Elementary reactions for glycine production in hot and dense interstellar media from CH 3 COOH , HCOOH, and NH 2 CH

CONTEXT

In this work, we investigate three elementary reactions involved in the production of glycine in the interstellar medium (ISM) employing trustworthy electronic structure and chemical kinetics methodologies. We considered three elementary reactions: HCOOH + NH 2 CH → NH 2 CH 2 COOH (R 1 ),CH 3 COOH + NH → CH 2 COOH + NH 2 (R 2 ) andCH 2 COOH + NH 2 → NH 2 CH 2 COOH ( R 3 ) under conditions consistent with hot molecular cores of massive star-forming regions. Our results indicate that the elementary reactions are feasible in these environments, with reaction barriers of 18.8 ( R 1 ) and 18.4 kcal · mol - 1 ( R 2 ). The rate coefficients for these reactions were calculated to be 1.4 × 10 - 17 and 9.3 × 10 - 16 cm 3 · molecule - 1 · s - 1 at 1000 K. Additionally, if the products of ( R 2 ) couple on a singlet surface, R 3 connects to the ground state of glycine via a barrierless path presenting a rate coefficient equal to 8.7 × 10 - 9 cm 3 · molecule - 1 · s - 1 at 298.15 K. Given that the molecules involved in these reactions have been detected in regions such as Sgr B2, our findings suggest that these elementary reactions should be included in mechanisms to study the production of glycine in such locations.

METHODS

The single-reference electronic structure calculations were carried out with the ORCA 4.1.2 package while the multi-reference calculations were performed with the COLUMBUS 7.0 package. The DFT functionals employed were M06-2X, ω B97X, and ω B97X-D3, with the 6-31+G* and def2-TZVP, and for the wave function-based calculations, the CCSD(T), DLPNO-CCSD(T), MRCI, and CASSF methods were employed using the aug-cc-pVDZ, aug-cc-pVTZ, and aug-cc-pVQZ basis sets. The chemical kinetic calculations for the elementary reactions with well-defined saddle points were performed using the Pilgrim package employing the TST, CVT, and CVT/SCT approaches.

Contrast and Complexity in the Low-Temperature Kinetics of CN(v = 1) with O2 and NO: Simultaneous Kinetics and Ringdown in a Uniform Supersonic Flow

Bimolecular rate coefficients were determined for the reaction CN(v = 1) + NO and O2 using continuous wave cavity ringdown spectroscopy in a uniform supersonic flow (UF-CRDS). The well-matched time scales for ringdown and reaction under pseudo-first-order conditions allow for the use of the SKaR method (simultaneous kinetics and ringdown) in which the full kinetic trace is obtained on each ringdown. The reactions offer an interesting contrast in that the CN(v = 1) + NO system is nonreactive and proceeds by complex-mediated vibrational relaxation, while the CN(v = 1) + O2 reaction is primarily reactive. The measured rate coefficients at 70 K are (2.49 ± 0.08) × 10-11 and (10.49 ± 0.22) × 10-11 cm3 molecule-1 s-1 for the reaction with O2 and NO, respectively. The rate for reaction with O2 is a factor 2 lower than previously reported for v = 0 in the same temperature range, a surprising result, while that for NO is consistent with extrapolation of previous high-temperature measurements to 70 K. The latter is also discussed in light of theoretical calculations and measurements of the rate constants for the association reaction in the high-pressure limit. The measurements are complicated by the presence of a metastable population of high-J CN formed by photolysis of the precursor BrCN, and a kinetic model is developed to treat the competing relaxation and reaction. It is particularly problematic for reactions at low temperatures where the rotational relaxation and reaction have similar rates, precluding a reliable determination of the rate coefficients at 30 K. Also presented are important modifications to the data acquisition and control for the instrument that have yielded considerably enhanced stability and throughput.

Chemical reaction thresholds according to classical-limit quantum dynamics

Classical-limit quantum dynamics is used to explain the origin of the quantum thresholds of chemical reactions from their classical dynamics when these are vibrationally nonadiabatic across the interaction region. This study is performed within the framework of an elementary model of chemical reaction that mimics the passage from the free rotation of the reagents to the bending vibration at the transition state to the free rotation of the products.

Acid Enriched with Methanol: Formation of a Prebiotic Cluster in the Interstellar Medium

Organic molecules are a potential source of prebiotic chemistry in the interstellar medium (ISM). Methanol (MetOH) is a very important source of more complex molecules. H 3 O + (aq) and Cl - (aq) are fundamental to living organisms and can be generated in the ISM from the dissociation of HCl with just four water molecules, yielding the (H 3 O) + (H 2 O) 3 Cl - ion-pair. Here, a detailed mechanism, based on density functional theory (DFT) and ab-initio (2 nd order Mfller-Plesset perturbation theory, MP2) calculations, is suggested for the substitution reactions of these water molecules by MetOH. The time required for formation of an appreciable amount of the product ((H 3 O) + (MetOH) 3 Cl - ) can be only few years. Such reaction can take place in Sagittarius B2, where HCl, H 2 O and MetOH have already been identified and it can be an important source for the formation of more complex prebiotic structures.

Capture Theory Models: An overview of their development, experimental verification, and applications to ion-molecule reactions

Since Arrhenius first proposed an equation to account for the behaviour of thermally activated reactions in 1889, significant progress has been made in our understanding of chemical reactivity. A number of capture theory models have been developed over the past several decades to predict the rate coefficients for reactions between ions and molecules-ranging from the Langevin equation (for reactions between ions and non-polar molecules) to more recent fully quantum theories (for reactions at ultra-cold temperatures). A number of different capture theory methods are discussed, with the key assumptions underpinning each approach clearly set out. The strengths and limitations of these capture theory methods are examined through detailed comparisons between low-temperature experimental measurements and capture theory predictions. Guidance is provided on the selection of an appropriate capture theory method for a given class of ion-molecule reaction and set of experimental conditions-identifying when a capture-based model is likely to provide an accurate prediction. Finally, the impact of capture theories on fields such as astrochemical modelling is noted, with some potential future directions of capture-based approaches outlined.

Quasi-Classical Trajectory Study of the CN + NH3 Reaction Based on a Global Potential Energy Surface

Based on a combination of valence-bond and molecular mechanics functions which were fitted to high-level ab initio calculations, we constructed an analytical full-dimensional potential energy surface, named PES-2020, for the hydrogen abstraction title reaction for the first time. This surface is symmetrical with respect to the permutation of the three hydrogens in ammonia, it presents numerical gradients and it improves the description presented by previous theoretical studies. In order to analyze its quality and accuracy, stringent tests were performed, exhaustive kinetics and dynamics studies were carried out using quasi-classical trajectory calculations, and the results were compared with the available experimental evidence. Firstly, the properties (geometry, vibrational frequency and energy) of all stationary points were found to reasonably reproduce the ab initio information used as input; due to the complicated topology with deep wells in the entrance and exit channels and a “submerged” transition state, the description of the intermediate complexes was poorer, although it was adequate to reasonably simulate the kinetics and dynamics of the title reaction. Secondly, in the kinetics study, the rate constants simulated the experimental data in the wide temperature range of 25–700 K, improving the description presented by previous theoretical studies. In addition, while previous studies failed in the description of the kinetic isotope effects, our results reproduced the experimental information. Finally, in the dynamics study, we analyzed the role of the vibrational and rotational excitation of the CN(v,j) reactant and product angular scattering distribution. We found that vibrational excitation by one quantum slightly increased reactivity, thus reproducing the only experimental measurement, while rotational excitation strongly decreased reactivity. The scattering distribution presented a forward-backward shape, associated with the presence of deep wells along the reaction path. These last two findings await experimental confirmation.

An accurate full-dimensional potential energy surface for the reaction OH + SO → H + SO2

An accurate full-dimensional PES for the OH + SO ↔ H + SO₂ reaction is developed by the permutation invariant polynomial-neural network approach.

A uniform flow-cavity ring-down spectrometer (UF-CRDS): A new setup for spectroscopy and kinetics at low temperature

The UF-CRDS (Uniform Flow-Cavity Ring Down Spectrometer) is a new setup coupling for the first time a pulsed uniform (Laval) flow with a continuous wave CRDS in the near infrared for spectroscopy and kinetics at low temperature. This high resolution and sensitive absorption spectrometer opens a new window into the phenomena occurring within UFs. The approach extends the detection range to new electronic and rovibrational transitions within Laval flows and offers the possibility to probe numerous species which have not been investigated yet. This new tool has been designed to probe radicals and reaction intermediates but also to follow the chemistry of hydrocarbon chains and PAHs which play a crucial role in the evolution of astrophysical environments. For kinetics measurements, the UF-CRDS combines the CRESU technique (French acronym meaning reaction kinetics in uniform supersonic flows) with the SKaR (Simultaneous Kinetics and Ring-Down) approach where, as indicated by its name, the entire reaction is monitored during each intensity decay within the high finesse cavity. The setup and the approach are demonstrated with the study of the reaction between CN (v = 1) and propene at low temperature. The recorded data are finally consistent with a previous study of the same reaction for CN (v = 0) relying on the CRESU technique with laser induced fluorescence detection.

Theoretical Study of Barrierless Chemical Reactions Involving Nearly Elastic Rebound: The Case of S(1D) + X2, X = H, D

For some values of the total angular momentum consistent with reaction, the title processes involve nonreactive trajectories proceeding through a single rebound mechanism during which the internal motion of the reagent diatom is nearly unperturbed. When such paths are in a significant amount, the classical reaction probability is found to be markedly lower than the quantum mechanical one. This finding was recently attributed to an unusual quantum effect called diffraction-mediated trapping, and a semiclassical correction was proposed in order to take into account this effect in the classical trajectory method. In the present work, we apply the resulting approach to the calculation of opacity functions as well as total and state-resolved integral cross sections (ICSs) and compare the values obtained with exact quantum ones, most of which are new. As the title reactions proceed through a deep insertion well, mean potential statistical calculations are also presented. Seven values of the collision energy, ranging from 30 to 1127 K, are considered. Two remarkable facts stand out: (i) The corrected classical treatment strongly improves the accuracy of the opacity function as compared to the usual classical treatment. When the entrance transition state is tight, however, those trajectories crossing it with a bending vibrational energy below the zero point energy must be discarded. (ii) The quantum opacity function, particularly its cutoff, is finely reproduced by the statistical approach. Consequently, the total ICS is also very well described by the two previous approximate methods. These, however, do not predict state-resolved ICSs with the same accuracy, proving thereby that (i) one or several genuine quantum effects involved in the dynamics are missed by the corrected classical treatment and (ii) the dynamics are not fully statistical.

Kinetic Study of the Gas-Phase Reactions of Nitrate Radicals with Methoxyphenol Compounds: Experimental and Theoretical Approaches

The gas-phase reactions of five methoxyphenols (three disubstituted and two trisubstituted) with nitrate radicals were studied in an 8000 L atmospheric simulation chamber at atmospheric pressure and 294 ± 2 K. The NO3 rate constants were investigated with the relative kinetic method using PTR-ToF-MS and GC-FID to measure the concentrations of the organic compounds. The rate constants (in units of cm(3) molecule(-1) s(-1)) determined were: 2-methoxyphenol (guaiacol; 2-MP), k(2-MP) = (2.69 ± 0.57 × 10(-11); 3-methoxyphenol (3-MP), k(3-MP) = (1.15 ± 0.21) × 10(-11); 4-methoxyphenol (4-MP), k(4-MP) = (13.75 ± 7.97) × 10(-11); 2-methoxy-4-methylphenol, k(2-M-4-MeP) = (8.41 ± 5.58) × 10(-11) and 2,6-dimethoxyphenol (syringol; 2,6-DMP), k(2,6-DMP) = (15.84 ± 8.10) × 10(-11). The NO3 rate constants of the studied methoxyphenols are compared with those of other substituted aromatics, and the differences in the reactivity are construed regarding the substituents (type, number and position) on the aromatic ring. This study was also supplemented by a theoretical approach of the methoxyphenol reactions with nitrate radicals. The upper limits of the NO3 overall rate constants calculated were in the same order of magnitude than those experimentally determined. Theoretical calculations of the minimum energies of the adducts formed from the reaction of NO3 radicals with the methoxyphenols were also performed using a DFT approach (M06-2X/6-31G(d,p)). The results indicate that the NO3 addition reactions on the aromatic ring of the methoxyphenols are exothermic, with energy values ranging between -13 and -21 kcal mol(-1), depending on the environment of the carbon on which the oxygen atom of NO3 is attached. These energy values allowed identifying the most suitable carbon sites for the NO3 addition on the aromatic ring of the methoxyphenols: at the exception of the 3-MP, the NO3 ipso-addition to the hydroxyl group is one of the favored sites for all the studies compounds.

Reaction Kinetics of Meteoric Sodium Reservoirs in the Upper Atmosphere

The gas-phase reactions of a selection of sodium-containing species with atmospheric constituents, relevant to the chemistry of meteor-ablated Na in the upper atmosphere, were studied in a fast flow tube using multiphoton ionization time-of-flight mass spectrometry. For the first time, unambiguous observations of NaO and NaOH in the gas phase under atmospheric conditions have been achieved. This enabled the direct measurement of the rate constants for the reactions of NaO with H2, H2O, and CO, and of NaOH with CO2, which at 300-310 K were found to be (at 2σ confidence level): k(NaO + H2O) = (2.4 ± 0.6) × 10(-10) cm(3) molecule (-1) s(-1), k(NaO + H2) = (4.9 ± 1.2) × 10(-12) cm(3) molecule (-1) s(-1), k(NaO + CO) = (9 ± 4) × 10(-11) cm(3) molecule (-1) s(-1), and k(NaOH + CO2 + M) = (7.6 ± 1.6) × 10(-29) cm(6) molecule (-2) s(-1) (P = 1-4 Torr). The NaO + H2 reaction was found to make NaOH with a branching ratio ≥ 99%. A combination of quantum chemistry and statistical rate theory calculations are used to interpret the reaction kinetics and extrapolate the atmospherically relevant experimental results to mesospheric temperatures and pressures. The NaO + H2O and NaOH + CO2 reactions act sequentially to provide the major atmospheric sink of meteoric Na and therefore have a significant impact on the underside of the Na layer in the terrestrial mesosphere: the newly determined rate constants shift the modeled peak to about 93 km, i.e., 2 km higher than observed by ground-based lidars. This highlights further uncertainties in the Na chemistry cycle such as the unknown rate constant of the NaOH + H reaction. The fast Na-recycling reaction between NaO and CO and a re-evaluated rate constant of the NaO + CO2 sink should be now considered in chemical models of the Martian Na layer.

A quasi-classical trajectory study of the OH + SO reaction: the role of ro-vibrational energy

The reaction cross section and the reaction probability after forming the complex as a function of vibrational energy of reactants.

Low-temperature rate coefficients for the reaction of ethynyl radical (C2H) with benzene

The reaction of the C2H radical with benzene is studied at low temperature using a pulsed Laval nozzle apparatus. The C2H radical is prepared by 193-nm photolysis of acetylene, and the C2H concentration is monitored using CH(A2Delta) chemiluminescence from the C2H + O2 reaction. Measurements at very low photolysis energy are performed using CF3C2H as the C2H precursor to study the influence of benzene photodissociation on the rate coefficient. Rate coefficients are obtained over a temperature range between 105 and 298 K. The average rate coefficient is found to be five times greater than the estimated value presently used in the photochemical modeling of Titan's atmosphere. The reaction exhibits a slight negative temperature dependence which can be fitted to the expression k(cm3 molecule(-1) s(-1)) = 3.28(+/-1.0) x 10(-10) (T/298)(-0.18(+/-0.18)). The results show that this reaction has no barrier and may play an important role in the formation of large molecules and aerosols at low temperature. Our results are consistent with the formation of a short lifetime intermediate that decomposes to give the final products.

Rate coefficients for reaction and for rotational energy transfer in collisions between CN in selected rotational levels (XΣ+2, v=2, N=0, 1, 6, 10, 15, and 20) and C2H2

Rate coefficients (ktot,Ni) are reported (a) for total removal (reactive+inelastic) of CN(X2Sigma+,v=2,Ni) radicals from selected rotational levels (Ni=0, 1, 6, 10, 15, and 20) and (b) for state-to-state rotational energy transfer (ki-->f) between levels Ni and other rotational levels Nf in collisions with C2H2. CN radicals were generated by pulsed laser photolysis of NCNO at 573 nm. A fraction of the radicals was then promoted to a selected rotational level in v=2 using a tunable infrared "pump" laser operating at approximately 2.45 microm, and the subsequent fate of this subset of radicals was monitored using pulsed laser-induced fluorescence (PLIF). Values of ktot,Ni were determined by observing the decay of the PLIF signals as the delay between pump and probe laser pulses was systematically varied. In a second series of experiments, double resonance spectra were recorded at a short delay between the pump and probe laser pulses. Analysis of these spectra yielded state-to-state rate coefficients for rotational energy transfer, ki-->f. The difference between the sum of these rate coefficients, Sigmafki-->f, and the value of ktot,Ni for the same level Ni is attributed to the occurrence of chemical reaction, yielding values of the rotationally selected rate coefficients (kreac,Ni) for reaction of CN from specified rotational levels. These rate coefficients decrease from (7.9+/-2.2)x10(-10) cm3molecule-1 s-1 for Ni=0 to (0.8+/-1.3)x10(-10) cm3 molecule-1 s-1 for Ni=20. The results are briefly discussed in the context of microcanonical transition state theory and the statistical adiabatic channel model.

Reactions at Very Low Temperatures: Gas Kinetics at a New Frontier

Advances in experimental techniques, especially the development of the CRESU (Cinétique de Réaction en Ecoulement Supersonique Uniforme) method, allow many gas-phase molecular processes to be studied at very low temperatures. This Review focuses on the reactions of molecular and atomic radicals with neutral molecules. Rate constants for almost 50 such reactions have been measured at temperatures as low as 13 K by using the CRESU method. The surprising demonstration that so many reactions between electrically neutral species can be extremely rapid at these very low temperatures has excited interest both from theoreticians and from those seeking to understand the chemistry that gives rise to the 135 or so molecules that are present in low-temperature molecular clouds in the interstellar medium. Theoretical treatments of these reactions are based on the idea that a reaction occurs when the long-range potential between the reagent species brings them into close contact. The astrochemical context, theoretical studies, and the determination of the rate constants of these low-temperature reactions are critically discussed.

The temperature-dependence of rapid low temperature reactions: experiment, understanding and prediction

Despite the success of the CRESU (Cinétique de Réaction en Ecoulement Supersonique Uniforme) method in measuring rate coefficients for neutral-neutral reactions of radicals down close to the very low temperatures prevalent in dense interstellar clouds (ISCs), there are still many reactions of potential importance in the chemistry of these objects for which there have been no measurements of low temperature rate coefficients. One important class of reactions is that between atomic and molecular free radicals and unsaturated hydrocarbons; that is, alkynes and alkenes. Based on semi-empirical arguments and correlations of 'room temperature' rate coefficients, k(298 K), for reactions of this type with the difference between the ionisation energy of the alkyne/alkene and the electron affinity of the radical, we suggest which reactions between the radicals, C(3P), O(3P), N(4S), CH, C2H and CN, and carbon chain molecules (Cn) and cyanopolyynes (HC2nCN and NCC2nCN) are likely to be fast at the temperature of dense ISCs. These reactions and rate coefficients have been incorporated into a purely gas-phase model (osu2005) of ISC chemistry. The results of these calculations are presented and discussed.