The Role of Aqueous Aerosols in the “Glyoxylate Scenario”: An Experimental Approach

The hierarchical organization of autocatalytic reaction networks and its relevance to the origin of life

Prior work on abiogenesis, the emergence of life from non-life, suggests that it requires chemical reaction networks that contain self-amplifying motifs, namely, autocatalytic cores. However, little is known about how the presence of multiple autocatalytic cores might allow for the gradual accretion of complexity on the path to life. To explore this problem, we develop the concept of a seed-dependent autocatalytic system (SDAS), which is a subnetwork that can autocatalytically self-maintain given a flux of food, but cannot be initiated by food alone. Rather, initiation of SDASs requires the transient introduction of chemical “seeds.” We show that, depending on the topological relationship of SDASs in a chemical reaction network, a food-driven system can accrete complexity in a historically contingent manner, governed by rare seeding events. We develop new algorithms for detecting and analyzing SDASs in chemical reaction databases and describe parallels between multi-SDAS networks and biological ecosystems. Applying our algorithms to both an abiotic reaction network and a biochemical one, each driven by a set of simple food chemicals, we detect SDASs that are organized as trophic tiers, of which the higher tier can be seeded by relatively simple chemicals if the lower tier is already activated. This indicates that sequential activation of trophically organized SDASs by seed chemicals that are not much more complex than what already exist could be a mechanism of gradual complexification from relatively simple abiotic reactions to more complex life-like systems. Interestingly, in both reaction networks, higher-tier SDASs include chemicals that might alter emergent features of chemical systems and could serve as early targets of selection. Our analysis provides computational tools for analyzing very large chemical/biochemical reaction networks and suggests new approaches to studying abiogenesis in the lab.

The level of complexity seen in even the simplest living system is too great to have arisen in its current form without a long history of complexification. In this paper, we explore the view that open environments on the early Earth that received an ongoing flux of food chemicals could have complexified gradually by the sequential activation of autocatalytic chemical reaction systems. We develop the concept of seed-dependent autocatalytic systems (SDASs)–subnetworks whose components can self-propagate once activated by “seed” molecules, which might result from rare reactions or import from other environments. We developed new computational tools for detecting SDASs in reaction databases and determining if they are hierarchically organized, such that the activation of a lower-tier SDAS allows a higher-tier SDAS to then be seeded, much like the relationship between producers and consumers in an ecosystem. We apply our algorithms to two chemical reaction networks, one biological and the other abiotic, and find that both contain hierarchically organized SDASs. These results support the fundamental continuity of the way that the chemistry of non-life and life is organized and suggest new classes of laboratory experiment.

Prebiotic synthesis of noncanonical nucleobases under plausible alkaline hydrothermal conditions

Herein, the potential of alkaline hydrothermal environments for the synthesis of possible ancestral pre-RNA nucleobases using cyanide as a primary source of carbon and nitrogen is described. Water cyanide polymerizations were assisted by microwave radiation to obtain high temperature and a relatively high pressure (MWR, 180 °C, 15 bar) and were also carried out using a conventional thermal system (CTS, 80 °C, 1 bar) to simulate subaerial and aerial hydrothermal conditions, respectively, on the early Earth. For these syntheses, the initial concentration of cyanide and the diffusion effects were studied. In addition, it is well known that hydrolysis conditions are directly related to the amount and diversity of organic molecules released from cyanide polymers. Thus, as a first step, we studied the effect of several hydrolysis procedures, generally used in prebiotic chemistry, on some of the potential pre-RNA nucleobases of interest, together with some of their isomers and/or deamination products, also presumably formed in these complex reactions. The results show that the alkaline hydrothermal scenarios with a relatively constant pH are good geological scenarios for the generation of noncanonical nucleobases using cyanide as a prebiotic precursor.

Cyanide as a primordial reductant enables a protometabolic reductive glyoxylate pathway

Investigation of prebiotic metabolic pathways is predominantly based on abiotically replicating the reductive citric acid cycle. While attractive from a parsimony point of view, attempts using metal/mineral-mediated reductions have produced complex mixtures with inefficient and uncontrolled reactions. Here we show that cyanide acts as a mild and efficient reducing agent mediating abiotic transformations of tricarboxylic acid intermediates and derivatives. The hydrolysis of the cyanide adducts followed by their decarboxylation enables the reduction of oxaloacetate to malate and of fumarate to succinate, whereas pyruvate and α-ketoglutarate themselves are not reduced. In the presence of glyoxylate, malonate and malononitrile, alternative pathways emerge that bypass the challenging reductive carboxylation steps to produce metabolic intermediates and compounds found in meteorites. These results suggest a simpler prebiotic forerunner of today's metabolism, involving a reductive glyoxylate pathway without oxaloacetate and α-ketoglutarate-implying that the extant metabolic reductive carboxylation chemistries are an evolutionary invention mediated by complex metalloproteins.

p-Aminobenzoic acid protonation dynamics in an evaporating droplet by ab initio molecular dynamics

Protonation equilibria are known to vary from the bulk to microdroplet conditions, which could induce many chemical and physical phenomena. Protonated p-aminobenzoic acid (PABA + H⁺) can be considered a model for probing the protonation dynamics in an evaporating droplet, as its protonation equilibrium is highly dependent on the formation conditions from solution via atmospheric pressure ionization sources. Experiments using diverse experimental techniques have shown that protic solvents allow formation of the O-protomer (PABA protonated in the carboxylic acid group) stable in the gas phase, while aprotic solvents yield the N-protomer (protonated in the amino group) that is the most stable protomer in solution. In this work, we explore the protonation equilibrium of PABA solvated by different numbers of water molecules (n = 0 to 32) using ab initio molecular dynamics. For n = 8-32, the protonation is either at the NH₂ group or in the solvent network. The solvent network interacts with the carboxylic acid group, but there is no complete proton transfer to form the O-protomer. For smaller clusters, however, solvent-mediated proton transfers to the carboxylic acid were observed, both via the Grotthuss mechanism and the vehicle or shuttle mechanism (for n = 1 and 2). Thermodynamic considerations allowed a description of the origins of the kinetic trapping effect, which explains the observation of the solution structure in the gas phase. This effect likely occurs in the final evaporation steps, which are outside the droplet size range covered by previous classical molecular dynamics simulations of charged droplets. These results may be considered relevant in determining the nature of the species observed in the ubiquitous ESI based mass spectrometry analysis, and in general for droplet chemistry, explaining how protonation equilibria are drastically changed from bulk to microdroplet conditions.

A Lizardite-HCN Interaction Leading the Increasing of Molecular Complexity in an Alkaline Hydrothermal Scenario: Implications for Origin of Life Studies

Hydrogen cyanide, HCN, is considered a fundamental molecule in chemical evolution. The named HCN polymers have been suggested as precursors of important bioorganics. Some novel researches have focused on the role of mineral surfaces in the hydrolysis and/or polymerization of cyanide species, but until now, their role has been unclear. Understanding the role of minerals in chemical evolution processes is crucial because minerals undoubtedly interacted with the organic molecules formed on the early Earth by different process. Therefore, we simulated the probable interactions between HCN and a serpentinite-hosted alkaline hydrothermal system. We studied the effect of serpentinite during the thermolysis of HCN at basic conditions (i.e., HCN 0.15 M, 50 h, 100 °C, pH > 10). The HCN-derived thermal polymer and supernatant formed after treatment were analyzed by several complementary analytical techniques. The results obtained suggest that: (I) the mineral surfaces can act as mediators in the mechanisms of organic molecule production such as the polymerization of HCN; (II) the thermal and physicochemical properties of the HCN polymer produced are affected by the presence of the mineral surface; and (III) serpentinite seems to inhibit the formation of bioorganic molecules compared with the control (without mineral).

A Comprehensive Review of HCN-Derived Polymers

HCN-derived polymers are a heterogeneous group of complex substances synthesized from pure HCN; from its salts; from its oligomers, specifically its trimer and tetramer, amino-nalono-nitrile (AMN) and diamino-maleo-nitrile (DAMN), respectively; or from its hydrolysis products, such as formamide, under a wide range of experimental conditions. The characteristics and properties of HCN-derived polymers depend directly on the synthetic conditions used for their production and, by extension, their potential applications. These puzzling systems have been known mainly in the fields of prebiotic chemistry and in studies on the origins of life and astrobiology since the first prebiotic production of adenine by Oró in the early years of the 1960s. However, the first reference regarding their possible role in prebiotic chemistry was mentioned in the 19th century by Pflüger. Currently, HCN-derived polymers are considered keys in the formation of the first and primeval protometabolic and informational systems, and they may be among the most readily formed organic macromolecules in the solar system. In addition, HCN-derived polymers have attracted a growing interest in materials science due to their potential biomedical applications as coatings and adhesives; they have also been proposed as valuable models for multifunctional materials with emergent properties such as semi-conductivity, ferroelectricity, catalysis and photocatalysis, and heterogeneous organo-synthesis. However, the real structures and the formation pathways of these fascinating substances have not yet been fully elucidated; several models based on either computational approaches or spectroscopic and analytical techniques have endeavored to shed light on their complete nature. In this review, a comprehensive perspective of HCN-derived polymers is presented, taking into account all the aspects indicated above.

A dual perspective on the microwave-assisted synthesis of HCN polymers towards the chemical evolution and design of functional materials

In this paper, the first study on NH4CN polymerization induced by microwave radiation is described, where a singular kinetic behaviour, especially when this reaction is conducted in the absence of air, is found. As a result, a complex conjugated N-heterocyclic polymer system is obtained, whose properties are very different, and even improved according to morphological features, characterized by their X-ray diffraction patterns and scanning electron microscopy analysis, with respect to those produced under conventional thermal treatment. In addition, a wide variety of relevant bioorganics have been identified, such as amino acids, nucleobases, co-factors, etc., from the synthetized NH4CN polymers. These particular families of polymers are of high interest in the fields of astrobiology and prebiotic chemistry and, more recently, in the development of smart multifunctional materials. From an astrobiological perspective, microwave-driven syntheses may simulate hydrothermal environments, which are considered ideal niches for increasing organic molecular complexity, and eventually as scenarios for an origin of life. From an industrial point of view and for potential applications, a microwave irradiation process leads to a notable decrease in the reaction times, and tune the properties of these new series macromolecular systems. The characteristics found for these materials encourage the development of further systematic research on this alternative HCN polymerization.

Characterization of HCN-Derived Thermal Polymer: Implications for Chemical Evolution

Hydrogen cyanide (HCN)-derived polymers have been recognized as sources of relevant organic molecules in prebiotic chemistry and material sciences. However, there are considerable gaps in the knowledge regarding the polymeric nature, the physicochemical properties, and the chemical pathways along polymer synthesis. HCN might have played an important role in prebiotic hydrothermal environments; however, only few experiments use cyanide species considering hydrothermal conditions. In this work, we synthesized an HCN-derived thermal polymer simulating an alkaline hydrothermal environment (i.e., HCN (l) 0.15 M, 50 h, 100 °C, pH approximately 10) and characterized its chemical structure, thermal behavior, and the hydrolysis effect. Elemental analysis and infrared spectroscopy suggest an important oxidation degree. The thermal behavior indicates that the polymer is more stable compared to other HCN-derived polymers. The mass spectrometric thermal analysis showed the gradual release of several volatile compounds along different thermal steps. The results suggest a complicate macrostructure formed by amide and hydroxyl groups, which are joined to the main reticular chain with conjugated bonds (C=O, N=O, –O–C=N). The hydrolysis treatment showed the pH conditions for the releasing of organics. The study of the synthesis of HCN-derived thermal polymers under feasible primitive hydrothermal conditions is relevant for considering hydrothermal vents as niches of chemical evolution on early Earth.

A Comparative Study on HCN Polymers Synthesized by Polymerization of NH4 CN or Diaminomaleonitrile in Aqueous Media: New Perspectives for Prebiotic Chemistry and Materials Science

HCN polymers are a group of complex and heterogeneous substances that are widely known in the fields of astrobiology and prebiotic chemistry. In addition, they have recently received considerable attention as potential functional material coatings. However, the real nature and pathways of formation of HCN polymers remain open questions. It is well established that the tuning of macromolecular structures determines the properties and practical applications of a polymeric material. Herein, different synthetic conditions were explored for the production of HCN polymers from NH₄ CN or diaminomaleonitrile in aqueous media with different concentrations of the starting reactants and several reaction times. By using a systematic methodology, both series of polymers were shown to exhibit similar, but not identical, spectroscopic and thermal fingerprints, which resulted in a clear differentiation of their morphological and electrochemical properties. New macrostructures are proposed for HCN polymers, and promising insights are discussed for prebiotic chemistry and materials science on the basis of the experimental results.

Synthesis and breakdown of universal metabolic precursors promoted by iron

Life builds its molecules from carbon dioxide (CO₂) and breaks them back down again through the intermediacy of just five metabolites, which are the universal hubs of biochemistry¹. However, it is unclear how core biological metabolism began and why it uses the intermediates, reactions and pathways that it does. Here we describe a purely chemical reaction network promoted by ferrous iron, in which aqueous pyruvate and glyoxylate-two products of abiotic CO₂ reduction^2-4-build up 9 of the 11 intermediates of the biological Krebs (or tricarboxylic acid) cycle, including all 5 universal metabolic precursors. The intermediates simultaneously break down to CO₂ in a life-like regime that resembles biological anabolism and catabolism⁵. Adding hydroxylamine^6-8 and metallic iron into the system produces four biological amino acids in a manner that parallels biosynthesis. The observed network overlaps substantially with the Krebs and glyoxylate cycles^9,10, and may represent a prebiotic precursor to these core metabolic pathways.

Prebiotic chemistry in neutral/reduced-alkaline gas-liquid interfaces

The conditions for the potential abiotic formation of organic compounds from inorganic precursors have great implications for our understanding of the origin of life on Earth and for its possible detection in other environments of the Solar System. It is known that aerosol-interfaces are effective at enhancing prebiotic chemical reactions, but the roles of salinity and pH have been poorly investigated to date. Here, we experimentally demonstrate the uniqueness of alkaline aerosols as prebiotic reactors that produce an undifferentiated accumulation of a variety of multi-carbon biomolecules resulting from high-energy processes (in our case, electrical discharges). Using simulation experiments, we demonstrate that the detection of important biomolecules in tholins increases when plausible and particular local planetary environmental conditions are simulated. A greater diversity in amino acids, carboxylic acids, N-heterocycles, and ketoacids, such as glyoxylic and pyruvic acid, was identified in tholins synthetized from reduced and neutral atmospheres in the presence of alkaline aqueous aerosols than that from the same atmospheres but using neutral or acidic aqueous aerosols.

Experimental conditions affecting the kinetics of aqueous HCN polymerization as revealed by UV-vis spectroscopy

HCN polymerization is one of the most important and fascinating reactions in prebiotic chemistry, and interest in HCN polymers in the field of materials science is growing. However, little is known about the kinetics of the HCN polymerization process. In the present study, a first approach to the kinetics of two sets of aqueous HCN polymerizations, from NH₄CN and NaCN, at middle temperatures between 4 and 38°C, has been carried out. For each series, the presence of air and salts in the reaction medium has been systematically explored. A previous kinetic analysis was conducted during the conversion of the insoluble black HCN polymers obtained as gel fractions in these precipitation polymerizations for a reaction of one month, where a limit conversion was achieved at the highest polymerization temperature. The kinetic description of the gravimetric data for this complex system shows a clear change in the linear dependence with the polymerization temperature for the reaction from NH₄CN, besides a relevant catalytic effect of ammonium, in comparison with those data obtained from the NaCN series. These results also demonstrated the notable influence of air, oxygen, and the saline medium in HCN polymer formation. Similar conclusions were reached when the sol fractions were monitored by UV-vis spectroscopy, and a Hill type correlation was used to describe the polymerization profiles obtained. This technique was chosen because it provides an easy, prompt and fast method to follow the evolution of the liquid or continuous phase of the process under study.

Modelling the kinetics and structural property evolution of a versatile reaction: aqueous HCN polymerization

The structural characterization and kinetics of HCN polymers were studied and the Kamal autocatalytic model can describe this aqueous precipitation polymerization.