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Fontecilla-Camps JC. Reflections on the Origin of Coded Protein Biosynthesis. Biomolecules 2024; 14:518. [PMID: 38785925 PMCID: PMC11117964 DOI: 10.3390/biom14050518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
The principle of continuity posits that some central features of primordial biocatalytic mechanisms should still be present in the genetically dependent pathway of protein synthesis, a crucial step in the emergence of life. Key bimolecular reactions of this process are catalyzed by DNA-dependent RNA polymerases, aminoacyl-tRNA synthetases, and ribosomes. Remarkably, none of these biocatalysts contribute chemically active groups to their respective reactions. Instead, structural and functional studies have demonstrated that nucleotidic α-phosphate and β-d-ribosyl 2' OH and 3' OH groups can help their own catalysis, a process which, consequently, has been called "substrate-assisted". Furthermore, upon binding, the substrates significantly lower the entropy of activation, exclude water from these catalysts' active sites, and are readily positioned for a reaction. This binding mode has been described as an "entropy trap". The combination of this effect with substrate-assisted catalysis results in reactions that are stereochemically and mechanistically simpler than the ones found in most modern enzymes. This observation is consistent with the way in which primordial catalysts could have operated; it may also explain why, thanks to their complementary reactivities, β-d-ribose and phosphate were naturally selected to be the central components of early coding polymers.
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2
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Mrnjavac N, Wimmer JLE, Brabender M, Schwander L, Martin WF. The Moon-Forming Impact and the Autotrophic Origin of Life. Chempluschem 2023; 88:e202300270. [PMID: 37812146 PMCID: PMC7615287 DOI: 10.1002/cplu.202300270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/10/2023]
Abstract
The Moon-forming impact vaporized part of Earth's mantle, and turned the rest into a magma ocean, from which carbon dioxide degassed into the atmosphere, where it stayed until water rained out to form the oceans. The rain dissolved CO2 and made it available to react with transition metal catalysts in the Earth's crust so as to ultimately generate the organic compounds that form the backbone of microbial metabolism. The Moon-forming impact was key in building a planet with the capacity to generate life in that it converted carbon on Earth into a homogeneous and accessible substrate for organic synthesis. Today all ecosystems, without exception, depend upon primary producers, organisms that fix CO2 . According to theories of autotrophic origin, it has always been that way, because autotrophic theories posit that the first forms of life generated all the molecules needed to build a cell from CO2 , forging a direct line of continuity between Earth's initial CO2 -rich atmosphere and the first microorganisms. By modern accounts these were chemolithoautotrophic archaea and bacteria that initially colonized the crust and still inhabit that environment today.
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Affiliation(s)
- Natalia Mrnjavac
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Jessica L. E. Wimmer
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Max Brabender
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Loraine Schwander
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - William F. Martin
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
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3
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Fontecilla-Camps JC. Reflections on the Origin and Early Evolution of the Genetic Code. Chembiochem 2023; 24:e202300048. [PMID: 37052530 DOI: 10.1002/cbic.202300048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/01/2023] [Indexed: 04/14/2023]
Abstract
Examination of the genetic code (GeCo) reveals that amino acids coded by (A/U) codons display a large functional spectrum and bind RNA whereas, except for Arg, those coded by (G/C) codons do not. From a stereochemical viewpoint, the clear preference for (A/U)-rich codons to be located at the GeCo half blocks suggests they were specifically determined. Conversely, the overall lower affinity of cognate amino acids for their (G/C)-rich anticodons points to their late arrival to the GeCo. It is proposed that i) initially the code was composed of the eight (A/U) codons; ii) these codons were duplicated when G/C nucleotides were added to their wobble positions, and three new codons with G/C in their first position were incorporated; and iii) a combination of A/U and G/C nucleotides progressively generated the remaining codons.
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Pinna S, Kunz C, Halpern A, Harrison SA, Jordan SF, Ward J, Werner F, Lane N. A prebiotic basis for ATP as the universal energy currency. PLoS Biol 2022; 20:e3001437. [PMID: 36194581 PMCID: PMC9531788 DOI: 10.1371/journal.pbio.3001437] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 08/30/2022] [Indexed: 11/07/2022] Open
Abstract
ATP is universally conserved as the principal energy currency in cells, driving metabolism through phosphorylation and condensation reactions. Such deep conservation suggests that ATP arose at an early stage of biochemical evolution. Yet purine synthesis requires 6 phosphorylation steps linked to ATP hydrolysis. This autocatalytic requirement for ATP to synthesize ATP implies the need for an earlier prebiotic ATP equivalent, which could drive protometabolism before purine synthesis. Why this early phosphorylating agent was replaced, and specifically with ATP rather than other nucleoside triphosphates, remains a mystery. Here, we show that the deep conservation of ATP might reflect its prebiotic chemistry in relation to another universally conserved intermediate, acetyl phosphate (AcP), which bridges between thioester and phosphate metabolism by linking acetyl CoA to the substrate-level phosphorylation of ADP. We confirm earlier results showing that AcP can phosphorylate ADP to ATP at nearly 20% yield in water in the presence of Fe3+ ions. We then show that Fe3+ and AcP are surprisingly favoured. A wide range of prebiotically relevant ions and minerals failed to catalyse ADP phosphorylation. From a panel of prebiotic phosphorylating agents, only AcP, and to a lesser extent carbamoyl phosphate, showed any significant phosphorylating potential. Critically, AcP did not phosphorylate any other nucleoside diphosphate. We use these data, reaction kinetics, and molecular dynamic simulations to infer a possible mechanism. Our findings might suggest that the reason ATP is universally conserved across life is that its formation is chemically favoured in aqueous solution under mild prebiotic conditions.
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Affiliation(s)
- Silvana Pinna
- Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, Darwin Building, London, United Kingdom
| | - Cäcilia Kunz
- Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, Darwin Building, London, United Kingdom
| | - Aaron Halpern
- Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, Darwin Building, London, United Kingdom
| | - Stuart A. Harrison
- Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, Darwin Building, London, United Kingdom
| | - Sean F. Jordan
- Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, Darwin Building, London, United Kingdom
| | - John Ward
- Department of Biochemical Engineering, University College London, London, United Kingdom
| | - Finn Werner
- Institute for Structural and Molecular Biology, University College London, Darwin Building, London, United Kingdom
| | - Nick Lane
- Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, Darwin Building, London, United Kingdom
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5
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Abánades Lázaro I, Forgan RS, Cirujano FG. MOF nanoparticles as heterogeneous catalysts for direct amide bond formations. Dalton Trans 2022; 51:8368-8376. [PMID: 35583628 DOI: 10.1039/d2dt00369d] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The influence of composition and textural characteristics of a family of ultra-small isoreticular UiO-type metal-organic frameworks (MOFs) with different functionalized and extended linkers on their catalytic performance is evaluated. Two direct amide bond formations across four different substrates (benzylamine + phenylacetic acid and aniline + formic acid) are employed as proof-of-concept reactions to test the activity of the Zr-MOF nanoparticles. The reaction rates of amide bond formation are evaluated against physico-chemical properties such as crystallinity, porosity, particle size or linker functionality, alongside the Lewis acid and hydrophobic properties of the MOFs, in order to gain insights into the catalytic mechanism and optimal properties for its enhancement.
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Affiliation(s)
- Isabel Abánades Lázaro
- Instituto de Ciencia Molecular (ICMol), Universitat de Valencia, Catedrático José Beltrán Martínez n° 2, 46980 Paterna, Valencia, Spain.
| | - Ross S Forgan
- WestCHEM School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, UK
| | - Francisco G Cirujano
- Instituto de Ciencia Molecular (ICMol), Universitat de Valencia, Catedrático José Beltrán Martínez n° 2, 46980 Paterna, Valencia, Spain.
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6
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Fontecilla-Camps JC, Volbeda A. Quinolinate Synthase: An Example of the Roles of the Second and Outer Coordination Spheres in Enzyme Catalysis. Chem Rev 2022; 122:12110-12131. [PMID: 35536891 DOI: 10.1021/acs.chemrev.1c00869] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The activation energy barrier of biochemical reactions is normally lowered by an enzyme catalyst, which directly helps the weakening of the bond(s) to be broken. In many metalloenzymes, this is a first coordination sphere effect. Besides having a direct catalytic action, enzymes can fix their reactive groups and substrates so that they are optimally positioned and also modify the water activity in the system. They can either activate substrates prior to their reaction or bind preactivated substrates, thereby drastically reducing local entropic effects. The latter type is well represented by some bisubstrate reactions, where they have been defined as "entropic traps". These can be described as "second coordination sphere" processes, but enzymes can also control the reactivity beyond this point through local conformational changes belonging to an "outer coordinate sphere" that can be modulated by substrate binding. We have chosen the [4Fe-4S] cluster-dependent enzyme quinolinate synthase to illustrate each one of these processes. In addition, this very old metalloenzyme shows low in vitro substrate binding specificity, atypical reactivity that produces dead-end products, and a unique modulation of its active site volume.
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Affiliation(s)
| | - Anne Volbeda
- Université Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
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7
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Tracing the Primordial Chemical Life of Glycine: A Review from Quantum Chemical Simulations. Int J Mol Sci 2022; 23:ijms23084252. [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] [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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9
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de Azambuja F, Loosen A, Conic D, van den Besselaar M, Harvey JN, Parac-Vogt TN. En Route to a Heterogeneous Catalytic Direct Peptide Bond Formation by Zr-Based Metal–Organic Framework Catalysts. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01782] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Alexandra Loosen
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Dragan Conic
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | | | - Jeremy N. Harvey
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
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10
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Nano-FTIR spectroscopic identification of prebiotic carbonyl compounds in Dominion Range 08006 carbonaceous chondrite. Sci Rep 2021; 11:11656. [PMID: 34079034 PMCID: PMC8172632 DOI: 10.1038/s41598-021-91200-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 05/24/2021] [Indexed: 12/02/2022] Open
Abstract
Meteorites contain organic matter that may have contributed to the origin of life on Earth. Carbonyl compounds such as aldehydes and carboxylic acids, which occur in meteorites, may be precursors of biologically necessary organic materials in the solar system. Therefore, such organic matter is of astrobiological importance and their detection and characterization can contribute to the understanding of the early solar system as well as the origin of life. Most organic matter is typically sub-micrometer in size, and organic nanoglobules are even smaller (50–300 nm). Novel analytical techniques with nanoscale spatial resolution are required to detect and characterize organic matter within extraterrestrial materials. Most techniques require powdered samples, consume the material, and lose petrographic context of organics. Here, we report the detection of nanoglobular aldehyde and carboxylic acids in a highly primitive carbonaceous chondrite (DOM 08006) with ~ 20 nm spatial resolution using nano-FTIR spectroscopy. Such organic matter is found within the matrix of DOM 08006 and is typically 50–300 nm in size. We also show petrographic context and nanoscale morphologic/topographic features of the organic matter. Our results indicate that prebiotic carbonyl nanoglobules can form in a less aqueous and relatively elevated temperature-environment (220–230 °C) in a carbonaceous parent body.
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11
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Fontecilla-Camps JC. Primordial bioenergy sources: The two facets of adenosine triphosphate. J Inorg Biochem 2020; 216:111347. [PMID: 33450675 DOI: 10.1016/j.jinorgbio.2020.111347] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/14/2020] [Accepted: 12/21/2020] [Indexed: 01/10/2023]
Abstract
Life requires energy to exist, to reproduce and to survive. Two major hypotheses have been put forward concerning the source of this energy at the very early stages of life evolution: (i) abiotic organics either brought to Earth by comets and/or meteorites, or produced at its atmosphere, and (ii) mineral surface-dependent bioinorganic catalytic reactions. Considering the latter possibility, I propose that, besides being a precursor of nucleic acids, adenosine triphosphate (ATP), which probably was used very early to improve the fidelity of nucleic acid polymerization, played an essential role in the transition between mineral-bound protocells and their free counterparts. Indeed, phosphorylation by ATP renders carboxylate groups electrophilic enough to react with nucleophiles such as amines, an effect that, thanks to their Lewis acid character, also have dehydrated metal ions on mineral surfaces. Early ATP synthesis for metabolic processes most likely depended on substrate level phosphorylation. However, the exaptation of a hexameric helicase-like ATPase and a transmembrane H+ pump (which evolved to counteract the acidity caused by fermentation reactions within the protocell) generated a much more efficient membrane-bound ATP synthase that uses chemiosmosis to make ATP.
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12
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Pantaleone S, Rimola A, Sodupe M. Canonical, deprotonated, or zwitterionic? II. A computational study on amino acid interaction with the TiO 2(110) rutile surface: comparison with the anatase (101) surface. Phys Chem Chem Phys 2020; 22:16862-16876. [PMID: 32666992 DOI: 10.1039/d0cp01429j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The adsorption of 11 amino acids (Gly, Leu, Met, Phe, Ser, Cys, Glu, Gln, Arg, Lys, and His) on the TiO2(110) rutile surface is investigated adopting a theoretical approach, using the PBE-D2* functional as implemented in the periodic VASP code. The adsorption of the amino acids is considered in their canonical, deprotonated and zwitterionic forms. For all cases, the most stable adsorption mode adopts a bidentate (O,O) binding with surface undercoordinated Ti atoms, in agreement with previous experimental and computational studies using glycine as a test case. Such a binding mode is possible due to the surface morphology, because the Ti-Ti distances match very well with the carboxylic O-O distance. The most stable adsorption states are the deprotonated and the zwitterionic ones, the canonical one lying significantly above in energy. The relative stability between the deprotonated and the zwitterionic states results in a delicate trade-off among dative interactions (O, N, and S atoms of the amino acids with Ti atoms of the surface), H-bond interactions, dispersive forces and, to a lesser extent, steric hindrance of the amino acidic lateral chains. Finally, the difference in the amino acid adsorption between the (110) rutile and the (101) anatase surfaces is discussed both from the energetic and surface morphological standpoints, highlighting the larger reactivity of the rutile polymorph in adsorbing and deprotonating the amino acids compared with the anatase one.
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Affiliation(s)
- S Pantaleone
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia, Spain.
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13
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Martínez-Bachs B, Rimola A. Prebiotic Peptide Bond Formation Through Amino Acid Phosphorylation. Insights from Quantum Chemical Simulations. Life (Basel) 2019; 9:life9030075. [PMID: 31527465 PMCID: PMC6789625 DOI: 10.3390/life9030075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/08/2019] [Accepted: 09/09/2019] [Indexed: 12/11/2022] Open
Abstract
Condensation reactions between biomolecular building blocks are the main synthetic channels to build biopolymers. However, under highly diluted prebiotic conditions, condensations are thermodynamically hampered since they release water. Moreover, these reactions are also kinetically hindered as, in the absence of any catalyst, they present high activation energies. In living organisms, in the formation of peptides by condensation of amino acids, this issue is overcome by the participation of adenosine triphosphate (ATP), in which, previous to the condensation, phosphorylation of one of the reactants is carried out to convert it as an activated intermediate. In this work, we present for the first time results based on density functional theory (DFT) calculations on the peptide bond formation between two glycine (Gly) molecules adopting this phosphorylation-based mechanism considering a prebiotic context. Here, ATP has been modeled by a triphosphate (TP) component, and different scenarios have been considered: (i) gas-phase conditions, (ii) in the presence of a Mg2+ ion available within the layer of clays, and (iii) in the presence of a Mg2+ ion in watery environments. For all of them, the free energy profiles have been fully characterized. Energetics derived from the quantum chemical calculations indicate that none of the processes seem to be feasible in the prebiotic context. In scenarios (i) and (ii), the reactions are inhibited due to unfavorable thermodynamics associated with the formation of high energy intermediates, while in scenario (iii), the reaction is inhibited due to the high free energy barrier associated with the condensation reactions. As a final consideration, the role of clays in this TP-mediated peptide bond formation route is advocated, since the interaction of the phosphorylated intermediate with the internal clay surfaces could well favor the reaction free energies.
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Affiliation(s)
- Berta Martínez-Bachs
- Department de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Albert Rimola
- Department de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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14
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Tabacchi G, Fabbiani M, Mino L, Martra G, Fois E. The Case of Formic Acid on Anatase TiO 2 (101): Where is the Acid Proton? Angew Chem Int Ed Engl 2019; 58:12431-12434. [PMID: 31310450 DOI: 10.1002/anie.201906709] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Indexed: 01/20/2023]
Abstract
Carboxylic-acid adsorption on anatase TiO2 is a relevant process in many technological applications. Yet, despite several decades of investigations, the acid-proton localization-either on the molecule or on the surface-is still an open issue. By modeling the adsorption of formic acid on top of anatase(101) surfaces, we highlight the formation of a short strong hydrogen bond. In the 0 K limit, the acid-proton behavior is ruled by quantum delocalization effects in a single potential well, while at ambient conditions, the proton undergoes a rapid classical shuttling in a shallow two-well free-energy profile. This picture, supported by agreement with available experiments, shows that the anatase surface acts like a protecting group for the carboxylic acid functionality. Such a new conceptual insight might help rationalize chemical processes involving carboxylic acids on oxide surfaces.
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Affiliation(s)
- Gloria Tabacchi
- Department of Science and High Technology, University of Insubria and INSTM, via Valleggio 9, I-22100, Como, Italy
| | - Marco Fabbiani
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centre, University of Torino, via P. Giuria 7, I-10125, Torino, Italy
| | - Lorenzo Mino
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centre, University of Torino, via P. Giuria 7, I-10125, Torino, Italy
| | - Gianmario Martra
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centre, University of Torino, via P. Giuria 7, I-10125, Torino, Italy
| | - Ettore Fois
- Department of Science and High Technology, University of Insubria and INSTM, via Valleggio 9, I-22100, Como, Italy
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15
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Tabacchi G, Fabbiani M, Mino L, Martra G, Fois E. The Case of Formic Acid on Anatase TiO
2
(101): Where is the Acid Proton? Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906709] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Gloria Tabacchi
- Department of Science and High TechnologyUniversity of Insubria and INSTM via Valleggio 9 I-22100 Como Italy
| | - Marco Fabbiani
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centreUniversity of Torino via P. Giuria 7 I-10125 Torino Italy
| | - Lorenzo Mino
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centreUniversity of Torino via P. Giuria 7 I-10125 Torino Italy
| | - Gianmario Martra
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centreUniversity of Torino via P. Giuria 7 I-10125 Torino Italy
| | - Ettore Fois
- Department of Science and High TechnologyUniversity of Insubria and INSTM via Valleggio 9 I-22100 Como Italy
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16
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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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17
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Shchelokov A, Palko N, Potemkin V, Grishina M, Morozov R, Korina E, Uchaev D, Krivtsov I, Bol'shakov O. Adsorption of Native Amino Acids on Nanocrystalline TiO 2: Physical Chemistry, QSPR, and Theoretical Modeling. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:538-550. [PMID: 30554513 DOI: 10.1021/acs.langmuir.8b02007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The affinity of biomolecules, such as peptides and proteins, with inorganic surfaces, is a fundamental topic in biotechnology and bionanotechnology. Amino acids are often used as "model" bits of peptides or proteins for studying their properties in different environments and/or developing functional surfaces. Despite great demand for knowledge about amino acid interactions with metal oxide surfaces, studies on the issue represent a fragmentary picture. In this paper, we describe amino acid adsorption on nanocrystalline anatase systematically at uniform conditions. Analysis of the Gibbs free adsorption energy indicated how the aliphatic, aromatic, polar, and charged side chain groups affect the binding affinity of the amino acids. Thermodynamic features of the l-amino acid adsorption receive thorough interpretation with calculated molecular descriptors. Theoretical modeling shows that amino acids complex with TiO2 nanoparticles as zwitterions via ammonium group.
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Affiliation(s)
| | | | | | | | | | | | | | - Igor Krivtsov
- Department of Chemical and Environmental Engineering , University of Oviedo , 33006 Oviedo , Spain
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18
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Fontecilla-Camps JC. Geochemical Continuity and Catalyst/Cofactor Replacement in the Emergence and Evolution of Life. Angew Chem Int Ed Engl 2018; 58:42-48. [DOI: 10.1002/anie.201808438] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/27/2018] [Indexed: 12/29/2022]
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19
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Fontecilla-Camps JC. Geochemische Kontinuität und Katalysator/Cofaktor-Austausch für Ursprung und Evolution des Lebens. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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20
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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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21
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McKee AD, Solano M, Saydjari A, Bennett CJ, Hud NV, Orlando TM. A Possible Path to Prebiotic Peptides Involving Silica and Hydroxy Acid‐Mediated Amide Bond Formation. Chembiochem 2018; 19:1913-1917. [DOI: 10.1002/cbic.201800217] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Aaron D. McKee
- NSF/NASA Center for Chemical Evolution 901 Atlantic Drive Atlanta GA 30332 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology 901 Atlantic Drive Atlanta GA 30332 USA
| | - Martin Solano
- NSF/NASA Center for Chemical Evolution 901 Atlantic Drive Atlanta GA 30332 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology 901 Atlantic Drive Atlanta GA 30332 USA
| | - Andrew Saydjari
- NSF/NASA Center for Chemical Evolution 901 Atlantic Drive Atlanta GA 30332 USA
| | - Christopher J. Bennett
- NSF/NASA Center for Chemical Evolution 901 Atlantic Drive Atlanta GA 30332 USA
- Department of Physics University of Central Florida Physical Sciences Bldg. 430 4111 Libra Drive Orlando FL 32816 USA
| | - Nicholas V. Hud
- NSF/NASA Center for Chemical Evolution 901 Atlantic Drive Atlanta GA 30332 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology 901 Atlantic Drive Atlanta GA 30332 USA
| | - Thomas M. Orlando
- NSF/NASA Center for Chemical Evolution 901 Atlantic Drive Atlanta GA 30332 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology 901 Atlantic Drive Atlanta GA 30332 USA
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22
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Liu Y, Cherkasov N, Gao P, Fernández J, Lees MR, Rebrov EV. The enhancement of direct amide synthesis reaction rate over TiO 2 @SiO 2 @NiFe 2 O 4 magnetic catalysts in the continuous flow under radiofrequency heating. J Catal 2017. [DOI: 10.1016/j.jcat.2017.09.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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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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24
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Dunetz JR, Magano J, Weisenburger GA. Large-Scale Applications of Amide Coupling Reagents for the Synthesis of Pharmaceuticals. Org Process Res Dev 2016. [DOI: 10.1021/op500305s] [Citation(s) in RCA: 411] [Impact Index Per Article: 51.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Joshua R. Dunetz
- Process
Chemistry, Gilead Sciences, 333 Lakeside Drive, Foster City, California 94404, United States
| | - Javier Magano
- Chemical Research & Development, Pfizer Worldwide Research & Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Gerald A. Weisenburger
- Chemical Research & Development, Pfizer Worldwide Research & Development, Eastern Point Road, Groton, Connecticut 06340, United States
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25
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Liu Y, Gao P, Cherkasov N, Rebrov EV. Direct amide synthesis over core–shell TiO2@NiFe2O4 catalysts in a continuous flow radiofrequency-heated reactor. RSC Adv 2016. [DOI: 10.1039/c6ra22659k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A core–shell TiO2@NiFe2O4 catalyst showed high activity and stability in direct amide synthesis with easy regeneration from coke by a treatment with a 30 wt% hydrogen peroxide solution.
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Affiliation(s)
- Yawen Liu
- School of Engineering
- University of Warwick
- Coventry CV4 7AL
- UK
| | - Pengzhao Gao
- College of Materials Science and Engineering
- Hunan University
- Changsha 410082
- China
| | | | - Evgeny V. Rebrov
- School of Engineering
- University of Warwick
- Coventry CV4 7AL
- UK
- Department of Biotechnology and Chemistry
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26
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Behr A, Levikov D, Nürenberg E. Rhodium catalyzed one-step hydroamidation of cyclopentadiene and dicyclopentadiene. Catal Sci Technol 2015. [DOI: 10.1039/c5cy00168d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The carboxylic acid amide group is of great importance in the contemporary chemical and pharmaceutical industries. A one-step rhodium catalyzed direct route from alkene to amide is presented via the hydroamidation reaction of cyclopentadiene and dicyclopentadiene.
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Affiliation(s)
- Arno Behr
- Technische Universität Dortmund
- Lehrstuhl für Technische Chemie
- 44227 Dortmund
- Germany
| | - Denys Levikov
- Technische Universität Dortmund
- Lehrstuhl für Technische Chemie
- 44227 Dortmund
- Germany
| | - Edward Nürenberg
- Technische Universität Dortmund
- Lehrstuhl für Technische Chemie
- 44227 Dortmund
- Germany
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27
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Arena F, Deiana C, Lombardo AF, Ivanchenko P, Sakhno Y, Trunfio G, Martra G. Activity patterns of metal oxide catalysts in the synthesis of N-phenylpropionamide from propanoic acid and aniline. Catal Sci Technol 2015. [DOI: 10.1039/c4cy01504e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reactivities of various oxide samples in the heterogeneous catalytic synthesis of N-phenylpropionamide from aniline and propanoic acid have been investigated and related to the different structure of adsorbed carboxylates.
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Affiliation(s)
- Francesco Arena
- Dipartimento di Ingegneria Elettronica
- Chimica e Ingegneria Industriale
- Università degli Studi di Messina
- 98166 Messina
- Italy
| | - Chiara Deiana
- Department of Chemistry and Centre for “Nanostructured Interfaces and Surfaces-NIS”
- University of Torino
- 10125 Torino
- Italy
| | - Agata F. Lombardo
- Dipartimento di Ingegneria Elettronica
- Chimica e Ingegneria Industriale
- Università degli Studi di Messina
- 98166 Messina
- Italy
| | - Pavlo Ivanchenko
- Department of Chemistry and Centre for “Nanostructured Interfaces and Surfaces-NIS”
- University of Torino
- 10125 Torino
- Italy
| | - Yuriy Sakhno
- Dipartimento di Ingegneria Elettronica
- Chimica e Ingegneria Industriale
- Università degli Studi di Messina
- 98166 Messina
- Italy
| | - Giuseppe Trunfio
- Dipartimento di Ingegneria Elettronica
- Chimica e Ingegneria Industriale
- Università degli Studi di Messina
- 98166 Messina
- Italy
| | - Gianmario Martra
- Department of Chemistry and Centre for “Nanostructured Interfaces and Surfaces-NIS”
- University of Torino
- 10125 Torino
- Italy
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28
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Martra G, Deiana C, Sakhno Y, Barberis I, Fabbiani M, Pazzi M, Vincenti M. The Formation and Self-Assembly of Long Prebiotic Oligomers Produced by the Condensation of Unactivated Amino Acids on Oxide Surfaces. Angew Chem Int Ed Engl 2014; 53:4671-4. [DOI: 10.1002/anie.201311089] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Indexed: 11/11/2022]
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29
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Martra G, Deiana C, Sakhno Y, Barberis I, Fabbiani M, Pazzi M, Vincenti M. The Formation and Self-Assembly of Long Prebiotic Oligomers Produced by the Condensation of Unactivated Amino Acids on Oxide Surfaces. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201311089] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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30
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Calcio Gaudino E, Carnaroglio D, Nunes MAG, Schmidt L, Flores EMM, Deiana C, Sakhno Y, Martra G, Cravotto G. Fast TiO2-catalyzed direct amidation of neat carboxylic acids under mild dielectric heating. Catal Sci Technol 2014. [DOI: 10.1039/c4cy00038b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The development of green protocols for amide bond formation is a major socioeconomic goal for chemical and pharmaceutical industries and an important challenge for academic research.
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Affiliation(s)
- E. Calcio Gaudino
- Dipartimento di Scienza e Tecnologia del Farmaco and Interdepartmental Centre “Nanostructured Interfaces and Surfaces – NIS”
- University of Turin
- 10125 Torino, Italy
| | - D. Carnaroglio
- Dipartimento di Scienza e Tecnologia del Farmaco and Interdepartmental Centre “Nanostructured Interfaces and Surfaces – NIS”
- University of Turin
- 10125 Torino, Italy
| | - M. A. G. Nunes
- Dipartimento de Química
- Universidade Federal de Santa Maria
- Santa Maria, Brazil
| | - L. Schmidt
- Dipartimento de Química
- Universidade Federal de Santa Maria
- Santa Maria, Brazil
| | - E. M. M. Flores
- Dipartimento de Química
- Universidade Federal de Santa Maria
- Santa Maria, Brazil
| | - C. Deiana
- Department di Chimica and Interdepartmental Centre “Nanostructured Interfaces and Surfaces – NIS”
- University of Turin
- 10125 Torino, Italy
| | - Y. Sakhno
- Department di Chimica and Interdepartmental Centre “Nanostructured Interfaces and Surfaces – NIS”
- University of Turin
- 10125 Torino, Italy
| | - G. Martra
- Department di Chimica and Interdepartmental Centre “Nanostructured Interfaces and Surfaces – NIS”
- University of Turin
- 10125 Torino, Italy
| | - G. Cravotto
- Dipartimento di Scienza e Tecnologia del Farmaco and Interdepartmental Centre “Nanostructured Interfaces and Surfaces – NIS”
- University of Turin
- 10125 Torino, Italy
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