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Derbali I, Aroule O, Hoffmann G, Thissen R, Alcaraz C, Romanzin C, Zins EL. On the relevance of the electron density analysis for the study of micro-hydration and its impact on the formation of a peptide-like bond. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02893-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Schiller A, Meyer M, Martini P, Zappa F, Krasnokutski SA, Calvo F, Scheier P. Adsorption of Helium on Small Cationic PAHs: Influence of Hydrocarbon Structure on the Microsolvation Pattern. J Phys Chem A 2021; 125:7813-7824. [PMID: 34436885 PMCID: PMC8450901 DOI: 10.1021/acs.jpca.1c05150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/11/2021] [Indexed: 11/29/2022]
Abstract
The adsorption of up to ∼100 helium atoms on cations of the planar polycyclic aromatic hydrocarbons (PAHs) anthracene, phenanthrene, fluoranthene, and pyrene was studied by combining helium nanodroplet mass spectrometry with classical and quantum computational methods. Recorded time-of-flight mass spectra reveal a unique set of structural features in the ion abundance as a function of the number of attached helium atoms for each of the investigated PAHs. Path-integral molecular dynamics simulations were used with a polarizable potential to determine the underlying adsorption patterns of helium around the studied PAH cations and in good general agreement with the experimental data. The calculated structures of the helium-PAH complexes indicate that the arrangement of adsorbed helium atoms is highly sensitive toward the structure of the solvated PAH cation. Closures of the first solvation shell around the studied PAH cations are suggested to lie between 29 and 37 adsorbed helium atoms depending on the specific PAH cation. Helium atoms are found to preferentially adsorb on these PAHs following the 3 × 3 commensurate pattern common for graphitic surfaces, in contrast to larger carbonaceous molecules like corannulene, coronene, and fullerenes that exhibit a 1 × 1 commensurate phase.
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Affiliation(s)
- Arne Schiller
- Institut
für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Miriam Meyer
- Institut
für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Paul Martini
- Institut
für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Fabio Zappa
- Institut
für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Serge A. Krasnokutski
- Laboratory
Astrophysics Group of the MPI for Astronomy at the University of Jena, Helmholtzweg 3, D-07743 Jena, Germany
| | - Florent Calvo
- CNRS,
LiPhy, Univ. Grenoble Alpes, F-38000 Grenoble, France
| | - Paul Scheier
- Institut
für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
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Zins EL. Microhydration of a Carbonyl Group: How does the Molecular Electrostatic Potential (MESP) Impact the Formation of (H 2O) n:(R 2C═O)Complexes? J Phys Chem A 2020; 124:1720-1734. [PMID: 32049521 DOI: 10.1021/acs.jpca.9b09992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The presence of a carbonyl group in a molecule usually leads to the identification of a π-hole on the molecular electrostatic potential (MESP) of the species. How does this electrophilic site influence the formation of microhydrated complexes? To address this point, a panel of R2CO solutes with various MESPs was selected, and we identified the structures and properties of several complexes containing one, two, three and six water molecules. The following solutes were considered in the present study: H2CO, F2CO, Cl2CO,(NC)2CO and H2C═CO. Geometry optimizations and frequency calculations were carried out at the LC-ωPBE/6-311++G(d,p) level, with the GD3BJ empirical correction for dispersion. For a number of n water molecules around the R2CO solute, the structure and the features of the most stable (H2O)n:(R2CO) complexes are highly dependent on the MESP of the isolated R2CO solute. The formation of pi-hole bondings appears to play a decisive role in the initiation of a three-dimensional organization of water molecules around the solute.
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Affiliation(s)
- Emilie-Laure Zins
- De la Molécule aux Nano-Objets: Réactivité, Interactions Spectroscopies, MONARIS, CNRS, Sorbonne Université, 75005, Paris, France
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Kerkeni B, Bacchus-Montabonel MC. Proton-Induced Charge Transfer on Imidazole and 2-Aminoimidazole. Role of the Substituent and Influence of Stepwise Hydration. J Phys Chem A 2020; 124:1003-1010. [PMID: 31935089 DOI: 10.1021/acs.jpca.9b10602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The behavior of potential prebiotic species in space is of main concern in the chemistry at the origin of life. Their reactivity or stability in spatial conditions, under strong UV radiations or ion bombardments, remains an open question and needs wide investigations. As protons are by far the most abundant ions in space, we focus presently on proton-induced collisions on imidazole and 2-aminoimidazole evidenced as important prebiotic RNA intermediates. Unconstrained full optimization of the structures was performed with B3LYP/cc-pVTZ model chemistry. The calculations were performed in a wide collision energy range in order to model various astrophysical environments, from eV in the interstellar medium, up to keV for solar winds or supernovae shock-wave protons. Such a study provides for the first time a theoretical insight on the influence of the amino substituent on the proton-induced charge transfer. We evaluated the role of icy grain environments through a cluster approach modeling the effect of a stepwise microhydration on the process. Comparisons with oxygenated and sulfurated analogues address further qualitative trends on the respective stability or reactivity of such heterocycles which may be of tremendous interest in prebiotic chemistry. Charge transfer appears to be quite efficient for imidazole compounds and their sulfurated analogue compared to the oxygenated heterocycle.
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Affiliation(s)
- Boutheïna Kerkeni
- Département de Physique, Laboratoire de Physique de la Matière Condensée, Faculté des Sciences de Tunis , Université de Tunis el Manar , Campus Universitaire , 2092 Tunis , Tunisia.,Institut Supérieur des Arts Multimédia de la Manouba , Université de la Manouba , 2010 La Manouba , Tunisia.,Université Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 Villeurbanne , France
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Charge Transfer, Complexes Formation and Furan Fragmentation Induced by Collisions with Low-Energy Helium Cations. Int J Mol Sci 2019; 20:ijms20236022. [PMID: 31795357 PMCID: PMC6929036 DOI: 10.3390/ijms20236022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/14/2019] [Accepted: 11/25/2019] [Indexed: 01/24/2023] Open
Abstract
The present work focuses on unraveling the collisional processes leading to the fragmentation of the gas-phase furan molecules under the He+ and He2+ cations impact in the energy range 5–2000 eV. The presence of different mechanisms was identified by the analysis of the optical fragmentation spectra measured using the collision-induced emission spectroscopy (CIES) in conjunction with the ab initio calculations. The measurements of the fragmentation spectra of furan were performed at the different kinetic energies of both cations. In consequence, several excited products were identified by their luminescence. Among them, the emission of helium atoms excited to the 1s4d1D2, 3D1,2,3 states was recorded. The structure of the furan molecule lacks an He atom. Therefore, observation of its emission lines is spectroscopic evidence of an impact reaction occurring via relocation of the electronic charge between interacting entities. Moreover, the recorded spectra revealed significant variations of relative band intensities of the products along with the change of the projectile charge and its velocity. In particular, at lower velocities of He+, the relative cross-sections of dissociation products have prominent resonance-like maxima. In order to elucidate the experimental results, the calculations have been performed by using a high level of quantum chemistry methods. The calculations showed that in both impact systems two collisional processes preceded fragmentation. The first one is an electron transfer from furan molecules to cations that leads to the neutralization and further excitation of the cations. The second mechanism starts from the formation of the He−C4H4O+/2+ temporary clusters before decomposition, and it is responsible for the appearance of the narrow resonances in the relative cross-section curves.
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Yamabe S, Tsuchida N, Yamazaki S. A DFT study of the hydrolysis of hydantoin. INT J CHEM KINET 2019. [DOI: 10.1002/kin.21312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Noriko Tsuchida
- Department of Liberal Arts, Faculty of MedicineSaitama Medical University Saitama Japan
| | - Shoko Yamazaki
- Department of ChemistryNara University of Education Japan
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Bacchus-Montabonel MC. Role of sulfur in proton-induced collisions of RNA prebiotic precursors. Phys Chem Chem Phys 2019; 21:1428-1434. [PMID: 30601542 DOI: 10.1039/c8cp07204c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A main objective in the synthesis of prebiotic compounds is to remain consistent with reasonable geochemical scenarios, while avoiding concomitant formation of undesirable by-products. In this context, 2-aminothiazole has shown enhanced selectivity in the addition reaction with sugars promoting interest in this sulfur species compared to its oxygenated analogue, 2-aminooxazole. More generally, the role of sulfur in prebiotic chemistry needs to be widely investigated with regard to the numerous sulfur-containing molecules detected recently in different astrophysical environments. However, in parallel to the problematic formation of building blocks of life, how prebiotic molecules could survive under extreme astrophysical conditions remains an open question. Intense UV radiation or ion bombardment may indeed lead to fragmentation and the specific behaviour of sulfur compounds has to be addressed. Focusing on its potentiality in prebiotic multistep synthesis, a detailed analysis of the proton impact on 2-aminothiazole has been investigated theoretically in a wide collision energy range chosen to model various astrophysical environments. The comparison with its oxygenated analogue may suggest qualitative trends on their respective stability under such processes which could be of crucial interest for prebiotic synthesis.
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Bacchus-Montabonel MC. Proton-induced collision dynamics on potential prebiotic sulfur species. Phys Chem Chem Phys 2018; 20:9084-9089. [PMID: 29561041 DOI: 10.1039/c8cp00886h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The formation of the building blocks of life and how they could survive under harsh astrophysical environments remains an open question of prebiotic chemistry. Effectively, ion bombardments or intense UV radiation may drive the destruction of prebiotic compounds. The possible role of sulfur in such processes is addressed here for the first time, by comparing directly proton-induced charge transfer for sulfur containing molecules and that for related COMs. The proton collision on mercaptoacetonitrile HSCH2C[triple bond, length as m-dash]N conformers has thus been investigated theoretically in a wide impact energy range modelling various astrophysical environments and compared to related COMs, namely HCN oligomers, in order to exhibit qualitative tendencies.
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