The Origin of Life--Out of the Blue

Cometary Delivery of Hydrogen Cyanide to the Early Earth

Delivery of water and organics by asteroid and comet impacts may have influenced prebiotic chemistry on the early Earth. Some recent prebiotic chemistry experiments emphasize hydrogen cyanide (HCN) as a feedstock molecule for the formation of sugars, ribonucleotides, amino acids, and lipid precursors. Here, we assess how much HCN originally contained in a comet would survive impact, using parametric temperature and pressure profiles together with a time-dependent chemistry model. We find that HCN survival mainly depends on whether the impact is hot enough to thermally decompose H₂O into reactive radicals, and HCN is therefore rather insensitive to the details of the chemistry. In the most favorable impacts (low impact angle, low velocity, small radius), this temperature threshold is not reached, and intact delivery of HCN is possible. We estimate the global delivery of HCN during a period of Early and Late Heavy Bombardment of the early Earth, as well as local HCN concentrations achieved by individual impacts. In the latter case, comet impacts can provide prebiotically interesting HCN levels for thousands to millions of years, depending on properties of the impactor and of the local environment.

Potentially Prebiotic Activation Chemistry Compatible with Nonenzymatic RNA Copying

The nonenzymatic replication of ribonucleic acid (RNA) may have enabled the propagation of genetic information during the origin of life. RNA copying can be initiated in the laboratory with chemically activated nucleotides, but continued copying requires a source of chemical energy for in situ nucleotide activation. Recent work has illuminated a potentially prebiotic cyanosulfidic chemistry that activates nucleotides, but its application to nonenzymatic RNA copying had not been demonstrated. Here, we report a novel pathway that activates RNA nucleotides in a manner compatible with template-directed nonenzymatic copying. We show that this pathway, which we refer to as bridge-forming activation, selectively yields the reactive imidazolium-bridged dinucleotide intermediate required for copying. Our results will enable more realistic simulations of RNA propagation based on continuous in situ nucleotide activation.

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.

Formic Acid, a Ubiquitous but Overlooked Component of the Early Earth Atmosphere

Terrestrial volcanism has been one of the dominant geological forces shaping our planet since its earliest existence. Its associated phenomena, like atmospheric lightning and hydrothermal activity, provide a rich energy reservoir for chemical syntheses. Based on our laboratory simulations, we propose that on the early Earth volcanic activity inevitably led to a remarkable production of formic acid through various independent reaction channels. Large-scale availability of atmospheric formic acid supports the idea of the high-temperature accumulation of formamide in this primordial environment.

Nonenzymatic Metabolic Reactions and Life's Origins

Prebiotic chemistry aims to explain how the biochemistry of life as we know it came to be. Most efforts in this area have focused on provisioning compounds of importance to life by multistep synthetic routes that do not resemble biochemistry. However, gaining insight into why core metabolism uses the molecules, reactions, pathways, and overall organization that it does requires us to consider molecules not only as synthetic end goals. Equally important are the dynamic processes that build them up and break them down. This perspective has led many researchers to the hypothesis that the first stage of the origin of life began with the onset of a primitive nonenzymatic version of metabolism, initially catalyzed by naturally occurring minerals and metal ions. This view of life's origins has come to be known as "metabolism first". Continuity with modern metabolism would require a primitive version of metabolism to build and break down ketoacids, sugars, amino acids, and ribonucleotides in much the same way as the pathways that do it today. This review discusses metabolic pathways of relevance to the origin of life in a manner accessible to chemists, and summarizes experiments suggesting several pathways might have their roots in prebiotic chemistry. Finally, key remaining milestones for the protometabolic hypothesis are highlighted.

Mirror Symmetry Breaking in Liquids and Their Impact on the Development of Homochirality in Abiogenesis: Emerging Proto-RNA as Source of Biochirality?

Recent progress in mirror symmetry breaking and chirality amplification in isotropic liquids and liquid crystalline cubic phases of achiral molecule is reviewed and discussed with respect to its implications for the hypothesis of emergence of biological chirality. It is shown that mirror symmetry breaking takes place in fluid systems where homochiral interactions are preferred over heterochiral and a dynamic network structure leads to chirality synchronization if the enantiomerization barrier is sufficiently low, i.e., that racemization drives the development of uniform chirality. Local mirror symmetry breaking leads to conglomerate formation. Total mirror symmetry breaking requires either a proper phase transitions kinetics or minor chiral fields, leading to stochastic and deterministic homochirality, respectively, associated with an extreme chirality amplification power close to the bifurcation point. These mirror symmetry broken liquids are thermodynamically stable states and considered as possible systems in which uniform biochirality could have emerged. A model is hypothesized, which assumes the emergence of uniform chirality by chirality synchronization in dynamic “helical network fluids” followed by polymerization, fixing the chirality and leading to proto-RNA formation in a single process.

Encoding Multiple Reactivity Modes within a Single Synthetic Replicator

Establishing programmable and self-sustaining replication networks in pools of chemical reagents is a key challenge in systems chemistry. Self-replicating templates are formed from two constituent components with complementary recognition and reactive sites via a slow bimolecular pathway and a fast template-directed pathway. Here, we re-engineer one of the components of a synthetic replicator to encode an additional recognition function, permitting the assembly of a binary complex between the components that mediates replicator formation through a template-independent pathway, which achieves maximum rate acceleration at early time points in the replication process. The complementarity between recognition sites creates a key conformational equilibrium between the catalytically inert product, formed via the template-independent pathway, and the catalytically active replicator that mediates the template-directed pathway. Consequently, the rapid formation of the catalytically inert isomer kick-starts replication through the template-directed pathway. Through kinetic analyses, we demonstrate that the presence of the two recognition-mediated reactivity modes results in enhanced template formation in comparison to that of systems capable of exploiting only a single recognition-mediated pathway. Finally, kinetic simulations reveal that the conformational equilibrium and both the relative and absolute efficiencies of the recognition-mediated pathways affect the extent to which self-replicating systems can benefit from this additional template-independent reactivity mode. These results allow us to formulate the rules that govern the coupling of replication processes to alternative recognition-mediated reactivity modes. The interplay between template-directed and template-independent pathways for replicator formation has significant relevance to ongoing efforts to design programmable and adaptable replicator networks.

Theoretical Investigations on the Possibility of Prebiotic HCN Formation via O-Addition Reactions

Until now, reactions between methane photolysis products (CH₃^•, CH₂) and active N atom or reactive NO radical are proposed as routes of HCN formation in the prebiotic Earth. Scientists think that the reducing atmosphere of primitive Earth was made of H₂, He, N₂, NO, CH₄, H₂O, CO₂, etc., and there was no molecular oxygen. However, it has been evident from experiments that the vacuum ultraviolet (VUV) photolysis of CO₂ can produce atomic oxygen. Therefore, it can be presumed that atomic oxygen was likely present in early Earth's atmosphere. Was there any impact of atomic oxygen in production of early atmospheric HCN for the emergence of life? To hunt for the answer, we have employed computational methods to study the mechanism and kinetics of CH₃NO + O(¹D) and CH₂NO^• + O(³P) addition reactions. Current study suggests that the addition of O(¹D) into nitrosomethane (CH₃NO) and the addition of O(³P) into nitrosomethylene radical (CH₂NO^•) can efficiently produce HCN through an effectively barrierless pathway. At STP, Bartis-Widom phenomenological loss rate coefficients of O(¹D) and O(³P) are obtained as 2.47 × 10^-12 and 4.67 × 10^-11 cm³ molecule^-1 s^-1, respectively. We propose that addition reactions of atomic oxygen with CH₃NO and CH₂NO^• might act as a potential source for early atmospheric HCN.

Organo-Halogens and their Possible Involvement in Prebiotic Chemistry

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In this review, we examined the possibility that some halogenated organic derivatives were used in the primitive ocean at the beginning of life on Earth. Firstly, we described the existence of extraterrestrial halogenated molecules, then we studied their nonbiological syntheses on the present Earth, especially in volcanic environments. In order to demonstrate the diversity of today’s halogenated biomolecules, representative examples are given and the biosynthesis of some of them is summarized. Finally, we proposed two aspects of the chemistry of halogenated compounds that may have been useful en route to biomolecules, firstly the use of methyl chloride as the first methylation reagent, secondly the synthesis and use of α-chloro-carbonyl derivatives.

The kinetics and mechanisms of reactions in the flow systems glycine-sodium trimetaphosphate-imidazoles: the crucial role of imidazoles in prebiotic peptide syntheses

The kinetics of oligopeptides formation in the flow systems glycine-sodium trimetaphosphate-imidazole/N-methylimidazole at thermocyclic regime has been investigated by HPLC and ³¹P NMR methods in the ranges of temperature from 45 to 90 °C and pH from 8.5 to 11.5. Detailed reaction mechanisms have been proposed and justified by quantum chemical calculations using DFT method at the CAM-B3LYP/TZVP level with accounting solvent effect by the C-PCM model. A new imidazole catalysis mechanism by which imidazole reacts with cyclic N,O-phosphoryl glycine giving N-imidazolyl-O-glycyl phosphate as a key intermediate was proposed and validated. It is emphasized that while in the absence of imidazoles, prebiotic activation of amino acids occurs at the N-terminus, in the presence of imidazoles it shifts to the O-terminus. This means that in the peptide elongation N-imidazolyl-O-aminoacyl phosphates play in prebiotic systems the outstanding role similar to that of aminoacyl adenylates formed at the ATP and aminoacyl-tRNA synthetases presence in biosystems. The new crucial role of imidazoles in prebiotic evolution has been noticed. The systems used and modes of their conversion can be good models for prebiotic peptide syntheses in a flow thermocyclic regime.

Supply of phosphate to early Earth by photogeochemistry after meteoritic weathering

During terrestrial differentiation, the relatively small amount of phosphorus that migrated to the lithosphere was incorporated into igneous rock, predominantly in the form of basic calcium orthophosphate (Ca₁₀(PO₄)₆(OH,F,Cl)₂, apatite). Yet, the highly insoluble nature of calcium apatite presents a significant problem to those contemplating the origin of life given the foundational role of phosphate (PO₄ ^3-) in extant biology and the apparent requirement for PO₄ ^3- as a catalyst, buffer and reagent in prebiotic chemistry. Reduced meteorites such as enstatite chondrites are highly enriched in phosphide minerals, and upon reaction with water these minerals can release phosphorus species of various oxidation states. Here, we demonstrate how reduced phosphorus species can be fully oxidized to PO₄ ^3- simply by the action of ultraviolet light on H₂S/HS^-. We used low pressure Hg lamps to simulate UV output from the young Sun and ³¹P NMR spectroscopy to monitor the progress of reactions. Our experimental findings provide a cosmochemically and geochemically plausible means for supply of PO₄ ^3- that was widely available to prebiotic chemistry and nascent life on early Earth, and potentially on other planets.

Semipermeable Mixed Phospholipid-Fatty Acid Membranes Exhibit K+/Na+ Selectivity in the Absence of Proteins

Two important ions, K⁺ and Na⁺, are unequally distributed across the contemporary phospholipid-based cell membrane because modern cells evolved a series of sophisticated protein channels and pumps to maintain ion gradients. The earliest life-like entities or protocells did not possess either ion-tight membranes or ion pumps, which would result in the equilibration of the intra-protocellular K⁺/Na⁺ ratio with that in the external environment. Here, we show that the most primitive protocell membranes composed of fatty acids, that were initially leaky, would eventually become less ion permeable as their membranes evolved towards having increasing phospholipid contents. Furthermore, these mixed fatty acid-phospholipid membranes selectively retain K⁺ but allow the passage of Na⁺ out of the cell. The K⁺/Na⁺ selectivity of these mixed fatty acid-phospholipid semipermeable membranes suggests that protocells at intermediate stages of evolution could have acquired electrochemical K⁺/Na⁺ ion gradients in the absence of any macromolecular transport machinery or pumps, thus potentially facilitating rudimentary protometabolism.

In vitro selection of ribozyme ligases that use prebiotically plausible 2-aminoimidazole-activated substrates

The hypothesized central role of RNA in the origin of life suggests that RNA propagation predated the advent of complex protein enzymes. A critical step of RNA replication is the template-directed synthesis of a complementary strand. Two experimental approaches have been extensively explored in the pursuit of demonstrating protein-free RNA synthesis: template-directed nonenzymatic RNA polymerization using intrinsically reactive monomers and ribozyme-catalyzed polymerization using more stable substrates such as biological 5'-triphosphates. Despite significant progress in both approaches in recent years, the assembly and copying of functional RNA sequences under prebiotic conditions remains a challenge. Here, we explore an alternative approach to RNA-templated RNA copying that combines ribozyme catalysis with RNA substrates activated with a prebiotically plausible leaving group, 2-aminoimidazole (2AI). We applied in vitro selection to identify ligase ribozymes that catalyze phosphodiester bond formation between a template-bound primer and a phosphor-imidazolide-activated oligomer. Sequencing revealed the progressive enrichment of 10 abundant sequences from a random sequence pool. Ligase activity was detected in all 10 RNA sequences; all required activation of the ligator with 2AI and generated a 3'-5' phosphodiester bond. We propose that ribozyme catalysis of phosphodiester bond formation using intrinsically reactive RNA substrates, such as imidazolides, could have been an evolutionary step connecting purely nonenzymatic to ribozyme-catalyzed RNA template copying during the origin of life.

A Peptide-Nucleic Acid Replicator Origin for Life

Evolution requires self-replication. But, what was the very first self-replicator directly ancestral to all life? The currently favoured RNA World theory assigns this role to RNA alone but suffers from a number of seemingly intractable problems. Instead, we suggest that the self-replicator consisted of both peptides and nucleic acid strands. Such a nucleopeptide replicator is more feasible both in the light of the replication machinery currently found in cells and the complexity of the evolutionary path required to reach them. Recent theoretical and mathematical work supports this idea and provide a blueprint for future investigations.

Prebiotic Peptides: Molecular Hubs in the Origin of Life

The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.

The Future of Origin of Life Research: Bridging Decades-Old Divisions

Research on the origin of life is highly heterogeneous. After a peculiar historical development, it still includes strongly opposed views which potentially hinder progress. In the 1st Interdisciplinary Origin of Life Meeting, early-career researchers gathered to explore the commonalities between theories and approaches, critical divergence points, and expectations for the future. We find that even though classical approaches and theories-e.g. bottom-up and top-down, RNA world vs. metabolism-first-have been prevalent in origin of life research, they are ceasing to be mutually exclusive and they can and should feed integrating approaches. Here we focus on pressing questions and recent developments that bridge the classical disciplines and approaches, and highlight expectations for future endeavours in origin of life research.

Role of the Dihydrodipicolinate Synthase DapA1 on Iron Homeostasis During Cyanide Assimilation by the Alkaliphilic Bacterium Pseudomonas pseudoalcaligenes CECT5344

Cyanide is a toxic compound widely used in mining and jewelry industries, as well as in the synthesis of many different chemicals. Cyanide toxicity derives from its high affinity for metals, which causes inhibition of relevant metalloenzymes. However, some cyanide-degrading microorganisms like the alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344 may detoxify hazardous industrial wastewaters that contain elevated cyanide and metal concentrations. Considering that iron availability is strongly reduced in the presence of cyanide, mechanisms for iron homeostasis should be required for cyanide biodegradation. Previous omic studies revealed that in the presence of a cyanide-containing jewelry residue the strain CECT5344 overproduced the dihydrodipicolinate synthase DapA1, a protein involved in lysine metabolism that also participates in the synthesis of dipicolinates, which are excellent metal chelators. In this work, a dapA1 ^- mutant of P. pseudoalcaligenes CECT5344 has been generated and characterized. This mutant showed reduced growth and cyanide consumption in media with the cyanide-containing wastewater. Intracellular levels of metals like iron, copper and zinc were increased in the dapA1 ^- mutant, especially in cells grown with the jewelry residue. In addition, a differential quantitative proteomic analysis by LC-MS/MS was carried out between the wild-type and the dapA1 ^- mutant strains in media with jewelry residue. The mutation in the dapA1 gene altered the expression of several proteins related to urea cycle and metabolism of arginine and other amino acids. Additionally, the dapA1 ^- mutant showed increased levels of the global nitrogen regulator PII and the glutamine synthetase. This proteomic study has also highlighted that the DapA1 protein is relevant for cyanide resistance, oxidative stress and iron homeostasis response, which is mediated by the ferric uptake regulator Fur. DapA1 is required to produce dipicolinates that could act as iron chelators, conferring protection against oxidative stress and allowing the regeneration of Fe-S centers to reactivate cyanide-damaged metalloproteins.

Proton-Induced Charge Transfer on Imidazole and 2-Aminoimidazole. Role of the Substituent and Influence of Stepwise Hydration

The behavior of potential prebiotic species in space is of main concern in the chemistry at the origin of life. Their reactivity or stability in spatial conditions, under strong UV radiations or ion bombardments, remains an open question and needs wide investigations. As protons are by far the most abundant ions in space, we focus presently on proton-induced collisions on imidazole and 2-aminoimidazole evidenced as important prebiotic RNA intermediates. Unconstrained full optimization of the structures was performed with B3LYP/cc-pVTZ model chemistry. The calculations were performed in a wide collision energy range in order to model various astrophysical environments, from eV in the interstellar medium, up to keV for solar winds or supernovae shock-wave protons. Such a study provides for the first time a theoretical insight on the influence of the amino substituent on the proton-induced charge transfer. We evaluated the role of icy grain environments through a cluster approach modeling the effect of a stepwise microhydration on the process. Comparisons with oxygenated and sulfurated analogues address further qualitative trends on the respective stability or reactivity of such heterocycles which may be of tremendous interest in prebiotic chemistry. Charge transfer appears to be quite efficient for imidazole compounds and their sulfurated analogue compared to the oxygenated heterocycle.

Programmed Recognition between Complementary Dinucleolipids To Control the Self-Assembly of Lipidic Amphiphiles

One of the major goals in systems chemistry is to create molecular assemblies with emergent properties that are characteristic of life. An interesting approach toward this goal is based on merging different biological building blocks into synthetic systems with properties arising from the combination of their molecular components. The covalent linkage of nucleic acids (or their constituents: nucleotides, nucleosides and nucleobases) with lipids in the same hybrid molecule leads, for example, to the so-called nucleolipids. Herein, we describe nucleolipids with a very short sequence of two nucleobases per lipid, which, in combination with hydrophobic effects promoted by the lipophilic chain, allow control of the self-assembly of lipidic amphiphiles to be achieved. The present work describes a spectroscopic and microscopy study of the structural features and dynamic self-assembly of dinucleolipids that contain adenine or thymine moieties, either pure or in mixtures. This approach leads to different self-assembled nanostructures, which include spherical, rectangular and fibrillar assemblies, as a function of the sequence of nucleobases and chiral effects of the nucleolipids involved. We also show evidence that the resulting architectures can encapsulate hydrophobic molecules, revealing their potential as drug delivery vehicles or as compartments to host interesting chemistries in their interior.

Chemistry of Abiotic Nucleotide Synthesis

The chemistry of abiotic nucleotide synthesis of RNA and DNA in the context of their prebiotic origins on early earth is a continuing challenge. How did (or how can) the nucleotides form and assemble from the small molecule inventories and under conditions that prevailed on early earth 3.5-4 billion years ago? This review provides a background and up-to-date progress that will allow the reader to judge where the field stands currently and what remains to be achieved. We start with a brief primer on the biological synthesis of nucleotides, followed by an extensive focus on the prebiotic formation of the components of nucleotides-either via the synthesis of ribose and the canonical nucleobases and then joining them together or by building both the conjoined sugar and nucleobase, part-by-part-toward the ultimate goal of forming RNA and DNA by polymerization. The review will emphasize that there are-and will continue to be-many more questions than answers from the synthetic, mechanistic, and analytical perspectives. We wrap up the review with a cautionary note in this context about coming to conclusions as to whether the problem of chemistry of prebiotic nucleotide synthesis has been solved.

Exploiting complexity to implement function in chemical systems

This feature article reflects a personal overview of the importance of complexity as an additional parameter to be considered in chemical research, being illustrated with selected examples in molecular recognition and catalysis.

The primary photo-dissociation dynamics of amino acids in aqueous solution: breaking the Cα-bond

Photo-excitation of aqueous amino acids at 200 nm breaks the C_α-bond.

Thermophoresis of biological and biocompatible compounds in aqueous solution

With rising popularity of microscale thermophoresis for the characterisation of protein-ligand binding reactions and possible applications in microfluidic devices, there is a growing interest in considering thermodiffusion in the context of life sciences. But although the understanding of thermodiffusion in non-polar mixtures has grown rapidly in recent years, predictions for associated mixtures like aqueous solutions remain challenging. This review aims to give an overview of the literature on thermodiffusion in aqueous systems, show the difficulties in theoretical description that arise from the non-ideal behaviour of water-mixtures, and highlight the relevance of thermodiffusion in a biological context. We find that the thermodiffusion in aqueous systems is dominated by contributions from heat of transfer, hydrogen bond interactions and charge effects. However, the separation of these effects is often difficult, especially in case of biological systems where a systematic exclusion of contributions may not be feasible.

CH3NO as a potential intermediate for early atmospheric HCN: a quantum chemical insight

Hydrogen cyanide (HCN) has played a central role in the production of several biological molecules under prebiotic conditions on primitive Earth. Previously, K. J. Zahnle (J. Geophys. Res.: Atmos., 1986, 91, 2819) and Tian et al. (Earth Planet. Sci. Lett., 2011, 308, 417) emphasized that HCN production in the early Earth's CH₄-rich atmosphere could have been possible through the reaction between active nitrogen atoms (N) and methane photolysis products. Here, we have proposed alternative pathways for the formation of early atmospheric HCN via the decomposition of CH₃NO as an intermediate. In the early Earth's O₂-free atmosphere, CH₃˙ could preferentially attach to NO, which was generated via early atmospheric volcanism or lightning and photochemical processes. We have quantum chemically explored both unimolecular and bimolecular decomposition pathways of CH₃NO via the assistance of another CH₃NO molecule and via H₂O, NH₃, HCl, HCOOH, HNO₃ and H₂SO₄ catalysis. Both energetic and kinetic analyses reveal that H₂SO₄ is more efficient in this regard than other atmospheric species. Overall, it has been suggested that the proposed bimolecular decomposition pathways might have been alternative pathways for the formation of HCN under certain conditions on prebiotic Earth, while the unimolecular decomposition of CH₃NO could lead to the formation of HCN in the high temperature volcanic environment on early Earth.

Prebiotic Chemistry that Could Not Not Have Happened

We present a direct route by which RNA might have emerged in the Hadean from a fayalite–magnetite mantle, volcanic SO₂ gas, and well-accepted processes that must have created substantial amounts of HCHO and catalytic amounts of glycolaldehyde in the Hadean atmosphere. In chemistry that could not not have happened, these would have generated stable bisulfite addition products that must have rained to the surface, where they unavoidably would have slowly released reactive species that generated higher carbohydrates. The formation of higher carbohydrates is self-limited by bisulfite formation, while borate minerals may have controlled aldol reactions that occurred on any semi-arid surface to capture that precipitation. All of these processes have well-studied laboratory correlates. Further, any semi-arid land with phosphate should have had phosphate anhydrides that, with NH₃, gave carbohydrate derivatives that directly react with nucleobases to form the canonical nucleosides. These are phosphorylated by magnesium borophosphate minerals (e.g., lüneburgite) and/or trimetaphosphate-borate with Ni²⁺ catalysis to give nucleoside 5′-diphosphates, which oligomerize to RNA via a variety of mechanisms. The reduced precursors that are required to form the nucleobases came, in this path-hypothesis, from one or more mid-sized (10²³–10²⁰ kg) impactors that almost certainly arrived after the Moon-forming event. Their iron metal content almost certainly generated ammonia, nucleobase precursors, and other reduced species in the Hadean atmosphere after it transiently placed the atmosphere out of redox equilibrium with the mantle. In addition to the inevitability of steps in this path-hypothesis on a Hadean Earth if it had semi-arid land, these processes may also have occurred on Mars. Adapted from a lecture by the Corresponding Author at the All-Russia Science Festival at the Lomonosov Moscow State University on 12 October 2019, and is an outcome of a three year project supported by the John Templeton Foundation and the NASA Astrobiology program. Dedicated to David Deamer, on the occasion of his 80th Birthday.

Membrane Lipid Composition and Amino Acid Excretion Patterns of Methanothermococcus okinawensis Grown in the Presence of Inhibitors Detected in the Enceladian Plume

Lipids and amino acids are regarded as important biomarkers for the search for extraterrestrial life in the Solar System. Such biomarkers may be used to trace methanogenic life on other planets or moons in the Solar System, such as Saturn's icy moon Enceladus. However, little is known about the environmental conditions shaping the synthesis of lipids and amino acids. Here, we present the lipid production and amino acid excretion patterns of the methanogenic archaeon Methanothermococcus okinawensis after exposing it to different multivariate concentrations of the inhibitors ammonium, formaldehyde, and methanol present in the Enceladian plume. M. okinawensis shows different patterns of lipid and amino acids excretion, depending on the amount of these inhibitors in the growth medium. While methanol did not show a significant impact on growth, lipid or amino acid production rates, ammonium and formaldehyde strongly affected these parameters. These findings are important for understanding the eco-physiology of methanogens on Earth and have implications for the use of biomarkers as possible signs of extraterrestrial life for future space missions in the Solar System.

Prebiotic condensation through wet-dry cycling regulated by deliquescence

Wet-dry cycling is widely regarded as a means of driving condensation reactions under prebiotic conditions to generate mixtures of prospective biopolymers. A criticism of this model is its reliance on unpredictable rehydration events, like rainstorms. Here, we report the ability of deliquescent minerals to mediate the oligomerization of glycine during iterative wet-dry cycles. The reaction mixtures evaporate to dryness at high temperatures and spontaneously reacquire water vapor to form aqueous solutions at low temperatures. Deliquescent mixtures can foster yields of oligomerization over ten-fold higher than non-deliquescent controls. The deliquescent mixtures tightly regulate their moisture content, which is crucial, as too little water precludes dissolution of the reactants while too much water favors hydrolysis over condensation. The model also suggests a potential reason why life evolved to favor the enrichment of potassium: so living systems could acquire and retain sufficient water to serve as a solvent for biochemical reactions.

A Stark Contrast to Modern Earth: Phosphate Mineral Transformation and Nucleoside Phosphorylation in an Iron- and Cyanide-Rich Early Earth Scenario

Organophosphates were likely an important class of prebiotic molecules. However, their presence on the early Earth is strongly debated because the low availability of phosphate, which is generally assumed to have been sequestered in insoluble calcium and iron minerals, is widely viewed as a major barrier to organophosphate generation. Herein, we demonstrate that cyanide (an essential prebiotic precursor) and urea-based solvents could promote nucleoside phosphorylation by transforming insoluble phosphate minerals in a "warm little pond" scenario into more soluble and reactive species. Our results suggest that cyanide and its derivatives (metal cyanide complexes, urea, ammonium formate, and formamide) were key reagents for the participation of phosphorus in chemical evolution. These results allow us to propose a holistic scenario in which an evaporitic environment could concentrate abiotically formed organics and transform the underlying minerals, allowing significant organic phosphorylation under plausible prebiotic conditions.

Insights Into the Origin of Life: Did It Begin from HCN and H2O?

The seminal Urey-Miller experiments showed that molecules crucial to life such as HCN could have formed in the reducing atmosphere of the Hadean Earth and then dissolved in the oceans. Subsequent proponents of the "RNA World" hypothesis have shown aqueous HCN to be the starting point for the formation of the precursors of RNA and proteins. However, the conditions of early Earth suggest that aqueous HCN would have had to react under a significant number of constraints. Therefore, given the limiting conditions, could RNA and protein precursors still have formed from aqueous HCN? If so, what mechanistic routes would have been followed? The current computational study, with the aid of the ab initio nanoreactor (AINR), a powerful new tool in computational chemistry, addresses these crucial questions. Gratifyingly, not only do the results from the AINR approach show that aqueous HCN could indeed have been the source of RNA and protein precursors, but they also indicate that just the interaction of HCN with water would have sufficed to begin a series of reactions leading to the precursors. The current work therefore provides important missing links in the story of prebiotic chemistry and charts the road from aqueous HCN to the precursors of RNA and proteins.

Prebiotic synthesis at impact craters: the role of Fe-clays and iron meteorites

Besides delivering plausible prebiotic feedstock molecules and high-energy initiators, extraterrestrial impacts could also affect the process of abiogenesis by altering the early Earth's geological environment in which primitive life was conceived. We show that iron-rich smectites formed by reprocessing of basalts due to the residual post-impact heat could catalyze the synthesis and accumulation of important prebiotic building blocks such as nucleobases, amino acids and urea.

How Small Heterocycles Make a Reaction Network of Amino Acids and Nucleotides Efficient in Water

Organisms use enzymes to ensure a flow of substrates through biosynthetic pathways. How the earliest form of life established biosynthetic networks and prevented hydrolysis of intermediates without enzymes is unclear. Organocatalysts may have played the role of enzymes. Quantitative analysis of reactions of adenosine 5'-monophosphate and glycine that produce peptides, pyrophosphates, and RNA chains reveals that organocapture by heterocycles gives hydrolytically stabilized intermediates with balanced reactivity. We determined rate constants for 20 reactions in aqueous solutions containing a carbodiimide and measured product formation with cyanamide as a condensing agent. Organocapture favors reactions that are kinetically slow but productive, and networks, over single transformations. Heterocycles can increase the metabolic efficiency more than two-fold, with up to 0.6 useful bonds per fuel molecule spent, boosting the efficiency of life-like reaction systems in the absence of enzymes.

Compositional Persistence in a Multicyclic Network of Synthetic Replicators

The emergence of collections of simple chemical entities that create self-sustaining reaction networks, embedding replication and catalysis, is cited as a potential mechanism for the appearance on the early Earth of systems that satisfy minimal definitions of life. In this work, a functional reaction network that creates and maintains a set of privileged replicator structures through auto- and cross-catalyzed reaction cycles is created from the pairwise combinations of four reagents. We show that the addition of individual preformed templates to this network, representing instructions to synthesize a specific replicator, induces changes in the output composition of the system that represent a network-level response. Further, we establish through sets of serial transfer experiments that the catalytic connections that exist between the four replicators in this network and the system-level behavior thereby encoded impose limits on the compositional variability that can be induced by repeated exposure to instructional inputs, in the form of preformed templates, to the system. The origin of this persistence is traced through kinetic simulations to the properties and inter-relationships between the critical ternary complexes formed by the auto- and crosscatalytic templates. These results demonstrate that in an environment where there is no continuous selection pressure the network connectivity, described by the catalytic relationships and system-level interactions between the replicators, is persistent, thereby limiting the ability of this network to adapt and evolve.

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.

Provisioning the origin and early evolution of life

There is a lot of controversy in the origin and early evolution of life field, but most people agree that at the advent of genetically coded protein synthesis, cells must have had access to ribonucleotides, amino acids, lipids and some sort of energy source. However, the provenance of these materials is a contentious issue — did early life obtain its building blocks prefabricated from the environment, or did it synthesise them from feedstocks such as CO₂ and N₂? In the first case, synthesis conditions need not have been compatible with life and any kind of reaction network that furnished the building blocks — and not much else — could have provisioned the subsequent origin and early evolution of life. In the second case, synthesis must have been under life-compatible conditions, with the reaction network either along the same lines as extant biology or along different ones. On the basis of experimental evidence, we will argue in favour of prefabrication and against synthesis by life in its nascent state, especially synthesis that resembles extant biosynthesis, which we suggest would have been well-nigh impossible without biological catalysts.

Investigating Prebiotic Protocells for A Comprehensive Understanding of the Origins of Life: A Prebiotic Systems Chemistry Perspective

Protocells are supramolecular systems commonly used for numerous applications, such as the formation of self-evolvable systems, in systems chemistry and synthetic biology. Certain types of protocells imitate plausible prebiotic compartments, such as giant vesicles, that are formed with the hydration of thin films of amphiphiles. These constructs can be studied to address the emergence of life from a non-living chemical network. They are useful tools since they offer the possibility to understand the mechanisms underlying any living cellular system: Its formation, its metabolism, its replication and its evolution. Protocells allow the investigation of the synergies occurring in a web of chemical compounds. This cooperation can explain the transition between chemical (inanimate) and biological systems (living) due to the discoveries of emerging properties. The aim of this review is to provide an overview of relevant concept in prebiotic protocell research.

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.

Early Life: Embracing the RNA World

Protein complexes with artificial aptamers exhibit a bias towards arginine, tryptophan and tyrosine, providing insights into physicochemical traits of the interactions between amino acids and RNA that may have led to the origin of the genetic code and the ribosome.

Two Synthetic Replicators Compete To Process a Dynamic Reagent Pool

Complementary building blocks, comprising a set of four aromatic aldehydes and a set of four nucleophiles-three anilines and one hydroxylamine-combine through condensation reactions to afford a dynamic covalent library (DCL) consisting of the eight starting materials and 16 condensation products. One of the aldehydes and, consequently, all of the DCL members derived from this compound bear an amidopyridine recognition site. Exposure of this DCL to two maleimides, M^p and M^m, each equipped with a carboxylic acid recognition site, results in the formation of a series of products through irreversible 1,3-dipolar cycloaddition reactions with the four nitrones present in the DCL. However, only the two cycloadducts in the product pool that incorporate both recognition sites, T^p and T^m, are self-replicators that can harness the DCL as feedstock for their own formation, facilitating their own synthesis via autocatalytic and cross-catalytic pathways. The ability of these replicators to direct their own formation from the components present in the dynamic reagent pool in response to the input of instructions in the form of preformed replicators is demonstrated through a series of quantitative ¹⁹F{¹H} NMR spectroscopy experiments. Simulations establish the critical relationships between the kinetic and thermodynamic parameters of the replicators, the initial reagent concentrations, and the presence or absence of the DCL and their influence on the competition between T^p and T^m. Thus, we establish the rules that govern the behavior of the competing replicators under conditions where their formation is coupled tightly to the processing of a DCL.

Absolute asymmetric Strecker synthesis in a mixed aqueous medium: reliable access to enantioenriched α-aminonitrile

Without using chiral sources, the Strecker reaction of achiral hydrogen cyanide, p-tolualdehyde and benzhydrylamine gave enantioenriched l- or d-N-benzhydryl-α-(p-tolyl)glycine nitriles with up to >99% ee in a mixed solvent of water and methanol. Therefore, total spontaneous resolution of α-aminonitriles could occur through a prebiotic mechanism of α-amino acid synthesis. Moreover, it was demonstrated that the repetition of partial dissolution and crystallization of a suspended conglomerate of aminonitrile under solution-phase racemization could generate the enantiomeric imbalance to afford, in combination with the amplification of chirality, an enantioenriched product in every case. Among the 73 experiments that were carried out, d- and l-enriched isomers occurred 36 and 37 times, respectively. This stochastic behavior, under achiral or racemic starting conditions, meets the requirements of the spontaneous absolute asymmetric Strecker synthesis. The implications of the present results for the origin of chirality of α-amino acids are discussed.

Regioselective 5'-position phosphorylation of ribose and ribonucleosides: phosphate transfer in the activated pyrophosphate complex in the gas phase

Herein, we present a rapid, efficient and regioselective phosphorylation method at the 5'-position of unprotected ribose and ribonucleosides with pyrophosphate in the gas phase, which involves the formation of anionic complexes via electrospray ionization and collisional activation to induce phosphorylation within the complexes.