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Samrout OE, Berlier G, Lambert JF. Amino Acid Polymerization on Silica Surfaces. Chempluschem 2024; 89:e202300642. [PMID: 38226922 DOI: 10.1002/cplu.202300642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/05/2024] [Accepted: 01/15/2024] [Indexed: 01/17/2024]
Abstract
The polymerization of unactivated amino acids (AAs) is an important topic because of its applications in various fields including industrial medicinal chemistry and prebiotic chemistry. Silica as a promoter for this reaction, is of great interest owing to its large abundance and low cost. The amide/peptide bond synthesis on silica has been largely demonstrated but suffers from a lack of knowledge regarding its reaction mechanism, the key parameters, and surface features that influence AA adsorption and reactivity, the selectivity of the reaction product, the role of water in the reaction, etc. The present review addresses these problems by summarizing experimental and modeling results from the literature and attempts to rationalize some apparent divergences in published results. After briefly presenting the main types of silica surface sites and other relevant macroscopic features, we discuss the different deposition procedures of AAs, whose importance is often neglected. We address the possible AA adsorption mechanisms including covalent grafting and H-bonding and show that they are highly dependent on silanol types and density. We then consider how the adsorption mechanisms determine the occurrence and outcome of AA condensation (formation of cyclic dimers or of long linear chains), and outline some recent results that suggest significant polymerization selectivity in systems containing several AAs, as well as the formation of specific elements of secondary structure in the growing polypeptide chains.
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Affiliation(s)
- Ola El Samrout
- Department of Chemistry, University of Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Gloria Berlier
- Department of Chemistry, University of Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Jean-François Lambert
- Laboratoire de Réactivité de Surface, LRS, Sorbonne Université Place Jussieu, 75005, Paris, France
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Lombard CJ, van Sittert CGCE, Mugo JN, Perry C, Willock DJ. Computational investigation of α-SiO 2 surfaces as a support for Pd. Phys Chem Chem Phys 2023; 25:6121-6130. [PMID: 36752082 DOI: 10.1039/d2cp04722e] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The properties of a supported metal catalyst depend crucially on the interaction between the active metal and the support. A case in point is Pd supported on silica, Pd/SiO2, which is widely used in oxidation catalysis. There is a need for a broad range of computational models that describe the interaction of Pd with silica surfaces so that active site models can be proposed and tested. In this work, we create well-defined, reproducible, periodic models of SiO2 surfaces and investigate their interaction with Pd using dispersion-corrected DFT. We use crystalline α-SiO2 as a useful starting point for creating and estimating the adsorption properties of metals on SiO2 surfaces, which can represent the specific isolated functional groups present on more complex amorphous silica surfaces. We have modelled α-SiO2 (001), (100) and (101) surfaces containing isolated siloxane and silanol functional groups and estimated their affinity towards the adsorption of Pd atoms regarding an isolated gaseous Pd atom and the fcc Pd solid. This provides additional information on the ease with which Pd can be dispersed on the surfaces in question. From our model, we characterise the surface energies of the α-SiO2 (hkl) surfaces and calculate the geometries of the Pd1/α-SiO2 (hkl) adsorption site on each surface. We estimate that Pd1(g) will prefer to adsorb close to strained four-membered siloxane rings or on a vicinal silanol group of α-SiO2 (101).
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Affiliation(s)
- C J Lombard
- Laboratory for Applied Molecular Modelling, Research Focus Area: Chemical Resource Beneficiation, North-West University, Private Bag X6001, Potchefstroom, 252, South Africa.
| | - C G C E van Sittert
- Laboratory for Applied Molecular Modelling, Research Focus Area: Chemical Resource Beneficiation, North-West University, Private Bag X6001, Potchefstroom, 252, South Africa.
| | - J N Mugo
- Johnson Matthey Technology Center, Belasis Avenue, Billingham TS23 1LH, UK
| | - C Perry
- Johnson Matthey Technology Center, Blount's Court, Sonning Common, Reading RG4 9NH, UK
| | - D J Willock
- Max Planck-Cardiff Centre on the Fundamentals of Heterogeneous Catalysis FUNCAT, Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK.
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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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Tielens F, Gierada M, Handzlik J, Calatayud M. Characterization of amorphous silica based catalysts using DFT computational methods. Catal Today 2020. [DOI: 10.1016/j.cattod.2019.03.062] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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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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Volkov VV, Belton DJ, Perry CC. Do Material Discontinuities in Silica Affect Vibration Modes? J Phys Chem A 2018; 122:4997-5003. [DOI: 10.1021/acs.jpca.8b01688] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Victor V. Volkov
- Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, United Kingdom
| | - David J. Belton
- Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, United Kingdom
| | - Carole C. Perry
- Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, United Kingdom
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Abstract
Empty spaces are abhorred by nature, which immediately rushes in to fill the void. Humans have learnt pretty well how to make ordered empty nanocontainers, and to get useful products out of them. When such an order is imparted to molecules, new properties may appear, often yielding advanced applications. This review illustrates how the organized void space inherently present in various materials: zeolites, clathrates, mesoporous silica/organosilica, and metal organic frameworks (MOF), for example, can be exploited to create confined, organized, and self-assembled supramolecular structures of low dimensionality. Features of the confining matrices relevant to organization are presented with special focus on molecular-level aspects. Selected examples of confined supramolecular assemblies - from small molecules to quantum dots or luminescent species - are aimed to show the complexity and potential of this approach. Natural confinement (minerals) and hyperconfinement (high pressure) provide further opportunities to understand and master the atomistic-level interactions governing supramolecular organization under nanospace restrictions.
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Affiliation(s)
- Gloria Tabacchi
- Department of Science and High Technology, University of Insubria, Via Valleggio, 9 I-22100, Como, Italy
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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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