101
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Šponer JE, Šponer J, Nováková O, Brabec V, Šedo O, Zdráhal Z, Costanzo G, Pino S, Saladino R, Di Mauro E. Emergence of the First Catalytic Oligonucleotides in a Formamide-Based Origin Scenario. Chemistry 2016; 22:3572-86. [PMID: 26807661 DOI: 10.1002/chem.201503906] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Indexed: 02/02/2023]
Abstract
50 years after the historical Miller-Urey experiment, the formamide-based scenario is perhaps the most powerful concurrent hypothesis for the origin of life on our planet besides the traditional HCN-based concept. The information accumulated during the last 15 years in this topic is astonishingly growing and nowadays the formamide-based model represents one of the most complete and coherent pathways leading from simple prebiotic precursors up to the first catalytically active RNA molecules. In this work, we overview the major events of this long pathway that have emerged from recent experimental and theoretical studies, mainly concentrating on the mechanistic, methodological, and structural aspects of this research.
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Affiliation(s)
- Judit E Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic. .,CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 62500, Brno, Czech Republic.
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic.,CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 62500, Brno, Czech Republic
| | - Olga Nováková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Viktor Brabec
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Ondrej Šedo
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 62500, Brno, Czech Republic
| | - Zbyněk Zdráhal
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 62500, Brno, Czech Republic
| | - Giovanna Costanzo
- Istituto di Biologia e Patologia Molecolari, CNR, P.le Aldo Moro, 5, Rome, 00185, Italy
| | - Samanta Pino
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", "Sapienza" Università di Roma, Piazzale Aldo Moro, 5, Rome, 00185, Italy
| | - Raffaele Saladino
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Via San Camillo De Lellis, 01100, Viterbo, Italy
| | - Ernesto Di Mauro
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", "Sapienza" Università di Roma, Piazzale Aldo Moro, 5, Rome, 00185, Italy
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102
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Cassone G, Creazzo F, Giaquinta PV, Saija F, Marco Saitta A. Ab initio molecular dynamics study of an aqueous NaCl solution under an electric field. Phys Chem Chem Phys 2016; 18:23164-73. [DOI: 10.1039/c6cp03926j] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ab initio molecular dynamics simulations of salty water under an electric field reveal two regimes of the relative mobilities of chlorine and sodium ions. When water dissociation and proton transfer are actived at strong field intensities, the presence of the ions hinders the efficiency of the proton transfer mechanism.
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Affiliation(s)
- Giuseppe Cassone
- Institute of Biophysics – Czech Academy of Sciences
- 61265 Brno
- Czech Republic
| | - Fabrizio Creazzo
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environment
- UMR8587 (CHARMMMAT)
- Université d'Evry val d'Essone
- 91025 Evry
- France
| | - Paolo V. Giaquinta
- Università degli Studi di Messina
- Dipartimento di Scienze Matematiche e Informatiche
- Scienze Fisiche e Scienze della Terra
- 98166 Messina
- Italy
| | | | - A. Marco Saitta
- Sorbonne Universités
- Université Pierre et Marie Curie Paris 06
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie
- 75005 Paris
- France
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103
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Formamide reaction network in gas phase and solution via a unified theoretical approach: Toward a reconciliation of different prebiotic scenarios. Proc Natl Acad Sci U S A 2015; 112:15030-5. [PMID: 26598679 DOI: 10.1073/pnas.1512486112] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Increasing experimental and theoretical evidence points to formamide as a possible hub in the complex network of prebiotic chemical reactions leading from simple precursors like H2, H2O, N2, NH3, CO, and CO2 to key biological molecules like proteins, nucleic acids, and sugars. We present an in-depth computational study of the formation and decomposition reaction channels of formamide by means of ab initio molecular dynamics. To this aim we introduce a new theoretical method combining the metadynamics sampling scheme with a general purpose topological formulation of collective variables able to track a wide range of different reaction mechanisms. Our approach is flexible enough to discover multiple pathways and intermediates starting from minimal insight on the systems, and it allows passing in a seamless way from reactions in gas phase to reactions in liquid phase, with the solvent active role fully taken into account. We obtain crucial new insight into the interplay of the different formamide reaction channels and into environment effects on pathways and barriers. In particular, our results indicate a similar stability of formamide and hydrogen cyanide in solution as well as their relatively facile interconversion, thus reconciling experiments and theory and, possibly, two different and competing prebiotic scenarios. Moreover, although not explicitly sought, formic acid/ammonium formate is produced as an important formamide decomposition byproduct in solution.
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104
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Bergeler M, Simm GN, Proppe J, Reiher M. Heuristics-Guided Exploration of Reaction Mechanisms. J Chem Theory Comput 2015; 11:5712-22. [DOI: 10.1021/acs.jctc.5b00866] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maike Bergeler
- Laboratory
of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Gregor N. Simm
- Laboratory
of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Jonny Proppe
- Laboratory
of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratory
of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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106
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Meteorite-catalyzed syntheses of nucleosides and of other prebiotic compounds from formamide under proton irradiation. Proc Natl Acad Sci U S A 2015; 112:E2746-55. [PMID: 25870268 DOI: 10.1073/pnas.1422225112] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Liquid formamide has been irradiated by high-energy proton beams in the presence of powdered meteorites, and the products of the catalyzed resulting syntheses were analyzed by mass spectrometry. Relative to the controls (no radiation, or no formamide, or no catalyst), an extremely rich, variegate, and prebiotically relevant panel of compounds was observed. The meteorites tested were representative of the four major classes: iron, stony iron, chondrites, and achondrites. The products obtained were amino acids, carboxylic acids, nucleobases, sugars, and, most notably, four nucleosides: cytidine, uridine, adenosine, and thymidine. In accordance with theoretical studies, the detection of HCN oligomers suggests the occurrence of mechanisms based on the generation of radical cyanide species (CN·) for the synthesis of nucleobases. Given that many of the compounds obtained are key components of extant organisms, these observations contribute to outline plausible exogenous high-energy-based prebiotic scenarios and their possible boundary conditions, as discussed.
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109
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Laporte S, Finocchi F, Paulatto L, Blanchard M, Balan E, Guyot F, Saitta AM. Strong electric fields at a prototypical oxide/water interface probed by ab initio molecular dynamics: MgO(001). Phys Chem Chem Phys 2015; 17:20382-90. [DOI: 10.1039/c5cp02097b] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a density-functional theory (DFT)-based study of the interface of bulk water with a prototypical oxide surface, MgO(001), and focus our study on the often-overlooked surface electric field.
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Affiliation(s)
- Sara Laporte
- Sorbonne Universités
- Université Pierre et Marie Curie Paris 06
- CNRS
- Muséum National d'Histoire Naturelle
- IRD
| | - Fabio Finocchi
- Sorbonne Universités
- Université Pierre et Marie Curie Paris 06
- CNRS
- UMR 7588
- Institut des NanoSciences de Paris
| | - Lorenzo Paulatto
- Sorbonne Universités
- Université Pierre et Marie Curie Paris 06
- CNRS
- Muséum National d'Histoire Naturelle
- IRD
| | - Marc Blanchard
- Sorbonne Universités
- Université Pierre et Marie Curie Paris 06
- CNRS
- Muséum National d'Histoire Naturelle
- IRD
| | - Etienne Balan
- Sorbonne Universités
- Université Pierre et Marie Curie Paris 06
- CNRS
- Muséum National d'Histoire Naturelle
- IRD
| | - François Guyot
- Sorbonne Universités
- Université Pierre et Marie Curie Paris 06
- CNRS
- Muséum National d'Histoire Naturelle
- IRD
| | - Antonino Marco Saitta
- Sorbonne Universités
- Université Pierre et Marie Curie Paris 06
- CNRS
- Muséum National d'Histoire Naturelle
- IRD
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