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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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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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Computational Analysis of a Prebiotic Amino Acid Synthesis with Reference to Extant Codon-Amino Acid Relationships. Life (Basel) 2021; 11:life11121343. [PMID: 34947874 PMCID: PMC8707928 DOI: 10.3390/life11121343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/26/2021] [Accepted: 11/30/2021] [Indexed: 11/28/2022] Open
Abstract
Novel density functional theory calculations are presented regarding a mechanism for prebiotic amino acid synthesis from alpha-keto acids that was suggested to happen via catalysis by dinucleotide species. Our results were analysed with comparison to the original hypothesis (Copley et al., PNAS, 2005, 102, 4442–4447). It was shown that the keto acid–dinucleotide hypothesis for possible prebiotic amino acid synthesis was plausible based on an initial computational analysis, and details of the structures for the intermediates and transition states showed that there was wide scope for interactions between the keto acid and dinucleotide moieties that could affect the free energy profiles and lead to the required proto-metabolic selectivity.
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Cassone G, Saija F. Interstellar chemical reactions toward the synthesis of the life's building blocks: Comment on "Insoluble organic matter in chondrites: Archetypal melanin-like PAH-based multifunctionality at the origin of life?" by M. d'Ischia et al. Phys Life Rev 2021; 38:140-142. [PMID: 34049816 DOI: 10.1016/j.plrev.2021.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 05/13/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Giuseppe Cassone
- CNR - Institute for Chemical-Physical Processes (IPCF), Viale Ferdinando Stagno d'Alcontres 37, I-98158 Messina, Italy
| | - Franz Saija
- CNR - Institute for Chemical-Physical Processes (IPCF), Viale Ferdinando Stagno d'Alcontres 37, I-98158 Messina, Italy.
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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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