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Cruz-Simbron RL, Picasso G, Cerda-Hernández J. Amino acid chiral amplification using Monte Carlo dynamic. J Chem Phys 2024; 160:084502. [PMID: 38407289 DOI: 10.1063/5.0190089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 01/21/2024] [Indexed: 02/27/2024] Open
Abstract
This study investigates the stability of chiral-molecule solution phases, with a specific focus on amino acids. The model framework is based on a two-dimensional square lattice model, where individual sites may be occupied by oriented chiral molecules or structureless solvent particles. Utilizing the Glauber dynamics and statistical mechanical formalism, as previously introduced and examined by Lombardo et al., we explore the influence of temperature, amino acid concentration, enantiomeric excess, and homochiral interaction strength on nucleation mechanisms, equilibrium phase behavior, and crystal composition. Our findings offer thermodynamic insights into the chiral amplification process of amino acids, contributing to a deeper understanding of the underlying processes.
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Affiliation(s)
- Romulo Leoncio Cruz-Simbron
- Technology of Materials for Environmental Remediation (TecMARA) Research Group, Faculty of Sciences, National University of Engineering, Av. Tupac Amaru 210, Lima, Peru
| | - Gino Picasso
- Technology of Materials for Environmental Remediation (TecMARA) Research Group, Faculty of Sciences, National University of Engineering, Av. Tupac Amaru 210, Lima, Peru
| | - José Cerda-Hernández
- Econometric Modelling and Data Science Research Group, National University of Engineering, Av. Tupac Amaru 210, Rimac, Lima, Peru
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2
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Roth M, Toker Y, Major DT. Monte Carlo-Simulated Annealing and Machine Learning-Based Funneled Approach for Finding the Global Minimum Structure of Molecular Clusters. ACS OMEGA 2024; 9:1298-1309. [PMID: 38222530 PMCID: PMC10785639 DOI: 10.1021/acsomega.3c07600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 01/16/2024]
Abstract
Understanding the physical underpinnings and geometry of molecular clusters is of great importance in many fields, ranging from studying the beginning of the universe to the formation of atmospheric particles. To this end, several approaches have been suggested, yet identifying the most stable cluster geometry (i.e., global potential energy minimum) remains a challenge, especially for highly symmetric clusters. Here, we suggest a new funneled Monte Carlo-based simulated annealing (SA) approach, which includes two key steps: generation of symmetrical clusters and classification of the clusters according to their geometry using machine learning (MCSA-ML). We demonstrate the merits of the MCSA-ML method in comparison to other approaches on several Lennard-Jones (LJ) clusters and four molecular clusters-Ser8(Cl-)2, H+(H2O)6, Ag+(CO2)8, and Bet4Cl-. For the latter of these clusters, the correct structure is unknown, and hence, we compare the experimental and simulated fragmentation patterns, and the fragmentation of the proposed global minimum matches experiments closely. Additionally, based on the fragmentation of the predicted betaine cluster, we were able to identify hitherto unknown neutral fragmentation channels. In comparison to results obtained with other methods, we demonstrated a superior ability of MCSA-ML to predict clusters with high symmetry and similar abilities to predict clusters with asymmetrical structures.
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Affiliation(s)
- Michal Roth
- Department
of Physics, Bar-Ilan University, Ramat-Gan 5290002, Israel
- Institute
of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Yoni Toker
- Department
of Physics, Bar-Ilan University, Ramat-Gan 5290002, Israel
- Institute
of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Dan T. Major
- Institute
of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
- Department
of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
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3
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Zhang G, Li R, Wang X, Chen X, Shen Y, Fu Y. The inhibiting water uptake mechanism of main-chain type N-spirocyclic quaternary ammonium ionene blended with polybenzimidazole as anion exchange membrane. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.120950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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4
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David J, Gómez S, Guerra D, Guerra D, Restrepo A. A Comprehensive Picture of the Structures, Energies, and Bonding in the Alanine Dimers. Chemphyschem 2021; 22:2401-2412. [PMID: 34554628 DOI: 10.1002/cphc.202100585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/22/2021] [Indexed: 12/14/2022]
Abstract
High level quantum mechanical computations and extensive stochastic searches of the potential energy surfaces of the Alanine dimers uncover rich and complex structural and interaction landscapes. A total of 416 strongly bound (up 13.4 kcal mol-1 binding energies at the DLPNO-CCSD(T)/6-311++G(d,p) level corrected by the basis set superposition error and by the zero point vibrational energies over B3LYP-D3 geometries), close energy equilibrium structures were located, bonded via 32 specific types of intermolecular contacts including Y⋅⋅⋅H-X primary and Y⋅⋅⋅H-C secondary hydrogen bonds, H⋅⋅⋅H dihydrogen contacts, and non conventional anti-electrostatic Y δ - ⋯ X δ - interactions. The putative global minimum is triply degenerate, corresponding to the structure of the common dimer of a carboxylic acid. All quantum descriptors of chemical bonding point to a multitude of weak individual interactions within each dimer, whose cumulative effect results in large binding energies and in an attractive fluxional wall of non-covalent interactions in the interstitial region between the monomers.
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Affiliation(s)
- Jorge David
- Escuela de Ciencias, Departamento de Ciencias Físicas, Universidad Eafit, AA 3300, Medellín, Colombia
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Doris Guerra
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Dario Guerra
- Departamento de Educación y Ciencias Básicas, Instituto Tecnológico Metropolitano, Calle 73 No. 76 A-354, Medellín, Colombia
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
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5
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Chen W, Wu X, Li T, Yan X, Zhang Y, Wang X, Zhang F, Zhang S, He G. Structural contribution of cationic groups to water sorption in anion exchange membranes: A combined DFT and MD simulation study. Chem Eng Sci 2021. [DOI: 10.1016/j.ces.2021.116791] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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6
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Koralewski M, Baranowski M, Ryzner A. Probing physical invariance between enantiomers: The magnetooptical and refractive properties of the simplest chiral amino acid – Alanine. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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7
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Nihamkin M, Isaak A, Albeck A, Mastai Y, Toker Y. Gas Phase Bond Formation in Dipeptide Clusters. J Phys Chem Lett 2020; 11:10100-10105. [PMID: 33190503 DOI: 10.1021/acs.jpclett.0c03195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Protein bonds between amino acids are one of the most important biological linkages that create life. The detection of amino acids in the interstellar environments and in meteorites may lead to the suggestion that amino acids came from outer space and that peptides bonds may have been created in the gas phase. Here we show experimentally the creation of covalent bonds, most likely peptide bonds, between serine dipeptides in the gas phase. More specifically, we show that spraying a solution of Ser-Ser dipeptides results, in addition to dipeptide clusters, in a peak with the same mass as the serine tetrapeptide, which also has the same fragmentation pattern. Moreover, we show that this mass is formed upon collision induced dissociation of clusters containing four serine dipeptides. Thence, if the dipeptide can be generated abiotically the polymerization process may occur spontaneously.
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Affiliation(s)
- Maria Nihamkin
- Department of Physics and Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Avinoam Isaak
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Amnon Albeck
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Yitzhak Mastai
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
- Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Yoni Toker
- Department of Physics and Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan 5290002, Israel
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Rousseau P, Piekarski DG, Capron M, Domaracka A, Adoui L, Martín F, Alcamí M, Díaz-Tendero S, Huber BA. Polypeptide formation in clusters of β-alanine amino acids by single ion impact. Nat Commun 2020; 11:3818. [PMID: 32732937 PMCID: PMC7393107 DOI: 10.1038/s41467-020-17653-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/01/2020] [Indexed: 11/17/2022] Open
Abstract
The formation of peptide bonds by energetic processing of amino acids is an important step towards the formation of biologically relevant molecules. As amino acids are present in space, scenarios have been developed to identify the roots of life on Earth, either by processes occurring in outer space or on Earth itself. We study the formation of peptide bonds in single collisions of low-energy He2+ ions (α-particles) with loosely bound clusters of β-alanine molecules at impact energies typical for solar wind. Experimental fragmentation mass spectra produced by collisions are compared with results of molecular dynamics simulations and an exhaustive exploration of potential energy surfaces. We show that peptide bonds are efficiently formed by water molecule emission, leading to the formation of up to tetrapeptide. The present results show that a plausible route to polypeptides formation in space is the collision of energetic ions with small clusters of amino acids.
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Affiliation(s)
- Patrick Rousseau
- Normandie Univ, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000, Caen, France.
| | - Dariusz G Piekarski
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Michael Capron
- Normandie Univ, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000, Caen, France
| | - Alicja Domaracka
- Normandie Univ, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000, Caen, France
| | - Lamri Adoui
- Normandie Univ, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000, Caen, France
| | - Fernando Martín
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencias (IMDEA-Nanociencia), Cantoblanco, 28049, Madrid, Spain
| | - Manuel Alcamí
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencias (IMDEA-Nanociencia), Cantoblanco, 28049, Madrid, Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Sergio Díaz-Tendero
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Bernd A Huber
- Normandie Univ, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000, Caen, France
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9
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DFT studies on the structure and stability of tetraaza macrocyclic nickel(II) complexes containing dicarbinolamine ligand moiety. J CHEM SCI 2019. [DOI: 10.1007/s12039-019-1688-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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10
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Ramamurthy K, Malar EJP, Selvaraju C. Hydrogen bonded dimers of ketocoumarin in the solid state and alcohol:water binary solvent: fluorescence spectroscopy, crystal structure and DFT investigation. NEW J CHEM 2019. [DOI: 10.1039/c9nj01053j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Fluorescence emission spectrum of ketocoumarin dimers in an alcohol:water binary mixture and the solid state.
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Affiliation(s)
- Kannan Ramamurthy
- National Centre for Ultrafast Processes, University of Madras
- Chennai 600 113
- India
| | - E. J. Padma Malar
- National Centre for Ultrafast Processes, University of Madras
- Chennai 600 113
- India
| | - Chellappan Selvaraju
- National Centre for Ultrafast Processes, University of Madras
- Chennai 600 113
- India
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