Prebiotic NH3 Formation: Insights from Simulations

Prebiotic Formation of Protoalkaloids within Alkaline Oceanic Hydrothermal Vents in the Hadean Seafloor as a Prerequisite for Evolutionary Biodiversity

The primordial origin of abiotic nitrogen fixation, which is not dependent on prokaryotes, reflects the importance of available nitrogenous compounds as an essential requirement for the emergence of life and evolutionary biodiversity. It has been hypothesized that synthesis of oxidized nitrogen in the form of nitrate (NO3−) and nitrite (NO₂⁻), occurred in the prebiotic anoxic Hadean atmosphere. The sustained influx of atmospheric NO₃⁻ and NO₂⁻ into prebiotic Hadean oceans have been proposed to provide the essential substrates for abiotic synthesis of compounds such as ammonia (NH₃) within oceanic alkaline hydrothermal vents in the seafloor. Because NH₃ is an essential chemical precursor for nitrogen-containing molecular components of proteins and nucleic acids, abiotic production in high concentrations within Hadean oceanic alkaline hydrothermal vents is required for the emergence of diverse life forms. The chemical evolution of nitrogenous compounds includes the functional development of alkaloids. This commentary aims to critically discuss the possible origin of nitrogen-containing alkaloids and evolutionary processes in higher organisms, including the diverse biomedical mechanisms involved.

Canonical, deprotonated, or zwitterionic? II. A computational study on amino acid interaction with the TiO2(110) rutile surface: comparison with the anatase (101) surface

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.

Recent Results on Computational Molecular Modeling of The Origins of Life

In the last decade of research in the origins of life, there has been an increase in the interest on theoretical molecular modeling methods aimed to improve the accuracy and speed of the algorithms that solve the molecular mechanics and chemical reactions of the matter. Research on the scenarios of prebiotic chemistry has also advanced. The presented work attempts to discuss the latest computational techniques and trends implemented so far. Although it is difficult to cover the full extent of the current publications, we tried to orient the reader into the modern tendencies and challenges faced by those who are in the origins of life field.

Effect of anion reorientation on proton mobility in the solid acids family CsHyXO4(X = S, P, Se,y= 1, 2) fromab initiomolecular dynamics simulations

The high temperature phases of the solid acids CsHSeO₄, CsHSO₄and CsH₂PO₄show extraordinary high proton conductivities, which are enabled by the interplay of high proton transfer rates and frequent anion reorientation.

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.

Redox and pH gradients drive amino acid synthesis in iron oxyhydroxide mineral systems

Iron oxyhydroxide minerals, known to be chemically reactive and significant for elemental cycling, are thought to have been abundant in early-Earth seawater, sediments, and hydrothermal systems. In the anoxic Fe²⁺-rich early oceans, these minerals would have been only partially oxidized and thus redox-active, perhaps able to promote prebiotic chemical reactions. We show that pyruvate, a simple organic molecule that can form in hydrothermal systems, can undergo reductive amination in the presence of mixed-valence iron oxyhydroxides to form the amino acid alanine, as well as the reduced product lactate. Furthermore, geochemical gradients of pH, redox, and temperature in iron oxyhydroxide systems affect product selectivity. The maximum yield of alanine was observed when the iron oxyhydroxide mineral contained 1:1 Fe(II):Fe(III), under alkaline conditions, and at moderately warm temperatures. These represent conditions that may be found, for example, in iron-containing sediments near an alkaline hydrothermal vent system. The partially oxidized state of the precipitate was significant in promoting amino acid formation: Purely ferrous hydroxides did not drive reductive amination but instead promoted pyruvate reduction to lactate, and ferric hydroxides did not result in any reaction. Prebiotic chemistry driven by redox-active iron hydroxide minerals on the early Earth would therefore be strongly affected by geochemical gradients of E_h, pH, and temperature, and liquid-phase products would be able to diffuse to other conditions within the sediment column to participate in further reactions.

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.

When the Surface Matters: Prebiotic Peptide-Bond Formation on the TiO2 (101) Anatase Surface through Periodic DFT-D2 Simulations

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.