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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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Thripati S. Computational studies on the possible formation of glycine via open shell gas-phase chemistry in the interstellar medium. Org Biomol Chem 2022; 20:4189-4203. [PMID: 35543204 DOI: 10.1039/d2ob00407k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Glycine is the simplest proteinogenic amino acid. It has significant astrobiological implications owing to the ongoing investigation for its detection in the interstellar medium (ISM). Hence, a suitable mechanistic elucidation for its formation in the ISM is of current research interest. In the present work, by employing electronic structure calculations [UCCSD(T) and density functional theory (DFT)], various plausible chemical pathways in the gas phase have been examined for the formation of glycine (whose existence has been indirectly proposed in the ISM) and other simple amino acids (yet to be detected in the ISM) from some simpler molecules present in the ISM. This work suggests that step 1: HO-CO (radical) + CH2NH → NHCH2COOH (radical) and step 2a: NHCH2COOH (radical) + H2 → glycine + H (radical) have very small barriers of 0.14 kcal mol-1 and ∼3 kcal mol-1, respectively (easily surmountable at a temperature of ∼50 K under putative interstellar conditions). Hence this should likely be feasible in interstellar gas-phase chemistry. Therefore, HO-CO (radical), CH2NH, and H2 could be the possible precursors for the formation of glycine (subject to the presence of the HO-CO radical). The energetic information related to the interstellar reactions, and how this work takes the putative interstellar conditions into account are presented. This paper also highlights how a reaction found to be unsuitable for interstellar molecular evolution via surface chemistry could nonetheless occur via gas-phase chemistry. Based on our results, this work also recommends detecting three new open-shell molecules, HO-CO radical, NHCH2COOH radical, and NH2CHCOOH radical, in the ISM.
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Affiliation(s)
- Sorakayala Thripati
- Department of Chemistry, Indian Institute of Science Education and Research Tirupati, Andhra Pradesh - 517507, India.
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Rimola A, Balucani N, Ceccarelli C, Ugliengo P. Tracing the Primordial Chemical Life of Glycine: A Review from Quantum Chemical Simulations. Int J Mol Sci 2022; 23:4252. [PMID: 35457069 PMCID: PMC9030215 DOI: 10.3390/ijms23084252] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 12/28/2022] Open
Abstract
Glycine (Gly), NH2CH2COOH, is the simplest amino acid. Although it has not been directly detected in the interstellar gas-phase medium, it has been identified in comets and meteorites, and its synthesis in these environments has been simulated in terrestrial laboratory experiments. Likewise, condensation of Gly to form peptides in scenarios resembling those present in a primordial Earth has been demonstrated experimentally. Thus, Gly is a paradigmatic system for biomolecular building blocks to investigate how they can be synthesized in astrophysical environments, transported and delivered by fragments of asteroids (meteorites, once they land on Earth) and comets (interplanetary dust particles that land on Earth) to the primitive Earth, and there react to form biopolymers as a step towards the emergence of life. Quantum chemical investigations addressing these Gly-related events have been performed, providing fundamental atomic-scale information and quantitative energetic data. However, they are spread in the literature and difficult to harmonize in a consistent way due to different computational chemistry methodologies and model systems. This review aims to collect the work done so far to characterize, at a quantum mechanical level, the chemical life of Gly, i.e., from its synthesis in the interstellar medium up to its polymerization on Earth.
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Affiliation(s)
- Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Catalonia, Spain
| | - Nadia Balucani
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy;
- Osservatorio Astrosico di Arcetri, Largo E. Fermi 5, 50125 Firenze, Italy
| | - Cecilia Ceccarelli
- CNRS, Institut de Planétologie et d’Astrophysique de Grenoble (IPAG), Université Grenoble Alpes, 38000 Grenoble, France;
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Centre, Università degli Studi di Torino, Via P. Giuria 7, 10125 Torino, Italy;
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Derbali I, Thissen R, Alcaraz C, Romanzin C, Zins EL. Study of the Reactivity of CH 3COOH +• and COOH + Ions with CH 3NH 2: Evidence of the Formation of New Peptide-like C(O)-N Bonds. J Phys Chem A 2021; 125:10006-10020. [PMID: 34761946 DOI: 10.1021/acs.jpca.1c06630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acetamide, a small organic compound containing a peptide bond, was observed in the interstellar medium, but reaction pathways leading to the formation of this prebiotic molecule remain uncertain. We investigated the possible formation of a peptide-like bond from the reaction between acetic acid (CH3-COOH) and methylamine (CH3-NH2) that were identified in the interstellar medium. From an experimental point of view, a quadrupole/octopole/quadrupole mass spectrometer was used in combination with synchrotron radiation as a tunable source of VUV photons for monitoring the reactivity of selected ions. Acetic acid was photoionized, and the reactivity of CH3COOH+• as well as COOH+ (produced from either acetic acid or formic acid) ions with neutral CH3NH2 was further studied. With no surprise, charge transfer, proton transfer, and concomitant dissociation processes were found to largely dominate the reactivity. However, a C(O)-N bond formation process between the two reactants was also evidenced, with a weak cross section reaction. From a theoretical point of view, results concerning reactivity and barrier heights were obtained using density functional theory, with the LC-ωPBE range-separated functional in combination with the 6-311++G(d,p) Pople basis set and are in perfect agreement with the experimental data.
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Affiliation(s)
- Imene Derbali
- De la Molécule aux Nano-Objets: Réactivité, Interactions Spectroscopies, MONARIS, Sorbonne Université, CNRS, 75005 Paris, France
| | - Roland Thissen
- Institut de Chimie Physique, UMR 8000, Université Paris-Saclay, CNRS, Bât. 350, 91405 Orsay, France.,SOLEIL Synchrotron, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Christian Alcaraz
- Institut de Chimie Physique, UMR 8000, Université Paris-Saclay, CNRS, Bât. 350, 91405 Orsay, France.,SOLEIL Synchrotron, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Claire Romanzin
- Institut de Chimie Physique, UMR 8000, Université Paris-Saclay, CNRS, Bât. 350, 91405 Orsay, France.,SOLEIL Synchrotron, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Emilie-Laure Zins
- De la Molécule aux Nano-Objets: Réactivité, Interactions Spectroscopies, MONARIS, Sorbonne Université, CNRS, 75005 Paris, France
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Perez-Mellor AF, Spezia R. Determination of kinetic properties in unimolecular dissociation of complex systems from graph theory based analysis of an ensemble of reactive trajectories. J Chem Phys 2021; 155:124103. [PMID: 34598552 DOI: 10.1063/5.0058382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In this paper, we report how graph theory can be used to analyze an ensemble of independent molecular trajectories, which can react during the simulation time-length, and obtain structural and kinetic information. This method is totally general and here is applied to the prototypical case of gas phase fragmentation of protonated cyclo-di-glycine. This methodology allows us to analyze the whole set of trajectories in an automatic computer-based way without the need of visual inspection but by getting all the needed information. In particular, we not only determine the appearance of different products and intermediates but also characterize the corresponding kinetics. The use of colored graph and canonical labeling allows for the correct characterization of the chemical species involved. In the present case, the simulations consist of an ensemble of unimolecular fragmentation trajectories at constant energy such that from the rate constants at different energies, the threshold energy can also be obtained for both global and specific pathways. This approach allows for the characterization of ion-molecule complexes, likely through a roaming mechanism, by properly taking into account the elusive nature of such species. Finally, it is possible to directly obtain the theoretical mass spectrum of the fragmenting species if the reacting system is an ion as in the specific example.
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Affiliation(s)
- Ariel F Perez-Mellor
- LAMBE UMR8587, Université d'Evry Val d'Essonne, CNRS, CEA, Université Paris-Saclay, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, 91025 Evry, France
| | - Riccardo Spezia
- Laboratoire de Chimie Théorique, Sorbonne Université and CNRS, F-75005 Paris, France
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Carrà A, Spezia R. In Silico
Tandem Mass Spectrometer: an Analytical and Fundamental Tool. ACTA ACUST UNITED AC 2021. [DOI: 10.1002/cmtd.202000071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Andrea Carrà
- Agilent Technologies Italia Via Piero Gobetti 2/C 20063 Cernusco SN, Milano Italy
| | - Riccardo Spezia
- Laboratoire de Chimie Théorique Sorbonne Université, UMR 7616 CNRS 4, Place Jussieu 75005 Paris France
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Prebiotic chemistry and origins of life research with atomistic computer simulations. Phys Life Rev 2020; 34-35:105-135. [DOI: 10.1016/j.plrev.2018.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/10/2018] [Indexed: 02/02/2023]
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Scuderi D, Pérez‐Mellor A, Lemaire J, Indrajith S, Bardaud J, Largo A, Jeanvoine Y, Spezia R. Infrared‐Assisted Synthesis of Prebiotic Glycine. Chemphyschem 2020; 21:503-509. [DOI: 10.1002/cphc.202000065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Indexed: 01/30/2023]
Affiliation(s)
- Debora Scuderi
- ICP, Institut de Chimie PhysiqueUniversité Paris Saclay, CNRS UMR 8000 15, rue Georges Clemenceau 91405 Orsay Cedex France
| | - Ariel Pérez‐Mellor
- LAMBEUniversité d'EvryCNRS, CEAUniversité Paris-Saclay 91025 Evry France
| | - Joël Lemaire
- ICP, Institut de Chimie PhysiqueUniversité Paris Saclay, CNRS UMR 8000 15, rue Georges Clemenceau 91405 Orsay Cedex France
| | - Suvasthika Indrajith
- ICP, Institut de Chimie PhysiqueUniversité Paris Saclay, CNRS UMR 8000 15, rue Georges Clemenceau 91405 Orsay Cedex France
| | | | - Antonio Largo
- Computational Chemistry GroupDepartamento de Quimica FisicaUniversidad de Valladolid Valladolid 47011 Spain
| | - Yannick Jeanvoine
- LAMBEUniversité d'EvryCNRS, CEAUniversité Paris-Saclay 91025 Evry France
| | - Riccardo Spezia
- Sorbonne UniversitéCNRS, Laboratoire de Chimie Théorique 4, Place Jussieu 75252 Paris Cedex 05 France
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Bodo E, Bovolenta G, Simha C, Spezia R. On the formation of propylene oxide from propylene in space: gas-phase reactions. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2485-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Macaluso V, Scuderi D, Crestoni ME, Fornarini S, Corinti D, Dalloz E, Martinez-Nunez E, Hase WL, Spezia R. l-Cysteine Modified by S-Sulfation: Consequence on Fragmentation Processes Elucidated by Tandem Mass Spectrometry and Chemical Dynamics Simulations. J Phys Chem A 2019; 123:3685-3696. [DOI: 10.1021/acs.jpca.9b01779] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Veronica Macaluso
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, 91025 Évry, France
| | - Debora Scuderi
- LCP, Laboratoire de Chimie Physique, Université Paris-Sud, Bat. 349, CNRS UMR8000, 15 rue Georges Clemenceau, 91405 Orsay Cedex, France
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Enzo Dalloz
- LCP, Laboratoire de Chimie Physique, Université Paris-Sud, Bat. 349, CNRS UMR8000, 15 rue Georges Clemenceau, 91405 Orsay Cedex, France
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Emilio Martinez-Nunez
- Departamento de Química Física, Facultade de Química, Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - William L. Hase
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Riccardo Spezia
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, 91025 Évry, France
- CNRS, Laboratoire de Chimie Théorique, LCT, Sorbonne Université, 4, Place Jussieu, 75252 Paris Cedex 05, France
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The formation of urea in space. II. MP2 versus PM6 dynamics in determining bimolecular reaction products. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2385-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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