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Liao Q, Xie P, Wang Z. Enantiodetermining processes in the synthesis of alanine, serine, and isovaline. Phys Chem Chem Phys 2023; 25:28829-28834. [PMID: 37853775 DOI: 10.1039/d3cp03212d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
In this study, quantum chemical calculations were used to explore the synthesis of three chiral α-amino acids, specifically alanine, serine, and isovaline, from reactants found in interstellar space. Our focus is on the crucial step in the synthesis pathway that determines the chirality of the amino acids. The results indicate that in the case of alanine, the determination of enantiomer is primarily influenced by the direction of the collision of molecules or functional groups, which leads to the formation of a chirality center in a crucial intermediate. However, contrary to chemical expectations, the enantiodetermining/enantioselection step for serine and isovaline synthesis occurs prior to the creation of a chirality center.
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Affiliation(s)
- Qingli Liao
- School of Physical Science and Technology, Guangxi University, Nanning 530004, China.
| | - Peng Xie
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Zhao Wang
- School of Physical Science and Technology, Guangxi University, Nanning 530004, China.
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Sato A, Shoji M, Watanabe N, Boero M, Shigeta Y, Umemura M. Origin of Homochirality in Amino Acids Induced by Lyman-α Irradiation in the Early Stage of the Milky Way. ASTROBIOLOGY 2023; 23:1019-1026. [PMID: 37737584 DOI: 10.1089/ast.2022.0140] [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: 09/23/2023]
Abstract
The enantiomeric excess (ee) of l-form amino acids found in the Murchison meteorite poses some issues about the cosmic origin of their chirality. Circular dichroism (CD) spectra of amino acids in the far-ultraviolet (FUV) at around 6.8 eV (182 nm) indicate that the circularly polarized light can induce ee through photochemical reactions. Here, we resort to ab initio calculations to extract the CD spectra up to the vacuum-ultraviolet (VUV) region (∼11 eV), and we propose a novel equation to compute the ee applicable to a wider range of light frequency than what is available to date. This allows us to show that the strength of the induced ee (|ee|) in the 10 eV VUV region is comparable to the one in the 6.8 eV FUV region. This feature is common for some key amino acids (alanine, 2-aminobutyric acid, and valine). In space, intense Lyman-α (Lyα) light of 10.2 eV is emitted from star forming regions. This study provides a theoretical basis that Lyα emitter from an early starburst in the Milky Way plays a crucial role in initiating the ee of amino acids.
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Affiliation(s)
- Akimasa Sato
- Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Japan
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
- JST-PRESTO, Kawaguchi, Japan
| | - Natsuki Watanabe
- Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Japan
| | - Mauro Boero
- Institut de Physique et Chimie des Matériaux de Strasbourg, CNRS, UMR 7504, University of Strasbourg, Strasbourg, France
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Masayuki Umemura
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
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Hori Y, Nakamura H, Sakawa T, Watanabe N, Kayanuma M, Shoji M, Umemura M, Shigeta Y. Theoretical Investigation into a Possibility of Formation of Propylene Oxide Homochirality in Space. ASTROBIOLOGY 2022; 22:1330-1336. [PMID: 36067332 PMCID: PMC9618371 DOI: 10.1089/ast.2022.0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
The preferential synthesis or destruction of a single enantiomer by ultraviolet circularly polarized light (UV-CPL) has been proposed as a possible triggering mechanism for the extraterrestrial origin of homochirality. Herein, we investigate the photoabsorption property of propylene oxide (c-C3H6O) for UV-CPL in the Lyman-α region. Our calculations show that c-C3H6O was produced by CH3+ and CH3CH(OH)CH3 or C3H7• and O (triplet). The computed electronic circular dichroism spectra show that c-C3H6O and the intermediate (CH3CH(OH)CH2+) could absorb the UV-CPL originating from the Lyman-α emitter spectrum, suggesting that the photolysis of c-C3H6O or CH3CH(OH)CH2+ upon irradiation could induce chiral symmetry breakage.
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Affiliation(s)
- Yuta Hori
- Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | - Honami Nakamura
- Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | - Takahide Sakawa
- Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | - Natsuki Watanabe
- Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | - Megumi Kayanuma
- Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | - Masayuki Umemura
- Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
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Shoji M, Watanabe N, Hori Y, Furuya K, Umemura M, Boero M, Shigeta Y. Comprehensive Search of Stable Isomers of Alanine and Alanine Precursors in Prebiotic Syntheses. ASTROBIOLOGY 2022; 22:1129-1142. [PMID: 35951031 DOI: 10.1089/ast.2022.0011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Enantiomeric excesses of l-amino acids have been detected in meteorites; however, their molecular mechanism and prebiotic syntheses are still a matter of debate. To elucidate the origin of homochirality, alanine and the chiral precursors formed in prebiotic processes were investigated with regard to their stabilities among their isomers by employing the minimum energy principle, namely, the abundancy of a molecule in the interstellar medium is directly correlated to the stability among isomers. To facilitate the search for possible isomers, we developed a new isomer search algorithm, the random connection method, and performed a thorough search for all the stable isomers within a given chemical formula. We found that alanine and most of its precursors are located at higher energy by more than 5.7 kcal mol-1, with respect to the most stable isomer that consists of a linear-chain structure, whereas only the 2-aminopropanenitrile is the most stable isomer among all others possible. The inherent stability of the α-amino nitrile suggests that the 2-aminopropanenitrile is the dominant contribution in the formation of the common enantiomeric excess over α-amino acids.
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Affiliation(s)
- Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
- JST-PRESTO, Kawaguchi, Japan
| | - Natsuki Watanabe
- Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yuta Hori
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Kenji Furuya
- National Astronomical Observatory of Japan, Mitaka, Japan
| | - Masayuki Umemura
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Mauro Boero
- University of Strasbourg, Institut de Physique et Chimie des Matériaux de Strasbourg, CNRS, UMR 7504, Strasbourg, France
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
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Thripati S. Computational studies on the possible formation of glycine via open shell gas-phase chemistry in the interstellar medium. Org Biomol Chem 2022; 20:4189-4203. [PMID: 35543204 DOI: 10.1039/d2ob00407k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Glycine is the simplest proteinogenic amino acid. It has significant astrobiological implications owing to the ongoing investigation for its detection in the interstellar medium (ISM). Hence, a suitable mechanistic elucidation for its formation in the ISM is of current research interest. In the present work, by employing electronic structure calculations [UCCSD(T) and density functional theory (DFT)], various plausible chemical pathways in the gas phase have been examined for the formation of glycine (whose existence has been indirectly proposed in the ISM) and other simple amino acids (yet to be detected in the ISM) from some simpler molecules present in the ISM. This work suggests that step 1: HO-CO (radical) + CH2NH → NHCH2COOH (radical) and step 2a: NHCH2COOH (radical) + H2 → glycine + H (radical) have very small barriers of 0.14 kcal mol-1 and ∼3 kcal mol-1, respectively (easily surmountable at a temperature of ∼50 K under putative interstellar conditions). Hence this should likely be feasible in interstellar gas-phase chemistry. Therefore, HO-CO (radical), CH2NH, and H2 could be the possible precursors for the formation of glycine (subject to the presence of the HO-CO radical). The energetic information related to the interstellar reactions, and how this work takes the putative interstellar conditions into account are presented. This paper also highlights how a reaction found to be unsuitable for interstellar molecular evolution via surface chemistry could nonetheless occur via gas-phase chemistry. Based on our results, this work also recommends detecting three new open-shell molecules, HO-CO radical, NHCH2COOH radical, and NH2CHCOOH radical, in the ISM.
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Affiliation(s)
- Sorakayala Thripati
- Department of Chemistry, Indian Institute of Science Education and Research Tirupati, Andhra Pradesh - 517507, India.
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Rimola A, Balucani N, Ceccarelli C, Ugliengo P. Tracing the Primordial Chemical Life of Glycine: A Review from Quantum Chemical Simulations. Int J Mol Sci 2022; 23:4252. [PMID: 35457069 PMCID: PMC9030215 DOI: 10.3390/ijms23084252] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 12/28/2022] Open
Abstract
Glycine (Gly), NH2CH2COOH, is the simplest amino acid. Although it has not been directly detected in the interstellar gas-phase medium, it has been identified in comets and meteorites, and its synthesis in these environments has been simulated in terrestrial laboratory experiments. Likewise, condensation of Gly to form peptides in scenarios resembling those present in a primordial Earth has been demonstrated experimentally. Thus, Gly is a paradigmatic system for biomolecular building blocks to investigate how they can be synthesized in astrophysical environments, transported and delivered by fragments of asteroids (meteorites, once they land on Earth) and comets (interplanetary dust particles that land on Earth) to the primitive Earth, and there react to form biopolymers as a step towards the emergence of life. Quantum chemical investigations addressing these Gly-related events have been performed, providing fundamental atomic-scale information and quantitative energetic data. However, they are spread in the literature and difficult to harmonize in a consistent way due to different computational chemistry methodologies and model systems. This review aims to collect the work done so far to characterize, at a quantum mechanical level, the chemical life of Gly, i.e., from its synthesis in the interstellar medium up to its polymerization on Earth.
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Affiliation(s)
- Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Catalonia, Spain
| | - Nadia Balucani
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy;
- Osservatorio Astrosico di Arcetri, Largo E. Fermi 5, 50125 Firenze, Italy
| | - Cecilia Ceccarelli
- CNRS, Institut de Planétologie et d’Astrophysique de Grenoble (IPAG), Université Grenoble Alpes, 38000 Grenoble, France;
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Centre, Università degli Studi di Torino, Via P. Giuria 7, 10125 Torino, Italy;
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Jonusas M, Leroux K, Krim L. N + H surface reaction under interstellar conditions: Does the NH/NH2/NH3 distribution depend on N/H ratio? J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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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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Renoud J, Indrajith S, Domaracka A, Rousseau P, Moretto-Capelle P, Huber BA, Champeaux JP. Interaction of hydantoin with solar wind minority ions: O 6+ and He 2. Phys Chem Chem Phys 2020; 22:5785-5796. [PMID: 32105280 DOI: 10.1039/c9cp06230k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The laboratory study of prebiotic molecules interacting with solar wind ions is important to understand their role in the emergence of life in the complex context of the astrochemistry of circumstellar environments. In this work, we present the first study of the interaction of hydantoin (C3N2O2H4, 100 a.m.u.) with solar wind minority multi-charged ions: O6+ at 30 keV and He2+ at 8 keV. The fragmentation mass spectra as well as correlation maps resulting from the interaction are presented and discussed in this paper. Prompt and delayed dissociations from metastable states of the ionized molecule have been observed and the corresponding lifetimes measured. Experimental results are completed by quantum Density Functional Theory (DFT) calculations for energies, structures and dynamics (Internal Reaction Coordinates and Dynamic Reaction Coordinates) of the molecule for its different reachable charge states and the major observed fragmentation pathways. These calculations show that the molecule can only support two charges before spontaneously dissociating in agreement with the experimental observations. Calculations also demonstrate that hydantoin's ring opens after double ionization of the molecule which may enhance its reactivity in the background of biological molecule formation in a cirmcumstellar environment. For the major experimentally observed fragmentations (like 44 a.m.u./56 a.m.u. dissociation), Internal Reaction Coordinate (IRC) calculations were performed pointing out for example the important role of hydrogen transfer in the fragmentation processes.
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Affiliation(s)
- Julie Renoud
- Laboratoire Collisions Agrégats et Réactivité, UMR 5589-CNRS Université Paul Sabatier Toulouse III, 118 Route de Narbonne, 31062 Toulouse Cedex 9, France.
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Yamabe S, Tsuchida N, Yamazaki S. A DFT study of the hydrolysis of hydantoin. INT J CHEM KINET 2019. [DOI: 10.1002/kin.21312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Noriko Tsuchida
- Department of Liberal Arts, Faculty of MedicineSaitama Medical University Saitama Japan
| | - Shoko Yamazaki
- Department of ChemistryNara University of Education Japan
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Kayanuma M, Shoji M, Furuya K, Kamiya K, Aikawa Y, Umemura M, Shigeta Y. First-Principles Study of the Reaction Mechanism of CHO + H on Graphene Surface. J Phys Chem A 2019; 123:5633-5639. [PMID: 31244121 DOI: 10.1021/acs.jpca.9b02345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many organic molecules observed in the interstellar medium are considered to be formed on dust grains and populated into the gas phase. We analyzed the reaction of HCO + H on a graphene surface using ab initio molecular dynamics simulations as a case study of the formation and desorption of organic molecules on interstellar dust particles. During the reactions of chemisorbed CHO (chemisorbed at the C atom) with free H, CO was generated and efficiently desorbed from the surface. These results suggest that the reactions, of which the reactant forms a covalent bond with the surface while the product does not, cause efficient desorption of the product upon reaction. In such reactions a repulsive force between the product and the surface would be generated and accelerate translation of the product in a specific direction. In addition, it was also shown that the branching ratio of the reactions between radical species on the surface would be affected by the form of the adsorption on the surface, e.g., when a free H reacted with the CHO chemisorbed at the C atom, CH2O was not generated.
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Affiliation(s)
- Megumi Kayanuma
- Research Center for Computational Design of Advanced Functional Materials , National Institute of Advanced Industrial Science and Technology , Central 2, 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan.,Center for Computational Sciences , University of Tsukuba , 1-1-1 Tennodai , Tsukuba , Ibaraki 305-8577 , Japan
| | - Mitsuo Shoji
- Center for Computational Sciences , University of Tsukuba , 1-1-1 Tennodai , Tsukuba , Ibaraki 305-8577 , Japan
| | - Kenji Furuya
- Center for Computational Sciences , University of Tsukuba , 1-1-1 Tennodai , Tsukuba , Ibaraki 305-8577 , Japan
| | - Katsumasa Kamiya
- Center for Basic Education and Integrated Learning , Kanagawa Institute of Technology , 1030 Shimoogino , Atsugi , Kanagawa 243-0292 , Japan
| | - Yuri Aikawa
- Department of Astronomy , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan
| | - Masayuki Umemura
- Center for Computational Sciences , University of Tsukuba , 1-1-1 Tennodai , Tsukuba , Ibaraki 305-8577 , Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences , University of Tsukuba , 1-1-1 Tennodai , Tsukuba , Ibaraki 305-8577 , Japan.,Institute of Space and Astronautical Science , Japan Aerospace Exploration Agency , 3-1-1 Yoshinodai, Chuo-ku , Sagamihara , Kanagawa 252-0222 , Japan
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Kolesniková L, León I, Alonso ER, Mata S, Alonso JL. Laser Ablation Assists Cyclization Reactions of Hydantoic Acid: A Proof for the Near-Attack Conformation Theory? J Phys Chem Lett 2019; 10:1325-1330. [PMID: 30807178 PMCID: PMC6534498 DOI: 10.1021/acs.jpclett.9b00208] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In the course of the investigation of the rotational spectrum of prebiotic hydantoic acid by Fourier transform microwave spectroscopy coupled to a laser ablation source in a supersonic expansion, rotational signatures of two cyclic molecules, hydantoin and 2,5-oxazolidinedione, have been unexpectedly observed along with the four most stable conformers of hydantoic acid. Interestingly, two of them presented folded geometric arrangements that might act as precursors in the cyclization reactions assisted by laser ablation. They could play the role of near-attack conformations (NACs) in the framework of the NAC theory for intramolecular reactions. A detailed analysis of the spectrum further revealed the simultaneous formation of other species in the jet, showing that the laser ablation of solid organic precursors constitutes an alternative tool in the generation of new chemical species.
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Affiliation(s)
- Lucie Kolesniková
- Grupo de Espectroscopia Molecular (GEM), Unidad Asociada CSIC, Laboratorios de Espectroscopia y Bioespectroscopia, Edificio Quifima, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Iker León
- Grupo de Espectroscopia Molecular (GEM), Unidad Asociada CSIC, Laboratorios de Espectroscopia y Bioespectroscopia, Edificio Quifima, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Elena R. Alonso
- Grupo de Espectroscopia Molecular (GEM), Unidad Asociada CSIC, Laboratorios de Espectroscopia y Bioespectroscopia, Edificio Quifima, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Santiago Mata
- Grupo de Espectroscopia Molecular (GEM), Unidad Asociada CSIC, Laboratorios de Espectroscopia y Bioespectroscopia, Edificio Quifima, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Jose L. Alonso
- Grupo de Espectroscopia Molecular (GEM), Unidad Asociada CSIC, Laboratorios de Espectroscopia y Bioespectroscopia, Edificio Quifima, Universidad de Valladolid, 47011 Valladolid, Spain
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