The chemistry of prebiotic N-containing compounds in the atmosphere of Titan and primitive Earth beyond a holistic approach

<p> </p> <p>How did life emerge from inanimate matter? The processes that led from complex organic molecules to the first self-replicating systems are no longer at play and we cannot easily reconstruct them because we do not have a geological record of the period when the transition from simple molecules to the very first forms of “life” have occurred. The presence of stable hydrosphere is considered as the first milestone in the timeline of the abiotic origin of life theory, with the second milestone being the massive accumulation of organic compounds necessary for the transition from organic chemistry to the biochemistry of life. But how Earth became so rich in complex organic molecules – up to the point that life spontaneously evolved from them - is still a matter of debate. At that stage, the abundance of liquid water, indeed, represents an obstacle for organic synthesis. Two theories have been suggested to solve this paradox, which are usually referred to as <em>endogenous synthesis</em> and <em>exogenous synthesis</em> scenarios [1]. But in both cases, prebiotic molecules (that is, molecules which are simple to be formed in abiotic processes but contain the functional groups typical of biological molecules or have the capability to easily evolve into them) are formed in gaseous media. Indeed, gas-phase prebiotic molecules have been observed in the upper atmosphere of Titan, the massive moon of Saturn, as well as in the interstellar clouds and cometary comae.</p> <p>The comprehension of the chemical processes that lead from simple atomic/diatomic species to prebiotic complex chemicals is an important part of the study on the origin of life. The study of these preliminary steps might seem relatively simple compared to the characterization of the other unknown phenomena that have led to the first living organisms. Nevertheless, the formation mechanisms of many of the prebiotic molecules that we observe nowadays in proto-stellar clouds or comets/meteorites or planetary atmospheres are far from being understood, while a comprehension of those processes can certainly help to set the stage for the emergence of life to occur.</p> <p>For this reason, in our laboratory we have started a systematic investigation of gas-phase reactions leading to simple prebiotic molecules within the Italian National Project of Astrobiology—Life in Space—Origin, Presence, Persistence of Life in Space, from Molecules to Extremophiles [2].</p> <p>In particular, by combining an experimental and theoretical approach, we have investigated a series of bimolecular reactions under single collision conditions. The aim is to provide detailed information on the elementary reactions which are employed in photochemical models of planetary atmosphere and cometary comae [3]. In particular, we have investigated several reactive systems leading to the formation of nitriles (such as dicyanoacetylene) and imines (such as ethanimine), as well as reactive radicals that can further react in subsequent reactions. We have also investigated reactions involving nitrogen atoms and aromatic compounds (benzene, pyridine, toluene) to address the role of these compounds in the growth of N-containing aromatic compounds, a proxy of DNA and RNA bases. In this contribution, the main results concerning the reactions involving atomic nitrogen, N, or cyano radicals, CN, and cyanoacetylene, acrylonitrile, benzene, toluene and pyridine will be illustrated and the implications for prebiotic chemistry noted.</p> <p>[1] C. Chyba and C. Sagan. Nature 1992, 355, 125.</p> <p>[2] S. Onofri, N. Balucani, V. Barone et al. Astrobiology 2020, 20, 580. DOI: 10.1089/ast.2020.2247</p> <p>[3] N. Balucani. Physics of Life Reviews 2020, 34–35, 136. DOI: 10.1016/j.plrev.2019.03.0061571-0645</p>

Behavior of light elements in iron-silicate-water-sulfur system during early Earth’s evolution

Hydrogen (H) is considered to be one of the candidates for light elements in the Earth’s core, but the amount and timing of delivery have been unknown. We investigated the effects of sulfur (S), another candidate element in the core, on deuteration of iron (Fe) in iron–silicate–water system up to 6–12 GPa, ~ 1200 K using in situ neutron diffraction measurements. The sample initially contained saturated water (D2O) as Mg(OD)2 in the ideal composition (Fe–MgSiO3–D2O) of the primitive Earth. In the existence of water and sulfur, phase transitions of Fe, dehydration of Mg(OD)2, and formation of iron sulfide (FeS) and silicates occurred with increasing temperature. The deuterium (D) solubility (x) in iron deuterides (FeDx) increased with temperature and pressure, resulting in a maximum of x = 0.33(4) for the hydrous sample without S at 11.2 GPa and 1067 K. FeS was hardly deuterated until Fe deuteration had completed. The lower D concentrations in the S-containing system do not exceed the miscibility gap (x < ~ 0.4). Both H and S can be incorporated into solid Fe and other light elements could have dissolved into molten iron hydride and/or FeS during the later process of Earth’s evolution.

Prebiotic Chemical Refugia: Multifaceted Scenario for the Formation of Biomolecules in Primitive Earth

The origin of life was a cosmic event happened on primitive Earth. A critical problem to better understand the origins of life in Earth is to glimpse in which chemical scenarios the basic building blocks of biological molecules could be produced. Classic works in pre-biotic chemistry frequently considered early Earth as a homogeneous atmosphere constituted by chemical elements such as methane (CH4), ammonia (NH3), water (H2O), hydrogen (H2) and hydrogen sulfide (H2S). Under that scenario, Stanley Miller was capable to produce amino acids and solved the question about the origin of proteins. Conversely, the origin of nucleic acids has tricked scientists for decades as nucleotides are complex though necessary molecules to allow the existence of life. Here we review possible chemical scenarios that allowed not only the formation of nucleotides but also other significant biomolecules. We aim to provide a theoretical solution for the origin of biomolecules at specific sites named &ldquo;Prebiotic Chemical Refugia&rdquo;. A prebiotic chemical refugium should therefore be understood as a geographic site in prebiotic Earth on which certain chemical elements were accumulated in higher proportion than expected, facilitating the production of basic biomolecules. Plus, this higher proportion should not be understood as static, but dynamic; once the physicochemical conditions of our planet changed periodically. This different concentration of elements, together with geochemical and astronomical changes along days, synodic months and years provided somewhat periodic changes in temperature, pressure, electromagnetic fields, and conditions of humidity; among other features. Recent and classic works suggesting most likely prebiotic refugia on which the main building blocks of biological molecules might be accumulated are reviewed and discussed.

Neopanspermia – Evidence That Life Continuously Arrives at the Earth from Space

The theory of panspermia in a variety of forms remains an important theory to account for the origin of life on Earth and possibly also on other planetary bodies orbiting the “habitable zones” of stars. A form of panspermia we review here, that can be called neopanspermia, encapsulates the concept that a continuing infall of microbiota from space contributes both to the inception of life on Earth and its subsequent evolution. We discuss the development of the theory of panspermia and show how, over the past decade, we have used balloon-borne samplers (lofted to heights approaching 30km) to isolate unusual Biological Entities (BEs) which, we maintain, are continuously arriving at the Earth from space. These BEs are carbon-based, show bilateral symmetry, contain DNA and are in the range 10-40 micrometres in dimension. Their sizes are an order of magnitude higher than par-ticles (including bacteria and viruses) of terrestrial origin that are normally recovered in the strato-sphere. The fact that Earth-organisms (e.g. pollen grains, grass-shards and fungal spores) have not been found in our samples provides additional evidence that the isolated BEs originate from space and are of extraterrestrial provenance. We propose that such incoming microorganisms led to the emergence of life on the primitive Earth between 3.83 and 4 billion years ago and thereafter have continuously contributed to its evolution.

Seven amino acid types suffice to reconstruct the core fold of RNA polymerase

The extant complex proteins must have evolved from ancient short and simple ancestors. Nevertheless, how such prototype proteins emerged on the primitive earth remains enigmatic. The double-psi beta-barrel (DPBB) is one of the oldest protein folds and conserved in various fundamental enzymes, such as the core domain of RNA polymerase. Here, by reverse engineering a modern DPBB domain, we reconstructed its evolutionary pathway started by “interlacing homo- dimerization” of a half-size peptide, followed by gene duplication and fusion. Furthermore, by simplifying the amino acid repertoire of the peptide, we successfully created the DPBB fold with only seven amino acid types (Ala, Asp, Glu, Gly, Lys, Arg, and Val), which can be coded by only GNN and ARR (R = A or G) codons in the modern translation system. Thus, the DPBB fold could have been materialized by the early translation system and genetic code.

Dynamic Self-organization in an Open Reaction Network as a Fundamental Mechanism for the Emergence of Life

<p>The emergence of life on the earth has attracted intense attention but the mechanism of it still remains an unsolved question. A key problem is that it has been left unclear why a living organism, which is regarded as an open reaction system, can demonstrate dynamic self-organization leading to highly-ordered structures and adaptive and evolutionary behavior. This paper shows by computer simulation that an open reaction network, which is characterized as a network of flexible constituent elements and irreversible processes, is converted to a self-organized system with adaptive and evolutionary ability when it has reached a fully-balanced stationary state. Strikingly, this result indicates that dynamic self-organization spontaneously emerges in a prebiotic chemical system placed under constant thermodynamic forces according to the second law of thermodynamics, not against it. The dynamic self-organization has potential for producing highly ordered chemical structures through evolution and is expected to have played a fundamental role in the emergence of life on the primitive earth.</p>

Dynamic Self-organization in an Open Reaction Network as a Fundamental Mechanism for the Emergence of Life

<p>The emergence of life on the earth has attracted intense attention but the mechanism of it still remains an unsolved question. A key problem is that it has been left unclear why a living organism, which is regarded as an open reaction system, can demonstrate dynamic self-organization leading to highly-ordered structures and adaptive and evolutionary behavior. This paper shows by computer simulation that an open reaction network, which is characterized as a network of flexible constituent elements and irreversible processes, is converted to a self-organized system with adaptive and evolutionary ability when it has reached a fully-balanced stationary state. Strikingly, this result indicates that dynamic self-organization spontaneously emerges in a prebiotic chemical system placed under constant thermodynamic forces according to the second law of thermodynamics, not against it. The dynamic self-organization has potential for producing highly ordered chemical structures through evolution and is expected to have played a fundamental role in the emergence of life on the primitive earth.</p>

Dynamic Self-organization in an Open Reaction Network as a Fundamental Mechanism for the Emergence of Life

The emergence of life on the earth has attracted intense attention but the mechanism of it still remains an unsolved question. A key problem is that it has been left unclear why a living organism, which is regarded as an open reaction system, can demonstrate dynamic self-organization leading to highly-ordered structures and adaptive and evolutionary behavior. This paper shows by computer simulation that (1) an open reaction network is a network of irreversible processes and for this reason spontaneously reaches a stationary state and (2) a stationary state thus formed is stable against a fluctuation, namely it has self-organizing ability. Strikingly, self-organizing ability can emerge in a prebiotic chemical system with no special mechanism for overcoming disturbances by the second law of thermodynamics. The above self-organizing ability leads to adaptive and evolutionary behavior and has large potential for producing highly organized chemical structures, and is expected to have played a fundamental role in the emergence of life on the primitive earth.

Dynamic Self-organization in an Open Reaction Network as a Fundamental Mechanism for the Emergence of Life

The emergence of life on the earth has attracted intense attention but the mechanism of it still remains an unsolved question. A key problem is that it has been left unclear why a living organism, which is regarded as an open reaction system, can demonstrate dynamic self-organization leading to highly-ordered structures and adaptive and evolutionary behavior. This paper shows by computer simulation that (1) an open reaction network is a network of irreversible processes and for this reason spontaneously reaches a stationary state and (2) a stationary state thus formed is stable against a fluctuation, namely it has self-organizing ability. Strikingly, self-organizing ability can emerge in a prebiotic chemical system with no special mechanism for overcoming disturbances by the second law of thermodynamics. The above self-organizing ability leads to adaptive and evolutionary behavior and has large potential for producing highly organized chemical structures, and is expected to have played a fundamental role in the emergence of life on the primitive earth.