1
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Thøgersen J, Madzharova F, Weidner T, Jensen F. Deep-Ultraviolet Photoexcitation of Aqueous Urea Forms Carbamic Acid/Carbamate in Less Than One Picosecond. Chemistry 2024:e202400728. [PMID: 38804868 DOI: 10.1002/chem.202400728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Indexed: 05/29/2024]
Abstract
Urea is believed to have been essential to the synthesis of prebiotic nucleotides and thereby the RNA or DNA of the first lifeforms. Models suggesting that life began in wet-dry cycles around shallow aquatic ponds imply that reactants such as urea were exposed to deep ultraviolet irradiation from the young sun. Detrimental photodissociation of urea induced by deep UV excitation potentially challenges these models. We here follow the primary deep ultraviolet photochemistry of aqueous urea. The data show that urea is barely excited at 200 nm due to weak ultraviolet absorption. The likelihood of photodissociation is further reduced by strong intra-molecular coupling of the CN and CO stretch vibrations accompanied by an efficient dissipation of the excitation energy to the surrounding water molecules mitigated by urea-water hydrogen bonds. We find that 54±5 % of the excited urea molecules dissociate. Reactions between the photoproducts and surrounding solvent molecules form carbamic acid or the carbamate anions within 0.6 ps. The molecules that do not dissociate return to the electronic ground state in 2 ps. Interestingly, the photodissociation processes of urea in the aqueous phase is different from earlier reported reactions observed following the VUV photolysis of urea in noble gas matrices and highlight the potential influence of water on the prebiotic photochemistry.
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Affiliation(s)
- Jan Thøgersen
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus, Denmark
| | - Fani Madzharova
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus, Denmark
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus, Denmark
| | - Frank Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus, Denmark
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2
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Prosdocimi F, de Farias ST. Origin of life: Drawing the big picture. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 180-181:28-36. [PMID: 37080436 DOI: 10.1016/j.pbiomolbio.2023.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/15/2023] [Accepted: 04/17/2023] [Indexed: 04/22/2023]
Abstract
Trying to provide a broad overview about the origin of life in Earth, the most significant transitions of life before cells are listed and discussed. The current approach emphasizes the symbiotic relationships that emerged with life. We propose a rational, stepwise scenario for the origin of life that starts with the origin of the first biomolecules and steps forward until the origins of the first cells. Along this path, we aim to provide a brief, though comprehensive theoretical model that will consider the following steps: (i) how nucleotides and other biomolecules could be made prebiotically in specific prebiotic refuges; (ii) how the first molecules of RNAs were formed; (iii) how the proto-peptidyl transferase center was built by the concatenation of proto-tRNAs; (iv) how the ribosome and the genetic code could be structured; (v) how progenotes could live and reproduce as "naked" ribonucleoprotein molecules; (vi) how peptides started to bind molecules in the prebiotic soup allowing biochemical pathways to evolve from those bindings; (vii) how genomes got bigger by the symbiotic relationship of progenotes and lateral transference of genetic material; (viii) how the progenote LUCA has been formed by assembling most biochemical routes; (ix) how the first virion capsids probably emerged and evolved; (x) how phospholipid membranes emerged probably twice by the evolution of lipid-binding proteins; (xi) how DNA synthesis have been formed in parallel in Bacteria and Archaea; and, finally, (xii) how DNA-based cells of Bacteria and Archaeabacteria have been constituted. The picture provided is conjectural and present epistemological gaps. Future research will help to advance into the elucidation of gaps and confirmation/refutation of current statements.
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Affiliation(s)
- Francisco Prosdocimi
- Laboratório de Biologia Teórica e de Sistemas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Sávio Torres de Farias
- Laboratório de Genética Evolutiva Paulo Leminski, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil; Network of Researchers on the Chemical Evolution of Life (NoRCEL), Leeds, LS7 3RB, UK
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3
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Salibi E, Peter B, Schwille P, Mutschler H. Periodic temperature changes drive the proliferation of self-replicating RNAs in vesicle populations. Nat Commun 2023; 14:1222. [PMID: 36869058 PMCID: PMC9984477 DOI: 10.1038/s41467-023-36940-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Growth and division of biological cells are based on the complex orchestration of spatiotemporally controlled reactions driven by highly evolved proteins. In contrast, it remains unknown how their primordial predecessors could achieve a stable inheritance of cytosolic components before the advent of translation. An attractive scenario assumes that periodic changes of environmental conditions acted as pacemakers for the proliferation of early protocells. Using catalytic RNA (ribozymes) as models for primitive biocatalytic molecules, we demonstrate that the repeated freezing and thawing of aqueous solutions enables the assembly of active ribozymes from inactive precursors encapsulated in separate lipid vesicle populations. Furthermore, we show that encapsulated ribozyme replicators can overcome freezing-induced content loss and successive dilution by freeze-thaw driven propagation in feedstock vesicles. Thus, cyclic freezing and melting of aqueous solvents - a plausible physicochemical driver likely present on early Earth - provides a simple scenario that uncouples compartment growth and division from RNA self-replication, while maintaining the propagation of these replicators inside new vesicle populations.
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Affiliation(s)
- Elia Salibi
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Benedikt Peter
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Hannes Mutschler
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.
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4
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Roche TP, Fialho DM, Menor-Salván C, Krishnamurthy R, Schuster GB, Hud NV. A Plausible Prebiotic Path to Nucleosides: Ribosides and Related Aldosides Generated from Ribulose, Fructose, and Similar Abiotic Precursors. Chemistry 2023; 29:e202203036. [PMID: 36261321 DOI: 10.1002/chem.202203036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Indexed: 12/12/2022]
Abstract
The prebiotic origins of ribose, nucleosides, and eventually RNA are enduring questions whose answers are central to the RNA world hypothesis. The abiotic synthesis of sugars was first demonstrated over a century ago, but no known prebiotic reaction produces ribose (an aldose sugar) selectively and in good yield. In contrast, ribulose, and fructose (ketose sugars) and other monosaccharides are formed in high yield by several robust abiotic reactions. It is reported here that ketose sugars - both ketopentoses and ketohexoes - serve as precursors for the formation of ribosides and other aldosides, as demonstrated by glycoside-forming reactions involving barbituric acid, a plausibly prebiotic nucleobase. Moreover, a one-pot reaction of glyceraldehyde and barbituric acid was discovered which under mild conditions, and without special minerals or other catalysts, results in the formation of glycosides. These results reveal that an exclusive or high-yielding generation of free ribose was not required for its incorporation into processes that provided the foundations for life.
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Affiliation(s)
- Tyler P Roche
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - David M Fialho
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Cesar Menor-Salván
- Departmento de Biología de Sistemas/IQAR, Universidad de Alcalá, Madrid, 28806, Spain
| | | | - Gary B Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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5
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Choe JC. Mechanism of Prebiotic Uracil Synthesis from Urea and HC 3O + in Space. ASTROBIOLOGY 2022; 22:1363-1369. [PMID: 36194055 DOI: 10.1089/ast.2022.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The potential energy surface for the formation of protonated uracil (UH+) from urea and HC3O+ was explored by performing quantum chemical complete basis set-QB3 calculations. A barrierless pathway was found for the formation of UH+, which was estimated to occur in the interstellar medium (ISM) much faster than the timescale of chemical revolution of typical dense interstellar clouds. Investigation of further reactions of UH+ formed through the obtained pathway led to the conclusion that uracil could be produced on icy grain surfaces but not in the gas phase of the ISM.
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Affiliation(s)
- Joong Chul Choe
- Department of Chemistry, Dongguk University-Seoul, Seoul, Korea
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6
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Prebiotic synthesis of noncanonical nucleobases under plausible alkaline hydrothermal conditions. Sci Rep 2022; 12:15140. [PMID: 36071125 PMCID: PMC9452575 DOI: 10.1038/s41598-022-19474-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/30/2022] [Indexed: 11/08/2022] Open
Abstract
Herein, the potential of alkaline hydrothermal environments for the synthesis of possible ancestral pre-RNA nucleobases using cyanide as a primary source of carbon and nitrogen is described. Water cyanide polymerizations were assisted by microwave radiation to obtain high temperature and a relatively high pressure (MWR, 180 °C, 15 bar) and were also carried out using a conventional thermal system (CTS, 80 °C, 1 bar) to simulate subaerial and aerial hydrothermal conditions, respectively, on the early Earth. For these syntheses, the initial concentration of cyanide and the diffusion effects were studied. In addition, it is well known that hydrolysis conditions are directly related to the amount and diversity of organic molecules released from cyanide polymers. Thus, as a first step, we studied the effect of several hydrolysis procedures, generally used in prebiotic chemistry, on some of the potential pre-RNA nucleobases of interest, together with some of their isomers and/or deamination products, also presumably formed in these complex reactions. The results show that the alkaline hydrothermal scenarios with a relatively constant pH are good geological scenarios for the generation of noncanonical nucleobases using cyanide as a prebiotic precursor.
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7
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Prosdocimi F, de Farias ST, José MV. Prebiotic chemical refugia: multifaceted scenario for the formation of biomolecules in primitive Earth. Theory Biosci 2022; 141:339-347. [PMID: 36042123 DOI: 10.1007/s12064-022-00377-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/17/2022] [Indexed: 11/25/2022]
Abstract
The origin of life was a cosmic event happened on primitive Earth. A critical problem to better understand the origins of life in Earth is the search for chemical scenarios on which the basic building blocks of biological molecules could be produced. Classic works in pre-biotic chemistry frequently considered early Earth as an homogeneous atmosphere constituted by chemical elements such as methane (CH4), ammonia (NH3), water (H2O), hydrogen (H2) and hydrogen sulfide (H2S). Under that scenario, Stanley Miller was capable to produce amino acids and solved the question about the abiotic origin of proteins. Conversely, the origin of nucleic acids has tricked scientists for decades once nucleotides are complex, though necessary molecules to allow the existence of life. Here we review possible chemical scenarios that allowed not only the formation of nucleotides but also other significant biomolecules. We aim to provide a theoretical solution for the origin of biomolecules at specific sites named "Prebiotic Chemical Refugia." Prebiotic chemical refugium should therefore be understood as a geographic site in prebiotic Earth on which certain chemical elements were accumulated in higher proportion than expected, facilitating the production of basic building blocks for biomolecules. This higher proportion should not be understood as static, but dynamic; once the physicochemical conditions of our planet changed periodically. These different concentration of elements, together with geochemical and astronomical changes along days, synodic months and years provided somewhat periodic changes in temperature, pressure, electromagnetic fields, and conditions of humidity, among other features. Recent and classic works suggesting most likely prebiotic refugia on which the main building blocks for biological molecules might be accumulated are reviewed and discussed.
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Affiliation(s)
- Francisco Prosdocimi
- Laboratório de Biologia Teórica E de Sistemas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal Do Rio de Janeiro, 21.941-902, Rio de Janeiro, Brazil. .,Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, CDMX, Mexico.
| | - Sávio Torres de Farias
- Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Marco V José
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, CDMX, Mexico.
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8
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Prosdocimi F, de Farias ST. Entering the labyrinth: A hypothesis about the emergence of metabolism from protobiotic routes. Biosystems 2022; 220:104751. [DOI: 10.1016/j.biosystems.2022.104751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/26/2022] [Accepted: 07/31/2022] [Indexed: 11/26/2022]
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9
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Menor‐Salván C, Burcar BT, Bouza M, Fialho DM, Fernández FM, Hud NV. A Shared Prebiotic Formation of Neopterins and Guanine Nucleosides from Pyrimidine Bases. Chemistry 2022; 28:e202200714. [PMID: 35537135 PMCID: PMC9401002 DOI: 10.1002/chem.202200714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Indexed: 11/09/2022]
Affiliation(s)
- César Menor‐Salván
- NSF-NASA Center for Chemical Evolution Georgia Institute of Technology Atlanta 30302 GA USA
- Dept. de Biología de Sistemas/IQAR Universidad de Alcalá 28806 Madrid Spain
| | - Bradley T. Burcar
- Dept. de Biología de Sistemas/IQAR Universidad de Alcalá 28806 Madrid Spain
- NASA HQ/Georgetown University/GSFC Greenbelt MD 20771
| | - Marcos Bouza
- Dept. de Biología de Sistemas/IQAR Universidad de Alcalá 28806 Madrid Spain
- Dept. of Physical and Analytical Chemistry Universidad de Jaen Jaén 23071 Jaen Spain
| | - David M. Fialho
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta 30302 GA USA
- Dept. de Biología de Sistemas/IQAR Universidad de Alcalá 28806 Madrid Spain
| | - Facundo M. Fernández
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta 30302 GA USA
- Dept. de Biología de Sistemas/IQAR Universidad de Alcalá 28806 Madrid Spain
| | - Nicholas V. Hud
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta 30302 GA USA
- Dept. de Biología de Sistemas/IQAR Universidad de Alcalá 28806 Madrid Spain
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10
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Oba Y, Takano Y, Furukawa Y, Koga T, Glavin DP, Dworkin JP, Naraoka H. Identifying the wide diversity of extraterrestrial purine and pyrimidine nucleobases in carbonaceous meteorites. Nat Commun 2022; 13:2008. [PMID: 35473908 PMCID: PMC9042847 DOI: 10.1038/s41467-022-29612-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/22/2022] [Indexed: 11/09/2022] Open
Abstract
The lack of pyrimidine diversity in meteorites remains a mystery since prebiotic chemical models and laboratory experiments have predicted that these compounds can also be produced from chemical precursors found in meteorites. Here we report the detection of nucleobases in three carbonaceous meteorites using state-of-the-art analytical techniques optimized for small-scale quantification of nucleobases down to the range of parts per trillion (ppt). In addition to previously detected purine nucleobases in meteorites such as guanine and adenine, we identify various pyrimidine nucleobases such as cytosine, uracil, and thymine, and their structural isomers such as isocytosine, imidazole-4-carboxylic acid, and 6-methyluracil, respectively. Given the similarity in the molecular distribution of pyrimidines in meteorites and those in photon-processed interstellar ice analogues, some of these derivatives could have been generated by photochemical reactions prevailing in the interstellar medium and later incorporated into asteroids during solar system formation. This study demonstrates that a diversity of meteoritic nucleobases could serve as building blocks of DNA and RNA on the early Earth.
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Affiliation(s)
- Yasuhiro Oba
- Institute of Low Temperature Science (ILTS), Hokkaido University, N19W8, Kita-ku, Sapporo, Hokkaido, 060-0189, Japan.
| | - Yoshinori Takano
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan
| | - Yoshihiro Furukawa
- Department of Earth Science, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Toshiki Koga
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan
| | - Daniel P Glavin
- Solar System Exploration Division, National Aeronautics and Space Administration (NASA), Goddard Space Flight Center (GSFC), Greenbelt, MD, 20771, USA
| | - Jason P Dworkin
- Solar System Exploration Division, National Aeronautics and Space Administration (NASA), Goddard Space Flight Center (GSFC), Greenbelt, MD, 20771, USA
| | - Hiroshi Naraoka
- Department of Earth and Planetary Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka, 819-0395, Japan
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11
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Visible-light photoionization of aromatic molecules in water-ice: Organic chemistry across the universe with less energy. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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12
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Schuster GB, Cafferty BJ, Karunakaran SC, Hud NV. Water-Soluble Supramolecular Polymers of Paired and Stacked Heterocycles: Assembly, Structure, Properties, and a Possible Path to Pre-RNA. J Am Chem Soc 2021; 143:9279-9296. [PMID: 34152760 DOI: 10.1021/jacs.0c13081] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hypothesis that RNA and DNA are products of chemical and biological evolution has motivated our search for alternative nucleic acids that may have come earlier in the emergence of life-polymers that possess a proclivity for covalent and non-covalent self-assembly not exhibited by RNA. Our investigations have revealed a small set of candidate ancestral nucleobases that self-assemble into hexameric rosettes that stack in water to form long, twisted, rigid supramolecular polymers. These structures exhibit properties that provide robust solutions to long-standing problems that have stymied the search for a prebiotic synthesis of nucleic acids. Moreover, their examination by experimental and computational methods provides insight into the chemical and physical principles that govern a particular class of water-soluble one-dimensional supramolecular polymers. In addition to efficient self-assembly, their lengths and polydispersity are modulated by a wide variety of positively charged, planar compounds; their assembly and disassembly are controlled over an exceedingly narrow pH range; they exhibit spontaneous breaking of symmetry; and homochirality emerges through non-covalent cross-linking during hydrogel formation. Some of these candidate ancestral nucleobases spontaneously form glycosidic bonds with ribose and other sugars, and, most significantly, functionalized forms of these heterocycles form supramolecular structures and covalent polymers under plausibly prebiotic conditions. This Perspective recounts a journey of discovery that continues to reveal attractive answers to questions concerning the origins of life and to uncover the principles that control the structure and properties of water-soluble supramolecular polymers.
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Affiliation(s)
- Gary B Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Brian J Cafferty
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Suneesh C Karunakaran
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
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13
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Menor Salván C, Bouza M, Fialho DM, Burcar BT, Fernández FM, Hud NV. Prebiotic Origin of Pre‐RNA Building Blocks in a Urea “Warm Little Pond” Scenario. Chembiochem 2020; 21:3504-3510. [DOI: 10.1002/cbic.202000510] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Indexed: 11/07/2022]
Affiliation(s)
- C. Menor Salván
- NSF-NASA Center for Chemical Evolution Georgia Institute of Technology Atlanta GA 30302 USA
- Dep. de Biología de Sistemas/IQAR Universidad de Alcalá 28806 Madrid Spain
| | - Marcos Bouza
- NSF-NASA Center for Chemical Evolution Georgia Institute of Technology Atlanta GA 30302 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA 30302 USA
| | - David M. Fialho
- NSF-NASA Center for Chemical Evolution Georgia Institute of Technology Atlanta GA 30302 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA 30302 USA
| | - Bradley T. Burcar
- NSF-NASA Center for Chemical Evolution Georgia Institute of Technology Atlanta GA 30302 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA 30302 USA
| | - Facundo M. Fernández
- NSF-NASA Center for Chemical Evolution Georgia Institute of Technology Atlanta GA 30302 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA 30302 USA
| | - Nicholas V. Hud
- NSF-NASA Center for Chemical Evolution Georgia Institute of Technology Atlanta GA 30302 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA 30302 USA
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14
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Wołos A, Roszak R, Żądło-Dobrowolska A, Beker W, Mikulak-Klucznik B, Spólnik G, Dygas M, Szymkuć S, Grzybowski BA. Synthetic connectivity, emergence, and
self-regeneration in the network of prebiotic
chemistry. Science 2020; 369:369/6511/eaaw1955. [DOI: 10.1126/science.aaw1955] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/28/2020] [Accepted: 07/24/2020] [Indexed: 12/13/2022]
Abstract
The challenge of prebiotic chemistry is to
trace the syntheses of life’s key building blocks
from a handful of primordial substrates. Here we
report a forward-synthesis algorithm that
generates a full network of prebiotic chemical
reactions accessible from these substrates under
generally accepted conditions. This network
contains both reported and previously unidentified
routes to biotic targets, as well as plausible
syntheses of abiotic molecules. It also exhibits
three forms of nontrivial chemical emergence, as
the molecules within the network can act as
catalysts of downstream reaction types; form
functional chemical systems, including
self-regenerating cycles; and produce surfactants
relevant to primitive forms of biological
compartmentalization. To support these claims,
computer-predicted, prebiotic syntheses of several
biotic molecules as well as a multistep,
self-regenerative cycle of iminodiacetic acid were
validated by experiment.
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Affiliation(s)
- Agnieszka Wołos
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
| | - Rafał Roszak
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
| | | | - Wiktor Beker
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
| | - Barbara Mikulak-Klucznik
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
| | - Grzegorz Spólnik
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
| | - Mirosław Dygas
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
| | - Sara Szymkuć
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
| | - Bartosz A. Grzybowski
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
- Center for Soft and Living Matter of
Korea’s Institute for Basic Science (IBS), Ulsan,
South Korea
- Department of Chemistry, Ulsan
National Institute of Science and Technology,
Ulsan, South Korea
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15
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Fialho DM, Roche TP, Hud NV. Prebiotic Syntheses of Noncanonical Nucleosides and Nucleotides. Chem Rev 2020; 120:4806-4830. [PMID: 32421316 DOI: 10.1021/acs.chemrev.0c00069] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The origin of nucleotides is a major question in origins-of-life research. Given the central importance of RNA in biology and the influential RNA World hypothesis, a great deal of this research has focused on finding possible prebiotic syntheses of the four canonical nucleotides of coding RNA. However, the use of nucleotides in other roles across the tree of life might be evidence that nucleotides have been used in noncoding roles for even longer than RNA has been used as a genetic polymer. Likewise, it is possible that early life utilized nucleotides other than the extant nucleotides as the monomers of informational polymers. Therefore, finding plausible prebiotic syntheses of potentially ancestral noncanonical nucleotides may be of great importance for understanding the origins and early evolution of life. Experimental investigations into abiotic noncanonical nucleotide synthesis reveal that many noncanonical nucleotides and related glycosides are formed much more easily than the canonical nucleotides. An analysis of the mechanisms by which nucleosides and nucleotides form in the solution phase or in drying-heating reactions from pre-existing sugars and heterocycles suggests that a wide variety of noncanonical nucleotides and related glycosides would have been present on the prebiotic Earth, if any such molecules were present.
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Affiliation(s)
- David M Fialho
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0440, United States
| | - Tyler P Roche
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0440, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0440, United States
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16
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Kaur N, Verma Y, Grewal P, Ahlawat N, Bhardwaj P, Jangid NK. Photochemical C–N bond forming reactions for the synthesis of five-membered fused N-heterocycles. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2020.1713378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Navjeet Kaur
- Department of Chemistry, Banasthali Vidyapith, Banasthali, India
| | - Yamini Verma
- Department of Chemistry, Banasthali Vidyapith, Banasthali, India
| | - Pooja Grewal
- Department of Chemistry, Banasthali Vidyapith, Banasthali, India
| | - Neha Ahlawat
- Department of Chemistry, Banasthali Vidyapith, Banasthali, India
| | - Pranshu Bhardwaj
- Department of Chemistry, Banasthali Vidyapith, Banasthali, India
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17
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Abstract
The chemistry of abiotic nucleotide synthesis of RNA and DNA in the context of their prebiotic origins on early earth is a continuing challenge. How did (or how can) the nucleotides form and assemble from the small molecule inventories and under conditions that prevailed on early earth 3.5-4 billion years ago? This review provides a background and up-to-date progress that will allow the reader to judge where the field stands currently and what remains to be achieved. We start with a brief primer on the biological synthesis of nucleotides, followed by an extensive focus on the prebiotic formation of the components of nucleotides-either via the synthesis of ribose and the canonical nucleobases and then joining them together or by building both the conjoined sugar and nucleobase, part-by-part-toward the ultimate goal of forming RNA and DNA by polymerization. The review will emphasize that there are-and will continue to be-many more questions than answers from the synthetic, mechanistic, and analytical perspectives. We wrap up the review with a cautionary note in this context about coming to conclusions as to whether the problem of chemistry of prebiotic nucleotide synthesis has been solved.
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Affiliation(s)
- Mahipal Yadav
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Ravi Kumar
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
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18
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Oba Y, Takano Y, Naraoka H, Watanabe N, Kouchi A. Nucleobase synthesis in interstellar ices. Nat Commun 2019; 10:4413. [PMID: 31562325 PMCID: PMC6764953 DOI: 10.1038/s41467-019-12404-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 09/03/2019] [Indexed: 11/09/2022] Open
Abstract
The synthesis of nucleobases in natural environments, especially in interstellar molecular clouds, is the focus of a long-standing debate regarding prebiotic chemical evolution. Here we report the simultaneous detection of all three pyrimidine (cytosine, uracil and thymine) and three purine nucleobases (adenine, xanthine and hypoxanthine) in interstellar ice analogues composed of simple molecules including H2O, CO, NH3 and CH3OH after exposure to ultraviolet photons followed by thermal processes, that is, in conditions that simulate the chemical processes accompanying star formation from molecular clouds. Photolysis of primitive gas molecules at 10 K might be one of the key steps in the production of nucleobases. The present results strongly suggest that the evolution from molecular clouds to stars and planets provides a suitable environment for nucleobase synthesis in space.
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Affiliation(s)
- Yasuhiro Oba
- Institute of Low Temperature Science (ILTS), Hokkaido University, N19W8, Kita-ku, Sapporo, Hokkaido, 060-0819, Japan.
| | - Yoshinori Takano
- Department of Biogeochemistry, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan.,Biogeochemistry Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan
| | - Hiroshi Naraoka
- Department of Earth and Planetary Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka, 819-0395, Japan.,Research Center for Planetary Trace Organic Compounds, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka, 819-0395, Japan
| | - Naoki Watanabe
- Institute of Low Temperature Science (ILTS), Hokkaido University, N19W8, Kita-ku, Sapporo, Hokkaido, 060-0819, Japan
| | - Akira Kouchi
- Institute of Low Temperature Science (ILTS), Hokkaido University, N19W8, Kita-ku, Sapporo, Hokkaido, 060-0819, Japan
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19
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Šponer JE, Šponer J, Di Mauro E. Structural and Energetic Compatibility: The Driving Principles of Molecular Evolution. ASTROBIOLOGY 2019; 19:1117-1122. [PMID: 31045430 DOI: 10.1089/ast.2018.1978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this work, we provide an answer to the question formulated by Albert Eschenmoser: "How would you envisage the bridge between potentially primordial geochemistry that had been disordered and one that gradually became self-organizing?" Analysis of the free-energy profiles of some of the key reactions leading to formation of nucleotides and their oligomers shows that, whereas the first part of the pathway, up to nucleotides, is energy-driven, in the second low-energy part entropic control in the form of structural compatibility becomes more important. We suggest that the birth of modern metabolism requires structural compatibility, which is enabled by the commensurability of the thermodynamics of the synthetic steps with the stabilizing effect of those intermolecular interactions that play a key role in dictating entropic control of these reactions.
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Affiliation(s)
- Judit E Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Ernesto Di Mauro
- Institute for Molecular Biology and Pathology, CNR, c/o Università Sapienza, Roma, Italy
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20
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Kaur S, Ohri A, Sharma P. Could Purines Be Formed from Cyanamide and Cyanoacetylene in a Prebiotic Earth Environment? ACS OMEGA 2019; 4:12771-12781. [PMID: 31460401 PMCID: PMC6682131 DOI: 10.1021/acsomega.9b01169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
Knowledge of prebiotic nucleobase formation is important for understanding the origin of contemporary genetics. Observation of nucleobase precursor radicals in previous impact laser plasma simulations of the late heavy bombardment period (FerusProc. Natl. Acad. Sci. U.S.A.2015, 112, 657) points toward possible nucleobase formation through free-radical pathways. However, previously explored radical routes to nucleobase formation involve a large number of reaction steps, repetitive addition of precursors, and a number of chemical transformations. The possibility of competing side reactions under such conditions questions the feasibility of such pathways. In view of these shortcomings, the present work employs density functional theory to explore purine formation pathways through reaction of cyanamide and cyanoacetylene with radicals via a five-membered intermediate, 4-cyanoimidazole in the presence of ammonia. Our analysis reveals that the skeletal components of 4-cyanoimidazole can be solely obtained from cyanamide and cyanoacetylene via barrierless cyclization and a small number of reaction steps. In addition, the proposed mechanisms are characterized by a small number of precursors and low energy barriers and are thus likely feasible under extreme conditions on the prebiotic earth such as meteoritic impact during late heavy bombardment period. Overall, the present study underscores the importance of cyanamide and cyanoacetylene precursors in kinetically accessible routes to purine formation.
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21
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Eckhardt AK, Bergantini A, Singh SK, Schreiner PR, Kaiser RI. Formation of Glyoxylic Acid in Interstellar Ices: A Key Entry Point for Prebiotic Chemistry. Angew Chem Int Ed Engl 2019; 58:5663-5667. [DOI: 10.1002/anie.201901059] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/05/2019] [Indexed: 11/10/2022]
Affiliation(s)
- André K. Eckhardt
- Institute of Organic ChemistryJustus Liebig University Giessen Heinrich-Buff-Ring 17 35392 Giessen Germany
| | - Alexandre Bergantini
- Department of ChemistryW. M. Keck Research Laboratory in AstrochemistryUniversity of Hawaii at Manoa 2545 McCarthy Mall Honolulu HI 96822 USA
| | - Santosh K. Singh
- Department of ChemistryW. M. Keck Research Laboratory in AstrochemistryUniversity of Hawaii at Manoa 2545 McCarthy Mall Honolulu HI 96822 USA
| | - Peter R. Schreiner
- Institute of Organic ChemistryJustus Liebig University Giessen Heinrich-Buff-Ring 17 35392 Giessen Germany
| | - Ralf I. Kaiser
- Department of ChemistryW. M. Keck Research Laboratory in AstrochemistryUniversity of Hawaii at Manoa 2545 McCarthy Mall Honolulu HI 96822 USA
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22
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Eckhardt AK, Bergantini A, Singh SK, Schreiner PR, Kaiser RI. Formation of Glyoxylic Acid in Interstellar Ices: A Key Entry Point for Prebiotic Chemistry. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- André K. Eckhardt
- Institute of Organic ChemistryJustus Liebig University Giessen Heinrich-Buff-Ring 17 35392 Giessen Germany
| | - Alexandre Bergantini
- Department of ChemistryW. M. Keck Research Laboratory in AstrochemistryUniversity of Hawaii at Manoa 2545 McCarthy Mall Honolulu HI 96822 USA
| | - Santosh K. Singh
- Department of ChemistryW. M. Keck Research Laboratory in AstrochemistryUniversity of Hawaii at Manoa 2545 McCarthy Mall Honolulu HI 96822 USA
| | - Peter R. Schreiner
- Institute of Organic ChemistryJustus Liebig University Giessen Heinrich-Buff-Ring 17 35392 Giessen Germany
| | - Ralf I. Kaiser
- Department of ChemistryW. M. Keck Research Laboratory in AstrochemistryUniversity of Hawaii at Manoa 2545 McCarthy Mall Honolulu HI 96822 USA
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23
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Prebiotic chemistry in neutral/reduced-alkaline gas-liquid interfaces. Sci Rep 2019; 9:1916. [PMID: 30760732 PMCID: PMC6374446 DOI: 10.1038/s41598-018-36579-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 11/25/2018] [Indexed: 11/09/2022] Open
Abstract
The conditions for the potential abiotic formation of organic compounds from inorganic precursors have great implications for our understanding of the origin of life on Earth and for its possible detection in other environments of the Solar System. It is known that aerosol-interfaces are effective at enhancing prebiotic chemical reactions, but the roles of salinity and pH have been poorly investigated to date. Here, we experimentally demonstrate the uniqueness of alkaline aerosols as prebiotic reactors that produce an undifferentiated accumulation of a variety of multi-carbon biomolecules resulting from high-energy processes (in our case, electrical discharges). Using simulation experiments, we demonstrate that the detection of important biomolecules in tholins increases when plausible and particular local planetary environmental conditions are simulated. A greater diversity in amino acids, carboxylic acids, N-heterocycles, and ketoacids, such as glyoxylic and pyruvic acid, was identified in tholins synthetized from reduced and neutral atmospheres in the presence of alkaline aqueous aerosols than that from the same atmospheres but using neutral or acidic aqueous aerosols.
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24
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Kaur S, Sharma P. Radical pathways for the formation of non-canonical nucleobases in prebiotic environments. RSC Adv 2019; 9:36530-36538. [PMID: 35539032 PMCID: PMC9075218 DOI: 10.1039/c9ra08001e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/04/2019] [Indexed: 11/21/2022] Open
Abstract
Due to the inability of canonical nucleobases (adenine, uracil, guanine and cytosine) to spontaneously form ribonucleosides and base pairs in free form in solution, RNA is believed to be preceded by a primitive information polymer (preRNA). The preRNA is proposed to contain non-canonical, heterocyclic bases that possess the above-mentioned capabilities. An extensive search for such candidate heterocycles has recently revealed that barbituric acid (BA), melamine (MM) and 2,4,6-triaminopyrimidine (TAP) have the capability to spontaneously form ribonucleosides and supramolecular assemblies that are held by Watson–Crick type hydrogen-bonded base pairs involving BA, MM, TAP and cyanuric acid (CA) heterocycles. However, despite this evidence, the prebiotic formation pathways of these heterocycles have not been fully explored. Further, for these heterocycles to interact and assemble into informational polymers under prebiotic conditions, it is expected that they should have formed in the proximity of each other. In this context, the present work employs density functional theory to propose the associated radical based formation pathways starting from cyanamide. Our pathways suggest that cyanamide, its derivatives (malonic acid and urea) and malononitrile can form BA, MM, CA and TAP in the presence of ammonia and hydroxyl radicals. In addition to originating from a common precursor, similarities in the highest reaction barriers (13 to 20 kcal mol−1) obtained for these pathways suggest that these heterocycles may likely form under similar conditions. Specifically, these pathways are relevant to high energy events such as meteoritic impact during the late heavy bombardment period on the early earth, which would have created conditions where radicals might have formed in reasonable concentrations. Overall, the present study emphasizes the importance of cyanamide in prebiotic heterocycle formation. The study explores radical-assisted formations of the nucleobase components of primitive genetics from cyanamide and related precursors in impact events.![]()
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Affiliation(s)
- Sarabjeet Kaur
- Computational Biochemistry Laboratory
- Department of Chemistry and Centre for Advanced Studies in Chemistry
- Panjab University
- Chandigarh
- India
| | - Purshotam Sharma
- Computational Biochemistry Laboratory
- Department of Chemistry and Centre for Advanced Studies in Chemistry
- Panjab University
- Chandigarh
- India
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25
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Chemomimesis and Molecular Darwinism in Action: From Abiotic Generation of Nucleobases to Nucleosides and RNA. Life (Basel) 2018; 8:life8020024. [PMID: 29925796 PMCID: PMC6027154 DOI: 10.3390/life8020024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/14/2018] [Accepted: 06/19/2018] [Indexed: 01/26/2023] Open
Abstract
Molecular Darwinian evolution is an intrinsic property of reacting pools of molecules resulting in the adaptation of the system to changing conditions. It has no a priori aim. From the point of view of the origin of life, Darwinian selection behavior, when spontaneously emerging in the ensembles of molecules composing prebiotic pools, initiates subsequent evolution of increasingly complex and innovative chemical information. On the conservation side, it is a posteriori observed that numerous biological processes are based on prebiotically promptly made compounds, as proposed by the concept of Chemomimesis. Molecular Darwinian evolution and Chemomimesis are principles acting in balanced cooperation in the frame of Systems Chemistry. The one-pot synthesis of nucleosides in radical chemistry conditions is possibly a telling example of the operation of these principles. Other indications of similar cases of molecular evolution can be found among biogenic processes.
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26
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Mattia Bizzarri B, Botta L, Pérez-Valverde MI, Saladino R, Di Mauro E, García-Ruiz JM. Silica Metal Oxide Vesicles Catalyze Comprehensive Prebiotic Chemistry. Chemistry 2018; 24:8126-8132. [PMID: 29603465 DOI: 10.1002/chem.201706162] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Indexed: 02/01/2023]
Abstract
It has recently been demonstrated that mineral self-assembled structures catalyzing prebiotic chemical reactions may form in natural waters derived from serpentinization, a geological process widespread in the early stages of Earth-like planets. We have synthesized self-assembled membranes by mixing microdrops of metal solutions with alkaline silicate solutions in the presence of formamide (NH2 CHO), a single-carbon molecule, at 80 °C. We found that these bilayer membranes, made of amorphous silica and metal oxide/hydroxide nanocrystals, catalyze the condensation of formamide, yielding the four nucleobases of RNA, three amino acids and, several carboxylic acids in a single-pot experiment. Besides manganese, iron and magnesium, two abundant elements in the earliest Earth crust that are key in serpentinization reactions, are enough to produce all these biochemical compounds. These results suggest that the transition from inorganic geochemistry to prebiotic organic chemistry is common on a universal scale and, most probably, occurred earlier than ever thought for our planet.
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Affiliation(s)
- Bruno Mattia Bizzarri
- Ecological and Biological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis snc, 01100, Viterbo, Italy
| | - Lorenzo Botta
- Ecological and Biological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis snc, 01100, Viterbo, Italy
| | - Maritza Iveth Pérez-Valverde
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la, Tierra, Consejo Superior de Investigaciones Científicas-Universidad de, Granada, Avenida de las Palmeras 4, Armilla, Granada, 18100, Spain
| | - Raffaele Saladino
- Ecological and Biological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis snc, 01100, Viterbo, Italy
| | - Ernesto Di Mauro
- Ecological and Biological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis snc, 01100, Viterbo, Italy
| | - Juan Manuel García-Ruiz
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la, Tierra, Consejo Superior de Investigaciones Científicas-Universidad de, Granada, Avenida de las Palmeras 4, Armilla, Granada, 18100, Spain
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27
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28
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Marín-Yaseli MR, Moreno M, de la Fuente JL, Briones C, Ruiz-Bermejo M. Experimental conditions affecting the kinetics of aqueous HCN polymerization as revealed by UV-vis spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 191:389-397. [PMID: 29065330 DOI: 10.1016/j.saa.2017.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 09/27/2017] [Accepted: 10/01/2017] [Indexed: 05/26/2023]
Abstract
HCN polymerization is one of the most important and fascinating reactions in prebiotic chemistry, and interest in HCN polymers in the field of materials science is growing. However, little is known about the kinetics of the HCN polymerization process. In the present study, a first approach to the kinetics of two sets of aqueous HCN polymerizations, from NH4CN and NaCN, at middle temperatures between 4 and 38°C, has been carried out. For each series, the presence of air and salts in the reaction medium has been systematically explored. A previous kinetic analysis was conducted during the conversion of the insoluble black HCN polymers obtained as gel fractions in these precipitation polymerizations for a reaction of one month, where a limit conversion was achieved at the highest polymerization temperature. The kinetic description of the gravimetric data for this complex system shows a clear change in the linear dependence with the polymerization temperature for the reaction from NH4CN, besides a relevant catalytic effect of ammonium, in comparison with those data obtained from the NaCN series. These results also demonstrated the notable influence of air, oxygen, and the saline medium in HCN polymer formation. Similar conclusions were reached when the sol fractions were monitored by UV-vis spectroscopy, and a Hill type correlation was used to describe the polymerization profiles obtained. This technique was chosen because it provides an easy, prompt and fast method to follow the evolution of the liquid or continuous phase of the process under study.
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Affiliation(s)
- Margarita R Marín-Yaseli
- Centro de Astrobiología (INTA-CSIC), Dpto. Evolución Molecular, Ctra. Torrejón-Ajalvir, km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Miguel Moreno
- Centro de Astrobiología (INTA-CSIC), Dpto. Evolución Molecular, Ctra. Torrejón-Ajalvir, km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - José L de la Fuente
- Instituto Nacional de Técnica Aeroespacial "Esteban Terradas" (INTA), Ctra. Torrejón-Ajalvir, km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Carlos Briones
- Centro de Astrobiología (INTA-CSIC), Dpto. Evolución Molecular, Ctra. Torrejón-Ajalvir, km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Marta Ruiz-Bermejo
- Centro de Astrobiología (INTA-CSIC), Dpto. Evolución Molecular, Ctra. Torrejón-Ajalvir, km 4, Torrejón de Ardoz, 28850 Madrid, Spain.
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29
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Calvo F, Bacchus-Montabonel MC. Size-Induced Segregation in the Stepwise Microhydration of Hydantoin and Its Role in Proton-Induced Charge Transfer. J Phys Chem A 2018; 122:1634-1642. [DOI: 10.1021/acs.jpca.7b10291] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Florent Calvo
- LiPhy, Université Grenoble 1 and CNRS UMR 5588, 140 Avenue
de la Physique, 38402 St Martin d’Hères, France
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30
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Menor-Salván C. From the Dawn of Organic Chemistry to Astrobiology: Urea as a Foundational Component in the Origin of Nucleobases and Nucleotides. PREBIOTIC CHEMISTRY AND CHEMICAL EVOLUTION OF NUCLEIC ACIDS 2018. [DOI: 10.1007/978-3-319-93584-3_4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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31
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Fiore M, Strazewski P. Zur präbiotischen Synthese von Nukleosiden und Nukleotiden. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Michele Fiore
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires; Université de Lyon, Claude Bernard Lyon 1; 43 bdv du 11 novembre 1918 69622 Villeurbanne Cedex Frankreich
| | - Peter Strazewski
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires; Université de Lyon, Claude Bernard Lyon 1; 43 bdv du 11 novembre 1918 69622 Villeurbanne Cedex Frankreich
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32
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Fiore M, Strazewski P. Bringing Prebiotic Nucleosides and Nucleotides Down to Earth. Angew Chem Int Ed Engl 2016; 55:13930-13933. [PMID: 27629398 DOI: 10.1002/anie.201606232] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Indexed: 12/20/2022]
Abstract
There may be more than one way leading to RNA: Recent discoveries in the synthesis of nucleoside and nucleotide precursors are described and put into the wider context of prebiotic systems chemistry. Mixing Butlerow's carbohydrate precursors with Traube's 5-formylaminopyrimidines has led to the formation of prebiotic purine nucleosides whereas the mixing of 5-phosphoribose with barbituric acid and melamine gave supramolecular fibers from stacks of Whitesides' rosettas.
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Affiliation(s)
- Michele Fiore
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 43 bdv du 11 novembre 1918, 69622, Villeurbanne Cedex, France
| | - Peter Strazewski
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 43 bdv du 11 novembre 1918, 69622, Villeurbanne Cedex, France.
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33
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Marín-Yaseli MR, González-Toril E, Mompeán C, Ruiz-Bermejo M. The Role of Aqueous Aerosols in the “Glyoxylate Scenario”: An Experimental Approach. Chemistry 2016; 22:12785-99. [DOI: 10.1002/chem.201602195] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Margarita R. Marín-Yaseli
- Departamento de Evolución Molecular; Centro de Astrobiología (INTA-CSIC); Ctra. Torrejón-Ajlavir km 4,8 28850 Torrejón de Ardoz Madrid Spain
| | - Elena González-Toril
- Departamento de Evolución Molecular; Centro de Astrobiología (INTA-CSIC); Ctra. Torrejón-Ajlavir km 4,8 28850 Torrejón de Ardoz Madrid Spain
| | - Cristina Mompeán
- Departamento de Evolución Molecular; Centro de Astrobiología (INTA-CSIC); Ctra. Torrejón-Ajlavir km 4,8 28850 Torrejón de Ardoz Madrid Spain
| | - Marta Ruiz-Bermejo
- Departamento de Evolución Molecular; Centro de Astrobiología (INTA-CSIC); Ctra. Torrejón-Ajlavir km 4,8 28850 Torrejón de Ardoz Madrid Spain
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34
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Kondoh A, Ota Y, Komuro T, Egawa F, Kanomata K, Terada M. Chiral Brønsted acid-catalyzed enantioselective Friedel-Crafts reaction of 2-methoxyfuran with aliphatic ketimines generated in situ. Chem Sci 2016; 7:1057-1062. [PMID: 29862000 PMCID: PMC5952551 DOI: 10.1039/c5sc03175c] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/29/2015] [Indexed: 11/28/2022] Open
Abstract
An enantioselective Friedel-Crafts reaction with aliphatic ketimines generated in situ from hemiaminal ethers catalyzed by a chiral Brønsted acid was investigated. The reaction of 2-methoxyfuran with (thio)hydantoin-derived hemiaminal methyl ether proceeded under the influence of a chiral phosphoric acid catalyst to afford the corresponding adduct possessing a quaternary stereogenic center in high yield with high enantioselectivity. Theoretical studies were also conducted to clarify the mechanism of the stereochemical outcome and the major factors contributing to the efficient enantioselection.
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Affiliation(s)
- Azusa Kondoh
- Research and Analytical Center for Giant Molecules , Graduate School of Science , Tohoku University , Aoba-ku , Sendai 980-8578 , Japan .
| | - Yusuke Ota
- Department of Chemistry , Graduate School of Science , Tohoku University , Aoba-ku , Sendai 980-8578 , Japan
| | - Takazumi Komuro
- Department of Chemistry , Graduate School of Science , Tohoku University , Aoba-ku , Sendai 980-8578 , Japan
| | - Fuyuki Egawa
- Department of Chemistry , Graduate School of Science , Tohoku University , Aoba-ku , Sendai 980-8578 , Japan
| | - Kyohei Kanomata
- Department of Chemistry , Graduate School of Science , Tohoku University , Aoba-ku , Sendai 980-8578 , Japan
| | - Masahiro Terada
- Research and Analytical Center for Giant Molecules , Graduate School of Science , Tohoku University , Aoba-ku , Sendai 980-8578 , Japan .
- Department of Chemistry , Graduate School of Science , Tohoku University , Aoba-ku , Sendai 980-8578 , Japan
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Rapf RJ, Vaida V. Sunlight as an energetic driver in the synthesis of molecules necessary for life. Phys Chem Chem Phys 2016; 18:20067-84. [DOI: 10.1039/c6cp00980h] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
This review considers how photochemistry and sunlight-driven reactions can abiotically generate prebiotic molecules necessary for the evolution of life.
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Affiliation(s)
- Rebecca J. Rapf
- Department of Chemistry and Biochemistry
- CIRES
- University of Colorado at Boulder
- Boulder
- USA
| | - Veronica Vaida
- Department of Chemistry and Biochemistry
- CIRES
- University of Colorado at Boulder
- Boulder
- USA
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Nguyen HT, Jeilani YA, Hung HM, Nguyen MT. Radical Pathways for the Prebiotic Formation of Pyrimidine Bases from Formamide. J Phys Chem A 2015. [DOI: 10.1021/acs.jpca.5b03625] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Yassin A. Jeilani
- Department
Chemistry and Biochemistry, Spelman College, Atlanta, Georgia 30314, United States
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Pearce BKD, Pudritz RE. SEEDING THE PREGENETIC EARTH: METEORITIC ABUNDANCES OF NUCLEOBASES AND POTENTIAL REACTION PATHWAYS. ACTA ACUST UNITED AC 2015. [DOI: 10.1088/0004-637x/807/1/85] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Cafferty BJ, Hud NV. Was a Pyrimidine-Pyrimidine Base Pair the Ancestor of Watson-Crick Base Pairs? Insights from a Systematic Approach to the Origin of RNA. Isr J Chem 2015. [DOI: 10.1002/ijch.201400206] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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39
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Parker DSN, Kaiser RI, Kostko O, Troy TP, Ahmed M, Mebel AM, Tielens AGGM. GAS PHASE SYNTHESIS OF (ISO)QUINOLINE AND ITS ROLE IN THE FORMATION OF NUCLEOBASES IN THE INTERSTELLAR MEDIUM. ACTA ACUST UNITED AC 2015. [DOI: 10.1088/0004-637x/803/2/53] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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40
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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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41
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Jeilani YA, Fearce C, Nguyen MT. Acetylene as an essential building block for prebiotic formation of pyrimidine bases on Titan. Phys Chem Chem Phys 2015; 17:24294-303. [DOI: 10.1039/c5cp03247d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Prebiotic building blocks for the formation of biomolecules are important in understanding the abiotic origin of biomolecules.
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Affiliation(s)
| | - Chelesa Fearce
- Department Chemistry and Biochemistry
- Spelman College
- Atlanta
- USA
| | - Minh Tho Nguyen
- Department of Chemistry
- University of Leuven
- B-3001 Leuven
- Belgium
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42
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Jeilani YA, Nguyen HT, Cardelino BH, Nguyen MT. Free radical pathways for the prebiotic formation of xanthine and isoguanine from formamide. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.02.053] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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43
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Jeilani YA, Orlando TM, Pope A, Pirim C, Nguyen MT. Prebiotic synthesis of triazines from urea: a theoretical study of free radical routes to melamine, ammeline, ammelide and cyanuric acid. RSC Adv 2014. [DOI: 10.1039/c4ra03717k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Prebiotic formation of triazines from urea was studied using density functional theory methods with the aim of understanding some of the neutral precursors that can lead to a mixture of triazines.
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Affiliation(s)
| | - Thomas M. Orlando
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta, USA
| | - Albryona Pope
- Department Chemistry and Biochemistry
- Spelman College
- Atlanta, USA
| | - Claire Pirim
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta, USA
| | - Minh Tho Nguyen
- Department of Chemistry
- University of Leuven
- B-3001 Leuven, Belgium
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Butch C, Cope ED, Pollet P, Gelbaum L, Krishnamurthy R, Liotta CL. Production of tartrates by cyanide-mediated dimerization of glyoxylate: a potential abiotic pathway to the citric acid cycle. J Am Chem Soc 2013; 135:13440-5. [PMID: 23914725 PMCID: PMC3777280 DOI: 10.1021/ja405103r] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An abiotic formation of meso- and DL-tartrates in 80% yield via the cyanide-catalyzed dimerization of glyoxylate under alkaline conditions is demonstrated. A detailed mechanism for this conversion is proposed, supported by NMR evidence and (13)C-labeled reactions. Simple dehydration of tartrates to oxaloacetate and an ensuing decarboxylation to form pyruvate are known processes that provide a ready feedstock for entry into the citric acid cycle. While glyoxylate and high hydroxide concentration are atypical in the prebiotic literature, there is evidence for natural, abiotic availability of each. It is proposed that this availability, coupled with the remarkable efficiency of tartrate production from glyoxylate, merits consideration of an alternative prebiotic pathway for providing constituents of the citric acid cycle.
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Affiliation(s)
- Christopher Butch
- School of Chemical and Biological Engineering and ‡School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
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Jeilani YA, Nguyen HT, Newallo D, Dimandja JMD, Nguyen MT. Free radical routes for prebiotic formation of DNA nucleobases from formamide. Phys Chem Chem Phys 2013; 15:21084-93. [DOI: 10.1039/c3cp53108b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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