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Hamilton BW, Kroonblawd MP, Strachan A. Extemporaneous Mechanochemistry: Shock-Wave-Induced Ultrafast Chemical Reactions Due to Intramolecular Strain Energy. J Phys Chem Lett 2022; 13:6657-6663. [PMID: 35838665 DOI: 10.1021/acs.jpclett.2c01798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Regions of energy localization referred to as hotspots are known to govern shock initiation and the run-to-detonation in energetic materials. Mounting computational evidence points to accelerated chemistry in hotspots from large intramolecular strains induced via the interactions between the shock wave and microstructure. However, definite evidence mapping intramolecular strain to accelerated or altered chemical reactions has so far been elusive. From a large-scale reactive molecular dynamics simulation of the energetic material 1,3,5-triamino-2,4,6-trinitrobenzene, we map decomposition kinetics to molecular temperature and intramolecular strain energy prior to reaction. Both temperature and intramolecular strain are shown to accelerate chemical kinetics. A detailed analysis of the atomistic trajectory shows that intramolecular strain can induce a mechanochemical alteration of decomposition mechanisms. The results in this paper could inform continuum-level chemistry models to account for a wide range of mechanochemical effects.
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Affiliation(s)
- Brenden W Hamilton
- School of Materials Engineering and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907, United States
| | - Matthew P Kroonblawd
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Alejandro Strachan
- School of Materials Engineering and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907, United States
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2
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Amante G, Sponer JE, Sponer J, Saija F, Cassone G. A Computational Quantum-Based Perspective on the Molecular Origins of Life's Building Blocks. ENTROPY (BASEL, SWITZERLAND) 2022; 24:1012. [PMID: 35892991 PMCID: PMC9394336 DOI: 10.3390/e24081012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/25/2022] [Accepted: 07/18/2022] [Indexed: 12/04/2022]
Abstract
The search for the chemical origins of life represents a long-standing and continuously debated enigma. Despite its exceptional complexity, in the last decades the field has experienced a revival, also owing to the exponential growth of the computing power allowing for efficiently simulating the behavior of matter-including its quantum nature-under disparate conditions found, e.g., on the primordial Earth and on Earth-like planetary systems (i.e., exoplanets). In this minireview, we focus on some advanced computational methods capable of efficiently solving the Schro¨dinger equation at different levels of approximation (i.e., density functional theory)-such as ab initio molecular dynamics-and which are capable to realistically simulate the behavior of matter under the action of energy sources available in prebiotic contexts. In addition, recently developed metadynamics methods coupled with first-principles simulations are here reviewed and exploited to answer to old enigmas and to propose novel scenarios in the exponentially growing research field embedding the study of the chemical origins of life.
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Affiliation(s)
- Gabriele Amante
- Department of Mathematical and Computer Science, Physical Sciences and Earth Sciences, Università degli Studi di Messina, V. le F. Stagno d’Alcontres 31, 98166 Messina, Italy;
| | - Judit E. Sponer
- Institute of Biophysics of the Czech Academy of Sciences (IBP-CAS), Kràlovopolskà 135, 61265 Brno, Czech Republic; (J.E.S.); (J.S.)
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences (IBP-CAS), Kràlovopolskà 135, 61265 Brno, Czech Republic; (J.E.S.); (J.S.)
| | - Franz Saija
- Institute for Physical-Chemical Processes, National Research Council of Italy (IPCF-CNR), V. le F. Stagno d’Alcontres 37, 98158 Messina, Italy
| | - Giuseppe Cassone
- Institute for Physical-Chemical Processes, National Research Council of Italy (IPCF-CNR), V. le F. Stagno d’Alcontres 37, 98158 Messina, Italy
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3
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New Signatures of Bio-Molecular Complexity in the Hypervelocity Impact Ejecta of Icy Moon Analogues. Life (Basel) 2022; 12:life12040508. [PMID: 35454999 PMCID: PMC9026792 DOI: 10.3390/life12040508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 01/05/2023] Open
Abstract
Impact delivery of prebiotic compounds to the early Earth from an impacting comet is considered to be one of the possible ways by which prebiotic molecules arrived on the Earth. Given the ubiquity of impact features observed on all planetary bodies, bolide impacts may be a common source of organics on other planetary bodies both in our own and other solar systems. Biomolecules such as amino acids have been detected on comets and are known to be synthesized due to impact-induced shock processing. Here we report the results of a set of hypervelocity impact experiments where we shocked icy mixtures of amino acids mimicking the icy surface of planetary bodies with high-speed projectiles using a two-stage light gas gun and analyzed the ejecta material after impact. Electron microscopic observations of the ejecta have shown the presence of macroscale structures with long polypeptide chains revealed from LCMS analysis. These results suggest a pathway in which impact on cometary ices containing building blocks of life can lead to the synthesis of material architectures that could have played a role in the emergence of life on the Earth and which may be applied to other planetary bodies as well.
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4
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Three-dimensional complex architectures observed in shock processed amino acid mixtures. EXPERIMENTAL RESULTS 2022. [DOI: 10.1017/exp.2021.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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5
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Chance and Necessity in the Evolution of Matter to Life: A Comprehensive Hypothesis. Symmetry (Basel) 2021. [DOI: 10.3390/sym13101918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Specialists in several branches of life sciences are trying to solve, piece by piece, the immensely complex puzzle of the origin of life. Some parts of the puzzle seem to appear with a rather high degree of clarity, while others remain totally obscure. We cannot be sure that life emerged only on our Earth, but we believe that the presence of large amounts of water in its liquid state is absolutely essential for the emergence and evolution of living matter. We can also assume that the latter exploits everywhere the same light elements, mainly C, H, O, N, S, and P, and somehow manipulates the same simple monomeric and polymeric organic compounds, such as alpha-amino acids, carbohydrates, nucleic bases, and surface-active carboxylic acids. The author contributes to the field by stating that all fundamental particles of our matter are “homochiral” and predominantly produce in an absolute asymmetric synthesis amino acids of L-configuration and carbohydrates of D-series. Another important point is that free atmospheric oxygen mainly stems from the photolysis of water molecules by cosmic irradiation and is not necessarily bound to living organisms on the planet.
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6
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Fárník M, Fedor J, Kočišek J, Lengyel J, Pluhařová E, Poterya V, Pysanenko A. Pickup and reactions of molecules on clusters relevant for atmospheric and interstellar processes. Phys Chem Chem Phys 2021; 23:3195-3213. [PMID: 33524089 DOI: 10.1039/d0cp06127a] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In this perspective, we review experiments with molecules picked up on large clusters in molecular beams with the focus on the processes in atmospheric and interstellar chemistry. First, we concentrate on the pickup itself, and we discuss the pickup cross sections. We measure the uptake of different atmospheric molecules on mixed nitric acid-water clusters and determine the accommodation coefficients relevant for aerosol formation in the Earth's atmosphere. Then the coagulation of the adsorbed molecules on the clusters is investigated. In the second part of this perspective, we review examples of different processes triggered by UV-photons or electrons in the clusters with embedded molecules. We start with the photodissociation of hydrogen halides and Freon CF2Cl2 on ice nanoparticles in connection with the polar stratospheric ozone depletion. Next, we mention reactions following the excitation and ionization of the molecules adsorbed on clusters. The first ionization-triggered reaction observed between two different molecules picked up on the cluster was the proton transfer between methanol and formic acid deposited on large argon clusters. Finally, negative ion reactions after slow electron attachment are illustrated by two examples: mixed nitric acid-water clusters, and hydrogen peroxide deposited on large ArN and (H2O)N clusters. The selected examples are discussed from the perspective of the atmospheric and interstellar chemistry, and several future directions are proposed.
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Affiliation(s)
- Michal Fárník
- J. Heyrovský Institute of Physical Chemistry, v.v.i., The Czech Academy of Sciences, Dolejškova 2155/3, 182 23 Prague, Czech Republic.
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7
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Prebiotic chemistry and origins of life research with atomistic computer simulations. Phys Life Rev 2020; 34-35:105-135. [DOI: 10.1016/j.plrev.2018.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/10/2018] [Indexed: 02/02/2023]
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8
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Singh SV, Vishakantaiah J, Meka JK, Sivaprahasam V, Chandrasekaran V, Thombre R, Thiruvenkatam V, Mallya A, Rajasekhar BN, Muruganantham M, Datey A, Hill H, Bhardwaj A, Jagadeesh G, Reddy KPJ, Mason NJ, Sivaraman B. Shock Processing of Amino Acids Leading to Complex Structures-Implications to the Origin of Life. Molecules 2020; 25:molecules25235634. [PMID: 33265981 PMCID: PMC7730583 DOI: 10.3390/molecules25235634] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/15/2020] [Accepted: 11/18/2020] [Indexed: 11/30/2022] Open
Abstract
The building blocks of life, amino acids, are believed to have been synthesized in the extreme conditions that prevail in space, starting from simple molecules containing hydrogen, carbon, oxygen and nitrogen. However, the fate and role of amino acids when they are subjected to similar processes largely remain unexplored. Here we report, for the first time, that shock processed amino acids tend to form complex agglomerate structures. Such structures are formed on timescales of about 2 ms due to impact induced shock heating and subsequent cooling. This discovery suggests that the building blocks of life could have self-assembled not just on Earth but on other planetary bodies as a result of impact events. Our study also provides further experimental evidence for the ‘threads’ observed in meteorites being due to assemblages of (bio)molecules arising from impact-induced shocks.
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Affiliation(s)
- Surendra V. Singh
- Atomic Molecular and Optical Physics Division, Physical Research Laboratory, Ahmedabad 380009, India; (S.V.S.); (J.K.M.)
- Discipline of Physics, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India
| | - Jayaram Vishakantaiah
- Solid State & Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India;
| | - Jaya K. Meka
- Atomic Molecular and Optical Physics Division, Physical Research Laboratory, Ahmedabad 380009, India; (S.V.S.); (J.K.M.)
| | - Vijayan Sivaprahasam
- Planetary Science Division, Physical Research Laboratory, Ahmedabad 380009, India; (V.S.); (A.B.)
| | | | - Rebecca Thombre
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Pune 411005, India;
| | - Vijay Thiruvenkatam
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India;
| | - Ambresh Mallya
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India;
| | | | | | - Akshay Datey
- Department of Aerospace Engineering, Indian Institute of Science, Bangalore 560012, India; (A.D.); (G.J.); (K.P.J.R.)
| | - Hugh Hill
- Physical Sciences, International Space University, 67400 Illkirch-Graffenstaden, France;
| | - Anil Bhardwaj
- Planetary Science Division, Physical Research Laboratory, Ahmedabad 380009, India; (V.S.); (A.B.)
| | - Gopalan Jagadeesh
- Department of Aerospace Engineering, Indian Institute of Science, Bangalore 560012, India; (A.D.); (G.J.); (K.P.J.R.)
| | - Kalidevapura P. J. Reddy
- Department of Aerospace Engineering, Indian Institute of Science, Bangalore 560012, India; (A.D.); (G.J.); (K.P.J.R.)
| | - Nigel J. Mason
- School of Physical Sciences, University of Kent, Canterbury CT2 7NZ, UK
- Correspondence: (N.J.M.); (B.S.)
| | - Bhalamurugan Sivaraman
- Atomic Molecular and Optical Physics Division, Physical Research Laboratory, Ahmedabad 380009, India; (S.V.S.); (J.K.M.)
- Correspondence: (N.J.M.); (B.S.)
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9
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Steele BA, Goldman N, Kuo IFW, Kroonblawd MP. Mechanochemical synthesis of glycine oligomers in a virtual rotational diamond anvil cell. Chem Sci 2020; 11:7760-7771. [PMID: 34123069 PMCID: PMC8163322 DOI: 10.1039/d0sc00755b] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 07/11/2020] [Indexed: 01/18/2023] Open
Abstract
Mechanochemistry of glycine under compression and shear at room temperature is predicted using quantum-based molecular dynamics (QMD) and a simulation design based on rotational diamond anvil cell (RDAC) experiments. Ensembles of high throughput semiempirical density functional tight binding (DFTB) simulations are used to identify chemical trends and bounds for glycine chemistry during rapid shear under compressive loads of up to 15.6 GPa. Significant chemistry is found to occur during compressive shear above 10 GPa. Recovered products consist of small molecules such as water, structural analogs to glycine, heterocyclic molecules, large oligomers, and polypeptides including the simplest polypeptide glycylglycine at up to 4% mass fraction. The population and size of oligomers generally increases with pressure. A number of oligomeric polypeptide precursors and intermediates are also identified that consist of two or three glycine monomers linked together through C-C, C-N, and/or C-O bridges. Even larger oligomers also form that contain peptide C-N bonds and exhibit branched structures. Many of the product molecules exhibit one or more chiral centers. Our simulations demonstrate that athermal mechanical compressive shearing of glycine is a plausible prebiotic route to forming polypeptides.
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Affiliation(s)
- Brad A Steele
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory Livermore CA 94550 USA
| | - Nir Goldman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory Livermore CA 94550 USA
| | - I-Feng W Kuo
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory Livermore CA 94550 USA
| | - Matthew P Kroonblawd
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory Livermore CA 94550 USA
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10
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Saladino R. Computational investigation of the primordial soup: Comment on "Prebiotic chemistry and origin of life research with atomistic computer simulations" by A. Pérez-Villa, F. Pietrucci, and A. M. Saitta. Phys Life Rev 2020; 34-35:149-152. [PMID: 31974057 DOI: 10.1016/j.plrev.2020.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/10/2020] [Indexed: 10/25/2022]
Affiliation(s)
- Raffaele Saladino
- Department of Ecological and Biological Sciences, Via S. Camillo de Lellis, University of Tuscia, 01100, Viterbo, Italy.
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11
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Kroonblawd MP, Lindsey RK, Goldman N. Synthesis of functionalized nitrogen-containing polycyclic aromatic hydrocarbons and other prebiotic compounds in impacting glycine solutions. Chem Sci 2019; 10:6091-6098. [PMID: 31360414 PMCID: PMC6585877 DOI: 10.1039/c9sc00155g] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/19/2019] [Indexed: 01/09/2023] Open
Abstract
Proteinogenic amino acids can be produced on or delivered to a planet via impacting abiotic sources and consequently were likely present before the emergence of life on Earth. However, the role that these materials played in prebiotic scenarios remains an open question, in part because little is known about the survivability and reactivity of astrophysical organic compounds upon impact with a planetary surface. To this end, we use a force-matched semi-empirical quantum simulation method to study impacts of aqueous proteinogenic amino acids at conditions reaching 48 GPa and 3000 K. Here, we probe a relatively unstudied mechanism for prebiotic synthesis where sudden heating and pressurization causes condensation of complex carbon-rich structures from mixtures of glycine, the simplest protein-forming amino acid. These carbon-containing clusters are stable on short timescales and undergo a fundamental structural transition upon expansion and cooling from predominantly sp3-bonded tetrahedral-like moieties to those that are more sp2-bonded and planar. The recovered sp2-bonded structures include large nitrogen containing polycyclic aromatic hydrocarbons (NPAHs) with a number of different functional groups and embedded bonded regions akin to oligo-peptides. A number of small organic molecules with prebiotic relevance are also predicted to form. This work presents an alternate route to gas-phase synthesis for the formation of NPAHs of high complexity and highlights the significance of both the thermodynamic path and local chemical self-assembly in forming prebiotic species during shock synthesis. Our results help determine the role of comets and other celestial bodies in both the delivery and synthesis of potentially significant life building compounds on early Earth.
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Affiliation(s)
- Matthew P Kroonblawd
- Physical and Life Sciences Directorate , Lawrence Livermore National Laboratory , Livermore , CA 94550 , USA .
| | - Rebecca K Lindsey
- Physical and Life Sciences Directorate , Lawrence Livermore National Laboratory , Livermore , CA 94550 , USA .
| | - Nir Goldman
- Physical and Life Sciences Directorate , Lawrence Livermore National Laboratory , Livermore , CA 94550 , USA .
- Department of Chemical Engineering , University of California , Davis , California 95616 , USA
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12
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Shimamura K, Shimojo F, Nakano A, Tanaka S. Ab initio molecular dynamics study of prebiotic production processes of organic compounds at meteorite impacts on ocean. J Comput Chem 2019; 40:349-359. [PMID: 30306615 DOI: 10.1002/jcc.25606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/03/2018] [Accepted: 09/04/2018] [Indexed: 02/05/2023]
Abstract
Recent experiments concerning prebiotic materials syntheses suggest that the iron-bearing meteorite impacts on ocean during Late Heavy Bombardment provided abundant organic compounds associated with biomolecules such as amino acids and nucleobases. However, the molecular mechanism of a series of chemical reactions to produce such compounds is not well understood. In this study, we simulate the shock compression state of a meteorite impact for a model system composed of CO2 , H2 O, and metallic iron slab by ab initio molecular dynamics combined with multiscale shock technique, and clarify possible elementary reaction processes up to production of organic compounds. The reactions included not only pathways similar to the Fischer-Tropsch process known as an important hydrocarbon synthesis in many planetary processes but also those resulting in production of a carboxylic acid. It is also found that bicarbonate ions formed from CO2 and H2 O participated in some forms in most of these observed elementary reaction processes. These findings would deepen the understanding of the full range of chemical reactions that could occur in the meteorite impact events. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Kohei Shimamura
- Graduate School of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501, Japan
| | - Fuyuki Shimojo
- Department of Physics, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Aiichiro Nakano
- Collaboratory for Advanced Computing and Simulations, Department of Physics & Astronomy, Department of Computer Science, Department of Chemical Engineering & Materials Science, and Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089-0242
| | - Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501, Japan
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13
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Kroonblawd MP, Pietrucci F, Saitta AM, Goldman N. Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model. J Chem Theory Comput 2018. [PMID: 29543444 DOI: 10.1021/acs.jctc.7b01266] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTB model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experimental observations of reaction energetics. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate for glycine condensation. Predictive accuracy of force-matched DFTB is demonstrated by direct comparison to DFT, with the two approaches yielding surfaces with large regions that differ by only a few kcal mol-1.
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Affiliation(s)
- Matthew P Kroonblawd
- Physical and Life Sciences Directorate , Lawrence Livermore National Laboratory , Livermore , California 94550 , United States
| | - Fabio Pietrucci
- Sorbonne Université, Muséum National d'Histoire Naturelle , UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC , F-75005 Paris , France
| | - Antonino Marco Saitta
- Sorbonne Université, Muséum National d'Histoire Naturelle , UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC , F-75005 Paris , France
| | - Nir Goldman
- Physical and Life Sciences Directorate , Lawrence Livermore National Laboratory , Livermore , California 94550 , United States.,Department of Chemical Engineering , University of California , Davis , California 95616 , United States
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14
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Consequences of EPR–Proton Qubits Populating DNA. ADVANCES IN QUANTUM CHEMISTRY 2018. [DOI: 10.1016/bs.aiq.2017.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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15
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Shimamura K, Shimojo F, Nakano A, Tanaka S. Meteorite impacts on ancient oceans opened up multiple NH 3 production pathways. Phys Chem Chem Phys 2017; 19:11655-11667. [PMID: 28435960 DOI: 10.1039/c7cp00870h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A recent series of shock experiments by Nakazawa et al. starting in 2005 (e.g. [Nakazawa et al., Earth Planet. Sci. Lett., 2005, 235, 356]) suggested that meteorite impacts on ancient oceans would have yielded a considerable amount of NH3 to the early Earth from atmospheric N2 and oceanic H2O through reduction by meteoritic iron. To clarify the mechanisms, we imitated the impact events by performing multi-scale shock technique-based ab initio molecular dynamics in the framework of density functional theory in combination with multi-scale shock technique (MSST) simulations. Our previous simulations with impact energies close to that of the experiments revealed picosecond-order rapid NH3 production during shock compression [Shimamura et al., Sci. Rep., 2016, 6, 38952]. It was also shown that the reduction of N2 took place with an associative mechanism as seen in the catalysis of nitrogenase enzymes. In this study, we performed an MSST-AIMD simulation to investigate the production by meteorite impacts with higher energies, which are closer to the expected values on the early Earth. It was found that the amount of NH3 produced further increased. We also found that the increased NH3 production is due to the emergence of multiple reaction mechanisms at increased impact energies. We elucidated that the reduction of N2 was not only attributed to the associative mechanism but also to a dissociative mechanism as seen in the Haber-Bosch process and to a mechanism through a hydrazinium ion. The emergence of these multiple production mechanisms capable of providing a large amount of NH3 would support the suggestions from recent experiments much more strongly than was previously believed, i.e., shock-induced NH3 production played a key role in the origin of life on Earth.
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Affiliation(s)
- Kohei Shimamura
- Graduate School of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan.
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16
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Pysanenko A, Kočišek J, Nachtigallová D, Poterya V, Fárník M. Clustering of Uracil Molecules on Ice Nanoparticles. J Phys Chem A 2017; 121:1069-1077. [PMID: 28098464 DOI: 10.1021/acs.jpca.6b12594] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We generate a molecular beam of ice nanoparticles (H2O)N, N̅ ≈ 130-220, which picks up several individual gas phase uracil (U) or 5-bromouracil (BrU) molecules. The mass spectra of the doped nanoparticles prove that the uracil and bromouracil molecules coagulate to clusters on the ice nanoparticles. Calculations of U and BrU monomers and dimers on the ice nanoparticles provide theoretical support for the cluster formation. The (U)mH+ and (BrU)mH+ intensity dependencies on m extracted from the mass spectra suggest a smaller tendency of BrU to coagulate compared to U, which is substantiated by a lower mobility of bromouracil on the ice surface. The hydrated Um·(H2O)nH+ series are also reported and discussed. On the basis of comparison with the previous experiments, we suggest that the observed propensity for aggregation on ice nanoparticles is a more general trend for biomolecules forming strong hydrogen bonds. This, together with their mobility, leads to their coagulation on ice nanoparticles which is an important aspect for astrochemistry.
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Affiliation(s)
- Andriy Pysanenko
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences , Dolejškova 3, 182 23 Prague, Czech Republic
| | - Jaroslav Kočišek
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences , Dolejškova 3, 182 23 Prague, Czech Republic
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences , Flemingovo nám. 2, 160610 Prague 6, Czech Republic
| | - Viktoriya Poterya
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences , Dolejškova 3, 182 23 Prague, Czech Republic
| | - Michal Fárník
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences , Dolejškova 3, 182 23 Prague, Czech Republic
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Koziol L, Fried LE, Goldman N. Using Force Matching To Determine Reactive Force Fields for Water under Extreme Thermodynamic Conditions. J Chem Theory Comput 2016; 13:135-146. [DOI: 10.1021/acs.jctc.6b00707] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lucas Koziol
- Physical and Life Sciences
Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Laurence E. Fried
- Physical and Life Sciences
Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Nir Goldman
- Physical and Life Sciences
Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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Shimamura K, Shimojo F, Nakano A, Tanaka S. Meteorite Impact-Induced Rapid NH 3 Production on Early Earth: Ab Initio Molecular Dynamics Simulation. Sci Rep 2016; 6:38953. [PMID: 27966594 PMCID: PMC5155216 DOI: 10.1038/srep38953] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/15/2016] [Indexed: 01/05/2023] Open
Abstract
NH3 is an essential molecule as a nitrogen source for prebiotic amino acid syntheses such as the Strecker reaction. Previous shock experiments demonstrated that meteorite impacts on ancient oceans would have provided a considerable amount of NH3 from atmospheric N2 and oceanic H2O through reduction by meteoritic iron. However, specific production mechanisms remain unclear, and impact velocities employed in the experiments were substantially lower than typical impact velocities of meteorites on the early Earth. Here, to investigate the issues from the atomistic viewpoint, we performed multi-scale shock technique-based ab initio molecular dynamics simulations. The results revealed a rapid production of NH3 within several picoseconds after the shock, indicating that shocks with greater impact velocities would provide further increase in the yield of NH3. Meanwhile, the picosecond-order production makes one expect that the important nitrogen source precursors of amino acids were obtained immediately after the impact. It was also observed that the reduction of N2 proceeded according to an associative mechanism, rather than a dissociative mechanism as in the Haber-Bosch process.
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Affiliation(s)
- Kohei Shimamura
- Graduate School of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Fuyuki Shimojo
- Department of Physics, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Aiichiro Nakano
- Collaboratory for Advanced Computing and Simulations, Department of Physics &Astronomy, Department of Computer Science, Department of Chemical Engineering &Materials Science, and Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0242, USA
| | - Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
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19
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Rubovič P, Pysanenko A, Lengyel J, Nachtigallová D, Fárník M. Biomolecule Analogues 2-Hydroxypyridine and 2-Pyridone Base Pairing on Ice Nanoparticles. J Phys Chem A 2016; 120:4720-30. [PMID: 26785038 DOI: 10.1021/acs.jpca.5b11359] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ice nanoparticles (H2O)N, N ≈ 450 generated in a molecular beam experiment pick up individual gas phase molecules of 2-hydroxypyridine and 2-pyridone (HP) evaporated in a pickup cell at temperatures between 298 and 343 K. The mass spectra of the doped nanoparticles show evidence for generation of clusters of adsorbed molecules (HP)n up to n = 8. The clusters are ionized either by 70 eV electrons or by two photons at 315 nm (3.94 eV). The two ionization methods yield different spectra, and their comparison provides an insight into the neutral cluster composition, ionization and intracluster ion-molecule reactions, and cluster fragmentation. Quite a few molecules were reported not to coagulate on ice nanoparticles previously. The (HP)n cluster generation on ice nanoparticles represents the first evidence for coagulating of molecules and cluster formation on free ice nanoparticles. For comparison, we investigate the coagulation of HP molecules picked up on large clusters ArN, N ≈ 205, and also (HP)n clusters generated in supersonic expansions with Ar buffer gas. This comparison points to a propensity for the (HP)2 dimer generation on ice nanoparticles. This shows the feasibility of base pairing for model of biological molecules on free ice nanoparticles. This result is important for hypotheses of the biomolecule synthesis on ice grains in the space. We support our findings by theoretical calculations that show, among others, the HP dimer structures on water clusters.
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Affiliation(s)
- Peter Rubovič
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
| | - Andriy Pysanenko
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
| | - Jozef Lengyel
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Michal Fárník
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
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20
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Goldman N, Fried LE, Koziol L. Using Force-Matched Potentials To Improve the Accuracy of Density Functional Tight Binding for Reactive Conditions. J Chem Theory Comput 2015; 11:4530-5. [DOI: 10.1021/acs.jctc.5b00742] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nir Goldman
- Physical
and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Laurence E. Fried
- Physical
and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Lucas Koziol
- Physical
and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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21
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Koziol L, Goldman N. PREBIOTIC HYDROCARBON SYNTHESIS IN IMPACTING REDUCED ASTROPHYSICAL ICY MIXTURES. ACTA ACUST UNITED AC 2015. [DOI: 10.1088/0004-637x/803/2/91] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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22
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Goldman N. Multi-center semi-empirical quantum models for carbon under extreme thermodynamic conditions. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.11.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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23
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Ribó JM, Blanco C, Crusats J, El-Hachemi Z, Hochberg D, Moyano A. Absolute Asymmetric Synthesis in Enantioselective Autocatalytic Reaction Networks: Theoretical Games, Speculations on Chemical Evolution and Perhaps a Synthetic Option. Chemistry 2014; 20:17250-71. [DOI: 10.1002/chem.201404534] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Indexed: 11/07/2022]
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24
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Ileri N, Goldman N. Graphene and nano-diamond synthesis in expansions of molten liquid carbon. J Chem Phys 2014; 141:164709. [PMID: 25362334 DOI: 10.1063/1.4899071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Despite their widespread use in high-pressure experiments, little is known about the physical and chemical properties of carbon-containing materials as they expand and cool to ambient conditions. As a result, interpretation of experiments can rely on use of unconstrained models with poor accuracy for the ensuing equation of state properties and final chemical products. To this end, we use quantum simulations to study the free expansion and cooling of carbon from metallic liquid states achieved during shock compression. Expansions from three different sets of shock conditions yielded of a variety of chain and ring structures. We then quantify the relative amounts of graphite-like and diamond-like particles formed during cooling and equilibration. We observe that for all cases, graphene sheets are the majority product formed with more extreme initial conditions producing increasingly larger amounts of diamond particles. Our results can address key needs for future meso-scale models of experiments, where knowledge of material properties and chemical end products can have a pronounced effect on interpreting experimental observables.
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Affiliation(s)
- Nazar Ileri
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Nir Goldman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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25
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Abstract
The celebrated Miller experiments reported on the spontaneous formation of amino acids from a mixture of simple molecules reacting under an electric discharge, giving birth to the research field of prebiotic chemistry. However, the chemical reactions involved in those experiments have never been studied at the atomic level. Here we report on, to our knowledge, the first ab initio computer simulations of Miller-like experiments in the condensed phase. Our study, based on the recent method of treatment of aqueous systems under electric fields and on metadynamics analysis of chemical reactions, shows that glycine spontaneously forms from mixtures of simple molecules once an electric field is switched on and identifies formic acid and formamide as key intermediate products of the early steps of the Miller reactions, and the crucible of formation of complex biological molecules.
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26
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Srinivasan SG, Goldman N, Tamblyn I, Hamel S, Gaus M. A density functional tight binding model with an extended basis set and three-body repulsion for hydrogen under extreme thermodynamic conditions. J Phys Chem A 2014; 118:5520-8. [PMID: 24960065 DOI: 10.1021/jp5036713] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a new DFTB-p3b density functional tight binding model for hydrogen at extremely high pressures and temperatures, which includes a polarizable basis set (p) and a three-body environmentally dependent repulsive potential (3b). We find that use of an extended basis set is necessary under dissociated liquid conditions to account for the substantial p-orbital character of the electronic states around the Fermi energy. The repulsive energy is determined through comparison to cold curve pressures computed from density functional theory (DFT) for the hexagonal close-packed solid, as well as pressures from thermally equilibrated DFT-MD simulations of the liquid phase. In particular, we observe improved agreement in our DFTB-p3b model with previous theoretical and experimental results for the shock Hugoniot of hydrogen up to 100 GPa and 25000 K, compared to a standard DFTB model using pairwise interactions and an s-orbital basis set, only. The DFTB-p3b approach discussed here provides a general method to extend the DFTB method for a wide variety of materials over a significantly larger range of thermodynamic conditions than previously possible.
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Affiliation(s)
- Sriram Goverapet Srinivasan
- Department of Mechanical and Nuclear Engineering, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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27
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Goldman N, Bastea S. Nitrogen Oxides As a Chemistry Trap in Detonating Oxygen-Rich Materials. J Phys Chem A 2014; 118:2897-903. [DOI: 10.1021/jp501455z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nir Goldman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue L-288, Livermore, California 94550, United States
| | - Sorin Bastea
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue L-288, Livermore, California 94550, United States
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28
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Goldman N, Tamblyn I. Reply to “Comment on ‘Prebiotic Chemistry Within a Simple Impacting Icy Mixture’”. J Phys Chem A 2013; 117:14295-7. [DOI: 10.1021/jp411584g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nir Goldman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Isaac Tamblyn
- Department of Physics, University of Ontario Institute of Technology, Oshawa, Ontario L1H 7K4, Canada
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29
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Ross DS. Comment on "prebiotic chemistry within a simple impacting icy mixture". J Phys Chem A 2013; 117:14293-4. [PMID: 24224564 DOI: 10.1021/jp409735g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- David S Ross
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
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