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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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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.
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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
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3
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Vos E, Hoehn SJ, Krul SE, Crespo-Hernández CE, González-Vázquez J, Corral I. Disclosing the Role of C4-Oxo Substitution in the Photochemistry of DNA and RNA Pyrimidine Monomers: Formation of Photoproducts from the Vibrationally Excited Ground State. J Phys Chem Lett 2022; 13:2000-2006. [PMID: 35191712 PMCID: PMC8900130 DOI: 10.1021/acs.jpclett.2c00052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Oxo and amino substituted purines and pyrimidines have been suggested as protonucleobases participating in ancient pre-RNA forms. Considering electromagnetic radiation as a key environmental selection pressure on early Earth, the investigation of the photophysics of modified nucleobases is crucial to determine their viability as nucleobases' ancestors and to understand the factors that rule the photostability of natural nucleobases. In this Letter, we combine femtosecond transient absorption spectroscopy and quantum mechanical simulations to reveal the photochemistry of 4-pyrimidinone, a close relative of uracil. Irradiation of 4-pyrimidinone with ultraviolet radiation populates the S1(ππ*) state, which decays to the vibrationally excited ground state in a few hundred femtoseconds. Analysis of the postirradiated sample in water reveals the formation of a 6-hydroxy-5H-photohydrate and 3-(N-(iminomethyl)imino)propanoic acid as the primary photoproducts. 3-(N-(Iminomethyl)imino)propanoic acid originates from the hydrolysis of an unstable ketene species generated from the C4-N3 photofragmentation of the pyrimidine core.
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Affiliation(s)
- Eva Vos
- Departamento
de Química, Módulo 13, Universidad
Autónoma de Madrid, 28049 Madrid, Spain
| | - Sean J. Hoehn
- Department
of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Sarah E. Krul
- Department
of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Carlos E. Crespo-Hernández
- Department
of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Jesús González-Vázquez
- Departamento
de Química, Módulo 13, Universidad
Autónoma de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Inés Corral
- Departamento
de Química, Módulo 13, Universidad
Autónoma de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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4
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Chatterjee K, Dopfer O. Spectroscopic identification of fragment ions of DNA/RNA building blocks: the case of pyrimidine. Phys Chem Chem Phys 2020; 22:17275-17290. [PMID: 32685941 DOI: 10.1039/d0cp02919j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Pyrimidine (Pym, 1,3-diazine, 1,3-diazabenzene) is an important N-heterocyclic building block of nucleobases. Understanding the structures of its fragment and precursor ions provides insight into its prebiotic and abiotic synthetic route. The long-standing controversial debate about the structures of the primary fragment ions of the Pym+ cation (C4H4N2+, m/z 80) resulting from loss of HCN, C3H3N+ (m/z 53), is closed herein with the aid of a combined approach utilizing infrared photodissociation (IRPD) spectroscopy in the CH and NH stretch ranges (νCH/NH) and density functional theory (DFT) calculations. IRPD spectra of cold Ar/N2-tagged fragment ions reveal that the C3H3N+ population is dominated by cis-/trans-HCCHNCH+ ions (∼90%) along with a minor contribution of the most stable H2CCCNH+ and cis-/trans-HCCHCNH+ isomers (∼10%). We also spectroscopically confirm that the secondary fragment resulting from further loss of HCN, C2H2+ (m/z 26), is the acetylene cation (HCCH+). The spectroscopic characterization of the identified C3H3N+ isomers and their hydrogen-bonded dimers with Ar and N2 provides insight into the acidity of their CH and NH groups. Finally, the vibrational properties of Pym+ in the 3 μm range are probed by IRPD of Pym+-(N2)1-2 clusters, which shows a high π-binding affinity of Pym+ toward a nonpolar hydrophobic ligand. Its νCH spectrum confirms the different acidity of the three nonequivalent CH groups.
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Affiliation(s)
- Kuntal Chatterjee
- Institut für Optik und Atomare Physik, TU Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, TU Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
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5
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Chatterjee K, Dopfer O. Microhydration of protonated biomolecular building blocks: protonated pyrimidine. Phys Chem Chem Phys 2020; 22:13092-13107. [PMID: 32490447 DOI: 10.1039/d0cp02110e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protonation and hydration of biomolecules govern their structure, conformation, and function. Herein, we explore the microhydration structure in mass-selected protonated pyrimidine-water clusters (H+Pym-Wn, n = 1-4) by a combination of infrared photodissociation spectroscopy (IRPD) between 2450 and 3900 cm-1 and density functional theory (DFT) calculations at the dispersion-corrected B3LYP-D3/aug-cc-pVTZ level. We further present the IR spectrum of H+Pym-N2 to evaluate the effect of solvent polarity on the intrinsic molecular parameters of H+Pym. Our combined spectroscopic and computational approach unequivocally shows that protonation of Pym occurs at one of the two equivalent basic ring N atoms and that the ligands in H+Pym-L (L = N2 or W) preferentially form linear H-bonds to the resulting acidic NH group. Successive addition of water ligands results in the formation of a H-bonded solvent network which increasingly weakens the NH group. Despite substantial activation of the N-H bond upon microhydration, no intracluster proton transfer occurs up to n = 4 because of the balance of relative proton affinities of Pym and Wn and the involved solvation energies. Comparison to neutral Pym-Wn clusters reveals the drastic effects of protonation on microhydration with respect to both structure and interaction strength.
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Affiliation(s)
- Kuntal Chatterjee
- Institut für Optik und Atomare Physik, TU Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
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6
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Materese CK, Nuevo M, Sandford SA, Bera PP, Lee TJ. The Production and Potential Detection of Hexamethylenetetramine-Methanol in Space. ASTROBIOLOGY 2020; 20:601-616. [PMID: 32105506 DOI: 10.1089/ast.2019.2147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Numerous laboratory studies of astrophysical ice analogues have shown that their exposure to ionizing radiation leads to the production of large numbers of new, more complex compounds, many of which are of astrobiological interest. We show here that the irradiation of astrophysical ice analogues containing H2O, CH3OH, CO, and NH3 yields quantities of hexamethylenetetramine-methanol (hereafter HMT-methanol; C7N4H14O) that are easily detectible in the resulting organic residues. This molecule differs from simple HMT, which is known to be abundant in similar ice photolysis residues, by the replacement of a peripheral H atom with a CH2OH group. As with HMT, HMT-methanol is likely to be an amino acid precursor. HMT has tetrahedral (Td) symmetry, whereas HMT-methanol has C1 symmetry. We report the computed expected infrared spectra for HMT and HMT-methanol obtained using ab initio quantum chemistry methods and show that there is a good match between the observed and computed spectra for regular HMT. Since HMT-methanol lacks the high symmetry of HMT, it produces rotational transitions that could be observed at longer wavelengths, although establishing the exact positions of these transitions may be challenging. It is likely that HMT-methanol represents an abundant member of a larger family of functionalized HMT molecules that may be present in cold astrophysical environments.
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Affiliation(s)
- Christopher K Materese
- NASA Ames Research Center, MS 245-6, Moffett Field, California 94035
- BAER Institute, NASA Research Park, MS 18-4, Moffett Field, California 94035
- NASA Goddard Space Flight Center, Code 691, Greenbelt, Maryland 20771
| | - Michel Nuevo
- NASA Ames Research Center, MS 245-6, Moffett Field, California 94035
- BAER Institute, NASA Research Park, MS 18-4, Moffett Field, California 94035
| | - Scott A Sandford
- NASA Ames Research Center, MS 245-6, Moffett Field, California 94035
| | - Partha P Bera
- NASA Ames Research Center, MS 245-6, Moffett Field, California 94035
- BAER Institute, NASA Research Park, MS 18-4, Moffett Field, California 94035
| | - Timothy J Lee
- NASA Ames Research Center, MS 245-3, Moffett Field, California 94035
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7
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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
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8
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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.
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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
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9
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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.
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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
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10
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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.
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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
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11
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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.
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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
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12
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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.
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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
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13
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Kokkila Schumacher SIL, Bera PP, Lee TJ. Characterization of the Azirinyl Cation and Its Isomers. J Phys Chem A 2016; 120:1275-82. [PMID: 26840658 DOI: 10.1021/acs.jpca.5b12373] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The azirinyl cation (C2H2N(+)) and its geometrical isomers could be present in the interstellar medium. The C2H2N(+) isomers are, however, difficult to identify in interstellar chemistry because of the lack of high-resolution spectroscopic data from laboratory experiments. Ab initio quantum chemical methods were used to characterize the structures, relative energies, and spectroscopic and physical properties of the low energy isomers of the azirinyl cation. We have employed second-order Møller-Plesset perturbation theory (MP2), second-order Z-averaged perturbation theory (ZAPT2), and coupled cluster theory with singles and doubles with perturbative triples CCSD(T) methods along with large correlation consistent basis sets such as cc-pVTZ, cc-pCVTZ, cc-pVQZ, cc-pCVQZ, and cc-pV5Z. Harmonic vibrational frequencies, dipole moments, rotational constants, and proton affinities for the lowest energy isomers were calculated using the CCSD(T) method. Azirinyl cation, a cyclic isomer, is lowest in energy at all levels of theory employed. Azirinyl cation is followed by the cyanomethyl cation (H2CCN)(+), isocyanomethyl cation (H2CNC)(+), and a quasilinear HCCNH(+) cation, which are 13.8, 17.3, and 21.5 kcal mol(-1) above the cyclic isomer, respectively, at the CCSD(T)/cc-pV5Z level of theory. The lowest three isomers all have C2v symmetry and (1)A1 ground electronic states. The quasilinear HCCNH(+) cation has a Cs symmetry planar structure, and a (3)A″ electronic ground state, unlike what some previous work suggested.
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Affiliation(s)
- Sara I L Kokkila Schumacher
- Space Science and Astrobiology Division, NASA Ames Research Center , Mountain View, California 94035, United States
| | - Partha P Bera
- Space Science and Astrobiology Division, NASA Ames Research Center , Mountain View, California 94035, United States.,Bay Area Environmental Research Institute , Petaluma, California 94952, United States
| | - Timothy J Lee
- Space Science and Astrobiology Division, NASA Ames Research Center , Mountain View, California 94035, United States
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Sandford SA, Bera PP, Lee TJ, Materese CK, Nuevo M. Photosynthesis and photo-stability of nucleic acids in prebiotic extraterrestrial environments. Top Curr Chem (Cham) 2015; 356:123-64. [PMID: 24500331 PMCID: PMC5737941 DOI: 10.1007/128_2013_499] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Laboratory experiments have shown that the UV photo-irradiation of low-temperature ices of astrophysical interest leads to the formation of organic molecules, including molecules important for biology such as amino acids, quinones, and amphiphiles. When pyrimidine is introduced into these ices, the products of irradiation include the nucleobases uracil, cytosine, and thymine, the informational sub-units of DNA and RNA, as well as some of their isomers. The formation of these compounds, which has been studied both experimentally and theoretically, requires a succession of additions of OH, NH₂, and CH₃groups to pyrimidine. Results show that H₂O ice plays key roles in the formation of the nucleobases, as an oxidant, as a matrix in which reactions can take place, and as a catalyst that assists proton abstraction from intermediate compounds. As H₂O is also the most abundant icy component in most cold astrophysical environments, it probably plays the same roles in space in the formation of biologically relevant compounds. Results also show that although the formation of uracil and cytosine from pyrimidine in ices is fairly straightforward, the formation of thymine is not. This is mostly due to the fact that methylation is a limiting step for its formation, particularly in H₂O-rich ices, where methylation must compete with oxidation. The relative inefficiency of the abiotic formation of thymine to that of uracil and cytosine, together with the fact that thymine has not been detected in meteorites, are not inconsistent with the RNA world hypothesis. Indeed, a lack of abiotically produced thymine delivered to the early Earth may have forced the choice for an RNA world, in which only uracil and cytosine are needed, but not thymine.
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Affiliation(s)
- Scott A Sandford
- Space Science and Astrobiology Division, NASA Ames Research Center, MS 245-6, Moffett Field, CA, 94035, USA,
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Wolff W, Luna H, Sigaud L, Tavares AC, Montenegro EC. Absolute total and partial dissociative cross sections of pyrimidine at electron and proton intermediate impact velocities. J Chem Phys 2014; 140:064309. [PMID: 24527917 DOI: 10.1063/1.4864322] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Absolute total non-dissociative and partial dissociative cross sections of pyrimidine were measured for electron impact energies ranging from 70 to 400 eV and for proton impact energies from 125 up to 2500 keV. MOs ionization induced by coulomb interaction were studied by measuring both ionization and partial dissociative cross sections through time of flight mass spectrometry and by obtaining the branching ratios for fragment formation via a model calculation based on the Born approximation. The partial yields and the absolute cross sections measured as a function of the energy combined with the model calculation proved to be a useful tool to determine the vacancy population of the valence MOs from which several sets of fragment ions are produced. It was also a key point to distinguish the dissociation regimes induced by both particles. A comparison with previous experimental results is also presented.
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Affiliation(s)
- Wania Wolff
- Instituto de Física, Universidade Federal do Rio de Janeiro, PO 68528, 21941-972 Rio de Janeiro, RJ, Brazil
| | - Hugo Luna
- Instituto de Física, Universidade Federal do Rio de Janeiro, PO 68528, 21941-972 Rio de Janeiro, RJ, Brazil
| | - Lucas Sigaud
- Instituto de Física, Universidade Federal do Rio de Janeiro, PO 68528, 21941-972 Rio de Janeiro, RJ, Brazil
| | - Andre C Tavares
- Departamento de Física, Pontificia Universidade Católica do Rio de Janeiro, PO 38071, Rua Marquês de São Vicente 225, 22453-900 Rio de Janeiro, RJ, Brazil
| | - Eduardo C Montenegro
- Instituto de Física, Universidade Federal do Rio de Janeiro, PO 68528, 21941-972 Rio de Janeiro, RJ, Brazil
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Nuevo M, Chen YJ, Hu WJ, Qiu JM, Wu SR, Fung HS, Chu CC, Yih TS, Ip WH, Wu CYR. Irradiation of pyrimidine in pure H2O ice with high-energy ultraviolet photons. ASTROBIOLOGY 2014; 14:119-31. [PMID: 24512484 PMCID: PMC3929345 DOI: 10.1089/ast.2013.1093] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 01/14/2014] [Indexed: 06/03/2023]
Abstract
The detection of nucleobases, the informational subunits of DNA and RNA, in several meteorites suggests that these compounds of biological interest were formed via astrophysical, abiotic processes. This hypothesis is in agreement with recent laboratory studies of irradiation of pyrimidine in H2O-rich ices with vacuum UV photons emitted by an H2-discharge lamp in the 6.9-11.3 eV (110-180 nm) range at low temperature, shown to lead to the abiotic formation of several compounds including the nucleobases uracil, cytosine, and thymine. In this work, we irradiated H2O:pyrimidine ice mixtures under astrophysically relevant conditions (14 K, ≤10(-9) torr) with high-energy UV photons provided by a synchrotron source in three different ranges: the 0(th) order light (4.1-49.6 eV, 25-300 nm), the He i line (21.2 eV, 58.4 nm), and the He ii line (40.8 eV, 30.4 nm). The photodestruction of pyrimidine was monitored with IR spectroscopy, and the samples recovered at room temperature were analyzed with liquid and gas chromatographies. Uracil and its precursor 4(3H)-pyrimidone were found in all samples, with absolute and relative abundances varying significantly from one sample to another. These results support a scenario in which compounds of biological interest can be formed and survive in environments subjected to high-energy UV radiation fields.
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Affiliation(s)
- Michel Nuevo
- NASA Ames Research Center, Space Science Division, Moffett Field, California, USA
- SETI Institute, Mountain View, California, USA
| | - Yu-Jung Chen
- Space Sciences Center and Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
- Department of Physics, National Central University, Jhongli, Taiwan
| | - Wei-Jie Hu
- Department of Physics, National Central University, Jhongli, Taiwan
| | - Jun-Ming Qiu
- Department of Physics, National Central University, Jhongli, Taiwan
| | - Shang-Ruei Wu
- Department of Physics, National Central University, Jhongli, Taiwan
| | - Hok-Sum Fung
- National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Ching-Chi Chu
- Department of Physics, National Central University, Jhongli, Taiwan
| | - Tai-Sone Yih
- Department of Physics, National Central University, Jhongli, Taiwan
| | - Wing-Huen Ip
- Graduate Institute of Astronomy, National Central University, Jhongli, Taiwan
| | - C.-Y. Robert Wu
- Space Sciences Center and Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
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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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Materese CK, Nuevo M, Bera PP, Lee TJ, Sandford SA. Thymine and other prebiotic molecules produced from the ultraviolet photo-irradiation of pyrimidine in simple astrophysical ice analogs. ASTROBIOLOGY 2013; 13:948-962. [PMID: 24143868 DOI: 10.1089/ast.2013.1044] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The informational subunits of RNA or DNA consist of substituted N-heterocyclic compounds that fall into two groups: those based on purine (C₅H₄N₄) (adenine and guanine) and those based on pyrimidine (C₄H₄N₂) (uracil, cytosine, and thymine). Although not yet detected in the interstellar medium, N-heterocycles, including the nucleobase uracil, have been reported in carbonaceous chondrites. Recent laboratory experiments and ab initio calculations have shown that the irradiation of pyrimidine in ices containing H₂O, NH₃, or both leads to the abiotic production of substituted pyrimidines, including the nucleobases uracil and cytosine. In this work, we studied the methylation and oxidation of pyrimidine in CH₃OH:pyrimidine, H₂O:CH₃OH:pyrimidine, CH₄:pyrimidine, and H₂O:CH₄:pyrimidine ices irradiated with UV photons under astrophysically relevant conditions. The nucleobase thymine was detected in the residues from some of the mixtures. Our results suggest that the abundance of abiotic thymine produced by ice photolysis and delivered to the early Earth may have been significantly lower than that of uracil. Insofar as the delivery of extraterrestrial molecules was important for early biological chemistry on early Earth, these results suggest that there was more uracil than thymine available for emergent life, a scenario consistent with the RNA world hypothesis.
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Affiliation(s)
- Christopher K Materese
- 1 NASA Ames Research Center , Space Science and Astrobiology Division, Moffett Field, California
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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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Nuevo M, Milam SN, Sandford SA. Nucleobases and prebiotic molecules in organic residues produced from the ultraviolet photo-irradiation of pyrimidine in NH(3) and H(2)O+NH(3) ices. ASTROBIOLOGY 2012; 12:295-314. [PMID: 22519971 DOI: 10.1089/ast.2011.0726] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Although not yet identified in the interstellar medium (ISM), N-heterocycles including nucleobases-the information subunits of DNA and RNA-are present in carbonaceous chondrites, which indicates that molecules of biological interest can be formed in non-terrestrial environments via abiotic pathways. Recent laboratory experiments and ab initio calculations have already shown that the irradiation of pyrimidine in pure H(2)O ices leads to the formation of a suite of oxidized pyrimidine derivatives, including the nucleobase uracil. In the present work, NH(3):pyrimidine and H(2)O:NH(3):pyrimidine ice mixtures with different relative proportions were irradiated with UV photons under astrophysically relevant conditions. Liquid- and gas-chromatography analysis of the resulting organic residues has led to the detection of the nucleobases uracil and cytosine, as well as other species of prebiotic interest such as urea and small amino acids. The presence of these molecules in organic residues formed under abiotic conditions supports scenarios in which extraterrestrial organics that formed in space and were subsequently delivered to telluric planets via comets and meteorites could have contributed to the inventory of molecules that triggered the first biological reactions on their surfaces.
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Affiliation(s)
- Michel Nuevo
- NASA Ames Research Center, Space Science Division, Moffett Field, California 94035, USA
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Wang T, Bowie JH. Can cytosine, thymine and uracil be formed in interstellar regions? A theoretical study. Org Biomol Chem 2012; 10:652-62. [DOI: 10.1039/c1ob06352a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Affiliation(s)
- Veronica Vaida
- Department of Chemistry and Biochemistry, CIRES, University of Colorado, Boulder, Colorado 80309-0215, USA
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