Ab initio simulations of desorption and reactivity of glycine at a water-pyrite interface at "iron-sulfur world" prebiotic conditions

Synthesis and Stability of Biomolecules in C-H-O-N Fluids under Earth's Upper Mantle Conditions

How life started on Earth is an unsolved mystery. There are various hypotheses for the location ranging from outer space to the seafloor, subseafloor, or potentially deeper. Here, we applied extensive ab initio molecular dynamics simulations to study chemical reactions between NH3, H2O, H2, and CO at pressures (P) and temperatures (T) approximating the conditions of Earth's upper mantle (i.e., 10-13 GPa, 1000-1400 K). Contrary to the previous assumptions that large organic molecules might readily disintegrate in aqueous solutions at extreme P-T conditions, we found that many organic compounds formed without any catalysts and persisted in C-H-O-N fluids under these extreme conditions, including glycine, ribose, urea, and uracil-like molecules. Particularly, our free-energy calculations showed that the C-N bond is thermodynamically stable at 10 GPa and 1400 K. Moreover, while the pyranose (six-membered ring) form of ribose is more stable than the furanose (five-membered ring) form at ambient conditions, we found that the formation of the five-membered-ring form of ribose is thermodynamically more favored at extreme conditions, which is consistent with the exclusive incorporation of β-d-ribofuranose in RNA. We have uncovered a previously unexplored pathway through which the crucial biomolecules could be abiotically synthesized from geofluids in the deep interior of Earth and other planets, and these formed biomolecules could potentially contribute to the early stage of the emergence of life.

Tracing the Primordial Chemical Life of Glycine: A Review from Quantum Chemical Simulations

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.

Toward the Specificity of Bare Nanomaterial Surfaces for Protein Corona Formation

Aiming at creating smart nanomaterials for biomedical applications, nanotechnology aspires to develop a new generation of nanomaterials with the ability to recognize different biological components in a complex environment. It is common opinion that nanomaterials must be coated with organic or inorganic layers as a mandatory prerequisite for applications in biological systems. Thus, it is the nanomaterial surface coating that predominantly controls the nanomaterial fate in the biological environment. In the last decades, interdisciplinary studies involving not only life sciences, but all branches of scientific research, provided hints for obtaining uncoated inorganic materials able to interact with biological systems with high complexity and selectivity. Herein, the fragmentary literature on the interactions between bare abiotic materials and biological components is reviewed. Moreover, the most relevant examples of selective binding and the conceptualization of the general principles behind recognition mechanisms were provided. Nanoparticle features, such as crystalline facets, density and distribution of surface chemical groups, and surface roughness and topography were encompassed for deepening the comprehension of the general concept of recognition patterns.

Defects on a pyrite(100) surface produce chemical evolution of glycine under inert conditions: experimental and theoretical approaches

The presence of non-stoichiometric sites on the pyrite(100) surface makes it a suitable substrate for driving the chemical evolution of the amino acid glycine over time, even under inert conditions. Spectroscopic molecular fingerprints prove a transition process from a zwitterionic species to an anionic species over time on the monosulfide enriched surface. By combining experimental and theoretical approaches, we propose a surface mechanism where the interaction between the amino acid species and the surface will be driven by the quenching of the surface states at Fe sites and favoured by sulfur vacancies. This study demonstrates the potential capability of pyrite to act as a surface catalyst.

Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinello Ab Initio Simulations

The catalytic effects of complex minerals or meteorites are often mentioned as important factors for the origins of life. To assess the possible role of nanoconfinement within a catalyst consisting of montmorillonite (MMT) and the impact of local electric field on the formation efficiency of the simple hypothetical precursors of nucleic acid bases or amino acids, we performed ab initio Car–Parrinello molecular dynamics simulations. We prepared four condensed-phase systems corresponding to previously suggested prototypes of a primordial soup. We monitored possible chemical reactions occurring within gas-like bulk and MMT-confined four simulation boxes on a 20-ps time scale at 1 atm and 300 K, 400 K, and 600 K. Elevated temperatures did not affect the reactivity of the elementary components of the gas-like boxes considerably; however, the presence of the MMT nanoclay substantially increased the formation probability of new molecules. Approximately 20 different new compounds were found in boxes containing carbon monoxide or formaldehyde molecules. This observation and an analysis of the atom–atom radial distribution functions indicated that the presence of Ca²⁺ ions at the surface of the internal MMT cavities may be an important factor in the initial steps of the formation of complex molecules at the early stages of the Earth’s history.

Pyrite and Organic Compounds Coexisting in Intrusive Mafic Xenoliths (Hyblean Plateau, Sicily): Implications for Subsurface Abiogenesis

Pyrite and organic matter closely coexist in some hydrothermally-altered gabbroic xenoliths from the Hyblean Plateau, Sicily. The representative sample consists of plagioclase, Fe-oxides, clinopyroxene, pyrite and minor amounts of many other minerals. Plagioclase displays incipient albitization, clinopyroxene is deeply corroded. Pyrite grains are widely replaced by spongy-textured magnetite, which locally hosts Ca-(and Fe-)sulfate micrograins and blebs of condensed organic matter. Whole-rock trace element distribution evidences that incompatible elements, particularly the fluid-mobile Ba, U and Pb, are significantly enriched with respect to N-MORB values. The mineralogical and geochemical characteristics of the sample, and its U-Pb zircon age of 216.9 ± 6.7 MA, conform to the xenolith-based viewpoint that the unexposed Hyblean basement is a relict of the Ionian Tethys lithospheric domain, mostly consisting of abyssal-type serpentinized peridotites with small gabbroic intrusions. Circulating hydrothermal fluids there favored the formation of hydrocarbons trough Fischer-Tropsch-type organic synthesis, giving also rise to sulfidization episodes. Subsequent variations in temperature and redox conditions of the system induced partial de-sulfidization, Fe-oxides precipitation and sulfate-forming reactions, also promoting poly-condensation and aromatization of the already-formed hydrocarbons. Here we show organic matter adhering to a crystal face of a microscopic pyrite grain. Pyrite surfaces, as abiotic analogues of enzymes, can adsorb and concentrate organic molecules, also acting as catalysts for a broad range of proto-biochemical reactions. The present data therefore may support established abiogenesis models suggesting that pyrite surfaces carried out primitive metabolic cycles in suitable environments of the early Earth, such as endolithic recesses in mafic rocks permeated by hydrothermal fluids.

Role of Mineral Surfaces in Prebiotic Chemical Evolution. In Silico Quantum Mechanical Studies

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.

Prebiotic NH3 Formation: Insights from Simulations

Simulations of prebiotic NH₃ synthesis from NO₃⁻ and NO₂⁻ on pyrite surfaces under hydrothermal conditions are reported. Ab initio metadynamics calculations have successfully explored the full reaction path which explains earlier experimental observations. We have found that the reaction mechanism can be constructed from stepwise single atom transfers which are compatible with the expected reaction time scales. The roles of the hot-pressurized water and of the pyrite surfaces have been addressed. The mechanistic picture that emerged from the simulations strengthens the theory of chemoautotrophic origin of life by providing plausible reaction pathways for the formation of ammonia within the iron-sulfur-world scenario.

Pyrite in contact with supercritical water: the desolation of steam

The supercritical water and pyrite interface has been studied by DFT calculations. A surprisingly dry surface has been found which points to a new reactivity under extreme conditions which has relevance in the iron–sulfur world prebiotic chemistry of the early Earth.

Adsorption of amino acids on the magnetite-(111)-surface: a force field study

Magnetite (Fe(3)O(4)) is an important biomineral, e.g., used by magnetotactic bacteria. The connection between the inorganic magnetite-(111)-surface and the organic parts of the bacteria is the magnetosome membrane. The membrane is built by different magnetosome membrane proteins (MMPs), which are dominated by the four amino acids glycine (Gly), aspartic acid (Asp), leucine (Leu) and glutamic acid (Glu). Force field simulations of the interaction of the magnetite-(111)-surface and the main amino acid compounds offer the possibility to investigate if and how the membrane proteins could interact with the mineral surface thus providing an atomistic view on the respective binding sites. In a force field simulation the four amino acids were docked on the Fe-terminated magnetite-(111)-surface. The results show that it is energetically favorable for the amino acids to adsorb on the surface with Fe-O-distances between 2.6 Å and 4.1 Å. The involved O-atoms belong to the carboxyl-group (Asp and Glu) or to the carboxylate-group (Gly, Leu and Glu). Electrostatic interactions dominate the physisorption of the amino acids. During the simulations, according to the frequency of the best results, the global minimum for the docking interaction could be attained for all amino acids analyzed.

Biomineralization: a proposed evolutionary origin for inorganic cofactors of enzymes

In this paper, three different reactions of nanoparticles and proteins are explained. As a model system, the interactions of birnessite, which is a common manganese oxide in the environment, and bovine serum albumin, as a protein that has a strong affinity for a variety of inorganic molecules, are studied. The author proposes that the cofactor-formation in particular enzymes may be considered as a biomineralization in the presence of the protein. One of the numerous and very small nanoparticles produced in the presence of protein could be formed in an appropriate location in proteins and be used as a primitive inorganic core (cofactor) of enzyme.

Formation versus hydrolysis of the peptide bond from a quantum-mechanical viewpoint: The role of mineral surfaces and implications for the origin of life

The condensation (polymerization by water elimination) of molecular building blocks to yield the first active biopolymers (e.g. of amino acids to form peptides) during primitive Earth is an intriguing question that nowadays still remains open since these processes are thermodynamically disfavoured in highly dilute water solutions. In the present contribution, formation and hydrolysis of glycine oligopeptides occurring on a cluster model of sanidine feldspar (001) surface have been simulated by quantum mechanical methods. Results indicate that the catalytic interplay between Lewis and Brønsted sites both present at the sanidine surface, in cooperation with the London forces acting between the biomolecules and the inorganic surface, plays a crucial role to: i) favour the condensation of glycine to yield oligopeptides as reaction products; ii) inhibit the hydrolysis of the newly formed oligopeptides. Both facts suggest that mineral surfaces may have helped in catalyzing, stabilizing and protecting from hydration the oligopeptides formed in the prebiotic era.

Adsorption and polymerization of amino acids on mineral surfaces: a review

The present paper offers a review of recent (post-1980) work on amino acid adsorption and thermal reactivity on oxide and sulfide minerals. This review is performed in the general frame of evaluating Bernal's hypothesis of prebiotic polymerization in the adsorbed state, but written from a surface scientist's point of view. After a general discussion of the thermodynamics of the problem and exactly what effects surfaces should have to make adsorbed-state polymerization a viable scenario, we examine some practical difficulties in experimental design and their bearing on the conclusions that can be drawn from extant works, including the relevance of the various available characterization techniques. We then present the state of the art concerning the mechanisms of the interactions of amino acids with mineral surfaces, including results from prebiotic chemistry-oriented studies, but also from several different fields of application, and discuss the likely consequences for adsorption selectivities. Finally, we briefly summarize the data concerning thermally activated amide bond formation of adsorbed amino acids without activating agents. The reality of the phenomenon is established beyond any doubt, but our understanding of its mechanism and therefore of its prebiotic potential is very fragmentary. The review concludes with a discussion of future work needed to fill the most conspicuous gaps in our knowledge of amino acids/mineral surfaces systems and their reactivity.

Aluminosilicate surfaces as promoters for peptide bond formation: an assessment of Bernal's hypothesis by ab initio methods

The role in prebiotic chemistry that Brønsted and Lewis sites, both present at the surface of common aluminosilicates, may have played in favoring the peptide bond formation has been addressed by ab initio methods within a cluster approach. B3LYP/6-31+G(d,p) free energy potential energy surfaces have been fully characterized for the model reaction glycine + NH3 --> 2-NH2 acetamide (mimicking the true 2 Gly --> GlyGly one) occurring on (i) a Lewis site, (ii) a Brønsted site, and (iii) a combined action of Lewis/Brønsted sites. Compared to the gas-phase (gp) activation free energy of 50 kcal/mol, the Lewis site alone reduces the gp barrier to 41 kcal/mol, whereas the activation by the Brønsted site dramatically reduces the barrier to about 18 kcal/mol. Nevertheless, formation of the prereactant complex in this latter case will rarely occur, since water will easily displace the glycine molecule interacting with the Brønsted site. However, if a realistic feldspar surface with neighboring Brønsted and Lewis sites is considered, the proper prereactant complex is highly stabilized by a simultaneous interaction with the Lewis and the Brønsted sites, in such a way that the Lewis site strongly attaches the glycine molecule to the surface whereas the Brønsted site efficiently catalyzes the condensation reaction, showing that the interplay between Lewis/Brønsted sites is an important issue. The free energy barrier computed for the realistic feldspar surface model is 26 kcal/mol. The role of dispersive interactions on the free energy barrier and the stabilization of the final product, not accounted for by the B3LYP functional, have been estimated and shown to be substantial. Speculations about further elongation of the formed dipeptide have been put forward on the basis of the relatively strong interaction energy of the formed GlyGly dipeptide with the aluminosilicate surface.