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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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2
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Gerakines PA, Qasim D, Frail S, Hudson RL. Radiolytic Destruction of Uracil in Interstellar and Solar System Ices. ASTROBIOLOGY 2022; 22:233-241. [PMID: 34672795 DOI: 10.1089/ast.2021.0053] [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: 06/13/2023]
Abstract
Uracil is one of the four RNA nucleobases and a component of meteoritic organics. If delivered to the early Earth, uracil could have been involved in the origins of the first RNA-based life, and so this molecule could be a biomarker on other worlds. Therefore, it is important to understand uracil's survival to ionizing radiation in extraterrestrial environments. Here we present a study of the radiolytic destruction kinetics of uracil and mixtures of uracil diluted in H2O or CO2 ice. All samples were irradiated by protons with an energy of 0.9 MeV, and experiments were performed at 20 and 150 K to determine destruction rate constants at temperatures relevant to interstellar and Solar System environments. We show that uracil is destroyed much faster when H2O ice or CO2 ice is present than when these two ices are absent. Moreover, destruction is faster for CO2-dominated ices than for H2O-dominated ones and, to a lesser extent, at 150 K compared with 20 K. Extrapolation of our laboratory results to astronomical timescales shows that uracil will be preserved in ices with half-lives of up to ∼107 years on cold planetary bodies such as comets or Pluto. An important implication of our results is that for extraterrestrial environments, the application of laboratory data measured for the radiation-induced destruction of pure (neat) uracil samples can greatly underestimate the molecule's rate of destruction and significantly overestimate its lifetime, which can lead to errors of over 1000%.
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Affiliation(s)
- Perry A Gerakines
- Astrochemistry Laboratory, NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
| | - Danna Qasim
- Astrochemistry Laboratory, NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Department of Physics and Astronomy, Howard University, Washington, District of Columbia, USA
- Center for Research and Exploration in Space Science and Technology, NASA/GSFC, Greenbelt, Maryland, USA
| | - Sarah Frail
- Astrochemistry Laboratory, NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Reggie L Hudson
- Astrochemistry Laboratory, NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
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3
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Wolf ME, Vandezande JE, Schaefer HF. Catalyzed reaction of isocyanates (RNCO) with water. Phys Chem Chem Phys 2021; 23:18535-18546. [PMID: 34612391 DOI: 10.1039/d1cp03302f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The reactions between substituted isocyanates (RNCO) and other small molecules (e.g. water, alcohols, and amines) are of significant industrial importance, particularly for the development of novel polyurethanes and other useful polymers. We present very high-level ab initio computations on the HNCO + H2O reaction, with results targeting the CCSDT(Q)/CBS//CCSD(T)/cc-pVQZ level of theory. Our results affirm that hydrolysis can occur across both the N[double bond, length as m-dash]C and C[double bond, length as m-dash]O bonds of HNCO via concerted mechanisms to form carbamate or imidic acid with ΔH0K barrier heights of 38.5 and 47.5 kcal mol-1. A total of 24 substituted RNCO + H2O reactions were studied. Geometries obtained with a composite method and refined with CCSD(T)/CBS single point energies determine that substituted RNCO species have a significant influence on these barrier heights, with an extreme case like fluorine lowering both barriers by close to 15 kcal mol-1 and most common alkyl substituents lowering both by approximately 3 kcal mol-1. Natural Bond Orbital (NBO) analysis provides evidence that the predicted barrier heights are strongly associated with the occupation of the in-plane C-O* orbital of the RNCO reactant. Key autocatalytic mechanisms are considered in the presence of excess water and RNCO species. Additional waters (one or two) are predicted to lower both barriers significantly at the CCSD(T)/aug-cc-pV(T+d)Z level of theory with strongly electron withdrawing RNCO substituents also increasing these effects, similar to the uncatalyzed case. The 298 K Gibbs energies are only marginally lowered by a second catalyst water molecule, indicating that the decreasing ΔH0K barriers are offset by loss of translational entropy with more than one catalyst water. Two-step 2RNCO + H2O mechanisms are characterized for the formation of carbamate and imidic acid. The second step of these two pathways exhibits the largest barrier and presents no clear pattern with respect to substituent choice. Our results indicate that an additional RNCO molecule might catalyze imidic acid formation but have less influence on the efficiency of carbamate formation. We expect that these results lay a firm foundation for the experimental study of substituted isocyanates and their relationship to the energetic pathways of related systems.
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Affiliation(s)
- Mark E Wolf
- Center for Computational Quantum Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, USA.
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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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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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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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7
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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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8
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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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9
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Cole CA, Wang ZC, Snow TP, Bierbaum VM. Anionic derivatives of uracil: fragmentation and reactivity. Phys Chem Chem Phys 2014; 16:17835-44. [DOI: 10.1039/c4cp02277g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Uracil is an essential biomolecule for terrestrial life, yet its prebiotic formation mechanisms have proven elusive for decades.
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Affiliation(s)
- Callie A. Cole
- Department of Chemistry and Biochemistry
- University of Colorado
- Boulder, USA
| | - Zhe-Chen Wang
- Department of Chemistry and Biochemistry
- University of Colorado
- Boulder, USA
| | - Theodore P. Snow
- Department of Astrophysical and Planetary Sciences
- University of Colorado
- Boulder, USA
- Center for Astrophysics and Space Astronomy
- University of Colorado
| | - Veronica M. Bierbaum
- Department of Chemistry and Biochemistry
- University of Colorado
- Boulder, USA
- Center for Astrophysics and Space Astronomy
- University of Colorado
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Tang Q, Guo Z, Li Q. A quantum chemical study of the structures, stability, and spectroscopy of halogen- and hydrogen-boned complexes between cyanoacetaldehyde and hypochlorous acids. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 121:157-163. [PMID: 24239758 DOI: 10.1016/j.saa.2013.10.088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 10/15/2013] [Indexed: 06/02/2023]
Abstract
The complexes of cyanoacetaldehyde and hypohalous acid (HOX, X=Cl, Br, and I) have been investigated. They can form six different structures (A, B, C, D, E, and F), the former three structures are mainly combined through a N(O)⋯X halogen bond and the latter three structures are maintained mainly by a N(O)⋯H hydrogen bond, although other weaker interactions are also present in most structures. The hydrogen-bonded structures are more stable than the respective halogen-bonded structures. The O-H and O-X bonds in the halogen- and hydrogen-bonded complexes are lengthened and show an observed red shift, while those in the weaker secondary interactions are contracted and display a small blue shift. The orbital interactions in NBO analysis and the electron densities in AIM analysis provide useful and reliable information for the strength of each type of interaction in different structures.
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Affiliation(s)
- Qingjie Tang
- College of Material Science and Engineering, Henan Polytechnic University, Jiaozuo 454000, China; Hebei North University, Zhangjiakou 075000, People's Republic of China
| | - Zhenfu Guo
- Hebei North University, Zhangjiakou 075000, People's Republic of China
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China.
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11
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Menor-Salván C, Marín-Yaseli MR. A New Route for the Prebiotic Synthesis of Nucleobases and Hydantoins in Water/Ice Solutions Involving the Photochemistry of Acetylene. Chemistry 2013; 19:6488-97. [DOI: 10.1002/chem.201204313] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 02/15/2013] [Indexed: 11/11/2022]
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12
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Wang T, Bowie JH. Hydrogen tunnelling influences the isomerisation of some small radicals of interstellar importance. A theoretical investigation. Org Biomol Chem 2012; 10:3219-28. [DOI: 10.1039/c2ob07102a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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