Destruction of dimethyl ether and methyl formate by collisions with He+^+

To correctly model the abundances of interstellar complex organic molecules (iCOMS) in different environments, both formation and destruction routes should be appropriately accounted for. While several scenarios have been explored for the formation of iCOMs via grain and gas-phase processes, much less work has been devoted to understanding the relevant destruction pathways, with special reference to (dissociative) charge exchange or proton transfer reactions with abundant atomic and molecular ions such as He$^+$, H$_3^+$ and HCO$^+$. By using a combined experimental and theoretical methodology we provide new values for the rate coefficients and branching ratios (BRs) of the reactions of He$^+$ ions with two important iCOMs, namely dimethyl ether (DME) and methyl formate (MF). We also review the destruction routes of DME and MF by other two abundant ions, namely H$_3^+$ and HCO$^+$. Based on our recent laboratory measurements of cross sections and BRs for the DME/MF + He$^+$ reactions over a wide collision energy range, we extend our theoretical insights on the selectivity of the microscopic dynamics to calculate the rate coefficients $k(T)$ in the temperature range from 10 to 298 K. We implement these new and revised kinetic data in a general model of cold and warm gas, simulating environments where DME and MF have been detected. Due to stereodynamical effects present at low collision energies, the rate coefficients, BRs and temperature dependences here proposed differ substantially from those reported in KIDA and UDfA, two of the most widely used astrochemical databases. These revised rates impact the predicted abundances of DME and MF, with variations up to 40% in cold gases and physical conditions similar to those present in prestellar coresComment: accepted for publication in Astronomy and Astrophysics (manuscript no. AA/2018/34585), 10 pages, 3 figure

Infrared action spectroscopy as tool for probing gas-phase dynamics: Protonated Dimethyl Ether, (CH3_3)2_2OH+^+, formed by the reaction of CH3_3OH2+_{2}^{+} with CH3_3OH

Methanol is one of the most abundant interstellar Complex Organic Molecules (iCOMs) and it represents a major building block for the synthesis of increasingly complex oxygen-containing molecules. The reaction between protonated methanol and its neutral counterpart, giving protonated dimethyl ether, (CH$_3$)$_2$OH$^+$, along with the ejection of a water molecule, has been proposed as a key reaction in the synthesis of dimethyl ether in space. Here, gas phase vibrational spectra of the (CH$_3$)$_2$OH$^+$ reaction product and of the [C$_2$H$_9$O$_2$]$^+$ intermediate complex(es), formed under different pressure and temperature conditions, are presented. The widely tunable free electron laser for infrared experiments, FELIX, was employed to record their vibrational fingerprint spectra using different types of infrared action spectroscopy in the $600-1700$ cm$^{-1}$ frequency range, complemented with measurements using an OPO/OPA system to cover the O-H stretching region $3400-3700$ cm$^{-1}$. The formation of protonated dimethyl ether as a product of the reaction is spectroscopically confirmed, providing the first gas-phase vibrational spectrum of this potentially relevant astrochemical ion.Comment: 15 pages, 6 figures, Molecular Physics, Published online: 22 Jun 2023, for associated data files see Zenodo repository at https://doi.org/10.5281/zenodo.786855

The GRETOBAPE gas-phase reaction network: the importance of being exothermic

The gas-phase reaction networks are the backbone of astrochemical models. However, due to their complexity and non-linear impact on the astrochemical modeling, they can be the first source of error in the simulations if incorrect reactions are present. Over time, following the increasing number of species detected, astrochemists have added new reactions, based on laboratory experiments and quantum mechanics (QM) computations as well as reactions inferred by chemical intuition and similarity principle. However, sometimes no verification of their feasibility in the interstellar conditions, namely their exothermicity, was performed. In this work, we present a new gas-phase reaction network, GRETOBAPE, based on the KIDA2014 network and updated with several reactions, cleaned from endothermic reactions not explicitly recognized as such. To this end, we characterized all the species in the GRETOBAPE network with accurate QM calculations. We found that 5% of the reactions in the original network are endothermic although most of them are reported as barrierless. The reaction network of Si-bearing species is the most impacted by the endothermicity cleaning process. We also produced a cleaned reduced network, GRETOBAPE-red, to be used to simulate astrochemical situations where only C-, O-, N- and S- bearing species with less than 6 atoms are needed. Finally, the new GRETOBAPE network, its reduced version, as well as the database with all the molecular properties are made publicly available. The species properties database can be used in the future to test the feasibility of possibly new reactions.Comment: ApJS submitte

Stereodynamical Effects by Anisotropic Intermolecular Forces

Electric and magnetic field gradients, arising from sufficiently strong anisotropic intermolecular forces, tend to induce molecular polarization which can often modify substantially the results of molecular collisions, especially at low rotational temperatures and low collision energies. The knowledge of these phenomena, today still not fully understood, is of general relevance for the control of the stereo-dynamics of elementary chemical-physical processes, involving neutral and ionic species under a variety of conditions. This paper reports on results obtained by combining information from scattering, spectroscopic and reactivity experiments, within a collaboration between the research groups in Perugia and Trento. We addressed particular attention to the reactions of small atomic ions with polar neutrals for their relevance in several environments, including interstellar medium, planetary atmospheres, and laboratory plasmas. In the case of ion-molecule reactions, alignment/orientation is a general phenomenon due to the electric field generated by the charged particle. Such phenomenon originates critical stereo-dynamic effects that can either suppress (when the orientation drives the collision complex into non-reactive or less reactive configurations), or enhance the reactivity (when orientation confines reagents in the most appropriate configuration for reaction). The associated rate coefficients show the propensity to follow an Arrhenius and a non-Arrhenius behavior, respectively

The Need for Laboratory Measurements and Ab Initio Studies to Aid Understanding of Exoplanetary Atmospheres

We are now on a clear trajectory for improvements in exoplanet observations that will revolutionize our ability to characterize their atmospheric structure, composition, and circulation, from gas giants to rocky planets. However, exoplanet atmospheric models capable of interpreting the upcoming observations are often limited by insufficiencies in the laboratory and theoretical data that serve as critical inputs to atmospheric physical and chemical tools. Here we provide an up-to-date and condensed description of areas where laboratory and/or ab initio investigations could fill critical gaps in our ability to model exoplanet atmospheric opacities, clouds, and chemistry, building off a larger 2016 white paper, and endorsed by the NAS Exoplanet Science Strategy report. Now is the ideal time for progress in these areas, but this progress requires better access to, understanding of, and training in the production of spectroscopic data as well as a better insight into chemical reaction kinetics both thermal and radiation-induced at a broad range of temperatures. Given that most published efforts have emphasized relatively Earth-like conditions, we can expect significant and enlightening discoveries as emphasis moves to the exotic atmospheres of exoplanets.Comment: Submitted as an Astro2020 Science White Pape

Global unfolding of proteins by partial NMR assignment

The effect of urea concentration on the backbone solution structure of the cyanide derivative of ferric Caretta caretta myoglobin (at pH 5.4) is reported. By addition of urea, sequential and long-range nuclear Overhauser effects (NOEs) are gradually lost. By using the residual NOE constraints to build the molecular model, a picture of the unfolding pathway was obtained. When the urea concentration is raised to 2.2 M, helices A and B appear largely disordered; helices C, D, and F loose structural constraints at 3.0 M urea. At urea concentration >6 M, the protein appears to be fully unfolded, including the GH hairpin and helix E stabilizing the prosthetic group. Reversible and cooperative denaturation isotherms obtained by following NOE peaks are considerably different from those obtained by monitoring electronic absorption changes. The reversible and cooperative urea-dependent folding-unfolding process of C. caretta myoglobin follows the minimum three-state mechanism N long left and right arrow X long left and right arrow D, where X represents a disordered globin structure (occurring at approximately 4 M urea) that still binds the heme

Quantum interference scattering of aligned molecules: Bonding in O-4 and role of spin coupling

Molecular beam experiments on collisions between oxygen molecules were performed at low energy and high angular resolution to permit observation of the ``glory'' interference effect. A novel technique for aligning the rotational angular momentum of the colliding molecules is exploited. Analysis of total scattering cross section data yields for the O2-O2 bond an energy of 1.65+/-0.08 kJ˙mol-1 for the most stable configuration (parallel molecules) at a distance of 0.356+/-0.007 nm. These results indicate that most of the bonding in the dimer comes from electrostatic (van der Waals) forces but chemical (spin-spin) contributions are not negligible.This work was supported by the Italian CNR and MURST, and the European Union (Contract No. ERG-FMRX-CT96-0088)Peer Reviewe

Experimental investigation of the reaction of helium ions with dimethyl ether:stereodynamics of the dissociative charge exchange process

\u3cp\u3eThe fate of dimethyl ether (DME, CH\u3csub\u3e3\u3c/sub\u3eOCH\u3csub\u3e3\u3c/sub\u3e) in collisions with He\u3csup\u3e+\u3c/sup\u3e ions is of high relevance for astrochemical models aimed at reproducing the abundances of complex organic molecules in the interstellar medium. Here we report an investigation on the reaction of He\u3csup\u3e+\u3c/sup\u3e ions with DME carried out using a Guided Ion Beam Mass Spectrometer (GIB-MS), which allows the measurement of reactive cross-sections and branching ratios (BRs) as a function of the collision energy. We obtain insights into the dissociative charge (electron) exchange mechanism by investigating the nature of the non-adiabatic transitions between the relevant potential energy surfaces (PESs) in an improved Landau-Zener approach. We find that the large interaction anisotropy could induce a pronounced orientation of the polar DME molecule in the electric field generated by He\u3csup\u3e+\u3c/sup\u3e so that at short distances the collision complex is confined within pendular states, a particular case of bending motion, which gives rise to intriguing stereodynamic effects. The positions of the intermolecular potential energy curve crossings indicate that He\u3csup\u3e+\u3c/sup\u3e captures an electron from an inner valence orbital of DME, thus causing its dissociation. In addition to the crossing positions, the symmetry of the electron density distribution of the involved DME orbitals turns out to be a further major point affecting the probability of electron transfer. Thus, the anisotropy of the intermolecular interaction and the electron densities of the orbitals involved in the reaction are the key ingredients for describing the dynamics of this dissociative charge transfer.\u3c/p\u3