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Abadian H, Cornette P, Costa D, Mezzetti A, Gervais C, Lambert JF. Leucine on Silica: A Combined Experimental and Modeling Study of a System Relevant for Origins of Life, and the Role of Water Coadsorption. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:8038-8053. [PMID: 35737817 DOI: 10.1021/acs.langmuir.2c00841] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Leucine on silica constitutes an interesting system from the point of view of origins of life studies since leucine coadsorbed on SiO2 together with glutamic acid can give rise to rather long linear polypeptides upon activation. It is also an ideal system to test methods of molecular characterization of biomolecules deposited on mineral surfaces since it combines a small-scale model of peptides and proteins, which are among the most important components of biodevices, with one of the most widely used inorganic materials. We have deposited l-leucine on a high surface fumed silica in the submonolayer range and characterized it by a multipronged approach including macroscopic information (thermogravimetry, X-ray diffraction), in situ spectroscopic methods (IR, multinuclear solid-state NMR including single-pulse and CP-MAS, 2-D HETCOR), and molecular modeling by density functional theory (DFT), including calculation of NMR parameters. Specific information can be obtained on the adsorption and interaction mechanism. Leucine is rather strongly adsorbed without any covalent bonds, through the formation of a specific lattice of H-bonds that often involve coadsorbed water molecules. Its state is indeed strongly dependent on the drying procedure: insufficient drying results in liquid-like surroundings for the leucine functional groups, while vacuum drying only retains a limited number of waters (of the order of 5 per leucine molecule). The most stable models have zwitterionic leucine interacting directly with surface silanols through their ammonium group, while the carboxylate interacts through bridging waters. Experimental NMR chemical shifts are satisfactorily predicted for these models, and leucine can be viewed as a probe for specific groups of surface sites known as silanol nests.
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Affiliation(s)
- Hagop Abadian
- Laboratoire de Réactivité de Surface (LRS, UMR 7609 CNRS), Case courrier 178, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
- Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP, UMR 7574 CNRS), Case courrier 174, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Pauline Cornette
- Laboratoire de Réactivité de Surface (LRS, UMR 7609 CNRS), Case courrier 178, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Dominique Costa
- Institut de Recherche de Chimie Paris (IRCP, UMR8247 CNRS), 11 rue Pierre et Marie Curie, 75005 Paris, France
| | - Alberto Mezzetti
- Laboratoire de Réactivité de Surface (LRS, UMR 7609 CNRS), Case courrier 178, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Christel Gervais
- Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP, UMR 7574 CNRS), Case courrier 174, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Jean-François Lambert
- Laboratoire de Réactivité de Surface (LRS, UMR 7609 CNRS), Case courrier 178, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
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Barcaro G, Sementa L, Carravetta V, Yano TA, Hara M, Monti S. Experimental and theoretical elucidation of catalytic pathways in TiO 2-initiated prebiotic polymerization. Phys Chem Chem Phys 2019; 21:5435-5447. [PMID: 30793143 DOI: 10.1039/c9cp00167k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The tendency of glycine to form polymer chains on a rutile(110) surface under wet/dry conditions (dry-wet cycles at high temperature) is studied through a conjunction of surface sensitive experimental techniques and sequential periodic multilevel calculations that mimics the experimental procedures with models of decreasing complexity and increasing accuracy. X-ray photoemission spectroscopy (XPS) and thermal desorption spectroscopy (TDS) experimentally confirmed that the dry-wet cycles lead to Gly polymerization on the oxide support. This was supported by all the theoretical characterizations. First, classical reactive molecular dynamics (MD) simulations based on the ReaxFF approach were used to reproduce the adsorption of the experimental glycine solution droplets sprayed onto an oxide support and to identify the most probable arrangement of the molecules that triggered the polymerization mechanisms. Then, quantum chemistry density functional tight binding (DF-TB) MDs and static density functional theory (DFT) calculations were carried out to further explore favorable configurations and to evaluate the energy barriers of the most promising reaction pathways for the peptide bond-formation reactions. The results confirmed the fundamental role played by the substrate to thermodynamically and kinetically favor the process and disclosed its main function as an immobilizing agent: the molecules accommodated in the surface channels close to each other were the ones starting the key events of the dimerization process and the most favorable mechanism was the one where a water molecule acted as a proton exchange mediator in the condensation process.
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Affiliation(s)
- Giovanni Barcaro
- CNR-IPCF, Institute of Chemical and Physical Processes, via G. Moruzzi 1, I-56124 Pisa, Italy.
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Sakhno Y, Battistella A, Mezzetti A, Jaber M, Georgelin T, Michot L, Lambert JF. One Step up the Ladder of Prebiotic Complexity: Formation of Nonrandom Linear Polypeptides from Binary Systems of Amino Acids on Silica. Chemistry 2019; 25:1275-1285. [PMID: 30284764 DOI: 10.1002/chem.201803845] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Indexed: 12/17/2022]
Abstract
Evidence for the formation of linear oligopeptides with nonrandom sequences from mixtures of amino acids coadsorbed on silica and submitted to a simple thermal activation is presented. The amino acid couples (glutamic acid+leucine) and (aspartic acid+valine) were deposited on a fumed silica and submitted to a single heating step at moderate temperature. The evolution of the systems was characterized by X-ray diffraction, infrared spectroscopy, thermosgravimetric analysis, HPLC, and electrospray ionization mass spectrometry (ESI-MS). Evidence for the formation of amide bonds was found in all systems studied. While the products of single amino acids activation on silica could be considered as evolutionary dead ends, (glutamic acid+leucine) and, at to some extent, (aspartic acid+valine) gave rise to the high yield formation of linear peptides up to the hexamers. Oligopeptides of such length have not been observed before in surface polymerization scenarios (unless the amino acids had been deposited by chemical vapor deposition, which is not realistic in a prebiotic environment). Furthermore, not all possible amino acid sequences were present in the activation products, which is indicative of polymerization selectivity. These results are promising for origins of life studies because they suggest the emergence of nonrandom biopolymers in a simple prebiotic scenario.
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Affiliation(s)
- Yuriy Sakhno
- Laboratoire de Réactivité de Surface, UMR 7197, Sorbonne Université, Case Courrier 178, 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
| | - Alice Battistella
- Laboratoire de Réactivité de Surface, UMR 7197, Sorbonne Université, Case Courrier 178, 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
| | - Alberto Mezzetti
- Laboratoire de Réactivité de Surface, UMR 7197, Sorbonne Université, Case Courrier 178, 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
| | - Maguy Jaber
- Laboratoire d'Archéologie Moléculaire et Structurale, UMR 8220, Sorbonne Université, Case Courrier 178, 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
| | - Thomas Georgelin
- Laboratoire de Réactivité de Surface, UMR 7197, Sorbonne Université, Case Courrier 178, 4 Pl. Jussieu, 75252, Paris CEDEX 05, France.,Temporary address: Centre de Biophysique Moléculaire, UPR 4301, CNRS, Rue Charles Sadron CS 80054, 45071, Orléans CEDEX 2, France
| | - Laurent Michot
- Laboratoire de Physicochimie des Electrolytes et Nanosystèmes Interfaciaux, UMR 8234, Sorbonne Université, Case Courrier 178, 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
| | - Jean-François Lambert
- Laboratoire de Réactivité de Surface, UMR 7197, Sorbonne Université, Case Courrier 178, 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
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Highly crystalline sphere and rod-shaped TiO 2 nanoparticles: A facile route to bio-polymer grafting. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.flm.2017.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Kitadai N, Oonishi H, Umemoto K, Usui T, Fukushi K, Nakashima S. Glycine Polymerization on Oxide Minerals. ORIGINS LIFE EVOL B 2017; 47:123-143. [PMID: 27473494 DOI: 10.1007/s11084-016-9516-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/14/2016] [Indexed: 11/24/2022]
Abstract
It has long been suggested that mineral surfaces played an important role in peptide bond formation on the primitive Earth. However, it remains unclear which mineral species was key to the prebiotic processes. This is because great discrepancies exist among the reported catalytic efficiencies of minerals for amino acid polymerizations, owing to mutually different experimental conditions. This study examined polymerization of glycine (Gly) on nine oxide minerals (amorphous silica, quartz, α-alumina and γ-alumina, anatase, rutile, hematite, magnetite, and forsterite) using identical preparation, heating, and analytical procedures. Results showed that a rutile surface is the most effective site for Gly polymerization in terms of both amounts and lengths of Gly polymers synthesized. The catalytic efficiency decreased as rutile > anatase > γ-alumina > forsterite > α- alumina > magnetite > hematite > quartz > amorphous silica. Based on reported molecular-level information for adsorption of Gly on these minerals, polymerization activation was inferred to have arisen from deprotonation of the NH3+ group of adsorbed Gly to the nucleophilic NH2 group, and from withdrawal of electron density from the carboxyl carbon to the surface metal ions. The orientation of adsorbed Gly on minerals is also a factor influencing the Gly reactivity. The examination of Gly-mineral interactions under identical experimental conditions has enabled the direct comparison of various minerals' catalytic efficiencies and has made discussion of polymerization mechanisms and their relative influences possible Further systematic investigations using the approach reported herein (which are expected to be fruitful) combined with future microscopic surface analyses will elucidate the role of minerals in the process of abiotic peptide bond formation.
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Affiliation(s)
- Norio Kitadai
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
| | - Hiroyuki Oonishi
- Institute of Nature and Environmental Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan
| | - Koichiro Umemoto
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Tomohiro Usui
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Keisuke Fukushi
- Institute of Nature and Environmental Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan
| | - Satoru Nakashima
- Department of Earth and Space Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
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Phosphoribosyl Pyrophosphate: A Molecular Vestige of the Origin of Life on Minerals. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702633] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Akouche M, Jaber M, Maurel MC, Lambert JF, Georgelin T. Phosphoribosyl Pyrophosphate: A Molecular Vestige of the Origin of Life on Minerals. Angew Chem Int Ed Engl 2017; 56:7920-7923. [PMID: 28558156 DOI: 10.1002/anie.201702633] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 04/15/2017] [Indexed: 11/07/2022]
Abstract
In this contribution, we report the formation under prebiotic conditions of phosphoribosyl pyrophosphate (PRPP) as a molecular precursor in the one-pot synthesis of a canonical nucleotide, namely adenosine monophosphate (AMP) from its building blocks (KH2 PO4 or Pi , adenine, and d-ribose), on a fumed silica surface. The on-the-rocks approach has been successfully applied to the simultaneous phosphorylation and glycosylation of ribose. The one-pot formation mechanism of AMP involves a two-step pathway via an activated intermediate, namely PRPP, obtained by multiple ribose phosphorylations upon mild thermal activation.
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Affiliation(s)
- Mariame Akouche
- Sorbonne Universités, UPMC Paris 06, CNRS UMR 7197, Laboratoire de Réactivité de Surface, 4 place Jussieu, 75005, Paris, France
| | - Maguy Jaber
- Sorbonne Universités, UPMC Paris06, CNRS UMR 8220, Laboratoire d'Archéologie Moléculaire et Structurale, 4 place Jussieu, 75005, Paris, France
| | | | - Jean-Francois Lambert
- Sorbonne Universités, UPMC Paris 06, CNRS UMR 7197, Laboratoire de Réactivité de Surface, 4 place Jussieu, 75005, Paris, France
| | - Thomas Georgelin
- Sorbonne Universités, UPMC Paris 06, CNRS UMR 7197, Laboratoire de Réactivité de Surface, 4 place Jussieu, 75005, Paris, France
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Akouche M, Jaber M, Zins EL, Maurel MC, Lambert JF, Georgelin T. Thermal Behavior of d-Ribose Adsorbed on Silica: Effect of Inorganic Salt Coadsorption and Significance for Prebiotic Chemistry. Chemistry 2016; 22:15834-15846. [PMID: 27624284 DOI: 10.1002/chem.201601418] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Indexed: 12/13/2022]
Abstract
Understanding ribose reactivity is a crucial step in the "RNA world" scenario because this molecule is a component of all extant nucleotides that make up RNA. In solution, ribose is unstable and susceptible to thermal destruction. We examined how ribose behaves upon thermal activation when adsorbed on silica, either alone or with the coadsorption of inorganic salts (MgCl2 , CaCl2 , SrCl2 , CuCl2 , FeCl2 , FeCl3 , ZnCl2 ). A combination of 13 C NMR, in situ IR, and TGA analyses revealed a variety of phenomena. When adsorbed alone, ribose remains stable up to 150 °C, at which point ring opening is observed, together with minor oxidation to a lactone. All the metal salts studied showed specific interactions with ribose after dehydration, resulting in the formation of polydentate metal ion complexes. Anomeric equilibria were affected, generally favoring ribofuranoses. Zn2+ stabilized ribose up to higher temperatures than bare silica (180 to 200 °C). Most other cations had an adverse effect on ribose stability, with ring opening already upon drying at 70 °C. In addition, alkaline earth cations catalyzed the dehydration of ribose to furfural and, to variable degrees, its further decarbonylation to furan. Transition-metal ions with open d-shells took part in redox reactions with ribose, either as reagents or as catalysts. These results allow the likelihood of prebiotic chemistry scenarios to be evaluated, and may also be of interest for the valorization of biomass-derived carbohydrates by heterogeneous catalysis.
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Affiliation(s)
- Mariame Akouche
- Sorbonne Universités, UPMC Univ Paris 06 and CNRS UMR 7197, LRS case courrier 178, UPMC 4 Pl. Jussieu, 75252, PARIS CEDEX 05, France
| | - Maguy Jaber
- Sorbonne Universités, UPMC Univ Paris 06 and CNRS UMR 8220, LAMS, case courrier 225, UPMC 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
| | - Emilie-Laure Zins
- Sorbonne Universités, UPMC Univ Paris 06 and CNRS UMR 8233, MONARIS, case courrier, UPMC 4 Pl. Jussieu, 75252, Paris CEDEX 05, France
| | | | - Jean-Francois Lambert
- Sorbonne Universités, UPMC Univ Paris 06 and CNRS UMR 7197, LRS case courrier 178, UPMC 4 Pl. Jussieu, 75252, PARIS CEDEX 05, France.
| | - Thomas Georgelin
- Sorbonne Universités, UPMC Univ Paris 06 and CNRS UMR 7197, LRS case courrier 178, UPMC 4 Pl. Jussieu, 75252, PARIS CEDEX 05, France.
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Tielens F, Gervais C, Deroy G, Jaber M, Stievano L, Coelho Diogo C, Lambert JF. Characterization of Phosphate Species on Hydrated Anatase TiO2 Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:997-1008. [PMID: 26734828 DOI: 10.1021/acs.langmuir.5b03519] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The adsorption/interaction of KH2PO4 with solvated (100) and (101) TiO2 anatase surfaces is investigated using periodic DFT calculations in combination with GIPAW NMR calculations and experimental IR and solid state (17)O, and (31)P NMR spectroscopies. A complete and realistic model has been used to simulate the solvent by individual water molecules. The most stable adsorption configurations are characterized theoretically at the atomic scale, and experimentally supported by NMR and IR spectroscopies. It is shown that H2PO4(-) chemisorbs on the (100) and (101) anatase surfaces, preferentially via a bidentate geometry. Dimer (H3P2O7(-)) and trimer (H4P3O10(-)) adsorption models are confronted with monomer adsorption models, in order to rationalize their occurrence.
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Affiliation(s)
- Frederik Tielens
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 7574, Laboratoire de Chimie de la Matière Condensée de Paris, Collège de France, 11 place Marcelin Berthelot, 75231 Cedex 05 Paris, France
| | - Christel Gervais
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 7574, Laboratoire de Chimie de la Matière Condensée de Paris, Collège de France, 11 place Marcelin Berthelot, 75231 Cedex 05 Paris, France
| | - Geraldine Deroy
- Sorbonne Université, UPMC Univ Paris 06, UMR 7197, Laboratoire de Réactivité de Surface. 3 rue Galilée, F-94200 Ivry-Sur-Seine, France
| | - Maguy Jaber
- Sorbonne Université, UPMC Univ Paris 06, UMR 8220 Laboratoire d'Archéologie Moléculaire et Structurale, 4 Place Jussieu, 75005 Paris, France
| | - Lorenzo Stievano
- Université Montpellier, ICGM, UMR 5253, 2 Place Eugène Bataillon - CC 1502, 34095 Montpellier CEDEX 5, France
| | - Cristina Coelho Diogo
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 7574, Laboratoire de Chimie de la Matière Condensée de Paris, Collège de France, 11 place Marcelin Berthelot, 75231 Cedex 05 Paris, France
- IMPC, Institut des Matériaux de Paris Centre FR2482, 75252 cedex 05 Paris, France
| | - Jean-François Lambert
- Sorbonne Université, UPMC Univ Paris 06, UMR 7197, Laboratoire de Réactivité de Surface. 3 rue Galilée, F-94200 Ivry-Sur-Seine, France
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Bian L, Xu JB, Song MX, Dong FQ, Dong HL, Shi FN, Wang L, Ren W. Designing perovskite BFO (111) membrane as an electrochemical sensor for detection of amino acids: A simulation study. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.06.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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