1
|
Knížek A, Petera L, Laitl V, Ferus M. Decomposition of HCN during Experimental Impacts in Dry and Wet Planetary Atmospheres. ACS EARTH & SPACE CHEMISTRY 2024; 8:1246-1258. [PMID: 38919854 PMCID: PMC11195306 DOI: 10.1021/acsearthspacechem.4c00064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/09/2024] [Accepted: 05/14/2024] [Indexed: 06/27/2024]
Abstract
Hydrogen cyanide (HCN), a key molecule of significant importance in contemporary perspectives on prebiotic chemistry, originates in planetary atmospheres from various processes, such as photochemistry, thermochemistry, and impact chemistry, as well as from delivery by impacts. The resilience of HCN during periods of heavy bombardment, a phenomenon caused by an influx of material on unstable trajectories after accretion, remains relatively understudied. This study extensively investigates the stability of HCN under impact conditions simulated using a laboratory Nd:YAG laser in the ELISE experimental setup. High-resolution infrared spectroscopy was employed to monitor the gas phase composition during these simulations. Impact chemistry was simulated in bulk nitrogen atmospheres with varying mixing ratios of HCN and water vapor. The probed range of compositions spans from ∼0 to 1.8% of HCN and 0 to 2.7% of H2O in a ∼1 bar nitrogen atmosphere. The primary decomposition products of HCN are CO and CO2 in the presence of water and unidentified solid phase products in dry conditions. Our experiments revealed a range of initial HCN decomposition rates between 2.43 × 1015 and 5.17 × 1017 molec J-1 of input energy depending on the initial composition. Notably, it is shown that the decomposition process induced by the laser spark simulating the impact plasma is nonlinear, with the duration of the irradiation markedly affecting the decomposition rate. These findings underscore the necessity for careful consideration and allowance for margins when applying these rates to chemical models of molecular synthesis and decomposition in planetary atmospheres.
Collapse
Affiliation(s)
- Antonín Knížek
- J.Heyrovský
Institute of Physical Chemistry, Czech Academy
of Sciences, Dolejškova
2155/3, CZ18223 Prague, Czech Republic
| | - Lukáš Petera
- J.Heyrovský
Institute of Physical Chemistry, Czech Academy
of Sciences, Dolejškova
2155/3, CZ18223 Prague, Czech Republic
- Department
of Inorganic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ12800 Prague, Czech Republic
| | - Vojtěch Laitl
- J.Heyrovský
Institute of Physical Chemistry, Czech Academy
of Sciences, Dolejškova
2155/3, CZ18223 Prague, Czech Republic
- Faculty
of Science, University of Antwerp, Groenenborgerlaan 171, BE2020 Antwerpen, Belgium
| | - Martin Ferus
- J.Heyrovský
Institute of Physical Chemistry, Czech Academy
of Sciences, Dolejškova
2155/3, CZ18223 Prague, Czech Republic
| |
Collapse
|
2
|
Root-Bernstein R, Brown AW. Novel Apparatuses for Incorporating Natural Selection Processes into Origins-of-Life Experiments to Produce Adaptively Evolving Chemical Ecosystems. Life (Basel) 2022; 12:1508. [PMID: 36294944 PMCID: PMC9605314 DOI: 10.3390/life12101508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/21/2022] Open
Abstract
Origins-of-life chemical experiments usually aim to produce specific chemical end-products such as amino acids, nucleic acids or sugars. The resulting chemical systems do not evolve or adapt because they lack natural selection processes. We have modified Miller origins-of-life apparatuses to incorporate several natural, prebiotic physicochemical selection factors that can be tested individually or in tandem: freezing-thawing cycles; drying-wetting cycles; ultraviolet light-dark cycles; and catalytic surfaces such as clays or minerals. Each process is already known to drive important origins-of-life chemical reactions such as the production of peptides and synthesis of nucleic acid bases and each can also destroy various reactants and products, resulting selection within the chemical system. No previous apparatus has permitted all of these selection processes to work together. Continuous synthesis and selection of products can be carried out over many months because the apparatuses can be re-gassed. Thus, long-term chemical evolution of chemical ecosystems under various combinations of natural selection may be explored for the first time. We argue that it is time to begin experimenting with the long-term effects of such prebiotic natural selection processes because they may have aided biotic life to emerge by taming the combinatorial chemical explosion that results from unbounded chemical syntheses.
Collapse
Affiliation(s)
| | - Adam W. Brown
- Department of Art, Art History and Design, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
3
|
Bera PP, Noneman KK, Lee TJ. Energy Landscape and Structural and Spectroscopic Characterization of Diazirine and Its Cyclic Isomers. J Phys Chem A 2022; 126:4700-4708. [PMID: 35853204 DOI: 10.1021/acs.jpca.2c01444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Identifying new nitrogenated hydrocarbon molecules in the interstellar medium (ISM) is challenging because of the lack of comprehensive spectroscopic data from experiments. In this computational work, we focus on investigating the structures, relative energies, spectroscopic constants, and energy landscape of the cyclic isomers of diazirine (c-CH2N2) using ab initio quantum chemical methods. Density functional theory (DFT) methods and coupled cluster theory with singles and doubles including perturbative triples [CCSD(T)] and CCSD(T) with the explicitly correlated F12b correction [CCSD(T)-F12b] were employed for this purpose along with large correlation consistent cc-pVTZ, cc-pVQZ, and cc-pV5Z basis sets. Harmonic vibrational frequencies, infrared vibrational intensities, rotational constants, and dipole moments are reported. Anharmonic vibrational fundamentals along with centrifugal distortion constants, and vibration-rotation interaction constants are also reported for all the cyclic isomers. The energies computed with the CCSD(T) and CCSD(T)-F12b methods were extrapolated to the one-particle complete basis set (CBS) limit following a three-point formula. At the CCSD(T)-F12b/CBS level of theory, the 3,3H-diazirine (c-CH2N2) is the lowest energy cyclic isomer followed by 1,3H-diazirine, (E)-1,2H-diazirine, and (Z)-1,2H-diazirine, which are 20.1, 47.8, and 51.3 kcal mol-1 above the 3,3H-diazirine, respectively. Accurate structures and spectroscopic constants that are reported here could be useful for future identification of these cyclic nitrogenated organic molecules in the interstellar medium or circumstellar disks.
Collapse
Affiliation(s)
- Partha P Bera
- Bay Area Environmental Research Institute, Moffett Field, California 94035, United States
- Space Science and Astrobiology Division, NASA Ames Research Center, Mountain View, California 94035, United States
| | - Kendra K Noneman
- Space Science and Astrobiology Division, NASA Ames Research Center, Mountain View, California 94035, United States
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Drive, Boise, Idaho 83725, United States
| | - Timothy J Lee
- Space Science and Astrobiology Division, NASA Ames Research Center, Mountain View, California 94035, United States
| |
Collapse
|
4
|
Ertem G. The Role of Minerals in Events That Led to the Origin of Life. ASTROBIOLOGY 2021; 21:137-150. [PMID: 33544652 DOI: 10.1089/ast.2020.2245] [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: 06/12/2023]
Abstract
The role of minerals in the events that led to the origin of life is discussed with regard to (1) their catalytic role for the formation of RNA-like oligomers from their monomers and (2) their protective role for organic molecules formed in space that were delivered to planetary surfaces. Results obtained in the laboratory demonstrate that minerals do catalyze the oligomerization of ribonucleic acid (RNA) monomers to produce short RNA chains. Furthermore, and more importantly, these synthetic RNA chains formed by mineral catalysis serve as a template for the formation of complementary RNA chains, which is a significant finding that demonstrates the role of minerals in the origin of life. Simulation experiments run under Mars-like conditions have also shown that Mars analog minerals can shield the precursors of RNA and proteins against the harmful effects of UV and gamma radiation at the martian surface and 5 cm below the surface.
Collapse
Affiliation(s)
- Gözen Ertem
- Carl Sagan Center, SETI Institute, Mountain View, California, USA
- University of Maryland, College Park, Maryland, USA
| |
Collapse
|
5
|
Sandford SA, Nuevo M, Bera PP, Lee TJ. Prebiotic Astrochemistry and the Formation of Molecules of Astrobiological Interest in Interstellar Clouds and Protostellar Disks. Chem Rev 2020; 120:4616-4659. [DOI: 10.1021/acs.chemrev.9b00560] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Scott A. Sandford
- NASA Ames Research Center, MS 245-6, Moffett Field, California 94035, United States
| | - Michel Nuevo
- NASA Ames Research Center, MS 245-6, Moffett Field, California 94035, United States
- BAER Institute, NASA Research Park, MS 18-4, Moffett Field, California 94035, United States
| | - Partha P. Bera
- NASA Ames Research Center, MS 245-6, Moffett Field, California 94035, United States
- BAER Institute, NASA Research Park, MS 18-4, Moffett Field, California 94035, United States
| | - Timothy J. Lee
- NASA Ames Research Center, MS 245-3, Moffett Field, California 94035, United States
| |
Collapse
|
6
|
Hendrix J, Bera PP, Lee TJ, Head-Gordon M. Cation, Anion, and Radical Isomers of C 4H 4N: Computational Characterization and Implications for Astrophysical and Planetary Environments. J Phys Chem A 2020; 124:2001-2013. [PMID: 32077700 DOI: 10.1021/acs.jpca.9b11305] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Nitrogen-containing ions and molecules in the gas phase have been detected in non-Earth environments such as dark molecular clouds and more recently in the atmosphere of Saturn's moon Titan. These molecules may serve as precursors to larger heterocyclic structures that provide the foundation of complex biological molecules. On Titan, molecules of m/z 66 have been detected by the Cassini mission, and species of the empirical formula C4H4N may contribute to this signature. We have characterized seven isomers of C4H4N in anionic, neutral radical, and cationic states using density functional theory. Structures were optimized using the range-separated hybrid ωB97X-V with the cc-pVTZ and aug-cc-pVTZ basis sets. Anionic and radical C4H4N favor cyclic structures with aromatic and quasi-aromatic electron arrangements, respectively. Interestingly, ionization from the radical surface to the cation induces significant changes in structural stability, and the global minimum for positively charged isomers is CH2CCHCNH+, a pseudo-linear species reminiscent of cyanoallene. Select formation pathways to these structures from Titan's existing or postulated gas-phase species, reactions that are also relevant for other astrophysical environments, are discussed. By characterizing C4H4N isomers, we have identified energetically stable anionic, radical, and cationic structures that may be present in Titan's atmosphere and dark molecular clouds.
Collapse
Affiliation(s)
- Josie Hendrix
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Partha P Bera
- NASA Ames Research Center, Moffett Field, Mountain View, California 94035, United States.,Bay Area Environmental Research Institute, Moffett Field, Mountain View, California 94952, United States
| | - Timothy J Lee
- NASA Ames Research Center, Moffett Field, Mountain View, California 94035, United States
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| |
Collapse
|
7
|
Majer K, Signorell R, Heringa MF, Goldmann M, Hemberger P, Bodi A. Valence Photoionization of Thymine: Ionization Energies, Vibrational Structure, and Fragmentation Pathways from the Slow to the Ultrafast. Chemistry 2019; 25:14192-14204. [PMID: 31469456 DOI: 10.1002/chem.201903282] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Indexed: 11/06/2022]
Abstract
The photoionization of thymine has been studied by using vacuum ultraviolet radiation and imaging photoelectron photoion coincidence spectroscopy after aerosol flash vaporization and bulk evaporation. The two evaporation techniques have been evaluated by comparison of the photoelectron spectra and breakdown diagrams. The adiabatic ionization energies for the first four electronic states were determined to be 8.922±0.008, 9.851±0.008, 10.30±0.02, and 10.82±0.01 eV. Vibrational features have been assigned for the first three electronic states with the help of Franck-Condon factor calculations based on density functional theory and wave function theory vibrational analysis within the harmonic approximation. The breakdown diagram of thymine, as supported by composite method ab initio calculations, suggests that the main fragment ions are formed in sequential HNCO-, CO-, and H-loss dissociation steps from the thymine parent ion, with the first step corresponding to a retro-Diels-Alder reaction. The dissociation rate constants were extracted from the photoion time-of-flight distributions and used together with the breakdown curves to construct a statistical model to determine 0 K appearance energies of 11.15±0.16 and 11.95±0.09 eV for the m/z 83 and 55 fragment ions, respectively. These results have allowed us to revise previously proposed fragmentation mechanisms and to propose a model for the final, nonstatistical H-loss step in the breakdown diagram, yielding the m/z 54 fragment ion at an appearance energy of 13.24 eV.
Collapse
Affiliation(s)
- Katharina Majer
- Paul Scherrer Institute, 5232, Villigen, Switzerland.,Department of Chemistry and Applied Biosciences, Laboratory of Physical Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | - Ruth Signorell
- Department of Chemistry and Applied Biosciences, Laboratory of Physical Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | - Maarten F Heringa
- Paul Scherrer Institute, 5232, Villigen, Switzerland.,Present address: Givaudan Schweiz AG, 8310, Kemptthal, Switzerland
| | - Maximilian Goldmann
- Gymnasium Lerbermatt, 3098, Köniz, Switzerland.,Hochschule Luzern - Technik & Architektur, 6048, Horw, Switzerland
| | | | - Andras Bodi
- Paul Scherrer Institute, 5232, Villigen, Switzerland
| |
Collapse
|
8
|
Cruikshank DP, Materese CK, Pendleton YJ, Boston PJ, Grundy WM, Schmitt B, Lisse CM, Runyon KD, Keane JT, Beyer RA, Summers ME, Scipioni F, Stern SA, Dalle Ore CM, Olkin CB, Young LA, Ennico K, Weaver HA, Bray VJ. Prebiotic Chemistry of Pluto. ASTROBIOLOGY 2019; 19:831-848. [PMID: 30907634 DOI: 10.1089/ast.2018.1927] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We present the case for the presence of complex organic molecules, such as amino acids and nucleobases, formed by abiotic processes on the surface and in near-subsurface regions of Pluto. Pluto's surface is tinted with a range of non-ice substances with colors ranging from light yellow to red to dark brown; the colors match those of laboratory organic residues called tholins. Tholins are broadly characterized as complex, macromolecular organic solids consisting of a network of aromatic structures connected by aliphatic bridging units (e.g., Imanaka et al., 2004; Materese et al., 2014, 2015). The synthesis of tholins in planetary atmospheres and in surface ices has been explored in numerous laboratory experiments, and both gas- and solid-phase varieties are found on Pluto. A third variety of tholins, exposed at a site of tectonic surface fracturing called Virgil Fossae, appears to have come from a reservoir in the subsurface. Eruptions of tholin-laden liquid H2O from a subsurface aqueous repository appear to have covered portions of Virgil Fossae and its surroundings with a uniquely colored deposit (D.P. Cruikshank, personal communication) that is geographically correlated with an exposure of H2O ice that includes spectroscopically detected NH3 (C.M. Dalle Ore, personal communication). The subsurface organic material could have been derived from presolar or solar nebula processes, or might have formed in situ. Photolysis and radiolysis of a mixture of ices relevant to Pluto's surface composition (N2, CH4, CO) have produced strongly colored, complex organics with a significant aromatic content having a high degree of nitrogen substitution similar to the aromatic heterocycles pyrimidine and purine (Materese et al., 2014, 2015; Cruikshank et al., 2016). Experiments with pyrimidines and purines frozen in H2O-NH3 ice resulted in the formation of numerous nucleobases, including the biologically relevant guanine, cytosine, adenine, uracil, and thymine (Materese et al., 2017). The red material associated with the H2O ice may contain nucleobases resulting from energetic processing on Pluto's surface or in the interior. Some other Kuiper Belt objects also exhibit red colors similar to those found on Pluto and may therefore carry similar inventories of complex organic materials. The widespread and ubiquitous nature of similarly complex organic materials observed in a variety of astronomical settings drives the need for additional laboratory and modeling efforts to explain the origin and evolution of organic molecules. Pluto observations reveal complex organics on a small body that remains close to its place of origin in the outermost regions of the Solar System.
Collapse
Affiliation(s)
- D P Cruikshank
- 1NASA Ames Research Center, Moffett Field, California, USA
| | - C K Materese
- 2Goddard Space Flight Center, Greenbelt, Maryland, USA
| | - Y J Pendleton
- 1NASA Ames Research Center, Moffett Field, California, USA
| | - P J Boston
- 1NASA Ames Research Center, Moffett Field, California, USA
| | - W M Grundy
- 3Lowell Observatory, Flagstaff, Arizona, USA
| | - B Schmitt
- 4Université Grenoble Alpes, CNRS, IPAG, Grenoble, France
| | - C M Lisse
- 5Applied Physics Laboratory, Johns Hopkins University, Laurel, Maryland, USA
| | - K D Runyon
- 5Applied Physics Laboratory, Johns Hopkins University, Laurel, Maryland, USA
| | - J T Keane
- 6California Institute of Technology, Pasadena, California, USA
| | - R A Beyer
- 1NASA Ames Research Center, Moffett Field, California, USA
| | - M E Summers
- 7Department of Physics and Astronomy, George Mason University, Fairfax, Virginia, USA
| | - F Scipioni
- 1NASA Ames Research Center, Moffett Field, California, USA
| | - S A Stern
- 8Southwest Research Institute, Boulder, Colorado, USA
| | - C M Dalle Ore
- 1NASA Ames Research Center, Moffett Field, California, USA
| | - C B Olkin
- 8Southwest Research Institute, Boulder, Colorado, USA
| | - L A Young
- 8Southwest Research Institute, Boulder, Colorado, USA
| | - K Ennico
- 1NASA Ames Research Center, Moffett Field, California, USA
| | - H A Weaver
- 5Applied Physics Laboratory, Johns Hopkins University, Laurel, Maryland, USA
| | - V J Bray
- 9Lunar and Planetary Laboratory, University of Arizona, Tucson, Arizona, USA
| |
Collapse
|
9
|
Dickerson CE, Bera PP, Lee TJ. Characterization of Azirine and Its Structural Isomers. J Phys Chem A 2018; 122:8898-8904. [PMID: 30350988 DOI: 10.1021/acs.jpca.8b07788] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structures and spectroscopic properties of azirine (C2H3N), a nitrogen-containing three-membered cyclic molecule, and its isomers were studied with state-of-the-art ab initio quantum chemical methods. Azirine is isomeric with methyl cyanide (CH3CN) and methyl isocyanide (CH3NC)-both observed in the star-forming regions of Sgr B2. In this study, we characterize the stationary points on the potential energy surface, relative energies, dipole moments, rotational constants, and harmonic vibrational frequencies of the 2 H-azirine ( a), 1 H-2,2 H-azirine ( b, carbene isomer), and 1 H-azirine ( c) cyclic isomers. The CCSD(T) method and density functional theory (DFT), using the ωB97-X functional, along with Dunning's cc-pVXZ (X = T and Q) basis sets were used to optimize molecular geometries and calculate vibrational frequencies. The 2 H-azirine, an imine isomer ( a), was found to be the lowest in energy among the cyclic isomers, followed by the carbene isomer ( b), and last the 1 H-azirine, an enamine isomer ( c). All three cyclic isomers have a C s symmetry equilibrium structure. Azirines, if identified (three linear C2H3N isomers are already identified in the same source toward the galactic center, Sgr B2), would be the first nitrogen-containing cyclic molecules identified in an astronomical observation.
Collapse
Affiliation(s)
| | - Partha P Bera
- Space Science and Astrobiology Division , NASA Ames Research Center , Mountain View , California 94035 , United States.,Bay Area Environmental Research Institute , Moffett Field , California 94035 , United States
| | - Timothy J Lee
- Space Science and Astrobiology Division , NASA Ames Research Center , Mountain View , California 94035 , United States
| |
Collapse
|
10
|
Cataldo F. Radiolysis and radioracemization of RNA ribonucleosides: implications for the origins of life. J Radioanal Nucl Chem 2018. [DOI: 10.1007/s10967-018-6276-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
11
|
Nakashima S, Kebukawa Y, Kitadai N, Igisu M, Matsuoka N. Geochemistry and the Origin of Life: From Extraterrestrial Processes, Chemical Evolution on Earth, Fossilized Life's Records, to Natures of the Extant Life. Life (Basel) 2018; 8:E39. [PMID: 30241342 PMCID: PMC6315873 DOI: 10.3390/life8040039] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/15/2018] [Accepted: 09/17/2018] [Indexed: 11/18/2022] Open
Abstract
In 2001, the first author (S.N.) led the publication of a book entitled "Geochemistry and the origin of life" in collaboration with Dr. Andre Brack aiming to figure out geo- and astro-chemical processes essential for the emergence of life. Since then, a great number of research progress has been achieved in the relevant topics from our group and others, ranging from the extraterrestrial inputs of life's building blocks, the chemical evolution on Earth with the aid of mineral catalysts, to the fossilized records of ancient microorganisms. Here, in addition to summarizing these findings for the origin and early evolution of life, we propose a new hypothesis for the generation and co-evolution of photosynthesis with the redox and photochemical conditions on the Earth's surface. Besides these bottom-up approaches, we introduce an experimental study on the role of water molecules in the life's function, focusing on the transition from live, dormant, and dead states through dehydration/hydration. Further spectroscopic studies on the hydrogen bonding behaviors of water molecules in living cells will provide important clues to solve the complex nature of life.
Collapse
Affiliation(s)
- Satoru Nakashima
- Department of Earth and Space Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
- Undergraduate School of Physics, Osaka University, Toyonaka, Osaka 560-0043, Japan.
| | - Yoko Kebukawa
- Department of Earth and Space Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
- Faculty of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan.
| | - Norio Kitadai
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
| | - Motoko Igisu
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa 237-0061, Japan.
| | - Natsuki Matsuoka
- Undergraduate School of Physics, Osaka University, Toyonaka, Osaka 560-0043, Japan.
| |
Collapse
|
12
|
Karsili TNV, Fennimore MA, Matsika S. Electron-induced origins of prebiotic building blocks of sugars: mechanism of self-reactions of a methanol anion dimer. Phys Chem Chem Phys 2018; 20:12599-12607. [DOI: 10.1039/c8cp00148k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reactions of methanol dimers in interstellar medium driven by low energy irradiation may lead to prebiotic precursors.
Collapse
|
13
|
Materese CK, Nuevo M, Sandford SA. The Formation of Nucleobases from the Ultraviolet Photoirradiation of Purine in Simple Astrophysical Ice Analogues. ASTROBIOLOGY 2017; 17:761-770. [PMID: 28723229 PMCID: PMC5808537 DOI: 10.1089/ast.2016.1613] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Nucleobases are the informational subunits of RNA and DNA and are essential to all known forms of life. The nucleobases can be divided into two groups of molecules: the pyrimidine-based compounds that include uracil, cytosine, and thymine, and the purine-based compounds that include adenine and guanine. Previous work in our laboratory has demonstrated that uracil, cytosine, thymine, and other nonbiological, less common nucleobases can form abiotically from the UV photoirradiation of pyrimidine in simple astrophysical ice analogues containing combinations of H2O, NH3, and CH4. In this work, we focused on the UV photoirradiation of purine mixed with combinations of H2O and NH3 ices to determine whether or not the full complement of biological nucleobases can be formed abiotically under astrophysical conditions. Room-temperature analyses of the resulting photoproducts resulted in the detection of adenine, guanine, and numerous other functionalized purine derivatives. Key Words: Pyrimidine-Nucleobases-Interstellar; Ices-Cometary; Ices-Molecular processes-Prebiotic chemistry. Astrobiology 17, 761-770.
Collapse
Affiliation(s)
- Christopher K. Materese
- NASA Ames Research Center, Space Science and Astrobiology Division, MS 245-6, Moffett Field, CA 94035, USA
- Bay Area Environmental Research Institute, 625 2 St., Suite 209, Petaluma, CA 94952, USA
| | - Michel Nuevo
- NASA Ames Research Center, Space Science and Astrobiology Division, MS 245-6, Moffett Field, CA 94035, USA
- Bay Area Environmental Research Institute, 625 2 St., Suite 209, Petaluma, CA 94952, USA
| | - Scott A. Sandford
- NASA Ames Research Center, Space Science and Astrobiology Division, MS 245-6, Moffett Field, CA 94035, USA
| |
Collapse
|
14
|
Bera PP, Stein T, Head-Gordon M, Lee TJ. Mechanisms of the Formation of Adenine, Guanine, and Their Analogues in UV-Irradiated Mixed NH 3:H 2O Molecular Ices Containing Purine. ASTROBIOLOGY 2017; 17:771-785. [PMID: 28708419 PMCID: PMC5734622 DOI: 10.1089/ast.2016.1614] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We investigated the formation mechanisms of the nucleobases adenine and guanine and the nucleobase analogues hypoxanthine, xanthine, isoguanine, and 2,6-diaminopurine in a UV-irradiated mixed 10:1 H2O:NH3 ice seeded with precursor purine by using ab initio and density functional theory computations. Our quantum chemical investigations suggest that a multistep reaction mechanism involving purine cation, hydroxyl and amino radicals, together with water and ammonia, explains the experimentally obtained products in an independent study. The relative abundances of these products appear to largely follow from relative thermodynamic stabilities. The key role of the purine cation is likely to be the reason why purine is not functionalized in pure ammonia ice, where cations are promptly neutralized by free electrons from NH3 ionization. Amine group addition to purine is slightly favored over hydroxyl group attachment based on energetics, but hydroxyl is much more abundant due to higher abundance of H2O. The amino group is preferentially attached to the 6 position, giving 6-aminopurine, that is, adenine, while the hydroxyl group is preferentially attached to the 2 position, leading to 2-hydroxypurine. A second substitution by hydroxyl or amino group occurs at either the 6 or the 2 position depending on the first substitution. Given that H2O is far more abundant than NH3 in the experimentally studied ices (as well as based on interstellar abundances), xanthine and isoguanine are expected to be the most abundant bi-substituted photoproducts. Key Words: Astrophysical ice-Abiotic organic synthesis-Nucleic acids-Origin of life-RNA world. Astrobiology 17, 771-785.
Collapse
Affiliation(s)
- Partha P. Bera
- NASA Ames Research Center, Moffett Field, Mountain View, CA, USA
- Bay Area Environmental Research Institute, Petaluma, CA, USA
| | - Tamar Stein
- University of California, Berkeley, CA, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Martin Head-Gordon
- University of California, Berkeley, CA, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Timothy J. Lee
- NASA Ames Research Center, Moffett Field, Mountain View, CA, USA
| |
Collapse
|
15
|
Bera PP, Nuevo M, Materese CK, Sandford SA, Lee TJ. Mechanisms for the formation of thymine under astrophysical conditions and implications for the origin of life. J Chem Phys 2016; 144:144308. [PMID: 27083722 PMCID: PMC5809119 DOI: 10.1063/1.4945745] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Nucleobases are the carriers of the genetic information in ribonucleic acid and deoxyribonucleic acid (DNA) for all life on Earth. Their presence in meteorites clearly indicates that compounds of biological importance can form via non-biological processes in extraterrestrial environments. Recent experimental studies have shown that the pyrimidine-based nucleobases uracil and cytosine can be easily formed from the ultraviolet irradiation of pyrimidine in H2O-rich ice mixtures that simulate astrophysical processes. In contrast, thymine, which is found only in DNA, is more difficult to form under the same experimental conditions, as its formation usually requires a higher photon dose. Earlier quantum chemical studies confirmed that the reaction pathways were favorable provided that several H2O molecules surrounded the reactants. However, the present quantum chemical study shows that the formation of thymine is limited because of the inefficiency of the methylation of pyrimidine and its oxidized derivatives in an H2O ice, as supported by the laboratory studies. Our results constrain the formation of thymine in astrophysical environments and thus the inventory of organic molecules delivered to the early Earth and have implications for the role of thymine and DNA in the origin of life.
Collapse
Affiliation(s)
- Partha P. Bera
- Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, California 94035, USA
- Bay Area Environmental Research Institute, Petaluma, California 94952, USA
| | - Michel Nuevo
- Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, California 94035, USA
- Bay Area Environmental Research Institute, Petaluma, California 94952, USA
| | - Christopher K. Materese
- Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, California 94035, USA
- Bay Area Environmental Research Institute, Petaluma, California 94952, USA
| | - Scott A. Sandford
- Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, California 94035, USA
| | - Timothy J. Lee
- Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, California 94035, USA
| |
Collapse
|
16
|
Improta R, Santoro F, Blancafort L. Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases. Chem Rev 2016; 116:3540-93. [PMID: 26928320 DOI: 10.1021/acs.chemrev.5b00444] [Citation(s) in RCA: 341] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.
Collapse
Affiliation(s)
- Roberto Improta
- Istituto di Biostrutture Biommagini (IBB-CNR), CNR-Consiglio Nazionale delle Ricerche , Via Mezzocannone 16, I-80134, Napoli, Italy
| | - Fabrizio Santoro
- Area della Ricerca di Pisa, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), CNR-Consiglio Nazionale delle Ricerche , Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi , 17071 Girona, Spain
| |
Collapse
|
17
|
Abstract
Photoinduced processes in nucleic acids are phenomena of fundamental interest in diverse fields, from prebiotic studies, through medical research on carcinogenesis, to the development of bioorganic photodevices. In this contribution we survey many aspects of the research across the boundaries. Starting from a historical background, where the main milestones are identified, we review the main findings of the physical-chemical research of photoinduced processes on several types of nucleic-acid fragments, from monomers to duplexes. We also discuss a number of different issues which are still under debate.
Collapse
Affiliation(s)
- Mario Barbatti
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany,
| | | | | |
Collapse
|