Thermodynamic and kinetic aspects of glycine and its radical cation under interstellar medium conditions

Xavier, Neubi Francisco; Baptista, Leonardo; Bauerfeldt, Glauco F.

doi:10.1093/mnras/stz936

Cited by 13 publications

(22 citation statements)

References 67 publications

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“…In the glycine case, the isolated zwitterion is not a gas-phase stationary point. 68 Nevertheless, electronic energy calculations must be performed at the same level of the crystal lattice (PBE-D3/USPP) for the isolated zwitterionic geometry extracted from each polymorph. Calculated E latt are −281.20, −278.56, and −276.80 kJ mol −1 for α, β, and γglycine, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…As previously stated, the lattice energy, E latt refers to the energy necessary to form the crystal lattice from infinite separate species. In the glycine case, the isolated zwitterion is not a gas-phase stationary point . Nevertheless, electronic energy calculations must be performed at the same level of the crystal lattice (PBE-D3/USPP) for the isolated zwitterionic geometry extracted from each polymorph.…”

Section: Resultsmentioning

confidence: 99%

“…25,65−67 It is noteworthy that the zwitterionic form of glycine, present in the crystalline phase, is not a stationary point in the gasphase potential energy surface. A detailed investigation of the gas-phase glycine conformers is presented in previous work, 68 from which the three numbers identification of each conformer was proposed based on geometrical parameters and are summarized as follows: the first and second numbers are related to the H−O−CO and O−C−C−N dihedral angles, respectively, from which 0 is related to 0 and 1 to 180°. The third number is based on the C−C−N−H dihedral angle, assumed as 1 and 2 for values closer to ±60 and ±120°, respectively.…”

Section: Computational Detailsmentioning

confidence: 99%

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Determination of the Cohesive Properties and Sublimation Temperatures of Glycine Polymorphs

Xavier

Bauerfeldt

2021

Crystal Growth & Design

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The experimental data of sublimation properties is limited to important materials, encouraging the development and assessment of theoretical models. Here, such properties were evaluated from periodic density functional theory calculations for three glycine polymorphs (α, β, and γ-glycine) along with the quasi-harmonic approximation for the determination of thermodynamic properties. Careful treatment of cohesive properties was performed, which are shown to be fundamental in the glycine dynamic sublimation process due to its zwitterionic nature in the crystalline environment in contrast with the molecular form in the gas phase. Computational limitations are addressed, and a detailed treatment of vibrational modes of crystalline and vapor phases is discussed. Also, the agreement with the fundamental physical–chemical background on the glycine sublimation process, obtained from different computational methodologies, is discussed. The uncertainties of sublimation properties were evaluated. The maximum absolute deviation of the sublimation temperature, from the experimental data for α-glycine, within the pressure range from 0.1 to 1 Pa, was −5.31 K. Our findings corroborate the experimental evidence for the preferential recrystallization of gas-phase glycine into the metastable β phase.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Computational Detailsmentioning

confidence: 99%

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Determination of the Cohesive Properties and Sublimation Temperatures of Glycine Polymorphs

Xavier

Bauerfeldt

2021

Crystal Growth & Design

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“…Numerous studies were undertaken to throw light on this controversy. They focused on plausible interstellar pathways to glycine, its detectability and survival in the hostile ISM (see, e.g., Ehrenfreund et al 2001a;Blagojevic et al 2003;Largo et al 2010;Pilling et al 2011;Lattelais et al 2011;Rimola et al 2012;Garrod 2013;Jimenez-Serra et al 2014;Nhlabatsi et al 2016;Aponte et al 2017;Suzuki et al 2018;Xavier et al 2019). Special emphasis has been also placed on the formation routes of possible glycine precursors (see, e.g., Basiuk 2001;Largo et al 2004;Koch et al 2008;Knowles et al 2010;Barrientos et al 2012;Redondo et al 2015, and references therein) which are hot candidates for the observations in the ISM as well.…”

Section: Introductionmentioning

confidence: 99%

Millimetre-wave laboratory study of glycinamide and search for it with ALMA toward Sagittarius B2(N)

Kisiel,

Kolesniková,

Belloche

et al. 2021

Preprint

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Context. Glycinamide (NH 2 CH 2 C(O)NH 2 ) is considered to be one of the possible precursors of the simplest amino acid glycine. Its only rotational spectrum reported so far has been in the cm-wave region on a laser-ablation generated supersonic expansion sample. Aims. The aim of this work is to extend the laboratory spectrum of glycinamide into the millimetre wave region to support its searches in the interstellar medium and to perform the first check for its presence in the high-mass star forming region Sagittarius B2(N). Methods. Glycinamide was synthesised chemically and was studied with broadband rotational spectroscopy in the 90-329 GHz region with the sample in slow flow at 50 • C. Tunneling across a low energy barrier between two symmetry equivalent configurations of the molecule resulted in splitting of each vibrational state and many perturbations in associated rotational energy levels, requiring careful coupled state fits for each vibrational doublet. We searched for emission of glycinamide in the imaging spectral line survey ReMoCA performed with the Atacama Large Millimetre/submillimetre Array toward Sgr B2(N). The astronomical spectra were analysed under the assumption of local thermodynamic equilibrium. Results. We report the first analysis of the mm-wave rotational spectrum of glycinamide, resulting in fitting to experimental measurement accuracy of over 1200 assigned and measured transition frequencies for the ground state tunneling doublet, of many lines for tunneling doublets for two singly excited vibrational states, and determination of precise vibrational separation in each doublet. We did not detect emission from glycinamide in the hot molecular core Sgr B2(N1S). We derived a column density upper limit of 1.5 × 10 16 cm −2 , which implies that glycinamide is at least seven times less abundant than aminoacetonitrile and 1.8 times less abundant than urea in this source. A comparison with results of astrochemical kinetics models for species related to glycinamide suggests that its abundance may be at least one order of magnitude below the upper limit obtained toward Sgr B2(N1S). This means that glycinamide emission in this source likely lies well below the spectral confusion limit in the frequency range covered by the ReMoCA survey. Conclusions. Thanks to the spectroscopic data provided by this study, the search for glycinamide in the interstellar medium can continue on a firm basis. Targetting sources with a lower level of spectral confusion, such as the Galactic Center shocked region G+0.693-0.027, may be a promising avenue.

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“…For a better understanding and interpretation of experimental data, quantum chemistry methods are often applied. − In particular, for acetonitrile, previous theoretical investigations focused on high order molecular clusters stabilized by intermolecular interactions − and formation of cationic clusters and dissociation pathways, − as well as formation of anionic clusters …”

Section: Introductionmentioning

confidence: 99%

Structure, Stability, and Spectroscopic Properties of Small Acetonitrile Cation Clusters

et al. 2020

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Ionization and fragmentation pathways induced by ionizing agents are key to understanding the formation of complex molecules in astrophysical environments. Acetonitrile (CH 3 CN), the simplest organic nitrile, is an important molecule present in the interstellar medium. In this work, DFT and MP2 calculations were performed in order to obtain the low energy structures of the most relevant cations formed from electron-stimulated ion desorption of CH 3 CN ices. Selected reaction pathways and spectroscopic properties were also calculated. Our results indicate that the most stable acetonitrile cation structure is CH 2 CNH + and that hydrogenation can occur successively without isomerization steps until its complete saturation. Moreover, the stability of distinct cluster families formed from the interaction of acetonitrile with small fragments, such as CH n + , C 2 H n + , and CH n CNH + , is discussed in terms of their respective binding energies. Some of these molecular clusters are stabilized by hydrogen bonds, leading to species whose infrared features are characterized by a strong redshift of the N− H stretching mode. Finally, the rotational spectra of CH 3 CN and protonated acetonitrile, CH 3 CNH + , were simulated using distinct computational protocols based on DFT, MP2, and CCSD(T) considering centrifugal distortion, vibrational−rotational coupling, and vibrational anharmonicity corrections. By adopting an empirical scaling procedure for calculating spectroscopic parameters, we were able to estimate the rotational frequencies of CH 3 CNH + with an expected average error below 1 MHz for J values up to 10.

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Thermodynamic and kinetic aspects of glycine and its radical cation under interstellar medium conditions

Cited by 13 publications

References 67 publications

Determination of the Cohesive Properties and Sublimation Temperatures of Glycine Polymorphs

Determination of the Cohesive Properties and Sublimation Temperatures of Glycine Polymorphs

Millimetre-wave laboratory study of glycinamide and search for it with ALMA toward Sagittarius B2(N)

Structure, Stability, and Spectroscopic Properties of Small Acetonitrile Cation Clusters

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