Astrochemical Studies Research Articles

Identification and Limit of Detection of Benzene, Chlorobenzene, Benzoic Acid, Phthalic Acid, and Mellitic Acid in Water Solutions Using Excitation, Emission, and Single-band Synchronous Fluorescence Spectroscopy

Introduction: This paper first introduces the use of computer-simulated single-band synchronous fluorescence (SF) obtained from experimental excitation and emission fluorescence spectra of a pure compound in solution. The simulation produces a single narrow band with a peak wavelength that identifies the compound. Methods: The method is used to show single peak identification of benzene, chlorobenzene, benzoic acid, phthalic acid, and mellitic acid in water solutions. Synchronous fluorescence spectroscopy (SFS) is a variant of fluorescence technique in which excitation and emission scans are simultaneously acquired and multiplied with a predetermined wavelength difference (Δλ) between the two. Commercial instruments have this option to get the SFS signals. Results: In response to the Δλ selected, the result will be an SFS signal producing a series of peaks that could be assigned to compounds. Instead of running the same experiment with different Δλ values to identify the compounds, our simulation program determines a specific Δλ value that generates a narrow SF band with a distinctive peak wavelength for identification purposes. Conclusion: Finally, binary mixtures of chlorobenzene with each compound in water are prepared. The SFS of the solution is acquired and compared with the SFS bands of the components for identification purposes. With the commercial lamp fluorimeter employed, the limits of detection are obtained at the ng/g concentration level with fluorescence emission. Possible limits of detection at lower concentrations are discussed using a laser source. The presence of these molecules in astrochemical studies is discussed.

Predicting binding energies of astrochemically relevant molecules via machine learning

Context. The behaviour of molecules in space is to a large extent governed by where they freeze out or sublimate. The molecular binding energy is therefore an important parameter for many astrochemical studies. This parameter is usually determined with time-consuming experiments, computationally expensive quantum chemical calculations, or the inexpensive yet relatively inaccurate linear addition method. Aims. In this work, we propose a new method for predicting binding energies (BEs) based on machine learning that is accurate, yet computationally inexpensive. Methods. We created a machine-learning (ML) model based on Gaussian process regression (GPR) and trained it on a database of BEs of molecules collected from laboratory experiments presented in the literature. The molecules in the database are categorised by their features, such as mono- or multilayer coverage, binding surface, functional groups, valence electrons, and H-bond acceptors and donors. Results. We assessed the performance of the model with five-fold and leave-one-molecule-out cross validation. Predictions are generally accurate, with differences between predicted binding energies and values from the literature of less than ±20%. We used the validated model to predict the binding energies of 21 molecules that were recently detected in the interstellar medium, but for which binding energy values are unknown. We used a simplified model to visualise where the snow lines of these molecules would be located in a protoplanetary disk. Conclusions. This work demonstrates that ML can be employed to accurately and rapidly predict BEs of molecules. Machine learning complements current laboratory experiments and quantum chemical computational studies. The predicted BEs will find use in the modelling of astrochemical and planet-forming environments.

New Tools for Taming Complex Reaction Networks: The Unimolecular Decomposition of Indole Revisited.

The level of detail attained in the computational description of reaction mechanisms can be vastly improved through tools for automated chemical space exploration, particularly for systems of small to medium size. Under this approach, the unimolecular decomposition landscape for indole was explored through the automated reaction mechanism discovery program AutoMeKin. Nevertheless, the sheer complexity of the obtained mechanisms might be a hindrance regarding their chemical interpretation. In this spirit, the new Python library amk-tools has been designed to read and manipulate complex reaction networks, greatly simplifying their overall analysis. The package provides interactive dashboards featuring visualizations of the network, the three-dimensional (3D) molecular structures and vibrational normal modes of all chemical species, and the corresponding energy profiles for selected pathways. The combination of the joined mechanism generation and postprocessing workflow with the rich chemistry of indole decomposition enabled us to find new details of the reaction (obtained at the CCSD(T)/aug-cc-pVTZ//M06-2X/MG3S level of theory) that were not reported before: (i) 16 pathways leading to the formation of HCN and NH3 (via amino radical); (ii) a barrierless reaction between methylene radical and phenyl isocyanide, which might be an operative mechanism under the conditions of the interstellar medium; and (iii) reaction channels leading to both hydrogen cyanide and hydrogen isocyanide, of potential astrochemical interest as the computed HNC/HCN ratios greatly exceed the calculated equilibrium value at very low temperatures. The reported reaction networks can be very valuable to supplement databases of kinetic data, which is of remarkable interest for pyrolysis and astrochemical studies.

Polarizability in Astrochemical Studies of Complex Carbon-Based Compounds

Polarizability in Astrochemical Studies of Complex Carbon-Based Compounds

Identification of DNA Bases and Their Cations in Astrochemical Environments: Computational Spectroscopy of Thymine as a Test Case

Increased importance of vibrational fingerprints in the identification of molecular systems, can be highlighted by the upcoming interstellar medium (ISM) observations by the James Webb Space Telescope, or in a context of other astrochemical environments as meteorites or exoplanets, Mars robotic missions, such as instruments on board of Perseverance rover. These observations can be supported by combination of laboratory experiments and theoretical calculations, essential to verify and predict the spectral assignments. Astrochemical laboratory simulations have shown that complex organic molecules (COMs) can be formed from simple species by vacuum ultraviolet or X-ray irradiation expanding interest in searching for organic biological and prebiotic compounds. In this work an example of nucleobase, thymine, is selected as a test case for highlighting the utility of computational spectroscopic methods in astrochemical studies. We consider mid-infrared (MIR) and near-infrared (NIR) vibrational spectra of neutral (T) and cationic (T+) thymine ground states, and vibrationally-resolved photoelectron (PE) spectra in the far UV range from 8.7 to 9.4 eV. The theoretical framework is based on anharmonic calculations including overtones and combination bands. The same anharmonic wavenumbers are applied into the simulations of vibrationally-resolved photoelectron spectra based on Franck-Condon computations. The infrared and vibrationally-resolved photoelectron spectra are compared with the available experimental counterparts to verify their accuracy and provide assignment of the observed transitions. Finally, reliable predictions of spectra, going beyond currently available experimental data, either dealing with energy ranges, resolution or temperature, which can support astrochemistry studies are provided.

Interstellar detection of the simplest aminocarbyne H2NC: an ignored but abundant molecule

We report the first identification in space of H2NC, a high-energy isomer of H2CN that has been largely ignored in chemical and astrochemical studies. The observation of various unidentified lines around 72.2 GHz in the cold dark cloud L483 motivated the search and successful detection of additional groups of lines in harmonic relation. Following an exhaustive high-level ab initio screening of possible carriers, we confidently assign the unidentified lines to H2NC based on the good agreement between the astronomical and theoretical spectroscopic parameters alongside sound spectroscopic and astrochemical arguments. The observed frequencies are used to precisely characterize the rotational spectrum of H2NC. This species is also detected in the cold dark cloud B1-b and the z = 0.89 galaxy in front of the quasar PKS 1830−211. We derive H2NC/H2CN abundance ratios ~1 in L483 and B1-b and 0.27 toward PKS 1830−211. Neither H2NC nor H2CN are detected in the dark cloud TMC-1, which seriously undermines the previous identification of H2CN in this source. We suggest that the H2NC/H2CN ratio behaves as the HNC/HCN ratio, with values close to one in cold dense clouds and below one in diffuse clouds. The reactions N + CH3 and C + NH3 emerge as strong candidates for the production of H2NC in interstellar clouds. Further studies on these two reactions are needed to evaluate the yield of H2NC. Due to the small number of atoms involved, it should be feasible to constrain the chemistry behind H2NC and H2CN, just as has been done for HNC and HCN, as this could allow for the H2NC/H2CN ratio to be applied as a probe of chemical or physical conditions of the host clouds.

Astrochemical studies at the Cryogenic Storage Ring.

The new Cryogenic Storage Ring at the Max Planck Institute for Nuclear Physics (Heidelberg, Germany) has recently become operational. One of the main research areas foreseen for this unique facility is astrochemical studies with cold molecular ions. The spontaneous radiative cooling of the prototype interstellar molecule CH+ to its lowest rotational states has been demonstrated by photodissociation spectroscopy, paving the way for experiments under true interstellar conditions. To this end, a low-energy electron cooler and a neutral atom beam set-up for merged beams studies have been constructed. These experiments have the potential to provide energy-resolved rate coefficients for fundamental astrochemical processes involving state-selected molecular ions. The main target reactions include some of the key processes of interstellar chemistry, such as the electron recombination of H3+, charge exchange between H2+ and H, or the formation of CH+ in collisions of triatomic hydrogen ions and C atoms. This article is part of a discussion meeting issue 'Advances in hydrogen molecular ions: H3+, H5+ and beyond'.

High resolution rotational spectroscopy of elusive molecules at the Center for Astrochemical Studies (CAS@MPE)

AbstractThe laboratories at the Centre for Astrochemical Studies at the Max Planck Institute for Extraterrestrial Physics are devoted to spectroscopic studies of molecules of astrophysical relevance. In particular, in this paper we report on the two experiments that can produce and probe unstable molecules, like radicals and ions.

Photochemistry vs. radiation chemistry of cosmic ice analogs

AbstractWhile gas-phase reactions and surface reactions on bare carbonaceous or siliceous dust grains contribute to cosmic chemistry, the energetic processing of cosmic ices via photochemistry and radiation chemistry is thought to be the dominant mechanism for the cosmic synthesis of prebiotic molecules. Because most previous laboratory astrochemical studies have used light sources that produce >10 eV photons and are, therefore, capable of ionizing cosmic ice analogs, discerning the role of photochemistry vs. radiation chemistry in astrochemistry is challenging. By using a source whose photon energy does not exceed 8 eV, we have studied ammonia and methanol cosmic ice reactions attributable solely to photochemistry. We compare these results to those obtained in the same ultrahigh vacuum chamber with 1 keV electrons which instead initiate radiation chemistry in cosmic ice analogs.

A new look at sulphur chemistry in hot cores and corinos

Sulphur-bearing species are often used to probe the evolution of hot cores since their abundances are particularly sensitive to physical and chemical variations. However, the chemistry of sulphur is not well understood in these regions, notably because observations of several hot cores displayed a large variety of sulphur compositions, and because the reservoir of sulphur in dense clouds, in which hot cores form, is still poorly constrained. In order to help disentangled its complexity, we present a fresh comprehensive review of sulphur chemistry in hot cores along with a study of its sensibility to temperature and pre-collapse chemical composition. In parallel, we analyse the discrepencies that result from the use of two different types of models (static and dynamic) to highlight the sensitivity to the choice of model to be used in astrochemical studies. Our results show that the pre-collapse chemical composition is a critical parameter for sulphur chemistry in hot cores and could explain the different sulphur compositions observed. We also report that differences in abundances for a given species between the static and dynamic models can reach six orders of magnitude in the hot core, which reveals the key role of the choice of model in astrochemical studies.

Parameterizing the interstellar dust temperature

The temperature of interstellar dust particles is of great importance to astronomers. It plays a crucial role in the thermodynamics of interstellar clouds, because of the gas-dust collisional coupling. It is also a key parameter in astrochemical studies that governs the rate at which molecules form on dust. In 3D (magneto)hydrodynamic simulations often a simple expression for the dust temperature is adopted, because of computational constraints, while astrochemical modelers tend to keep the dust temperature constant over a large range of parameter space. Our aim is to provide an easy-to-use parametric expression for the dust temperature as a function of visual extinction ($A_{\rm V}$) and to shed light on the critical dependencies of the dust temperature on the grain composition. We obtain an expression for the dust temperature by semi-analytically solving the dust thermal balance for different types of grains and compare to a collection of recent observational measurements. We also explore the effect of ices on the dust temperature. Our results show that a mixed carbonaceous-silicate type dust with a high carbon volume fraction matches the observations best. We find that ice formation allows the dust to be warmer by up to 15% at high optical depths ($A_{\rm V}> 20$ mag) in the interstellar medium. Our parametric expression for the dust temperature is presented as $T_{\rm d} = \left[ 11 + 5.7\times \tanh\bigl( 0.61 - \log_{10}(A_{\rm V})\bigr) \right] \, \chi_{\rm uv}^{1/5.9}$, where $\chi_{\rm uv}$ is in units of the Draine (1978) UV field

A novel assessment of the role of the methyl radical and water formation channel in the CH3OH + H reaction.

A number of experimental and theoretical papers accounted almost exclusively for two channels in the reaction of atomic hydrogen with methanol: H-abstraction from the methyl (R1) and hydroxyl (R2) functional groups. Recently, several astrochemical studies claimed the importance of another channel for this reaction, which is crucial for kinetic simulations related to the abundance of molecular constituents in planetary atmospheres: methyl radical and water formation (R3 channel). Here, motivated by the lack of and uncertainties about the experimental and theoretical kinetic rate constants for the third channel, we developed first-principles Car-Parrinello molecular dynamics thermalized at two significant temperatures - 300 and 2500 K. Furthermore, the kinetic rate constant of all three channels was calculated using a high-level deformed-transition state theory (d-TST) at a benchmark electronic structure level. d-TST is shown to be suitable for describing the overall rate constant for the CH3OH + H reaction (an archetype of the moderate tunnelling regime) with the precision required for practical applications. Considering the experimental ratios at 1000 K, kR1/kR2 ≈ 0.84 and kR1/kR3 ≈ 15-40, we provided a better estimate when compared with previous theoretical work: 7.47 and 637, respectively. The combination of these procedures explicitly demonstrates the role of the third channel in a significant range of temperatures and indicates its importance considering the thermodynamic control to estimate methyl radical and water formation. We expect that these results can help to shed new light on the fundamental kinetic rate equations for the CH3OH + H reaction.

Astronomical complex organic molecules: Quantum chemistry meets rotational spectroscopy

AbstractAstrochemistry is an interdisciplinary field involving chemistry, physics, and astronomy, which encompasses astronomical observations, modeling, as well as theoretical and experimental laboratory investigations. In the frame of the latter, this contribution provides an overview on the computational approaches supporting and complementing rotational spectroscopy experiments applied to astrochemical studies. The focus is on the computational strategies that permit accurate computations of structural and rotational parameters as well as of energetics and on their application to case studies, with particular emphasis on the so‐called “astronomical complex” organic molecules.

Adsorption and Thermal Processing of Glycolaldehyde, Methyl Formate, and Acetic Acid on Graphite at 20 K.

We present the first detailed comparative study of the adsorption and thermal processing of the three astrophysically important C2O2H4 isomers glycolaldehyde, methyl formate, and acetic acid adsorbed on a graphitic grain analogue at 20 K. The ability of the individual molecule to form intermolecular hydrogen bonds is extremely important, dictating the growth modes of the ice on the surface and the measured desorption energies. Methyl formate forms only weak intermolecular bonds and hence wets the graphite surface, forming monolayer, bilayer, and multilayer ices, with the multilayer having a desorption energy of 35 kJ mol(-1). In contrast, glycolaldehyde and acetic acid dewet the surface, forming clusters even at the very lowest coverages. The strength of the intermolecular hydrogen bonding for glycolaldehyde and acetic acid is reflected in their desorption energies (46.8 and 55 kJ mol(-1), respectively), which are comparable to those measured for other hydrogen-bonded species such as water. Infrared spectra show that all three isomers undergo structural changes as a result of thermal processing. In the case of acetic acid and glycolaldehyde, this can be assigned to the formation of well-ordered, crystalline, structures where the molecules form chains of hydrogen-bonded moieties. The data reported here are of relevance to astrochemical studies of hot cores and star-forming regions and can be used to model desorption from interstellar ices during the warm up phase with particular importance for complex organic molecules.

Theoretical characterization of dimethyl carbonate at low temperatures.

Highly correlated ab initio methods (CCSD(T) and RCCSD(T)-F12) are employed for the spectroscopic characterization of the gas phase of dimethyl carbonate (DMC) at low temperatures. DMC, a relevant molecule for atmospheric and astrochemical studies, shows only two conformers, cis-cis and trans-cis, respectively, of C2v and Cs symmetries. cis-cis-DMC represents the most stable form. Using RCCSD(T)-F12 theory, the two sets of equilibrium rotational constants have been computed to be Ae = 10 493.15 MHz, Be = 2399.22 MHz, and Ce = 2001.78 MHz (cis-cis) and to be Ae = 6585.16 MHz, Be = 3009.04 MHz, and Ce = 2120.36 MHz (trans-cis). Centrifugal distortions constants and anharmonic frequencies for all of the vibrational modes are provided. Fermi displacements are predicted. The minimum energy pathway for the cis-cis → trans-cis interconversion process is restricted by a barrier of ∼3500 cm(-1). DMC displays internal rotation of two methyl groups. If the nonrigidity is considered, the molecule can be classified in the G36 (cis-cis) and the G18 (trans-cis) symmetry groups. For cis-cis-DMC, both internal tops are equivalent, and the torsional motions are restricted by V3 potential energy barriers of 384.7 cm(-1). trans-cis-DMC shows two different V3 barriers of 631.53 and 382.6 cm(-1). The far-infrared spectra linked to the torsional motion of both conformers are analyzed independently using a variational procedure and a two-dimensional flexible model. In cis-cis-DMC, the ground vibrational state splits into nine components: one nondegenerate, 0.000 cm(-1) (A1), four quadruply degenerate, 0.012 cm(-1) (G), and four doubly degenerate 0.024 cm(-1) (E1 and E3). The methyl torsional fundamentals are obtained to lie at 140.274 cm(-1) (ν15) and 132.564 cm(-1) (ν30).

Band spectra and dissociation energies: A physical chemistry experiment

An experiment that has proved successful in introducing the spectroscopic determination of molecular energy levels and thermodynamic quantities is the analysis of the visible band spectrum of either iodine or bromine. In addition, this experiment introduces techniques now widely used in high temperature and astro-chemical studies.