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Brigiano FS, Gierada M, Tielens F, Pietrucci F. Mechanism and Free-Energy Landscape of Peptide Bond Formation at the Silica–Water Interface. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Flavio Siro Brigiano
- General Chemistry (ALGC), Materials Modeling Group, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Maciej Gierada
- General Chemistry (ALGC), Materials Modeling Group, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Faculty of Chemical Engineering and Technology, Cracow University of Technology, ul. Warszawska 24, 31-155 Kraków, Poland
| | - Frederik Tielens
- General Chemistry (ALGC), Materials Modeling Group, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
| | - 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
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Adsorption and isomerization of amino acids within zeolites: Impacts of acidity, amine functionalization, pore topology and sidechains. MOLECULAR CATALYSIS 2020. [DOI: 10.1016/j.mcat.2020.111088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Theoretical and Experimental Study on the 7‐Hydroxy‐4‐Methylcoumarin Synthesis with H‐Beta Zeolite. ChemistrySelect 2019. [DOI: 10.1002/slct.201902596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Rimola A, Sodupe M, Ugliengo P. Role of Mineral Surfaces in Prebiotic Chemical Evolution. In Silico Quantum Mechanical Studies. Life (Basel) 2019; 9:E10. [PMID: 30658501 PMCID: PMC6463156 DOI: 10.3390/life9010010] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/10/2019] [Accepted: 01/12/2019] [Indexed: 01/07/2023] Open
Abstract
There is a consensus that the interaction of organic molecules with the surfaces of naturally-occurring minerals might have played a crucial role in chemical evolution and complexification in a prebiotic era. The hurdle of an overly diluted primordial soup occurring in the free ocean may have been overcome by the adsorption and concentration of relevant molecules on the surface of abundant minerals at the sea shore. Specific organic⁻mineral interactions could, at the same time, organize adsorbed molecules in well-defined orientations and activate them toward chemical reactions, bringing to an increase in chemical complexity. As experimental approaches cannot easily provide details at atomic resolution, the role of in silico computer simulations may fill that gap by providing structures and reactive energy profiles at the organic⁻mineral interface regions. Accordingly, numerous computational studies devoted to prebiotic chemical evolution induced by organic⁻mineral interactions have been proposed. The present article aims at reviewing recent in silico works, mainly focusing on prebiotic processes occurring on the mineral surfaces of clays, iron sulfides, titanium dioxide, and silica and silicates simulated through quantum mechanical methods based on the density functional theory (DFT). The DFT is the most accurate way in which chemists may address the behavior of the molecular world through large models mimicking chemical complexity. A perspective on possible future scenarios of research using in silico techniques is finally proposed.
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Affiliation(s)
- Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS), Università degli Studi di Torino, Via P. Giuria 7, 10125 Torino, Italy.
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Pantaleone S, Ugliengo P, Sodupe M, Rimola A. When the Surface Matters: Prebiotic Peptide-Bond Formation on the TiO 2 (101) Anatase Surface through Periodic DFT-D2 Simulations. Chemistry 2018; 24:16292-16301. [PMID: 30212609 DOI: 10.1002/chem.201803263] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Indexed: 12/13/2022]
Abstract
The mechanism of the peptide-bond formation between two glycine (Gly) molecules has been investigated by means of PBE-D2* and PBE0-D2* periodic simulations on the TiO2 (101) anatase surface. This is a process of great relevance both in fundamental prebiotic chemistry, as the reaction univocally belongs to one of the different organizational events that ultimately led to the emergence of life on Earth, as well as from an industrial perspective, since formation of amides is a key reaction for pharmaceutical companies. The efficiency of the surface catalytic sites is demonstrated by comparing the reactions in the gas phase and on the surface. At variance with the uncatalyzed gas-phase reaction, which involves a concerted nucleophilic attack and dehydration step, on the surface these two steps occur along a stepwise mechanism. The presence of surface Lewis and Brönsted sites exerts some catalytic effect by lowering the free energy barrier for the peptide-bond formation by about 6 kcal mol-1 compared to the gas-phase reaction. Moreover, the co-presence of molecules acting as proton-transfer assistants (i.e., H2 O and Gly) provide a more significant kinetic energy barrier decrease. The reaction on the surface is also favorable from a thermodynamic standpoint, involving very large and negative reaction energies. This is due to the fact that the anatase surface also acts as a dehydration agent during the condensation reaction, since the outermost coordinatively unsaturated Ti atoms strongly anchor the released water molecules. Our theoretical results provide a comprehensive atomistic interpretation of the experimental results of Martra et al. (Angew. Chem. Int. Ed. 2014, 53, 4671), in which polyglycine formation was obtained by successive feedings of Gly vapor on TiO2 surfaces in dry conditions and are, therefore, relevant in a prebiotic context envisaging dry and wet cycles occurring, at mineral surfaces, in a small pool.
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Affiliation(s)
- Stefano Pantaleone
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS), Inter-Departmental centre, Università degli Studi di Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
| | - Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
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Rimola A, Fabbiani M, Sodupe M, Ugliengo P, Martra G. How Does Silica Catalyze the Amide Bond Formation under Dry Conditions? Role of Specific Surface Silanol Pairs. ACS Catal 2018. [DOI: 10.1021/acscatal.7b03961] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Marco Fabbiani
- Dipartimento de Scienza e Alta Tecnologia, Università degli Studi dell’insubria, Via Valleggio 11, 22100 Como, Italy
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Inter-Departmental centre, Università degli Studi di Torino, Via P. Giuria 7, 10125 Torino, Italy
| | - Gianmario Martra
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Inter-Departmental centre, Università degli Studi di Torino, Via P. Giuria 7, 10125 Torino, Italy
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Moro D, Ulian G, Valdrè G. Single Molecule Investigation of Glycine-Chlorite Interaction by Cross-Correlated Scanning Probe Microscopy and Quantum Mechanics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:4453-4463. [PMID: 25830864 DOI: 10.1021/acs.langmuir.5b00161] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this work, we studied the interaction of glycine with the (001) surface of chlorite mineral at a single molecule level by cross-correlating scanning probe microscopy (SPM) and ab initio quantum mechanics (QM) investigations. Chlorite mineral is particularly interesting and peculiar for the interaction with organic molecules because it presents an alternated stacking of brucite-like (hydrophobic) and talc-like (hydrophilic) layers of different polarities. Brucite-like is positive, whereas talc-like is negative. The experimental atomic force microscopy (AFM) observations show that glycine is stably and selectively adsorbed on the brucite-like layer, organized in monolayers with different patterns. The sizes of single molecules of glycine measured by AFM are in agreement with those calculated by QM. Glycine molecules were found to align both at the edges and on the terraces of the brucitic surface. QM simulations confirmed the AFM observations that glycine molecule is adsorbed with high adsorption energy preferentially with its plane parallel to the (001) brucite-like surface. QM also provided the geometry conformation of the molecule and the bonding scheme between glycine and brucite surface. This kind of data can be very helpful both to biotechnological applications of this substrate and to depict some important processes that might have been occurred in prebiotic environments.
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Affiliation(s)
- Daniele Moro
- Centro di Ricerca Interdisciplinare di Biomineralogia, Cristallografia e Biomateriali, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna "Alma Mater Studiorum", Piazza di Porta San Donato 1, 40126 Bologna, Italy
| | - Gianfranco Ulian
- Centro di Ricerca Interdisciplinare di Biomineralogia, Cristallografia e Biomateriali, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna "Alma Mater Studiorum", Piazza di Porta San Donato 1, 40126 Bologna, Italy
| | - Giovanni Valdrè
- Centro di Ricerca Interdisciplinare di Biomineralogia, Cristallografia e Biomateriali, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna "Alma Mater Studiorum", Piazza di Porta San Donato 1, 40126 Bologna, Italy
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Lambert JF, Jaber M, Georgelin T, Stievano L. A comparative study of the catalysis of peptide bond formation by oxide surfaces. Phys Chem Chem Phys 2013; 15:13371-80. [DOI: 10.1039/c3cp51282g] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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