectra of protonated pyrene.

The equilibrium geometry and 75 vibrational normal-mode frequencies of the ground and first excited states of protonated pyrene isomers were calculated and characterized in the adiabatic representation by using the complete active space self-consistent field (CASSCF) method. Electronic absorption spectra of solid neon matrixes in the wavelength range 495-415 nm were determined by Maier et al. and they were analyzed using time-dependent density functional theory calculations (TDDFT). CASSCF calculations and absorption and emission spectra simulations by one-photon excitation equations were used to optimize the excited and ground state structures of protonated pyrene isomers. The absorption band was attributed to the S0 → S1 electronic transition in 1H-Py(+), and a band origin was used at 20580.96 cm(-1). The displaced harmonic oscillator approximation and Franck-Condon approximation were used to simulate the absorption spectrum of the (1) (1)A' ← X[combining tilde](1)A' transition of 1H-Py(+), and the main vibronic transitions were assigned for the first ππ* state. It shows that the vibronic structures were dominated by one of the eight active totally symmetric modes, with ν15 being the most crucial. This indicates that the electronic transition of the S1((1)A') state calculated in the adiabatic representation effectively includes a contribution from the adiabatic vibronic coupling through Franck-Condon factors perturbed by harmonic oscillators. The present method can adequately reproduce experimental absorption and fluorescence spectra of a gas phase.

Dynamics of the reaction of C2 with C6H2: an implication for the formation of interstellar C8H.

The reaction C2 + C6H2 → C8H + H was investigated for the first time. Reactant C2 (C6H2) was synthesized from 1% C3F6/He (5% C2H2/He) by pulsed high-voltage discharge. We measured the translational-energy distribution, the angular distribution, and the photoionization spectrum of product C8H in a crossed molecular-beam apparatus using synchrotron vacuum-ultraviolet ionization. This reaction released average translational energy of 8.5 kcal mol(-1) corresponding to a fraction of 0.37 in translation. C8H was identified as octatetranyl based on the maximal translational-energy release 23 ± 2 kcal mol(-1) and the ionization threshold 8.9 ± 0.2 eV. Kinematic constraints can qualitatively account for the nearly isotropic angular distribution. The quantum-chemical calculations indicate that the exothermic reactions C2 (X (1)Σg (+)/a (3)Πu) + HC6H → C8H + H can proceed without entrance and exit barriers, implying the importance in the cold interstellar medium. This work verifies that interstellar C8H can be formed through the C2 + C6H2 reaction.

Dynamics of the reaction of C3(a³Πu) radicals with C2H2: a new source for the formation of C5H.

The reaction C3(a(3)Πu) + C2H2 → C5H + H was investigated at collision energy 10.9 kcal mol(-1) that is less than the enthalpy of ground-state reaction C3(X(1)Σg (+)) + C2H2 → C5H + H. C3(a(3)Πu) radicals were synthesized from 1% C4F6/He by pulsed high-voltage discharge. The title reaction was conducted in a crossed molecular-beam apparatus equipped with a quadrupole-mass filter. Product C5H was interrogated with time-of-flight spectroscopy and synchrotron vacuum-ultraviolet ionization. Reactant C3(a(3)Πu) and product C5H were identified using photoionization spectroscopy. The ionization thresholds of C3(X(1)Σg(+)) and C3(a(3)Πu) are determined as 11.6 ± 0.2 eV and 10.0 ± 0.2 eV, respectively. The C5H product is identified as linear pentynylidyne that has an ionization energy 8.4 ± 0.2 eV. The title reaction releases translational energy 10.6 kcal mol(-1) in average and has an isotropic product angular distribution. The quantum-chemical calculation indicates that the C3(a(3)Πu) radical attacks one of the carbon atoms of C2H2 and subsequently a hydrogen atom is ejected to form C5H + H, in good agreement with the experimental observation. As far as we are aware, the C3(a(3)Πu) + C2H2 reaction is investigated for the first time. This work gives an implication for the formation of C5H from the C3(a(3)Πu) + C2H2 reaction occurring in a combustion or discharge process of C2H2.

Dynamics of carbon-hydrogen and carbon-methyl exchanges in the collision of 3P atomic carbon with propene.

We investigated the dynamics of the reaction of (3)P atomic carbon with propene (C3H6) at reactant collision energy 3.8 kcal mol(-1) in a crossed molecular-beam apparatus using synchrotron vacuum-ultraviolet ionization. Products C4H5, C4H4, C3H3, and CH3 were observed and attributed to exit channels C4H5 + H, C4H4 + 2H, and C3H3 + CH3; their translational-energy distributions and angular distributions were derived from the measurements of product time-of-flight spectra. Following the addition of a (3)P carbon atom to the C=C bond of propene, cyclic complex c-H2C(C)CHCH3 undergoes two separate stereoisomerization mechanisms to form intermediates E- and Z-H2CCCHCH3. Both the isomers of H2CCCHCH3 in turns decompose to C4H5 + H and C3H3 + CH3. A portion of C4H5 that has enough internal energy further decomposes to C4H4 + H. The three exit channels C4H5 + H, C4H4 + 2H, and C3H3 + CH3 have average translational energy releases 13.5, 3.2, and 15.2 kcal mol(-1), respectively, corresponding to fractions 0.26, 0.41, and 0.26 of available energy deposited to the translational degrees of freedom. The H-loss and 2H-loss channels have nearly isotropic angular distributions with a slight preference at the forward direction particularly for the 2H-loss channel. In contrast, the CH3-loss channel has a forward and backward peaked angular distribution with an enhancement at the forward direction. Comparisons with reactions of (3)P carbon atoms with ethene, vinyl fluoride, and vinyl chloride are stated.

Exploring the dynamics of C/H and C/Cl exchanges in the C(3P) + C2H3Cl reaction.

The dynamics of the C((3)P) + C2H3Cl reaction at collision energy 3.8 kcal mol(-1) was investigated in a crossed molecular-beam apparatus using synchrotron vacuum-ultraviolet ionization. Time-of-flight spectra of products C3H2Cl, C3H3, and Cl were recorded at various laboratory scattering angles, from which translational-energy distributions and angular distributions of product channels C3H2Cl + H and C3H3 + Cl were derived. Cl correlates satisfactorily with C3H3 in linear momentum and angular distributions, which confirms the production of C3H3 + Cl. The H-loss (Cl-loss) channel has average translational-energy release 14.3 (8.8) kcal mol(-1) corresponding to a fraction 0.30 (0.14) of available energy into the translational degrees of freedom of product HCCCHCl + H (H2CCCH + Cl). The branching ratio of channel H to channel Cl was determined approximately as 12:88. The measurements of translational-energy releases and photoionization thresholds cannot distinguish HCCCHCl from H2CCCCl because both isomers have similar enthalpy of formation and ionization energy; nevertheless, the Rice-Ramsperger-Kassel-Marcus calculation prefers HCCCHCl. The measurement of photoionization spectra identifies product C3H3 as H2CCCH (propargyl). Both products C3H2Cl + H and C3H3 + Cl might correlate to the same triplet intermediate H2CCCHCl but have distinct angular distributions; the former is nearly isotropic whereas the latter is forward biased. A comparison with the C((3)P) + C2H3F reaction is stated.

Dynamics of the C/H and C/F exchanges in the reaction of 3P carbon atoms with vinyl fluoride.

Two product channels C3H2F + H and C3H3 + F were identified in the reaction of C((3)P) atoms with vinyl fluoride (C2H3F) at collision energy 3.7 kcal mol(-1) in a crossed molecular-beam apparatus using selective photoionization. Time-of-flight (TOF) spectra of products C3H2F and C3H3 were measured at 12-16 laboratory angles as well as a TOF spectrum of atomic F, a counter part of C3H3, was recorded at single laboratory angle. From the best simulation of product TOF spectra, translational-energy distributions at seven scattering angles and a nearly isotropic (forward and backward peaked) angular distribution were derivable for exit channel C3H2F + H (C3H3 + F) that has average kinetic-energy release of 14.5 (4.9) kcal mol(-1). Products C3H2F + H and C3H3 + F were estimated to have a branching ratio of ~53:47. Furthermore, TOF spectra and photoionization spectra of products C3H2F and C3H3 were measured at laboratory angle 62° with photoionization energy ranging from 7 eV to 11.6 eV. The appearance of TOF spectra is insensitive to photon energy, implying that only single species overwhelmingly contributes to products C3H2F and C3H3. HCCCHF (H2CCCH) was identified as the dominant species based on the measured ionization threshold of 8.3 ± 0.2 (8.6 ± 0.2) eV and the maximal translational-energy release. The C/H and C/F exchange mechanisms are stated.

Exploring the dynamics of reaction C(3P) + C2H4 with crossed beam/photoionization experiments and quantum chemical calculations.

We investigated the title reaction at collision energy 3.5 kcal mol(-1) in a crossed molecular beam apparatus using undulator radiation as an ionization source. Time-of-flight (TOF) spectra of product C(3)H(3) were measured in laboratory angles from 20° to 100° using two photoionization energies 9.5 and 11.6 eV. These two sets of experimental data exhibit almost the same TOF distributions and laboratory angular distributions. From the best simulation, seven angle-specific kinetic-energy distributions and a nearly isotropic angular distribution are derived for product channel C(3)H(3) + H that has an average kinetic-energy release of 15.5 kcal mol(-1), corresponding to an average internal energy of 33.3 kcal mol(-1) in C(3)H(3). Furthermore, TOF spectra of product C(3)H(3) were measured at laboratory angle 52° with ionizing photon energies from 7 to 12 eV. The appearance of TOF spectra remains almost the same, indicating that a species exclusively contributes to product C(3)H(3); the species is identified as H(2)CCCH (propargyl) based on the ionization energy of 8.6 ± 0.2 eV and the maximal kinetic-energy release of 49 kcal mol(-1). Theoretical calculations indicate that the rapid inversion mechanism and rotation in intermediate H(2)CCCH(2) can result in a forward-backward symmetric angular distribution for product C(3)H(3) + H. The present work avoids the interference of reactions of C((1)D) and C(2) radicals with C(2)H(4) and rules out the probability of production of other isomers like c-C(3)H(3) and H(3)CCC proposed in the previous work at least at the investigated collision energy.