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Life
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Minerals and Origins of Life
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Minerals and Origins of Life

A special issue of Life (ISSN 2075-1729).

Deadline for manuscript submissions: closed (1 August 2018) | Viewed by 49026

Special Issue Editors

Dr. Jean-Francois Lambert

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Guest Editor
Laboratoire de Réactivité de Surface, Sorbonne Université, 75005 Paris, France
Interests: reactivity of biomolecules at interfaces (identification of adsorption sites on oxide surfaces); adsorption of small biological molecules; prebiotic chemistry; intercalation-bridging of lamellar structures (PILS); nanocomposite materials
Dr. Maguy Jaber

E-Mail Website
Guest Editor
1. Laboratoire d’Archéologie Moléculaire et Structurale, Institut Universitaire de France
2. Sorbonne Université, 75005 Paris, France
Interests: clays and their hybrid derivatives; nanocomposites materials; reactivity of biomolecules on oxide surfaces; materials synthesis and characterization; nanomaterials; prebiotic chemistry; fossilisation; cultural heritage; historical pigments

Special Issue Information

Dear Colleagues,

When life arose on our planet, a complex mineral world was already present and certainly interacted with the first biomolecules, for better or for worse. This interaction involved their surfaces which are the obligate zone of contact with the outside world. How it channeled chemical evolution has been the subject of much speculation; specific roles for minerals have been invoked for the emergence of the three main distinguishing features of life: Information storage, metabolism, and compartmentalization.

At one time, the provocative idea was put forward that clays, not only guided the first steps toward life, but actually were the first living organisms, storing information in the sequence of their layers. While there is little evidence for this far-reaching claim, mineral surfaces may have supplied selectivity in adsorption and/or polymerization, thus selecting a subset in the space of possible proteins and nucleic acids. A lot remains to be understood concerning the molecular structure of relevant surfaces and the precise mechanisms of their interactions with biomolecules.

As regards the emergence of metabolic activity, mineral surfaces are well-known as catalysts (industrial  heterogeneous catalysis), but they can also have played the role of alternate reaction media, offering thermochemical conditions different from those in solution, and allowing to harness macroscopic gradients and cyclical variations in temperature and humidity to produce the molecular-level imbalances that are characteristic of life. This includes the storage of chemical energy in the form of molecular-scale concentration gradients, one of the most original features of bioenergetics, and the appearance of proto-metabolic cycles including reactions with mineral surfaces, some vestigial remains of which could perhaps still be found in metabolism.

Minerals may also have played a role in compartmentalization, opposing the deadly drive to dilution that would otherwise have destroyed emerging prebiotic systems. Any type of adsorption has the potential to maintain high local concentration, but the micro-, meso-, and macroporosity of minerals from zeolite to pumice, and the tunable porosity of clay minerals, seem most attractive in this respect.

In this Special Issue, we wish to invite contributions, in the form of both experimental studies and theoretical reflections, on the implication of the mineral world in these crucial aspects of the emergence of life, and the integration of such steps in plausible origins scenarios.

Dr. Jean-Francois Lambert
Dr. Maguy Jaber
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • heterogeneous catalysis
  • nucleotides
  • peptides
  • oxide minerals
  • sulfide minerals
  • clays
  • non-equilibrium
  • compartmentalization
  • adsorption
  • bioenergetics
  • protometabolism

Published Papers (7 papers)

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Research

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25 pages, 21312 KiB  
Article
How do Nucleotides Adsorb Onto Clays?
by Ulysse Pedreira-Segade, Jihua Hao, Angelina Razafitianamaharavo, Manuel Pelletier, Virginie Marry, Sébastien Le Crom, Laurent J. Michot and Isabelle Daniel
Life 2018, 8(4), 59; https://doi.org/10.3390/life8040059 - 27 Nov 2018
Cited by 27 | Viewed by 6486
Abstract
Adsorption of prebiotic building blocks is proposed to have played a role in the emergence of life on Earth. The experimental and theoretical study of this phenomenon should be guided by our knowledge of the geochemistry of the habitable early Earth environments, which [...] Read more.
Adsorption of prebiotic building blocks is proposed to have played a role in the emergence of life on Earth. The experimental and theoretical study of this phenomenon should be guided by our knowledge of the geochemistry of the habitable early Earth environments, which could have spanned a large range of settings. Adsorption being an interfacial phenomenon, experiments can be built around the minerals that probably exhibited the largest specific surface areas and were the most abundant, i.e., phyllosilicates. Our current work aims at understanding how nucleotides, the building blocks of RNA and DNA, might have interacted with phyllosilicates under various physico-chemical conditions. We carried out and refined batch adsorption studies to explore parameters such as temperature, pH, salinity, etc. We built a comprehensive, generalized model of the adsorption mechanisms of nucleotides onto phyllosilicate particles, mainly governed by phosphate reactivity. More recently, we used surface chemistry and geochemistry techniques, such as vibrational spectroscopy, low pressure gas adsorption, X-ray microscopy, and theoretical simulations, in order to acquire direct data on the adsorption configurations and localization of nucleotides on mineral surfaces. Although some of these techniques proved to be challenging, questioning our ability to easily detect biosignatures, they confirmed and complemented our pre-established model. Full article
(This article belongs to the Special Issue Minerals and Origins of Life)
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12 pages, 1843 KiB  
Article
Ultraviolet Irradiation on a Pyrite Surface Improves Triglycine Adsorption
by Santos Galvez-Martinez and Eva Mateo-Marti
Life 2018, 8(4), 50; https://doi.org/10.3390/life8040050 - 25 Oct 2018
Cited by 6 | Viewed by 4781
Abstract
We characterized the adsorption of triglycine molecules on a pyrite surface under several simulated environmental conditions by X-ray photoemission spectroscopy. The triglycine molecular adsorption on a pyrite surface under vacuum conditions (absence of oxygen) shows the presence of two different states for the [...] Read more.
We characterized the adsorption of triglycine molecules on a pyrite surface under several simulated environmental conditions by X-ray photoemission spectroscopy. The triglycine molecular adsorption on a pyrite surface under vacuum conditions (absence of oxygen) shows the presence of two different states for the amine functional group (NH2 and NH3+), therefore two chemical species (anionic and zwitterionic). On the other hand, molecular adsorption from a solution discriminates the NH2 as a unique molecular adsorption form, however, the amount adsorbed in this case is higher than under vacuum conditions. Furthermore, molecular adsorption on the mineral surface is even favored if the pyrite surface has been irradiated before the molecular adsorption occurs. Pyrite surface chemistry is highly sensitive to the chemical changes induced by UV irradiation, as XPS analysis shows the presence of Fe2O3 and Fe2SO4—like environments on the surface. Surface chemical changes induced by UV help to increase the probability of adsorption of molecular species and their subsequent concentration on the pyrite surface. Full article
(This article belongs to the Special Issue Minerals and Origins of Life)
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13 pages, 3305 KiB  
Article
Formamide Adsorption at the Amorphous Silica Surface: A Combined Experimental and Computational Approach
by Matteo Signorile, Clara Salvini, Lorenzo Zamirri, Francesca Bonino, Gianmario Martra, Mariona Sodupe and Piero Ugliengo
Life 2018, 8(4), 42; https://doi.org/10.3390/life8040042 - 23 Sep 2018
Cited by 13 | Viewed by 5075
Abstract
Mineral surfaces have been demonstrated to play a central role in prebiotic reactions, which are understood to be at the basis of the origin of life. Among the various molecules proposed as precursors for these reactions, one of the most interesting is formamide. [...] Read more.
Mineral surfaces have been demonstrated to play a central role in prebiotic reactions, which are understood to be at the basis of the origin of life. Among the various molecules proposed as precursors for these reactions, one of the most interesting is formamide. Formamide has been shown to be a pluripotent molecule, generating a wide distribution of relevant prebiotic products. In particular, the outcomes of its reactivity are strongly related to the presence of mineral phases acting as catalysts toward specific reaction pathways. While the mineral–products relationship has been deeply studied for a large pool of materials, the fundamental description of formamide reactivity over mineral surfaces at a microscopic level is missing in the literature. In particular, a key step of formamide chemistry at surfaces is adsorption on available interaction sites. This report aims to investigate the adsorption of formamide over a well-defined amorphous silica, chosen as a model mineral surface. An experimental IR investigation of formamide adsorption was carried out and its outcomes were interpreted on the basis of first principles simulation of the process, adopting a realistic model of amorphous silica. Full article
(This article belongs to the Special Issue Minerals and Origins of Life)
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Review

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44 pages, 6365 KiB  
Review
Role of Mineral Surfaces in Prebiotic Chemical Evolution. In Silico Quantum Mechanical Studies
by Albert Rimola, Mariona Sodupe and Piero Ugliengo
Life 2019, 9(1), 10; https://doi.org/10.3390/life9010010 - 17 Jan 2019
Cited by 47 | Viewed by 7234
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Minerals and Origins of Life)
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20 pages, 300 KiB  
Review
The Paleomineralogy of the Hadean Eon Revisited
by Shaunna M. Morrison, Simone E. Runyon and Robert M. Hazen
Life 2018, 8(4), 64; https://doi.org/10.3390/life8040064 - 17 Dec 2018
Cited by 25 | Viewed by 6437
Abstract
A preliminary list of plausible near-surface minerals present during Earth’s Hadean Eon (>4.0 Ga) should be expanded to include: (1) phases that might have formed by precipitation of organic crystals prior to the rise of predation by cellular life; (2) minerals associated with [...] Read more.
A preliminary list of plausible near-surface minerals present during Earth’s Hadean Eon (>4.0 Ga) should be expanded to include: (1) phases that might have formed by precipitation of organic crystals prior to the rise of predation by cellular life; (2) minerals associated with large bolide impacts, especially through the generation of hydrothermal systems in circumferential fracture zones; and (3) local formation of minerals with relatively oxidized transition metals through abiological redox processes, such as photo-oxidation. Additional mineral diversity arises from the occurrence of some mineral species that form more than one ‘natural kind’, each with distinct chemical and morphological characteristics that arise by different paragenetic processes. Rare minerals, for example those containing essential B, Mo, or P, are not necessary for the origins of life. Rather, many common minerals incorporate those and other elements as trace and minor constituents. A rich variety of chemically reactive sites were thus available at the exposed surfaces of common Hadean rock-forming minerals. Full article
(This article belongs to the Special Issue Minerals and Origins of Life)
41 pages, 1540 KiB  
Review
Catalytic/Protective Properties of Martian Minerals and Implications for Possible Origin of Life on Mars
by Teresa Fornaro, Andrew Steele and John Robert Brucato
Life 2018, 8(4), 56; https://doi.org/10.3390/life8040056 - 05 Nov 2018
Cited by 35 | Viewed by 7703
Abstract
Minerals might have played critical roles for the origin and evolution of possible life forms on Mars. The study of the interactions between the “building blocks of life” and minerals relevant to Mars mineralogy under conditions mimicking the harsh Martian environment may provide [...] Read more.
Minerals might have played critical roles for the origin and evolution of possible life forms on Mars. The study of the interactions between the “building blocks of life” and minerals relevant to Mars mineralogy under conditions mimicking the harsh Martian environment may provide key insight into possible prebiotic processes. Therefore, this contribution aims at reviewing the most important investigations carried out so far about the catalytic/protective properties of Martian minerals toward molecular biosignatures under Martian-like conditions. Overall, it turns out that the fate of molecular biosignatures on Mars depends on a delicate balance between multiple preservation and degradation mechanisms, often regulated by minerals, which may take place simultaneously. Such a complexity requires more efforts in simulating realistically the Martian environment in order to better inspect plausible prebiotic pathways and shed light on the nature of the organic compounds detected both in meteorites and on the surface of Mars through in situ analysis. Full article
(This article belongs to the Special Issue Minerals and Origins of Life)
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26 pages, 3564 KiB  
Review
Chemical Diversity of Metal Sulfide Minerals and Its Implications for the Origin of Life
by Yamei Li, Norio Kitadai and Ryuhei Nakamura
Life 2018, 8(4), 46; https://doi.org/10.3390/life8040046 - 10 Oct 2018
Cited by 35 | Viewed by 9601
Abstract
Prebiotic organic synthesis catalyzed by Earth-abundant metal sulfides is a key process for understanding the evolution of biochemistry from inorganic molecules, yet the catalytic functions of sulfides have remained poorly explored in the context of the origin of life. Past studies on prebiotic [...] Read more.
Prebiotic organic synthesis catalyzed by Earth-abundant metal sulfides is a key process for understanding the evolution of biochemistry from inorganic molecules, yet the catalytic functions of sulfides have remained poorly explored in the context of the origin of life. Past studies on prebiotic chemistry have mostly focused on a few types of metal sulfide catalysts, such as FeS or NiS, which form limited types of products with inferior activity and selectivity. To explore the potential of metal sulfides on catalyzing prebiotic chemical reactions, here, the chemical diversity (variations in chemical composition and phase structure) of 304 natural metal sulfide minerals in a mineralogy database was surveyed. Approaches to rationally predict the catalytic functions of metal sulfides are discussed based on advanced theories and analytical tools of electrocatalysis such as proton-coupled electron transfer, structural comparisons between enzymes and minerals, and in situ spectroscopy. To this end, we introduce a model of geoelectrochemistry driven prebiotic synthesis for chemical evolution, as it helps us to predict kinetics and selectivity of targeted prebiotic chemistry under “chemically messy conditions”. We expect that combining the data-mining of mineral databases with experimental methods, theories, and machine-learning approaches developed in the field of electrocatalysis will facilitate the prediction and verification of catalytic performance under a wide range of pH and Eh conditions, and will aid in the rational screening of mineral catalysts involved in the origin of life. Full article
(This article belongs to the Special Issue Minerals and Origins of Life)
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