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Szabó P, Gustafsson M. Polyatomic radiative association by quasiclassical trajectory calculations: Formation of HCN and HNC molecules in H + CN collisions. J Chem Phys 2023; 159:144112. [PMID: 37831719 DOI: 10.1063/5.0170577] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 08/21/2023] [Indexed: 10/15/2023] Open
Abstract
We have developed the polyatomic extension of the established [M. Gustafsson, J. Chem. Phys. 138, 074308 (2013)] classical theory of radiative association in the absence of electronic transitions. The cross section and the emission spectrum of the process is calculated by a quasiclassical trajectory method combined with the classical Larmor formula which can provide the radiated power in collisions. We have also proposed a Monte Carlo scheme for efficient computation of ro-vibrationally quantum state resolved cross sections for radiative association. Besides the method development, the global potential energy and dipole surfaces for H + CN collisions have been calculated and fitted to test our polyatomic semiclassical method.
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Affiliation(s)
- Péter Szabó
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
- Royal Belgian Institute for Space Aeronomy (BIRA-IASB), Avenue Circulaire 3, 1180 Brussels, Belgium
- Applied Physics, Division of Materials Science, Department of Engineering Science and Mathematics, Luleå University of Technology, 97187 Luleå, Sweden
| | - Magnus Gustafsson
- Applied Physics, Division of Materials Science, Department of Engineering Science and Mathematics, Luleå University of Technology, 97187 Luleå, Sweden
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2
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Armas-Vázquez MZ, González-Espinoza CE, Segura A, Heredia A, Miranda-Rosete A. Impact of M Dwarfs Ultraviolet Radiation on Prebiotic Chemistry: The Case of Adenine. ASTROBIOLOGY 2023; 23:705-722. [PMID: 37115581 DOI: 10.1089/ast.2022.0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To date, several exoplanets have been found to orbit within the habitable zone of main sequence M stars (M dwarfs). These stars exhibit different levels of chromospheric activity that produces ultraviolet (UV) radiation. UV may be harmful to life, but it can also trigger reactions of prebiotic importance on the surface of a potentially habitable planet (PHP). We created a code to obtain the adenine yield for a known adenine synthesis route from diaminomaleonitrile (DAMN). We used computational methods to calculate the reaction coefficient rates (photolysis rate J and rate constant K) for the intermediate molecules DAMN, diaminofumaronitrile (DAFN), and 4-aminoimidazole-5-carbonitrile (AICN) of the adenine synthesis route. We used stellar UV sources and a mercury lamp to compare the theoretical results with experiments performed with lamps. The surface UV flux of planets in the habitable zone of two active M dwarfs (Proxima Centauri and AD Leonis) and the prebiotic Earth was calculated using the photochemical model ATMOS, considering a CO2-N2-H2O atmosphere. We obtained UV absorption coefficients for DAMN and DAFN and thermodynamic parameters that are useful for prebiotic chemistry studies. According to our results, experiments using UV lamps may underestimate the photolysis production of molecules of prebiotic importance. Our results indicate that photolysis reactions are fast with a yield of 50% of AICN in 10 s for the young Sun and ∼1 h for Proxima Centauri b. Planets around active M dwarfs may provide the most favorable environment for UV-mediated production of compounds relevant to the origins of life. The kinetic reaction AICN + HCN adenine is the bottleneck of the pathway with reaction rates <10-22 L/(mol·s).
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Affiliation(s)
- M Zulema Armas-Vázquez
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México (UNAM), Ciudad de Mexico, Mexico
| | | | - Antígona Segura
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México (UNAM), Ciudad de Mexico, Mexico
| | - Alejandro Heredia
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México (UNAM), Ciudad de Mexico, Mexico
| | - Arturo Miranda-Rosete
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México (UNAM), Ciudad de Mexico, Mexico
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3
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Hernández C, Michaelian K. Dissipative Photochemical Abiogenesis of the Purines. ENTROPY (BASEL, SWITZERLAND) 2022; 24:1027. [PMID: 35893007 PMCID: PMC9394256 DOI: 10.3390/e24081027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 01/27/2023]
Abstract
We have proposed that the abiogenesis of life around the beginning of the Archean may have been an example of "spontaneous" microscopic dissipative structuring of UV-C pigments under the prevailing surface ultraviolet solar spectrum. The thermodynamic function of these Archean pigments (the "fundamental molecules of life"), as for the visible pigments of today, was to dissipate the incident solar light into heat. We have previously described the non-equilibrium thermodynamics and the photochemical mechanisms which may have been involved in the dissipative structuring of the purines adenine and hypoxanthine from the common precursor molecules of hydrogen cyanide and water under this UV light. In this article, we extend our analysis to include the production of the other two important purines, guanine and xanthine. The photochemical reactions are presumed to occur within a fatty acid vesicle floating on a hot (∼80 ∘C) neutral pH ocean surface exposed to the prevailing UV-C light. Reaction-diffusion equations are resolved under different environmental conditions. Significant amounts of adenine (∼10-5 M) and guanine (∼10-6 M) are obtained within 60 Archean days, starting from realistic concentrations of the precursors hydrogen cyanide and cyanogen (∼10-5 M).
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Affiliation(s)
- Claudeth Hernández
- Department of Physics, Division of Exact and Natural Sciences, Campus Hermosillo, Universidad de Sonora, Hermosillo C.P. 83067, Mexico;
| | - Karo Michaelian
- Department of Nuclear Physics and Application of Radiation, Instituto de Física, Universidad Nacional Autónoma de México, Circuito Interior de la Investigación Científica, Cuidad Universitaria, Cuidad de México C.P. 04510, Mexico
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Zamir A, Stein T. Isomerization of hydrogen cyanide and hydrogen isocyanide in a cluster environment: quantum chemical study. J Chem Phys 2022; 156:054307. [DOI: 10.1063/5.0077000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Alon Zamir
- Fritz Haber Research Center for Molecular Dynamics, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Tamar Stein
- Fritz Haber Research Center for Molecular Dynamics, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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5
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Abstract
HCN-derived polymers are a heterogeneous group of complex substances synthesized from pure HCN; from its salts; from its oligomers, specifically its trimer and tetramer, amino-nalono-nitrile (AMN) and diamino-maleo-nitrile (DAMN), respectively; or from its hydrolysis products, such as formamide, under a wide range of experimental conditions. The characteristics and properties of HCN-derived polymers depend directly on the synthetic conditions used for their production and, by extension, their potential applications. These puzzling systems have been known mainly in the fields of prebiotic chemistry and in studies on the origins of life and astrobiology since the first prebiotic production of adenine by Oró in the early years of the 1960s. However, the first reference regarding their possible role in prebiotic chemistry was mentioned in the 19th century by Pflüger. Currently, HCN-derived polymers are considered keys in the formation of the first and primeval protometabolic and informational systems, and they may be among the most readily formed organic macromolecules in the solar system. In addition, HCN-derived polymers have attracted a growing interest in materials science due to their potential biomedical applications as coatings and adhesives; they have also been proposed as valuable models for multifunctional materials with emergent properties such as semi-conductivity, ferroelectricity, catalysis and photocatalysis, and heterogeneous organo-synthesis. However, the real structures and the formation pathways of these fascinating substances have not yet been fully elucidated; several models based on either computational approaches or spectroscopic and analytical techniques have endeavored to shed light on their complete nature. In this review, a comprehensive perspective of HCN-derived polymers is presented, taking into account all the aspects indicated above.
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6
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The Dissipative Photochemical Origin of Life: UVC Abiogenesis of Adenine. ENTROPY 2021; 23:e23020217. [PMID: 33579010 PMCID: PMC7916814 DOI: 10.3390/e23020217] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/22/2021] [Accepted: 02/03/2021] [Indexed: 11/21/2022]
Abstract
The non-equilibrium thermodynamics and the photochemical reaction mechanisms are described which may have been involved in the dissipative structuring, proliferation and complexation of the fundamental molecules of life from simpler and more common precursors under the UVC photon flux prevalent at the Earth’s surface at the origin of life. Dissipative structuring of the fundamental molecules is evidenced by their strong and broad wavelength absorption bands in the UVC and rapid radiationless deexcitation. Proliferation arises from the auto- and cross-catalytic nature of the intermediate products. Inherent non-linearity gives rise to numerous stationary states permitting the system to evolve, on amplification of a fluctuation, towards concentration profiles providing generally greater photon dissipation through a thermodynamic selection of dissipative efficacy. An example is given of photochemical dissipative abiogenesis of adenine from the precursor HCN in water solvent within a fatty acid vesicle floating on a hot ocean surface and driven far from equilibrium by the incident UVC light. The kinetic equations for the photochemical reactions with diffusion are resolved under different environmental conditions and the results analyzed within the framework of non-linear Classical Irreversible Thermodynamic theory.
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Ferus M, Rimmer P, Cassone G, Knížek A, Civiš S, Šponer JE, Ivanek O, Šponer J, Saeidfirozeh H, Kubelík P, Dudžák R, Petera L, Juha L, Pastorek A, Křivková A, Krůs M. One-Pot Hydrogen Cyanide-Based Prebiotic Synthesis of Canonical Nucleobases and Glycine Initiated by High-Velocity Impacts on Early Earth. ASTROBIOLOGY 2020; 20:1476-1488. [PMID: 32955922 DOI: 10.1089/ast.2020.2231] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Chemical environments of young planets are assumed to be significantly influenced by impacts of bodies lingering after the dissolution of the protoplanetary disk. We explore the chemical consequences of impacts of these bodies under reducing planetary atmospheres dominated by carbon monoxide, methane, and molecular nitrogen. Impacts were simulated by using a terawatt high-power laser system. Our experimental results show that one-pot impact-plasma-initiated synthesis of all the RNA canonical nucleobases and the simplest amino acid glycine is possible in this type of atmosphere in the presence of montmorillonite. This one-pot synthesis begins with de novo formation of hydrogen cyanide (HCN) and proceeds through intermediates such as cyanoacetylene and urea.
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Affiliation(s)
- Martin Ferus
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Paul Rimmer
- Department of Earth Sciences, University of Cambridge, Cambridge, United Kingdom
- Cavendish Astrophysics, University of Cambridge, Cambridge, United Kingdom
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Giuseppe Cassone
- Institute for Physical-Chemical Processes, National Research Council, Messina, Italy
| | - Antonín Knížek
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Svatopluk Civiš
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Judit E Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Ondřej Ivanek
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Homa Saeidfirozeh
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Kubelík
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Radiation and Chemical Physics, Institute of Physics, Czech Academy of Sciences, Prague, Czech Republic
| | - Roman Dudžák
- Department of Radiation and Chemical Physics, Institute of Physics, Czech Academy of Sciences, Prague, Czech Republic
- Institute of Plasma Physics, Czech Academy of Sciences, Prague, Czech Republic
| | - Lukáš Petera
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Libor Juha
- Department of Radiation and Chemical Physics, Institute of Physics, Czech Academy of Sciences, Prague, Czech Republic
- Institute of Plasma Physics, Czech Academy of Sciences, Prague, Czech Republic
| | - Adam Pastorek
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Prague, Czech Republic
| | - Anna Křivková
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Prague, Czech Republic
| | - Miroslav Krůs
- Institute of Plasma Physics, Czech Academy of Sciences, Prague, Czech Republic
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Chatterjee K, Dopfer O. Spectroscopic identification of fragment ions of DNA/RNA building blocks: the case of pyrimidine. Phys Chem Chem Phys 2020; 22:17275-17290. [PMID: 32685941 DOI: 10.1039/d0cp02919j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Pyrimidine (Pym, 1,3-diazine, 1,3-diazabenzene) is an important N-heterocyclic building block of nucleobases. Understanding the structures of its fragment and precursor ions provides insight into its prebiotic and abiotic synthetic route. The long-standing controversial debate about the structures of the primary fragment ions of the Pym+ cation (C4H4N2+, m/z 80) resulting from loss of HCN, C3H3N+ (m/z 53), is closed herein with the aid of a combined approach utilizing infrared photodissociation (IRPD) spectroscopy in the CH and NH stretch ranges (νCH/NH) and density functional theory (DFT) calculations. IRPD spectra of cold Ar/N2-tagged fragment ions reveal that the C3H3N+ population is dominated by cis-/trans-HCCHNCH+ ions (∼90%) along with a minor contribution of the most stable H2CCCNH+ and cis-/trans-HCCHCNH+ isomers (∼10%). We also spectroscopically confirm that the secondary fragment resulting from further loss of HCN, C2H2+ (m/z 26), is the acetylene cation (HCCH+). The spectroscopic characterization of the identified C3H3N+ isomers and their hydrogen-bonded dimers with Ar and N2 provides insight into the acidity of their CH and NH groups. Finally, the vibrational properties of Pym+ in the 3 μm range are probed by IRPD of Pym+-(N2)1-2 clusters, which shows a high π-binding affinity of Pym+ toward a nonpolar hydrophobic ligand. Its νCH spectrum confirms the different acidity of the three nonequivalent CH groups.
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Affiliation(s)
- Kuntal Chatterjee
- Institut für Optik und Atomare Physik, TU Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, TU Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
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9
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Choe JC. Formation of Cytosine and Uracil from Cyanoacetylaldehyde and Guanidine: A Computational Study. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.11971] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Joong Chul Choe
- Department of ChemistryDongguk University‐Seoul Seoul 04620 South Korea
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10
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Giacomozzi L, D’Angelo G, Diaz-Tendero S, de Ruette N, Stockett MH, Alcamí M, Cederquist H, Schmidt HT, Zettergren H. Decay pathways for protonated and deprotonated adenine molecules. J Chem Phys 2019; 151:044306. [DOI: 10.1063/1.5109963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- L. Giacomozzi
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
| | - G. D’Angelo
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - S. Diaz-Tendero
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - N. de Ruette
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
| | - M. H. Stockett
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
| | - M. Alcamí
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-NANO), 28049 Madrid, Spain
| | - H. Cederquist
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
| | - H. T. Schmidt
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
| | - H. Zettergren
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
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11
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Marais A, Adams B, Ringsmuth AK, Ferretti M, Gruber JM, Hendrikx R, Schuld M, Smith SL, Sinayskiy I, Krüger TPJ, Petruccione F, van Grondelle R. The future of quantum biology. J R Soc Interface 2018; 15:20180640. [PMID: 30429265 PMCID: PMC6283985 DOI: 10.1098/rsif.2018.0640] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/12/2018] [Indexed: 01/17/2023] Open
Abstract
Biological systems are dynamical, constantly exchanging energy and matter with the environment in order to maintain the non-equilibrium state synonymous with living. Developments in observational techniques have allowed us to study biological dynamics on increasingly small scales. Such studies have revealed evidence of quantum mechanical effects, which cannot be accounted for by classical physics, in a range of biological processes. Quantum biology is the study of such processes, and here we provide an outline of the current state of the field, as well as insights into future directions.
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Affiliation(s)
- Adriana Marais
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Betony Adams
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Andrew K Ringsmuth
- Institute for Lasers, Life and Biophotonics, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
- ARC Centre of Excellence for Engineered Quantum Systems, The University of Queensland, St Lucia 4072, Australia
| | - Marco Ferretti
- Institute for Lasers, Life and Biophotonics, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - J Michael Gruber
- Institute for Lasers, Life and Biophotonics, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Ruud Hendrikx
- Institute for Lasers, Life and Biophotonics, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Maria Schuld
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Samuel L Smith
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Ilya Sinayskiy
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa
- National Institute for Theoretical Physics, KwaZulu-Natal, South Africa
| | - Tjaart P J Krüger
- Department of Physics, Faculty of Natural and Agricultural Sciences, University of Pretoria, Hatfield, South Africa
| | - Francesco Petruccione
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa
- National Institute for Theoretical Physics, KwaZulu-Natal, South Africa
| | - Rienk van Grondelle
- Institute for Lasers, Life and Biophotonics, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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Benallou A. A new mechanistic insight of DNA base adenine formation from pentamer HCN in the gas phase of interstellar clouds. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2018. [DOI: 10.1080/16583655.2018.1543163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Abdelilah Benallou
- Team of Chemoinformatics Research and Spectroscopy and Quantum Chemistry, Department of Chemistry, Physical and Chemistry Lab, Faculty of Science, University Chouaib Doukkali, El Jadida, Morocco
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14
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Cunha T, Mendes M, Ferreira da Silva F, Eden S, García G, Bacchus-Montabonel MC, Limão-Vieira P. Electron transfer driven decomposition of adenine and selected analogs as probed by experimental and theoretical methods. J Chem Phys 2018; 148:134301. [PMID: 29626890 DOI: 10.1063/1.5021888] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report on a combined experimental and theoretical study of electron-transfer-induced decomposition of adenine (Ad) and a selection of analog molecules in collisions with potassium (K) atoms. Time-of-flight negative ion mass spectra have been obtained in a wide collision energy range (6-68 eV in the centre-of-mass frame), providing a comprehensive investigation of the fragmentation patterns of purine (Pu), adenine (Ad), 9-methyl adenine (9-mAd), 6-dimethyl adenine (6-dimAd), and 2-D adenine (2-DAd). Following our recent communication about selective hydrogen loss from the transient negative ions (TNIs) produced in these collisions [T. Cunha et al., J. Chem. Phys. 148, 021101 (2018)], this work focuses on the production of smaller fragment anions. In the low-energy part of the present range, several dissociation channels that are accessible in free electron attachment experiments are absent from the present mass spectra, notably NH2 loss from adenine and 9-methyl adenine. This can be understood in terms of a relatively long transit time of the K+ cation in the vicinity of the TNI tending to enhance the likelihood of intramolecular electron transfer. In this case, the excess energy can be redistributed through the available degrees of freedom inhibiting fragmentation pathways. Ab initio theoretical calculations were performed for 9-methyl adenine (9-mAd) and adenine (Ad) in the presence of a potassium atom and provided a strong basis for the assignment of the lowest unoccupied molecular orbitals accessed in the collision process.
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Affiliation(s)
- T Cunha
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - M Mendes
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - F Ferreira da Silva
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - S Eden
- School of Physical Sciences, The Open University, Walton Hall, MK7 6AA Milton Keynes, United Kingdom
| | - G García
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 113-bis, 28006 Madrid, Spain
| | - M-C Bacchus-Montabonel
- Institut Lumiére Matiére, Université Lyon, Université Claude Bernard Lyon 1, CNRS, 69622 Villeurbanne, France
| | - P Limão-Vieira
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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15
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Šponer JE, Szabla R, Góra RW, Saitta AM, Pietrucci F, Saija F, Di Mauro E, Saladino R, Ferus M, Civiš S, Šponer J. Prebiotic synthesis of nucleic acids and their building blocks at the atomic level - merging models and mechanisms from advanced computations and experiments. Phys Chem Chem Phys 2018; 18:20047-66. [PMID: 27136968 DOI: 10.1039/c6cp00670a] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The origin of life on Earth is one of the most fascinating questions of contemporary science. Extensive research in the past decades furnished diverse experimental proposals for the emergence of first informational polymers that could form the basis of the early terrestrial life. Side by side with the experiments, the fast development of modern computational chemistry methods during the last 20 years facilitated the use of in silico modelling tools to complement the experiments. Modern computations can provide unique atomic-level insights into the structural and electronic aspects as well as the energetics of key prebiotic chemical reactions. Many of these insights are not directly obtainable from the experimental techniques and the computations are thus becoming indispensable for proper interpretation of many experiments and for qualified predictions. This review illustrates the synergy between experiment and theory in the origin of life research focusing on the prebiotic synthesis of various nucleic acid building blocks and on the self-assembly of nucleotides leading to the first functional oligonucleotides.
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Affiliation(s)
- Judit E Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic. and CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Rafał Szabla
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic.
| | - Robert W Góra
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - A Marco Saitta
- Sorbonne Universités, Université Pierre et Marie Curie Paris 6, CNRS, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d'Histoire Naturelle, Institut de Recherche pour le Développement, UMR 7590, F-75005 Paris, France
| | - Fabio Pietrucci
- Sorbonne Universités, Université Pierre et Marie Curie Paris 6, CNRS, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d'Histoire Naturelle, Institut de Recherche pour le Développement, UMR 7590, F-75005 Paris, France
| | - Franz Saija
- CNR-IPCF, Viale Ferdinando Stagno d'Alcontres 37, 98158 Messina, Italy
| | - Ernesto Di Mauro
- 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
| | - Martin Ferus
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
| | - Svatopluk Civiš
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic. and CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
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16
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Kameneva SV, Tyurin DA, Feldman VI. Characterization of the HCNCO complex and its radiation-induced transformation to HNCCO in cold media: an experimental and theoretical investigation. Phys Chem Chem Phys 2018; 19:24348-24356. [PMID: 28849816 DOI: 10.1039/c7cp03518g] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The HCNCO complex and its X-ray induced transformation to HNCCO in solid noble gas (Ng) matrices (Ng = Ne, Ar, Kr, Xe) was first characterized by matrix isolation FTIR spectroscopy at 5 K. The HCNCO complex was obtained by deposition of HCN/CO/Ng gaseous mixtures. The assignment was based on extensive quantum chemical calculations at the CCSD(T) level of theory. The calculations predicted two computationally stable structures for HCNCO and three stable structures for HNCCO. However, only the most energetically favorable linear structures corresponding to the co-ordination between the H atom of HCN (HNC) and the C atom of CO have been found experimentally. The HCNCO complex demonstrates a considerable red shift of the H-C stretching vibrations (-24 to -38 cm-1, depending on the matrix) and a blue shift of the HCN bending vibrations (+29 to +32 cm-1) with respect to that of the HCN monomer, while the C[double bond, length as m-dash]O stretching mode is blue-shifted by 15 to 20 cm-1 as compared to the CO monomer. The HNCCO complex reveals a strong red shift of the H-N bending (-77 to -118 cm-1) and a strong blue shift of the HNC bending mode (ca. +100 cm-1) as compared to the HNC monomer, whereas the C[double bond, length as m-dash]O stretching is blue-shifted by 24 to 29 cm-1 with respect to that of the CO monomer. The interaction energies were determined to be 1.01 and 1.87 kcal mol-1 for HCNCO and HNCCO, respectively. It was found that the formation of complexes with CO had a remarkable effect on the radiation-induced transformations of HCN. While the dissociation of HCN to H and CN is suppressed in complexes, the isomerization of HCN to HNC is strongly catalyzed by the complexation with CO. The astrochemical implications of the results are discussed.
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Affiliation(s)
- Svetlana V Kameneva
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia.
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17
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Choe JC. Water-assisted Dimerization of Hydrogen Cyanide: A Computational Study. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11324] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Joong Chul Choe
- Department of Chemistry; Dongguk University-Seoul; Seoul 04620 Korea
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18
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de Oliveira PMC, Silva JAB, Longo RL. Benchmark, DFT assessments, cooperativity, and energy decomposition analysis of the hydrogen bonds in HCN/HNC oligomeric complexes. J Mol Model 2017; 23:56. [PMID: 28161784 DOI: 10.1007/s00894-017-3235-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 01/13/2017] [Indexed: 02/05/2023]
Abstract
Hydrogen cyanide (HCN) and its tautomer hydrogen isocyanide (HNC) are relevant for extraterrestrial chemistry and possible relation to the origin of biomolecules. Several processes and reactions involving these molecules depend on their intermolecular interactions that can lead to aggregates and liquids especially due to the hydrogen bonds. It is thus important to comprehend, to describe, and to quantify their hydrogen bonds, mainly their nature and the cooperativity effects. A systematic study of all linear complexes up to pentamers of HCN and HNC is presented. CCSD(T)/CBS energy calculations, with and without basis set superposition error (BSSE) corrections for energies and geometries, provided a suitable set of benchmarks. Approximated methods based on the density functional theory (DFT) such as BP86, PBE, TPSS, B3LYP, CAM-B3LYP with and without dispersion corrections and long-range corrections, were assessed to describe the interaction energies and cooperativity effects. These assessments are relevant to select DFT functionals for liquid simulations. Energy decomposition analysis was performed at the PBE/STO-TZ2P level and provided insights into the nature of the hydrogen bonds, which are dominated by the electrostatic component. In addition, several linear relationships between the various energy components and the interaction energy were obtained. The cooperativity energy was also found to be practically linear with respect to the interaction energy, which may be relevant for designing and/or correcting empirical force fields. Graphical Abstract Hydrogen bonds in HCN/HNC oligomeric complexesᅟ.
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Affiliation(s)
| | - Juliana A B Silva
- Centro Acadêmico do Agreste, Universidade Federal de Pernambuco, 55002-970, Caruaru, PE, Brazil
| | - Ricardo L Longo
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, 50740-540, Recife, PE, Brazil.
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19
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The mechanism determination of trimer and tetramer HCN for adenine formation in the gas phase of interstellar space. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2016.12.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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20
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Kameneva SV, Tyurin DA, Nuzhdin KB, Feldman VI. Matrix isolation andab initiostudy on HCN/CO2system and its radiation-induced transformations: Spectroscopic evidence for HCN⋯CO2andtrans-HCNH⋯CO2complexes. J Chem Phys 2016; 145:214309. [DOI: 10.1063/1.4969075] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Svetlana V. Kameneva
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Daniil A. Tyurin
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Kirill B. Nuzhdin
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir I. Feldman
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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21
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Information entropy of interstellar and circumstellar carbon-containing molecules: Molecular size against structural complexity. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.10.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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22
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Understanding the most favourable dimer of HCN for the oligomerization process in the gas phase of interstellar clouds. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.10.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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23
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Kameneva SV, Tyurin DA, Feldman VI. Structure and properties of the radiation-induced intermediates produced from HCN in noble gas matrices. Radiat Phys Chem Oxf Engl 1993 2016. [DOI: 10.1016/j.radphyschem.2015.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Carels N, Ponce de Leon M. An Interpretation of the Ancestral Codon from Miller's Amino Acids and Nucleotide Correlations in Modern Coding Sequences. Bioinform Biol Insights 2015; 9:37-47. [PMID: 25922573 PMCID: PMC4401237 DOI: 10.4137/bbi.s24021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/08/2015] [Accepted: 03/13/2015] [Indexed: 12/31/2022] Open
Abstract
Purine bias, which is usually referred to as an “ancestral codon”, is known to result in short-range correlations between nucleotides in coding sequences, and it is common in all species. We demonstrate that RWY is a more appropriate pattern than the classical RNY, and purine bias (Rrr) is the product of a network of nucleotide compensations induced by functional constraints on the physicochemical properties of proteins. Through deductions from universal correlation properties, we also demonstrate that amino acids from Miller’s spark discharge experiment are compatible with functional primeval proteins at the dawn of living cell radiation on earth. These amino acids match the hydropathy and secondary structures of modern proteins.
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Affiliation(s)
- Nicolas Carels
- Laboratório de Modelagem de Sistemas Biológicos, National Institute for Science and Technology on Innovation in Neglected Diseases (INCT/IDN), Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - Miguel Ponce de Leon
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria, Madrid, Spain
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25
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Cole CA, Wang ZC, Snow TP, Bierbaum VM. Deprotonated Purine Dissociation: Experiments, Computations, and Astrobiological Implications. J Phys Chem A 2015; 119:334-43. [DOI: 10.1021/jp509012s] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Callie A. Cole
- Department
of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, Colorado 80309, United States
| | - Zhe-Chen Wang
- Department
of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, Colorado 80309, United States
| | - Theodore P. Snow
- Department
of Astrophysical and Planetary Sciences, University of Colorado, 391 UCB, Boulder, Colorado 80309, United States
- Center
for Astrophysics and Space Astronomy, University of Colorado, 389 UCB, Boulder, Colorado 80309, United States
| | - Veronica M. Bierbaum
- Department
of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, Colorado 80309, United States
- Center
for Astrophysics and Space Astronomy, University of Colorado, 389 UCB, Boulder, Colorado 80309, United States
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26
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Affiliation(s)
- Kenneth M. Merz
- Quantum
Theory Project, University of Florida, 2234 New Physics Building, Gainesville, 32611 Florida, United States
- Institute for Cyber Enabled Research, Department of Chemistry,
and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Eduardo C. Aguiar
- Departamento
de Química Fundamental, Universidade Federal de Pernambuco, Recife, 54740-540 Pernambuco, Brazil
| | - Joao Bosco P. da Silva
- Departamento
de Química Fundamental, Universidade Federal de Pernambuco, Recife, 54740-540 Pernambuco, Brazil
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27
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Shivani, Misra A, Tandon P. Reaction between CH2 and HCCN: a theoretical approach to acrylonitrile formation in the interstellar medium. ORIGINS LIFE EVOL B 2014; 44:143-57. [PMID: 25416678 DOI: 10.1007/s11084-014-9373-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 10/26/2014] [Indexed: 11/29/2022]
Abstract
Acrylonitrile (CH2CHCN) was first detected in dense molecular cloud SgrB2. The synthesis of this interstellar molecule is reported to be quite difficult. Therefore, in the present work an attempt has been made to explore the possibility of formation of acrylonitrile from some simple molecules and radicals detected in interstellar space by radical-radical interaction scheme, both in the gas phase and in the icy grains. All calculations are performed using quantum chemical methods with density functional theory (DFT) at the B3LYP/6-311G (d,p) level and Møller-Plesset perturbation theory at the MP2/6-311G (d,p) level. In the discussed chemical pathway, the reaction is found to be totally exothermic and barrier less giving rise to a high probability of acrylonitrile formation in Interstellar space.
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Affiliation(s)
- Shivani
- Department of Mathematics & Astronomy, University of Lucknow, Lucknow, India
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28
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Jung SH, Choe JC. Mechanisms of prebiotic adenine synthesis from HCN by oligomerization in the gas phase. ASTROBIOLOGY 2013; 13:465-75. [PMID: 23659646 DOI: 10.1089/ast.2013.0973] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We explored the potential energy surfaces for adenine synthesis by oligomerizations of HCN or HNC from CBS-QB3 calculations. The pathways have been obtained for the formation of the covalently bound HCN dimer, trimer, tetramer, and pentamer (adenine) by sequential additions of HCN or HNC. The activation energies of the individual oligomerization stages are a few hundred kilojoules per mole, which prevent efficient adenine synthesis in interstellar space or in the atmosphere of Titan. On the other hand, when the oligomerizations start from HCNH(+), the activation energies of sequential HCN or HNC additions are significantly reduced. Kinetic analyses results suggest that adenine synthesis by proton-catalyzed oligomerizations cannot occur efficiently in interstellar space or in the atmosphere of Titan, even though some oligomerization stages can occur under the latter condition.
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Affiliation(s)
- Sun Hwa Jung
- Department of Chemistry, Dongguk University-Seoul, Seoul, Korea
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29
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Ferus M, Civiš S, Mládek A, Šponer J, Juha L, Šponer JE. On the Road from Formamide Ices to Nucleobases: IR-Spectroscopic Observation of a Direct Reaction between Cyano Radicals and Formamide in a High-Energy Impact Event. J Am Chem Soc 2012. [DOI: 10.1021/ja310421z] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Martin Ferus
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
- Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-182 21 Prague 8, Czech Republic
| | - Svatopluk Civiš
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
| | - Arnošt Mládek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic
- CEITEC-Central European Institute of Technology, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic
- CEITEC-Central European Institute of Technology, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Libor Juha
- Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-182 21 Prague 8, Czech Republic
| | - Judit E. Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic
- CEITEC-Central European Institute of Technology, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
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31
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Gupta VP, Tandon P. Conformational and vibrational studies of isomeric hydrogen cyanide tetramers by quantum chemical methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 89:55-66. [PMID: 22245939 DOI: 10.1016/j.saa.2011.12.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 11/18/2011] [Accepted: 12/15/2011] [Indexed: 05/31/2023]
Abstract
The results of structural studies and detailed harmonic and anharmonic vibrational analysis on two hydrogen cyanide (HCN) tetramers diaminomaleonitrile (DAMN) and diaminofumaronitrile (DAFN), which are important molecules for understanding the chemistry of interstellar space and nitrile rich environments, are being reported on the basis of density functional theory using second-order perturbation theory. Both the molecules are found to have C1 symmetry. While all the heavy atoms of DAMN lie in the same plane (maximum deviation 6°), the two nitrogen atoms in DAFN are out of plane by about 15°. The two amino groups are tetrahedral and do not have significant bond angle anisotropy. Detailed conformational studies are reported on the two molecules and their possible rotational isomers are identified. Complete vibrational analysis based on harmonic and anharmonic frequencies, intensity of infrared and activity of Raman bands and potential energy distribution over the internal coordinates has been provided for the two molecules. Affect of hydrogen bonding on molecular geometry and frequencies of the NH stretch modes has been studied by calculations on the dimers of the two molecules. A close agreement has been observed between the experimental and calculated frequencies. Vibrational-rotational constants such as rotational constants in the ground vibrational state (A0, B0, C0) and the effective rotational constants (Ae, Be and Ce), including terms due to quartic centrifugal distortion constants, rotation-vibration coupling constants, Wilson and Nielsen's centrifugal distortion constants have been calculated using B3LYP and B97-1 functionals and 6-31G**, 6-311+G** and TZVP basis sets.
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Affiliation(s)
- V P Gupta
- Department of Physics, University of Lucknow, Lucknow 226021, India.
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32
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Gupta V, Rawat P, Singh R, Tandon P. Formation of 2-imino-malononitrile and diaminomaleonitrile in nitrile rich environments: A quantum chemical study. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2011.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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33
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Šponer JE, Mládek A, Šponer J, Fuentes-Cabrera M. Formamide-Based Prebiotic Synthesis of Nucleobases: A Kinetically Accessible Reaction Route. J Phys Chem A 2011; 116:720-6. [DOI: 10.1021/jp209886b] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Judit E. Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265 Brno, Czech Republic
- CEITEC-Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Arnošt Mládek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265 Brno, Czech Republic
- CEITEC-Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Miguel Fuentes-Cabrera
- Center for Nanophase Materials Sciences and Computer Sciences and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, P.O. Box 2008, Oak Ridge, Tennessee 37831-6494, United States
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34
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Glaser R, Yin J, Miller S. Asymmetry in the N-Inversion of Heteroarene Imines: Pyrimidin-4(3H)-Imine, Pyridin-2(1H)-Imine, and 1H-Purine-6(9H)-Imine. J Org Chem 2010; 75:1132-42. [DOI: 10.1021/jo902358c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rainer Glaser
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211
| | - Jian Yin
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211
| | - Stephanie Miller
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211
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35
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Mateo-Martí E, Pradier CM, Martín-Gago JA. Ultraviolet photostability of adenine on gold and silicon surfaces. ASTROBIOLOGY 2009; 9:573-579. [PMID: 19663763 DOI: 10.1089/ast.2008.0317] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The adenine molecule is a DNA nucleobase, an essential component of genetic material. Because of the important role of DNA nucleobases in terrestrial biochemistry, we have studied the molecular adsorption, orientation, and chemical binding of adenine on metallic and semiconducting surfaces, such as gold and silicon, respectively, and their stability toward ultraviolet radiation by X-ray photoelectron spectroscopy (XPS) and reflection absorption infrared spectroscopy (RAIRS) techniques. We have exposed the adenine surface system to UV radiation (200-400 nm) under a high-vacuum environment (10(-7) mbar) to study the photostability and photochemistry of adenine on different surfaces. After 10 or 24 hours of exposure under interplanetary space conditions, UV radiation induces desorption and partial dissociation of the molecule, which is dependant on the nature of the surface. The electronic excitations, induced in the material by UV absorption, play a major role in the photodestruction of the absorbed molecules on the solid surfaces.
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Affiliation(s)
- Eva Mateo-Martí
- Centro de Astrobiología (CSIC-INTA), 28850-Torrejón de Ardoz, Madrid, Spain.
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36
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Pilling S, Andrade DPP, Neto ÁC, Rittner R, Naves de Brito A. DNA Nucleobase Synthesis at Titan Atmosphere Analog by Soft X-rays. J Phys Chem A 2009; 113:11161-6. [DOI: 10.1021/jp902824v] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sergio Pilling
- Pontifícia Universidade Católica do Rio de Janeiro (PUC-Rio), Rua Marques de São Vicente, 225 Gávea, CEP 22453-900, Rio de Janeiro, RJ, Brazil, State University of Campinas (Unicamp), CEP 3084-971, Campinas, SP, Brazil, and Laboratório Nacional de Luz Síncroton (LNLS), Rua Giuseppe Maximo Scolfaro, 10000, Guara, CEP 13083-970, Campinas, SP, Brazil
| | - Diana P. P. Andrade
- Pontifícia Universidade Católica do Rio de Janeiro (PUC-Rio), Rua Marques de São Vicente, 225 Gávea, CEP 22453-900, Rio de Janeiro, RJ, Brazil, State University of Campinas (Unicamp), CEP 3084-971, Campinas, SP, Brazil, and Laboratório Nacional de Luz Síncroton (LNLS), Rua Giuseppe Maximo Scolfaro, 10000, Guara, CEP 13083-970, Campinas, SP, Brazil
| | - Álvaro C. Neto
- Pontifícia Universidade Católica do Rio de Janeiro (PUC-Rio), Rua Marques de São Vicente, 225 Gávea, CEP 22453-900, Rio de Janeiro, RJ, Brazil, State University of Campinas (Unicamp), CEP 3084-971, Campinas, SP, Brazil, and Laboratório Nacional de Luz Síncroton (LNLS), Rua Giuseppe Maximo Scolfaro, 10000, Guara, CEP 13083-970, Campinas, SP, Brazil
| | - Roberto Rittner
- Pontifícia Universidade Católica do Rio de Janeiro (PUC-Rio), Rua Marques de São Vicente, 225 Gávea, CEP 22453-900, Rio de Janeiro, RJ, Brazil, State University of Campinas (Unicamp), CEP 3084-971, Campinas, SP, Brazil, and Laboratório Nacional de Luz Síncroton (LNLS), Rua Giuseppe Maximo Scolfaro, 10000, Guara, CEP 13083-970, Campinas, SP, Brazil
| | - Arnaldo Naves de Brito
- Pontifícia Universidade Católica do Rio de Janeiro (PUC-Rio), Rua Marques de São Vicente, 225 Gávea, CEP 22453-900, Rio de Janeiro, RJ, Brazil, State University of Campinas (Unicamp), CEP 3084-971, Campinas, SP, Brazil, and Laboratório Nacional de Luz Síncroton (LNLS), Rua Giuseppe Maximo Scolfaro, 10000, Guara, CEP 13083-970, Campinas, SP, Brazil
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Balucani N. Elementary reactions and their role in gas-phase prebiotic chemistry. Int J Mol Sci 2009; 10:2304-2335. [PMID: 19564951 PMCID: PMC2695279 DOI: 10.3390/ijms10052304] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2009] [Revised: 05/13/2009] [Accepted: 05/15/2009] [Indexed: 11/23/2022] Open
Abstract
The formation of complex organic molecules in a reactor filled with gaseous mixtures possibly reproducing the primitive terrestrial atmosphere and ocean demonstrated more than 50 years ago that inorganic synthesis of prebiotic molecules is possible, provided that some form of energy is provided to the system. After that groundbreaking experiment, gas-phase prebiotic molecules have been observed in a wide variety of extraterrestrial objects (including interstellar clouds, comets and planetary atmospheres) where the physical conditions vary widely. A thorough characterization of the chemical evolution of those objects relies on a multi-disciplinary approach: 1) observations allow us to identify the molecules and their number densities as they are nowadays; 2) the chemistry which lies behind their formation starting from atoms and simple molecules is accounted for by complex reaction networks; 3) for a realistic modeling of such networks, a number of experimental parameters are needed and, therefore, the relevant molecular processes should be fully characterized in laboratory experiments. A survey of the available literature reveals, however, that much information is still lacking if it is true that only a small percentage of the elementary reactions considered in the models have been characterized in laboratory experiments. New experimental approaches to characterize the relevant elementary reactions in laboratory are presented and the implications of the results are discussed.
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Affiliation(s)
- Nadia Balucani
- Dipartimento di Chimica, Università degli Studi di Perugia, 06123 Perugia, Italy; E-Mail:
; Tel. +39-075-585-5513; Fax: +39-075-585-5606
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38
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Brédy R, Bernard J, Chen L, Montagne G, Li B, Martin S. Fragmentation of adenine under energy control. J Chem Phys 2009; 130:114305. [DOI: 10.1063/1.3080162] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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Lehman N. A recombination-based model for the origin and early evolution of genetic information. Chem Biodivers 2008; 5:1707-17. [PMID: 18816523 DOI: 10.1002/cbdv.200890159] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Recombination is the exchange of groups of subunits between two entities. It is argued here that this process was central to the origin of life, because it allowed for the creation of useful information from a random pool of linear polymers. The length distribution of such a pool could be broadened if these polymers, such as RNA strands, have the capability of interacting and performing a cross-strand nucleophilic attack of a hydroxy group on a phosphate. Both the formation of stable secondary structures such as stem-loops and selection for self-replication can operate to push the equilibrium length distribution of the pool to longer and more catalytically proficient oligomers. There is empirical and theoretical support for these operations. Finally, in a collection of recombining linear oligomers, the advent of short recognition sequences that favor certain interactions over others, the property of a genotypic 'self' could develop, which later can shed its collective nature and be subject to Darwinian evolution. This could have given rise to true replicase enzymes, for example.
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Affiliation(s)
- Niles Lehman
- Department of Chemistry, Portland State University, PO Box 751, Portland, OR 97207, USA.
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VUV photophysics and dissociative photoionization of pyrimidine, purine, imidazole and benzimidazole in the 7–18eV photon energy range. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.08.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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41
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Abstract
AbstractTo understand the origin of protein/nucleic acid based life as we know it on Earth, we must “follow” the nitrogen. Because of its unique hydrogen bonding characteristics, nitrogen is the key element in catalytic and/or informational proteins and nucleic acids essential to cell function and reproduction. We present evidence that HCN is the original source of prebiotic protein and nucleobase nitrogen. We also present chemically rational models supporting the radical hypothesis that the polymerization of HCN yields ab initio mundi prebiotic protein and polynucleobase macromolecules of sufficient size and complexity to allow the spontaneous generation of pre-RNA World biopolymers capable of catalysis and information transfer.
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Shukla MK, Leszczynski J. Radiation Induced Molecular Phenomena In Nucleic Acids: A Brief Introduction. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2008. [DOI: 10.1007/978-1-4020-8184-2_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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Qian M, Yang S, Wu H, Majumdar P, Leigh N, Glaser R. Ammonia elimination from protonated nucleobases and related synthetic substrates. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:2040-57. [PMID: 17920289 PMCID: PMC2080854 DOI: 10.1016/j.jasms.2007.08.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2007] [Revised: 08/28/2007] [Accepted: 08/28/2007] [Indexed: 05/10/2023]
Abstract
The results are reported of mass-spectrometric studies of the nucleobases adenine 1h (1, R = H), guanine 2h, and cytosine 3h. The protonated nucleobases are generated by electrospray ionization of adenosine 1r (1, R = ribose), guanosine 2r, and deoxycytidine 3d (3, R = deoxyribose) and their fragmentations were studied with tandem mass spectrometry. In contrast to previous EI-MS studies of the nucleobases, NH(3) elimination does present a major path for the fragmentations of the ions [1h + H](+), [2h + H](+), and [3h + H](+). The ion [2h + H - NH(3)](+) also was generated from the acyclic precursor 5-cyanoamino-4-oxomethylene-dihydroimidazole 13h and from the thioether derivative 14h of 2h (NH(2) replaced by MeS). The analyses of the modes of initial fragmentation is supported by density functional theoretical studies. Conjugate acids 15-55 were studied to determine site preferences for the protonations of 1h, 2h, 3h, 13h, and 14h. The proton affinity of the amino group hardly ever is the substrate's best protonation site, and possible mechanisms for NH(3) elimination are discussed in which the amino group serves as the dissociative protonation site. The results provide semi-direct experimental evidence for the existence of the pyrimidine ring-opened cations that we had proposed on the basis of theoretical studies as intermediates in nitrosative nucleobase deamination.
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Affiliation(s)
- Ming Qian
- Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211, USA
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Roy D, Najafian K, von Ragué Schleyer P. Chemical evolution: the mechanism of the formation of adenine under prebiotic conditions. Proc Natl Acad Sci U S A 2007; 104:17272-7. [PMID: 17951429 PMCID: PMC2077245 DOI: 10.1073/pnas.0708434104] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Indexed: 11/18/2022] Open
Abstract
Fundamental building blocks of life have been detected extraterrestrially, even in interstellar space, and are known to form nonenzymatically. Thus, the HCN pentamer, adenine (a base present in DNA and RNA), was first isolated in abiogenic experiments from an aqueous solution of ammonia and HCN in 1960. Although many variations of the reaction conditions giving adenine have been reported since then, the mechanistic details remain unexplored. Our predictions are based on extensive computations of sequences of reaction steps along several possible mechanistic routes. H(2)O- or NH(3)-catalyzed pathways are more favorable than uncatalyzed neutral or anionic alternatives, and they may well have been the major source of adenine on primitive earth. Our report provides a more detailed understanding of some of the chemical processes involved in chemical evolution, and a partial answer to the fundamental question of molecular biogenesis. Our investigation should trigger similar explorations of the detailed mechanisms of the abiotic formation of the remaining nucleic acid bases and other biologically relevant molecules.
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Affiliation(s)
- Debjani Roy
- Center for Computational Chemistry, Department of Chemistry, University of Georgia, Athens, GA 30602-2525; and
| | - Katayoun Najafian
- Department of Chemistry, Acadia University, Wolfville, NS, Canada B4P 2R6
| | - Paul von Ragué Schleyer
- Center for Computational Chemistry, Department of Chemistry, University of Georgia, Athens, GA 30602-2525; and
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