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Co-polymerization of glycol nucleic acid monomers with dicarboxylic acid linkers under plausible early Earth dry-down scenario conditions.

Nucleic acid segregation and compartmentalization were likely essential functions that primitive compartment systems resolved during evolution. Recently, polyester microdroplets generated from dehydration synthesis of various α-hydroxy acids (αHA) were suggested as potential primitive compartments. Some of these droplets can differentially segregate and compartmentalize organic dyes, proteins, and nucleic acids. However, the previously studied polyester microdroplets included limited αHA chemical diversity, which may not reflect the chemical diversity available in the primitive Earth environment. Here, we increased the chemical diversity of polyester microdroplet systems by combinatorially adding an αHA monomer with a basic side chain, 4-amino-2-hydroxybutyric acid (4a2h), which was incorporated with different ratios of other αHAs containing uncharged side chains to form combinatorial heteropolyesters via dehydration synthesis. Incorporation of 4a2h in the polymers resulted in the assembly of some polyester microdroplets able to segregate fluorescent RNA or potentially acquire intrinsic fluorescent character, suggesting that minor modifications of polyester composition can significantly impact the functional properties of primitive compartments. This study suggests one process by which primitive chemical systems can increase diversity of compartment "phenotype" through simple modifications in their chemical composition.

The 1953 Miller–Urey experiment was a ground-breaking attempt to understand stages in the origins of life on Earth. In the experiment, Stanley Miller added water and reduced gases to a sealed flask to simulate the primitive atmosphere and hydrosphere, then subjected the contents to an electric discharge to simulate atmospheric lightning. Miller's chemical analysis of the products revealed a number of amino acids used by modern organisms to construct coded proteins, suggesting these may then have been available for the construction of the first organisms. The experiment was inspired by both Oparin's early writings on the origins of life and Urey's conception of the primitive atmosphere. Since the publication of the original results, there has been considerable development in thinking regarding the nature of the primitive environment, as well as a proliferation of alternative, detailed models for the origins of life which do not necessarily hinge on the results of this kind of experiment. Nevertheless, while considerable uncertainty lingers regarding the primitive environment, the Miller–Urey experiment remains relevant to many modern origins of life models, and its impact on modern thinking regarding the origins of life cannot be overstated.

Phosphorus (P) is a crucial structural component of living systems and central to modern bioenergetics. P cycles through terrestrial geochemical reservoirs via complex physical and chemical processes. Terrestrial life has altered these fluxes between reservoirs as it evolved, which is why it is of interest to explore planetary P flux evolution in the absence of biology. This is especially true, since environmental P availability affects life’s ability to alter other geochemical cycles, which could then be an example of niche construction. Understanding how P reservoir transport affects environmental P availability helps parameterize how the evolution of P reservoirs influenced the emergence of life on Earth, and potentially other planetary bodies. Geochemical P fluxes likely change as planets evolve, and element cycling models that take those changes into account can provide insights on how P fluxes evolve abiotically. There is considerable uncertainty in many aspects of modern and historical global P cycling, including Earth’s initial P endowment and distribution after core formation and how terrestrial P interactions between reservoirs and fluxes and their rates have evolved over time. We present here a dynamical box model for Earth’s abiological P reservoir and flux evolution. This model suggests that in the absence of biology, long term planetary geochemical cycling on planets similar to Earth with respect to geodynamism tends to bring P to surface reservoirs, and biology, including human civilization, tends to move P to subductable marine reservoirs.

Carboxylation and decarboxylation are two fundamental classes of reactions that impact the cycling of carbon in and on Earth’s crust. These reactions play important roles in both long-term (primarily abiotic) and short-term (primarily biotic) carbon cycling. Long-term cycling is important in the subsurface and at subduction zones where organic carbon is decomposed and outgassed or recycled back to the mantle. Short-term reactions are driven by biology and have the ability to rapidly convert CO2 to biomass and vice versa. For instance, carboxylation is a critical reaction in primary production and metabolic pathways like photosynthesis in which sunlight provides energy to drive carbon fixation, whereas decarboxylation is a critical reaction in metabolic pathways like respiration and the tricarboxylic acid cycle. Early life and prebiotic chemistry on Earth likely relied heavily upon the abiotic synthesis of carboxylic acids. Over time, life has diversified (de)carboxylation reactions and incorporated them into many facets of cellular metabolism. Here we present a broad overview of the importance of carboxylation and decarboxylation reactions from both abiotic and biotic perspectives to highlight the importance of these reactions and compounds to planetary evolution.

Prebiotic chemists often study how modern biopolymers, e.g., peptides and nucleic acids, could have originated in the primitive environment, though most contemporary biomonomers don’t spontaneously oligomerize under mild conditions without activation or catalysis. However, life may not have originated using the same monomeric components that it does presently. There may be numerous non-biological (or “xenobiological”) monomer types that were prebiotically abundant and capable of facile oligomerization and self-assembly. Many modern biopolymers degrade abiotically preferentially via processes which produce thermodynamically stable ring structures, e.g. diketopiperazines in the case of proteins and 2′, 3′-cyclic nucleotide monophosphates in the case of RNA. This weakness is overcome in modern biological systems by kinetic control, but this need not have been the case for primitive systems. We explored here the oligomerization of a structurally diverse set of prebiotically plausible xenobiological monomers, which can hydrolytically interconvert between cyclic and acyclic forms, alone or in the presence of glycine under moderate temperature drying conditions. These monomers included various lactones, lactams and a thiolactone, which varied markedly in their stability, propensity to oligomerize and apparent modes of initiation, and the oligomeric products of some of these formed self-organized microscopic structures which may be relevant to protocell formation.

We model nitrogen (N) partitioning in the magma ocean stage and cycling between the surface and mantle through Earth's history, and suggest that N in the present-day mantle may be set by subduction before the development of the modern N cycle. Introduction: On present-day Earth, N cycling between the surface and mantle is largely controlled by biological N fixation and aerobic biological processing. Biological N fixation brings the majority of inorganic N into the modern N cycle. In the oceans, dissolved nitrate is the main form of nitrogen available for life, and dissimilatory denitrification leads to residual nitrate being kinetically enriched in 15N by ~6‰. The isotopically enriched nitrate is then reduced to ammonium and finally trapped in sediments (e.g., Stüeken al. 2016). Though secular subduction of 15N-rich sediments should cause 15N enrichment in the mantle, the mantle N sampled from mid-ocean ridge basalt (MORB) is rather depleted in 15N (~-5‰), which is known as the N isotopic disequilibrium. Previous studies hypothesized that N in the mantle is a primordial component (Cartingy & Marty, 2013; Labidi et al. 2020). In the primordial origin scenario, the isotopic disequilibrium is attributed to atmospheric escape, which enriched the atmosphere with 15N. Another study proposed a recycling origin scenario in which the N isotopic composition of sediments has changed over time (Marty & Dauphas, 2003). Neither of these scenarios has been modeled quantitatively. Here we test the different scenarios by using numerical models coupled with N isotopes. Methods: We developed two sets of models for the origin of observed mantle N isotopic composition: i) the primordial origin and ii) the recycling origin. The results are either accepted or rejected by the comparison to the amounts and isotopic compositions of N in contemporary surface reservoirs and mantle (Johnson & Goldblatt, 2015; Labidi et al. 2020). For the primordial origin scenario, we calculate N partitioning between the atmosphere and mantle upon magma ocean solidification by using a melt-trapping model (Hier-Majumder & Hirschmann, 2017) and the partitioning coefficients between minerals, silicate melt, and the atmosphere (Li et al. 2013; Dalou et al. 2017). We consider the range of oxygen fugacity relevant to Earth's formation. We also estimate the 15N-enrichment effect due to EUV-driven escape (Watson et al. 1981) and solar-wind pick-up (Lichtenegger et al. 2010) to see how much atmospheric N should be removed to reproduce ~+5‰ difference between the atmosphere and mantle. For the recycling origin scenario, we calculate secular N exchange between the surface reservoirs and mantle. Our model is based on that of Labidi et al. (2020). The isotopic fractionation between the atmosphere and subducting sediments is taken to be ~-9‰ and ~+6‰ before and after the Great Oxidation Event at 2.4 Ga, respectively, considering the change from abiotic fixation and anaerobic processing to biological fixation and aerobic processing. We fix the subduction and degassing fluxes on present-day Earth, and their power-law indices as a function of time as parameters. Bulk N partitioning and the isotopic difference between the reservoirs in the initial state are also treated as parameters. Figure 1: Nitrogen partitioning between the atmosphere and mantle at the time of magma ocean solidification (PAN = present-day atmospheric nitrogen). The range of the modeled mantle N content reflects the uncertainty in the oxygen fugacity of the magma ocean. Figure 2: Evolution of masses (left) and 15N/14N ratios (right) in the surface reservoirs (blue) and mantle (red). Curves show accepted models having different initial conditions and fluxes. Gray areas are the estimates for present-day surface reservoirs and mantle. Results: Because N is relatively insoluble in silicate melts, it is mostly partitioned into the atmosphere even when trapping in interstitial melts is considered (Figure 1). Partitioning N into the mantle as much as present-day leads to 100 times excess in PAL N. We found that the excess amount of N can be removed neither by EUV- nor solar-wind-induced loss without excessive 15N enrichment in the atmosphere. Impact erosion by the late veneer bombardment removes atmospheric N without isotopic fractionation up to ~10 bar (Sakuraba et al. 2019), but it may not be sufficient to remove all excess N in the atmosphere. Since the results of our partitioning model suggest that the primordial origin is unlikely, next we tested the recycling scenario in our N cycling model (Figure 2). In our successful runs, the mantle is initially depleted in N, and N in the present-day mantle is a result of higher net subduction flux on early Earth where sedimentary N is depleted in 15N due to abiotic N fixation and anaerobic N processing. The change to modern N cycle is visible in the kink in δ15N evolution, which may provide a way to test our model with evidence from geologic record. Discussion: We suggest that N partitioning between the surface and deep Earth may be set by subduction driven by plate tectonics and partially by biology. This also suggests that the difference of atmospheric N contents between Venus and Earth, the former of which has three times more N in the atmosphere, is caused by their long-term evolution rather than early formation and differentiation processes. Conclusions: We conclude that N in the present-day mantle may be set by subduction before the development of the modern N cycle. Further results for parameter survey and discussion on other geological and geochemical constraints will be shown in our presentation.

While tensions may lie between science and policy, we argue that dissemination and public engagement are key in alleviating those perceived tensions. Science being valued by society results in fact-based policy-making being demanded by constituents. Constituents’ demands will yield representatives who are familiar with the scientific process and research to inform policy decisions.

Continuous reaction networks, which do not rely on purification or timely additions of reagents, serve as models for chemical evolution and have been demonstrated for compounds thought to have played important roles for the origins of life such as amino acids, hydroxy acids, and sugars. Step-by-step chemical protocols for ribonucleotide synthesis are known, but demonstrating their synthesis in the context of continuous reaction networks remains a major challenge. Herein, compounds proposed to be important for prebiotic RNA synthesis, including glycolaldehyde, cyanamide, 2-aminooxazole, and 2-aminoimidazole, are generated from a continuous reaction network, starting from an aqueous mixture of NaCl, NH(4)Cl, phosphate, and HCN as the only carbon source. No well-timed addition of any other reagents is required. The reaction network is driven by a combination of γ radiolysis and dry-down. γ Radiolysis results in a complex mixture of organics, including the glycolaldehyde-derived glyceronitrile and cyanamide. This mixture is then dried down, generating free glycolaldehyde that then reacts with cyanamide/NH(3) to furnish a combination of 2-aminooxazole and 2-aminoimidazole. This continuous reaction network models how precursors for generating RNA and other classes of compounds may arise spontaneously from a complex mixture that originates from simple reagents.

The chemistry occurring in the universe generates a huge variety of organic compounds abiotically. Significant progress has been made in understanding the types and distributions of these compounds...

We studied the radiolysis of a wide variety of N-heterocycles, including many of biological importance, and find that the majority are remarkably stable in the solid-state when subjected to large doses of ionizing gamma radiation from a 60Co source. Degradation of N-heterocycles as a function of dose rate and total dose was measured using high-performance liquid chromatography with UV detection. Many N-heterocycles show little degradation when γ-irradiated up to a total dose of ~1 MGy, which approximates hundreds of millions of years’ worth of radiation emitted in meteorite parent bodies due to slow radionuclide decay. Extrapolation of these results suggests that these N-heterocyclic compounds would be stable in dry parent bodies over solar system timescales. We suggest that the abundance of these N-heterocycles as measured presently in carbonaceous meteorites is largely reflective of their abundance at the time aqueous alteration stopped in their parent bodies and the absence of certain compounds in present-day samples is either due to the formation mechanisms or degradation which occurred during periods of aqueous alteration or thermal metamorphism.

Nitrogen is the major component of Earth's atmosphere and plays important roles in biochemistry. Biological systems have evolved a variety of mechanisms for fixing and recycling environmental nitrogen sources, which links them tightly with terrestrial nitrogen reservoirs. However, prior to the emergence of biology, all nitrogen cycling was abiological, and this cycling may have set the stage for the origin of life. It is of interest to understand how nitrogen cycling would proceed on terrestrial planets with comparable geodynamic activity to Earth, but on which life does not arise. We constructed a kinetic mass-flux model of nitrogen cycling in its various major chemical forms (e.g., N2, reduced (NHx) and oxidized (NOx) species) between major planetary reservoirs (the atmosphere, oceans, crust, and mantle) and included inputs from space. The total amount of nitrogen species that can be accommodated in each reservoir, and the ways in which fluxes and reservoir sizes may have changed over time in the absence of biology, are explored. Given a partition of volcanism between arc and hotspot types similar to the modern ones, our global nitrogen cycling model predicts a significant increase in oceanic nitrogen content over time, mostly as NHx, while atmospheric N2 content could be lower than today. The transport timescales between reservoirs are fast compared to the evolution of the environment; thus atmospheric composition is tightly linked to surface and interior processes.

In this review, we describe some of the central philosophical issues facing origins-of-life research and provide a targeted history of the developments that have led to the multidisciplinary field of origins-of-life studies. We outline these issues and developments to guide researchers and students from all fields. With respect to philosophy, we provide brief summaries of debates with respect to (1) definitions (or theories) of life, what life is and how research should be conducted in the absence of an accepted theory of life, (2) the distinctions between synthetic, historical, and universal projects in origins-of-life studies, issues with strategies for inferring the origins of life, such as (3) the nature of the first living entities (the “bottom up” approach) and (4) how to infer the nature of the last universal common ancestor (the “top down” approach), and (5) the status of origins of life as a science. Each of these debates influences the others. Although there are clusters of researchers that agree on some answers to these issues, each of these debates is still open. With respect to history, we outline several independent paths that have led to some of the approaches now prevalent in origins-of-life studies. These include one path from early views of life through the scientific revolutions brought about by Linnaeus (von Linn.), Wöhler, Miller, and others. In this approach, new theories, tools, and evidence guide new thoughts about the nature of life and its origin. We also describe another family of paths motivated by a” circularity” approach to life, which is guided by such thinkers as Maturana & Varela, Gánti, Rosen, and others. These views echo ideas developed by Kant and Aristotle, though they do so using modern science in ways that produce exciting avenues of investigation. By exploring the history of these ideas, we can see how many of the issues that currently interest us have been guided by the contexts in which the ideas were developed. The disciplinary backgrounds of each of these scholars has influenced the questions they sought to answer, the experiments they envisioned, and the kinds of data they collected. We conclude by encouraging scientists and scholars in the humanities and social sciences to explore ways in which they can interact to provide a deeper understanding of the conceptual assumptions, structure, and history of origins-of-life research. This may be useful to help frame future research agendas and bring awareness to the multifaceted issues facing this challenging scientific question., This project/publication was supported by the ELSI Origins Network (EON), which is supported by a grant from the John Templeton Foundation. T.F.’s work on this article was supported by an ELSI Origins Network (EON) Long-Term Visitor Award and by an UNAM-DGAPA-PAPIIT project (IA104717).

The surface metabolism theory posits that adaptive evolution initiated when autocatalytic chemical systems became spatially localized on mineral surfaces. We searched for such surface-limited metab...

Searching for life in the Universe depends on unambiguously distinguishing biological features from background signals, which could take the form of chemical, morphological, or spectral signatures. The discovery and direct measurement of organic compounds unambiguously indicative of extraterrestrial (ET) life is a major goal of Solar System exploration. Biology processes matter and energy differently from abiological systems, and materials produced by biological systems may become enriched in planetary environments where biology is operative. However, ET biology might be composed of different components than terrestrial life. As ET sample return is difficult, in situ methods for identifying biology will be useful. Mass spectrometry (MS) is a potentially versatile life detection technique, which will be used to analyze numerous Solar System environments in the near future. We show here that simple algorithmic analysis of MS data from abiotic synthesis (natural and synthetic), microbial cells, and thermally processed biological materials (lab-grown organisms and petroleum) easily identifies relational organic compound distributions that distinguish pristine and aged biological and abiological materials, which likely can be attributed to the types of compounds these processes produce, as well as how they are formed and decompose. To our knowledge this is the first comprehensive demonstration of the utility of this analytical technique for the detection of biology. This method is independent of the detection of particular masses or molecular species samples may contain. This suggests a general method to agnostically detect evidence of biology using MS given a sufficiently strong signal in which the majority of the material in a sample has either a biological or abiological origin. Such metrics are also likely to be useful for studies of possible emergent living phenomena, and paleobiological samples.

Rationale Spark discharge experiments, like those performed by Stanley Miller in the 1950s, generate complex, analytically challenging mixtures that contain biopolymer building blocks. Recently, α-amino acids and α-hydroxy acids (AHAs) were subjected to environmental cycling to form simple depsipeptides (peptides with both amide and ester linkages). The synthesis of AHAs under possible primordial environments must be examined to better understand this chemistry. Methods We report a direct, quantitative method for AHAs using ultrahigh-performance liquid chromatography and triple quadrupole mass spectrometry. Hexylamine ion-pairing chromatography and selected reaction monitoring detection were combined for the rapid analysis of ten AHAs in a single run. Additionally, prebiotic simulation experiments, including the first-ever reproduction of Miller's 1958 cyanamide spark discharge experiment, were performed to evaluate AHA synthesis over a wide range of possible primitive terrestrial environments. Results The quantitating transition for each of the AHAs targeted in this study produced a limit of detection in the nanomolar concentration range. For most species, a linear response over a range spanning two orders of magnitude was found. The AHAs glycolic acid, lactic acid, malic acid, and α-hydroxyglutaric acid were detected in electric discharge experiments in the low micromolar concentration range. Conclusions The results of this work suggest that the most abundant building blocks available for prebiotic depsipeptide synthesis would have been glycolic, lactic, malic, and α-hydroxyglutaric acids, and their corresponding amino acids, glycine, alanine, and aspartic and glutamic acids. Copyright © 2016 John Wiley & Sons, Ltd.

At the time before ∼3.5 Ga that life originated and began to spread on Earth, Mars was a wetter and more geologically dynamic planet than it is today. The Argyre basin, in the southern cratered highlands of Mars, formed from a giant impact at ∼3.93 Ga, which generated an enormous basin approximately 1800 km in diameter. The early post-impact environment of the Argyre basin possibly contained many of the ingredients that are thought to be necessary for life: abundant and long-lived liquid water, biogenic elements, and energy sources, all of which would have supported a regional environment favorable for the origin and the persistence of life. We discuss the astrobiological significance of some landscape features and terrain types in the Argyre region that are promising and accessible sites for astrobiological exploration. These include (i) deposits related to the hydrothermal activity associated with the Argyre impact event, subsequent impacts, and those associated with the migration of heated water along Argyre-induced basement structures; (ii) constructs along the floor of the basin that could mark venting of volatiles, possibly related to the development of mud volcanoes; (iii) features interpreted as ice-cored mounds (open-system pingos), whose origin and development could be the result of deeply seated groundwater upwelling to the surface; (iv) sedimentary deposits related to the formation of glaciers along the basin's margins, such as evidenced by the ridges interpreted to be eskers on the basin floor; (v) sedimentary deposits related to the formation of lakes in both the primary Argyre basin and other smaller impact-derived basins along the margin, including those in the highly degraded rim materials; and (vi) crater-wall gullies, whose morphology points to a structural origin and discharge of (wet) flows.

From a geochemical perspective, significant amounts of pure formamide (HCONH2) would have likely been rare on the early Earth. There may have been mixed formamide-water solutions, but even in the presence of catalyst, solutions with >20 weight% water in formamide would not have produced significant amounts of prebiotic compounds. It might be feasible to produce relatively pure formamide by a rare occurrence of freezing formamide/water mixtures at temperatures lower than formamide's freezing point (2.55 °C) but greater than the freezing point of water. Because of the high density of formamide ice it would have sunk and accumulated at the bottom of the solution. If the remaining water froze on the surface of this ice, and was then removed by a sublimation-ablation process, a small amount of pure formamide ice might have been produced. In addition a recent report suggested that ∼85 weight% formamide could be prepared by a geochemical type of fractional distillation process, offering another possible route for prebiotic formamide production.

A variety of organic chemicals were likely available on prebiotic Earth. These derived from diverse processes including atmospheric and geochemical synthesis and extraterrestrial input, and were delivered to environments including oceans, lakes, and subaerial hot springs. Prebiotic chemistry generates both molecules used by modern organisms, such as proteinaceous amino acids, as well as many molecule types not used in biochemistry. As prebiotic chemical diversity was likely high, and the core of biochemistry uses a rather small set of common building blocks, the majority of prebiotically available organic compounds may not have been those used in modern biochemistry. Chemical evolution was unlikely to have been able to discriminate which molecules would eventually be used in biology, and instead, interactions among compounds were governed simply by abundance and chemical reactivity. Previous work has shown that likely prebiotically available α-hydroxy acids can combinatorially polymerize into polyesters that self-assemble to create new phases which are able to compartmentalize other molecule types. The unexpectedly rich complexity of hydroxy acid chemistry and the likely enormous structural diversity of prebiotic organic chemistry suggests chemical evolution could have been heavily influenced by molecules not used in contemporary biochemistry, and that there is a considerable amount of prebiotic chemistry which remains unexplored.

The standard alphabet of the 20 genetically encoded amino acids is considered to have been selected during early evolution from a larger pool of α-amino acids based on its coverage of the chemical space. Chemical space is here defined by charge, size and hydrophobicity, leading to 6-tuples representing coverage, which is composed of range and evenness in these three physico-chemical properties. We summarize findings of previous studies on the adaptive properties of the 20 encoded amino acids and show how we extend these computational experiments to subsets of the standard alphabet.

Ribonucleic acid (RNA) is one of the two nucleic acids used by extant biochemistry and plays a central role as the intermediary carrier of genetic information in transcription and translation. If RNA was involved in the origin of life, it should have a facile prebiotic synthesis. A wide variety of such syntheses have been explored. However, to date no one-pot reaction has been shown capable of yielding RNA monomers from likely prebiotically abundant starting materials, though this does not rule out the possibility that simpler, more easily prebiotically accessible nucleic acids may have preceded RNA. Given structural constraints, such as the ability to form complementary base pairs and a linear covalent polymer, a variety of structural isomers of RNA could potentially function as genetic platforms. By using structure-generation software, all the potential structural isomers of the ribosides (BC5H9O4, where B is nucleobase), as well as a set of simpler minimal analogues derived from them, that can potentially serve as monomeric building blocks of nucleic acid–like molecules are enumerated. Molecules are selected based on their likely stability under biochemically relevant conditions (e.g., moderate pH and temperature) and the presence of at least two functional groups allowing the monomers to be incorporated into linear polymers. The resulting structures are then evaluated by using molecular descriptors typically applied in quantitative structure–property relationship (QSPR) studies and predicted physicochemical properties. Several databases have been queried to determine whether any of the computed isomers had been synthesized previously. Very few of the molecules that emerge from this structure set have been previously described. We conclude that ribonucleosides may have competed with a multitude of alternative structures whose potential proto-biochemical roles and abiotic syntheses remain to be explored. Key Words: Evolution—Chemical evolution—Exobiology—Prebiotic chemistry—RNA world. Astrobiology 15, 538–558.

α-Amino acids are fundamental to biochemistry as the monomeric building blocks with which cells construct proteins according to genetic instructions. However, the 20 amino acids of the standard genetic code represent a tiny fraction of the number of α-amino acid chemical structures that could plausibly play such a role, both from the perspective of natural processes by which life emerged and evolved, and from the perspective of human-engineered genetically coded proteins. Until now, efforts to describe the structures comprising this broader set, or even estimate their number, have been hampered by the complex combinatorial properties of organic molecules. Here, we use computer software based on graph theory and constructive combinatorics in order to conduct an efficient and exhaustive search of the chemical structures implied by two careful and precise definitions of the α-amino acids relevant to coded biological proteins. Our results include two virtual libraries of α-amino acid structures corresponding to these different approaches, comprising 121 044 and 3 846 structures, respectively, and suggest a simple approach to exploring much larger, as yet uncomputed, libraries of interest.

Spark discharge experiments, like those performed by Stanley Miller in the 1950s, generate complex, analytically challenging mixtures that contain biopolymer building blocks. Recently, α-amino acids and α-hydroxy acids (AHAs) were subjected to environmental cycling to form simple depsipeptides (peptides with both amide and ester linkages). The synthesis of AHAs under possible primordial environments must be examined to better understand this chemistry.We report a direct, quantitative method for AHAs using ultrahigh-performance liquid chromatography and triple quadrupole mass spectrometry. Hexylamine ion-pairing chromatography and selected reaction monitoring detection were combined for the rapid analysis of ten AHAs in a single run. Additionally, prebiotic simulation experiments, including the first-ever reproduction of Miller's 1958 cyanamide spark discharge experiment, were performed to evaluate AHA synthesis over a wide range of possible primitive terrestrial environments.The quantitating transition for each of the AHAs targeted in this study produced a limit of detection in the nanomolar concentration range. For most species, a linear response over a range spanning two orders of magnitude was found. The AHAs glycolic acid, lactic acid, malic acid, and α-hydroxyglutaric acid were detected in electric discharge experiments in the low micromolar concentration range.The results of this work suggest that the most abundant building blocks available for prebiotic depsipeptide synthesis would have been glycolic, lactic, malic, and α-hydroxyglutaric acids, and their corresponding amino acids, glycine, alanine, and aspartic and glutamic acids. Copyright © 2016 John WileySons, Ltd.

Self-assembly of a nucleoside on Au(111) was studied to ascertain whether polymerization on well-defined substrates constitutes a promising approach for making sequence-controlled polymers. Scanning tunneling microscopy and density functional theory were used to investigate the self-assembly on Au(111) of (RS)-N9-(2,3-dihydroxypropyl)adenine (DHPA), a plausibly prebiotic nucleoside analog of adenosine. It is found that DHPA molecules self-assemble into a hydrogen-bonded polymer that grows almost exclusively along the herringbone reconstruction pattern, has a two component sequence that is repeated over hundreds of nanometers and is erasable with electron-induced excitation. Although the sequence is simple, more complicated ones are envisioned if two or more nucleoside types are combined. Because polymerization occurs on a substrate in a dry environment, the success of each combination can be gauged with high-resolution imaging and accurate modeling techniques. These characteristics make nucleoside self-assembly on a substrate an attractive approach for designing sequence-controlled polymers. Further, by choosing plausibly prebiotic nucleosides, insights may be provided into how nature created the first sequence-controlled polymers capable of storing information. Such insights, in turn, can inspire new ways of synthesizing sequence-controlled polymers.

All terrestrial organisms depend on nucleic acids (RNA and DNA), which use pyrimidine and purine nucleobases to encode genetic information. Carbon-rich meteorites may have been important sources of organic compounds required for the emergence of life on the early Earth; however, the origin and formation of nucleobases in meteorites has been debated for over 50 y. So far, the few nucleobases reported in meteorites are biologically common and lacked the structural diversity typical of other indigenous meteoritic organics. Here, we investigated the abundance and distribution of nucleobases and nucleobase analogs in formic acid extracts of 12 different meteorites by liquid chromatography–mass spectrometry. The Murchison and Lonewolf Nunataks 94102 meteorites contained a diverse suite of nucleobases, which included three unusual and terrestrially rare nucleobase analogs: purine, 2,6-diaminopurine, and 6,8-diaminopurine. In a parallel experiment, we found an identical suite of nucleobases and nucleobase analogs generated in reactions of ammonium cyanide. Additionally, these nucleobase analogs were not detected above our parts-per-billion detection limits in any of the procedural blanks, control samples, a terrestrial soil sample, and an Antarctic ice sample. Our results demonstrate that the purines detected in meteorites are consistent with products of ammonium cyanide chemistry, which provides a plausible mechanism for their synthesis in the asteroid parent bodies, and strongly supports an extraterrestrial origin. The discovery of new nucleobase analogs in meteorites also expands the prebiotic molecular inventory available for constructing the first genetic molecules.

The abiotic polymerization of amino acids may have been important for the origin of life, as peptides may have been components of the first self-replicating systems. Though amino acid concentrations in the primitive oceans may have been too dilute for significant oligomerization to occur, mineral surface adsorption may have provided a concentration mechanism. As unactivated amino acid polymerization is thermodynamically unfavorable and kinetically slow in aqueous solution, we studied mainly the reverse reaction of polymer degradation to measure the impact of mineral surface catalysis on peptide bonds. Aqueous glycine (G), diglycine (GG), diketopiperazine (DKP), and triglycine (GGG) were reacted with minerals (calcite, hematite, montmorillonite, pyrite, rutile, or amorphous silica) in the presence of 0.05 M, pH 8.1, KHCO3 buffer and 0.1 M NaCl as background electrolyte in a thermostatted oven at 25, 50 or 70 °C. Below 70 °C, reaction kinetics were too sluggish to detect catalytic activity over amenable laboratory time-scales. Minerals were not found to have measurable effects on the degradation or elongation of G, GG or DKP at 70 °C in solution. At 70 °C pyrite was the most catalytic mineral with detectible effects on the degradation of GGG, although several others also displayed catalytic behavior. GGG degraded ∼1.5–4 times faster in the presence of pyrite than in control reactions, depending on the ratio of solution concentration to mineral surface area. The rate of pyrite catalysis of GGG hydrolysis was found to be saturable, suggesting the presence of discrete catalytic sites on the mineral surface. The mineral-catalyzed degradation of GGG appears to occur via a GGG → DKP + G mechanism, rather than via GGG → GG + G, as in solution-phase reactions. These results are compatible with many previous findings and suggest that minerals may have assisted in peptide synthesis in certain geological settings, specifically by speeding the approach to equilibrium in environments where amino acids were already highly concentrated, but that minerals may not significantly alter the expected solution-phase equilibria. Thus the abiotic synthesis of long peptides may have required activating agents, dry heating at higher temperatures, or some form of phase separation.

Nucleic acids, the storage molecules of genetic information, are composed of repeating polymers of ribonucleotides (in RNA) or deoxyribonucleotides (in DNA), which are themselves composed of a phosphate moiety, a sugar moiety, and a nitrogenous base. The interactions between these components and mineral surfaces are important because there is a tremendous flux of nucleic acids in the environment due to cell death and horizontal gene transfer. The adsorption of mono-, oligo-, and polynucleotides and their components on mineral surfaces may have been important for the origin of life. We have studied here interactions of nucleic acid components with rutile (TiO(2)), a mineral common in many terrestrial crustal rocks. Our results suggest roles for several nucleic acid functional groups (including sugar hydroxyl groups, the phosphate group, and extracyclic functional groups on the bases) in binding, in agreement with results obtained from studies of other minerals. In contrast with recent studies of nucleotide adsorption on ZnO, aluminum oxides, and hematite, our results suggest a different preferred orientation for the monomers on rutile surfaces. The conformations of the molecules bound to rutile surfaces appear to favor specific interactions, which in turn may allow identification of the most favorable mineral surfaces for nucleic acid adsorption.

Interactions between aqueous amino acids and mineral surfaces influence many geochemical processes from biomineralization to the origin of life. However, the specific reactions involved and the attachment mechanisms are mostly unknown. We have studied the adsorption of l -aspartate on the surface of rutile (α-TiO 2 , pH PPZC = 5.4) in NaCl(aq) over a wide range of pH, ligand-to-solid ratio and ionic strength, using potentiometric titrations and batch adsorption experiments. The adsorption is favored below pH 6 with a maximum of 1.2 μmol of adsorbed aspartate per m 2 of rutile at pH 4 in our experiments. The adsorption decreases at higher pH because the negatively charged aspartate molecule is repelled by the negatively charged rutile surface above pH PPZC . At pH values of 3–5, aspartate adsorption increases with decreasing ionic strength. The adsorption of aspartate on rutile is very similar to that previously published for glutamate ( Jonsson et al., 2009 ). An extended triple-layer model was used to provide a quantitative thermodynamic characterization of the aspartate adsorption data. Two reaction stoichiometries identical in reaction stoichiometry to those for glutamate were needed. At low surface coverages, aspartate, like glutamate, may form a bridging-bidentate surface species binding through both carboxyl groups, i.e. “lying down” on the rutile surface. At high surface coverages, the reaction stoichiometry for aspartate was interpreted differently compared to glutamate: it likely involves an outer-sphere or hydrogen bonded aspartate surface species, as opposed to a partly inner-sphere complex for glutamate. Both the proposed aspartate species are qualitatively consistent with previously published ATR–FTIR spectroscopic results for aspartate on amorphous titanium dioxide. The surface complexation model for aspartate was tested against experimental data for the potentiometric titration of aspartate in the presence of rutile. In addition, the model correctly predicted a decrease of the isoelectric point with increased aspartate concentration consistent with previously published studies of the aspartate–anatase system. Prediction of the surface speciation of aspartate on rutile indicates that the relative proportions of the two complexes are a strong function of environmental conditions, which should be taken into account in considerations of geochemical systems involving the interactions of biomolecules and minerals in electrolyte solutions.

Formaldehyde (HCHO), the simplest aldehyde, is an intermediate oxidation state one carbon molecule that exists transiently but prominently in the abiological carbon cycle, and is ubiquitous in the cosmos. Its potential prebiotic importance is suggested by the fact that it readily undergoes a variety of addition and redox reactions to give products of biological significance including sugars and amino acids. It is especially important with respect to the origin of an RNA or pre-RNA world, since HCHO may be a precursor to ribose and other sugars. HCHO is introduced to the environment by a number of processes including atmospheric and aqueous phase synthesis as well as extraterrestrial delivery, balanced by various destructive processes such as photolysis and redox equilibration in hydrothermal environments. While the Strecker synthesis of amino acids can occur at very low dilution, even best case scenarios for HCHO steady-state concentrations in the primitive oceans are too low for the formation of sugars to occur. Concentration mechanisms would thus be necessary. As HCHO is volatile, direct evaporation is not possible, but other geochemical mechanisms such as eutectic freezing and conversion to non-volatile derivatives by reaction with other species present in the primitive environment, followed by evaporation, could have concentrated HCHO sufficiently to allow for sugar synthesis.

Most prebiotic syntheses depend on the reaction of concentrated precursor compounds to produce bio-organic molecules. It is now believed that the early Earth's atmosphere was not reducing enough to have permitted copious synthesis of precursor molecules. Freezing allows reaction to occur even from dilute solution. This reaction has been demonstrated for the purines but not for the pyrimidines. It is shown here that dilute solutions of simple prebiotic molecules produce the biological pyrimidines cytosine and uracil upon freezing. Cold environments may have allowed synthesis of all of the RNA bases even from low organic yielding atmospheres, such as those of the early Earth, Mars, Titan and Europa.

The polymerization of concentrated NH4CN solutions has been studied at various temperatures and ammonia concentrations. The products of the oligomerization of ammonium cyanide include adenine and guanine, as well as trace amounts of 2,6-diaminopurine. Our results indicate that the adenine yield is not strongly dependent on temperature. Guanine is produced in lower yield. The original studies by Oró and Kimball (1961) showed that the 6 N HCl hydrolysis of the NH4CN polymerization supernatant greatly increased the adenine yield. However, this hydrolysis also decomposes adenine and other purines. Therefore, we have measured the yields from an NH4CN polymerization as a function of hydrolysis time, and found that shorter hydrolytic periods give higher yields of adenine. We have also investigated the hydrolysis of the supernatant at pH 8, which is a more reasonable model of primitive oceanic conditions, and found that the adenine yield is comparable to that obtained with acid hydrolysis (approximately 0.1%). The yield of adenine does not decline at longer hydrolysis times because of the greater stability of adenine at pH 8. The insoluble black polymer formed from NH4CN has been analyzed by both acid and neutral hydrolysis. In both cases adenine yields of approximately 0.05% were obtained. This suggests that the polymer may have been as important a prebiotic source of purines as the usually analyzed supernatant.

A wide variety of pyrimidines and purineswere identified as products of a dilute frozen ammoniumcyanide solution that had been held at –78°C for 27 years.This demonstrates that both pyrimidines and purines couldhave been produced on the primitive earth in a short time byeutectic concentration of HCN, even though the concentrationof HCN in the primitive ocean may have been low. We suggestthat eutectic freezing is the most plausible demonstratedmechanism by which HCN polymerizations could have producedbiologically important prebiotic compounds.

It has been suggested that hydrogen cyanide(HCN) would not have been present in sufficient concentrationto polymerize in the primitive ocean to produce nucleic acidbases and amino acids. We have measured the hydrolysis ratesof HCN and formamide over the range of 30–150 °C and pH 0–14,and estimated the steady state concentrations in theprimitive ocean. At 100 °C and pH 8, the steady stateconcentration of HCN and formamide were calculated to be7 × 10-13 M and 1 × 10-15 M, respectively. Thus, itseems unlikely that HCN could have polymerized in a warmprimitive ocean. It is suggested that eutectic freezing mighthave been required to have concentrated HCN sufficiantly forit to polymerize. If the HCN polymerization was important forthe origin of life, some regions of the primitive earth mighthave been frozen.

Many of the biosynthetic pathways, especially those leading to the coenzymes, must have originated very early, perhaps before enzymes were available to catalyze their synthesis. While a number of enzymatic reactions in metabolism are known to proceed nonenzymatically, there are no examples of entire metabolic sequences that can be achieved in this manner. The most primitive pathway for nicotinic acid biosynthesis is the reaction of aspartic acid with dihydroxyacetone phosphate. We report here that nicotinic acid (NAc) and its metabolic precursor, quinolinic acid (QA), are produced in yields as high as 7% in a six-step nonenzymatic sequence from aspartic acid and dihydroxyacetone phosphate (DHAP). The biosynthesis of ribose phosphate could have produced DHAP and other three carbon compounds. Aspartic acid could have been available from prebiotic synthesis or from the ribozyme synthesis of pyrimidines. These results suggest that NAD could have originated in the RNA world and that the nonenzymatic biosynthesis of the cofactor nicotinamide could have been an inevitable consequence of life based on carbohydrates and amino acids. The enzymes of the modern pathway were later added in any order.

It is frequently stated that UV light would cause massive destruction of prebiotic organic compounds because of the absence of an ozone layer. The elevated UV flux of the early sun compounds this problem. This applies to organic compounds of both terrestrial and extraterrestrial origin. Attempts to deal with this problem generally involve atmospheric absorbers. We show here that prebiotic organic polymers as well as several inorganic compounds are sufficient to protect oceanic organic molecules from UV degradation. This aqueous protection is in addition to any atmospheric UV absorbers and should be a ubiquitous planetary phenomenon serving to increase the size of planetary habitable zones.

Mineral-assisted thermal decomposition of formamide (HCONH(2)) is a heavily studied model prebiotic reaction that has offered valuable insights into the plausible pathways leading to the chemical building blocks of primordial informational polymers. To date, most efforts have focused on the analysis of formamide reaction products released in solution, although several studies have examined the role of mineral catalysts in promoting this chemistry. We show here that the direct investigation of reactive mineral surfaces by desorption electrospray ionization-mass spectrometry imaging (DESI-MSI) gives a new perspective on the important role of the mineral surface in the formation of reaction products. As a proof-of-principle example, we show that DESI-MSI allows interrogation of the molecular products produced on heterogeneous granite samples with minimal sample preparation. Purine and pyrimidine nucleobases and their derivatives are successfully detected by DESI-MSI, with a strong correlation of the spatial product distribution with the mineral microenvironment. To our knowledge, this study is the first application of DESI-MSI to the study of complex and porous mineral surfaces and their roles in chemical evolution. This DESI-MSI approach is generally applicable to a wide range of reactions or other processes involving minerals.

Life is believed to have originated on Earth ∼4.4–3.5 Ga ago, via processes in which organic compounds supplied by the environment self-organized, in some geochemical environmental niches, into systems capable of replication with hereditary mutation. This process is generally supposed to have occurred in an aqueous environment and, likely, in the presence of minerals. Mineral surfaces present rich opportunities for heterogeneous catalysis and concentration which may have significantly altered and directed the process of prebiotic organic complexification leading to life. We review here general concepts in prebiotic mineral-organic interfacial processes, as well as recent advances in the study of mineral surface-organic interactions of potential relevance to understanding the origin of life.

Life is believed to have originated on Earth ∼4.4–3.5 Ga ago, via processes in which organic compounds supplied by the environment self-organized, in some geochemical environmental niches, into systems capable of replication with hereditary mutation. This process is generally supposed to have occurred in an aqueous environment and, likely, in the presence of minerals. Mineral surfaces present rich opportunities for heterogeneous catalysis and concentration which may have significantly altered and directed the process of prebiotic organic complexification leading to life. We review here general concepts in prebiotic mineral-organic interfacial processes, as well as recent advances in the study of mineral surface-organic interactions of potential relevance to understanding the origin of life.

To adapt and survive, life as we know it must have a genetic component to pass on information accumulated during natural selection. It has been suggested that life may have begun with a self-replicating RNA molecule. This appears chemically untenable as the prebiotic synthesis of RNA was unlikely on the primitive Earth. It is now known that biological nucleic acids (DNA and RNA) are not chemically unique in their ability to serve as informational templates. Many structural isomers of nucleic acids are now known. Alternative genetic polymers that were more easily synthesized under plausible geochemical conditions may have preceded RNA. Despite some 50 years of research, many of the structural alterations of nucleic acids of possible relevance to the origin of life remain uninvestigated, though this may prove to be one of the most experimentally tractable areas in prebiotic chemistry. Various structures and the constraints posed by prebiotic chemistry are reviewed herein.

Stanley Miller's 1958 H(2)S-containing experiment, which included a simulated prebiotic atmosphere of methane (CH(4)), ammonia (NH(3)), carbon dioxide (CO(2)), and hydrogen sulfide (H(2)S) produced several alkyl amino acids, including the α-, β-, and γ-isomers of aminobutyric acid (ABA) in greater relative yields than had previously been reported from his spark discharge experiments. In the presence of H(2)S, aspartic and glutamic acids could yield alkyl amino acids via the formation of thioimide intermediates. Radical chemistry initiated by passing H(2)S through a spark discharge could have also enhanced alkyl amino acid synthesis by generating alkyl radicals that can help form the aldehyde and ketone precursors to these amino acids. We propose mechanisms that may have influenced the synthesis of certain amino acids in localized environments rich in H(2)S and lightning discharges, similar to conditions near volcanic systems on the early Earth, thus contributing to the prebiotic chemical inventory of the primordial Earth.

Carbonaceous chondrites are a type of meteorite with a high organic content, which formed early in the history of the solar system. In addition to large amounts of insoluble high molecular weight organic polymer, they contain a variety of small organic molecules such as polycyclic aromatic hydrocarbons, polyols and aldaric, aldonic, amino, hydroxy and sugar acids, among others. Intriguingly, some of the amino acids and hydroxy acids have been found to display a chiral bias. The types of compounds present, their isotopic distributions and relative abundances may provide clues to the mechanisms by which they were synthesized in meteorite parent bodies. A unified set of mechanisms which may explain some of these properties is presented here. It involves simple addition reactions of cosmically abundant 1-carbon compounds such as HCHO and HCN undergoing well-established aqueous chemistry. Although aqueous processes could amplify and pass a chiral bias from one type of compound to another, circularly polarized light or another pre-accretion mechanism may have been required to initiate the chiral bias observed. Most of the small organic molecules present in these meteorites (90 to > 99% by number) to date remain unidentified; these mechanisms may provide a framework for identifying them.

We studied the adsorption of short single-stranded deoxyribonucleic acid (ssDNA) oligomers, of approximately 30 nucleotides (nt) in length, of varying sequence, adenine + guanine + cytosine (AGC) content, and propensity to form secondary structure, to equal surface area samples of olivine, pyrite, calcite, hematite, and rutile in 0.1 M NaCl, 0.05 M pH 8.1 KHCO3 buffer. Although the mineral surfaces have widely varying points of zero charge, under these conditions they show remarkably similar adsorption of ssDNA regardless of oligomer characteristics. Mineral surfaces appear to accommodate ssDNA comparably, or ssDNA oligomers of this length are able to find binding sites of comparable strength and density due to their flexibility, despite the disparate surface properties of the different minerals. This may partially be due charge shielding by the ionic strength of the solutions tested, which are typical of many natural environments. These results may have some bearing on the adsorption and accumulation of biologically derived nucleic acids in sediments as well as the abiotic synthesis of nucleic acids before the origin of life.

Biology uses essentially 20 amino acids for its coded protein enzymes, representing a very small subset of the structurally possible set. Most models of the origin of life suggest organisms developed from environmentally available organic compounds. A variety of amino acids are easily produced under conditions which were believed to have existed on the primitive Earth or in the early solar nebula. The types of amino acids produced depend on the conditions which prevailed at the time of synthesis, which remain controversial. The selection of the biological set is likely due to chemical and early biological evolution acting on the environmentally available compounds based on their chemical properties. Once life arose, selection would have proceeded based on the functional utility of amino acids coupled with their accessibility by primitive metabolism and their compatibility with other biochemical processes. Some possible mechanisms by which the modern set of 20 amino acids was selected starting from prebiotic chemistry are discussed.

The Mars Organic Analyzer (MOA), a portable microfabricated capillary electrophoresis instrument being developed for planetary exploration, is used to analyze a wide variety of fluorescamine-labeled amine-containing biomarker compounds, including amino acids, mono and diaminoalkanes, amino sugars, nucleobases, and nucleobase degradation products. The nucleobases cytosine and adenine, which contain an exocyclic primary amine, were effectively labeled, separated, and detected at concentrations500 nM. To test the general applicability of the MOA for biomarker detection, amino acids and mono- and diamines were extracted from bacterial cells using both hydrolysis and sublimation followed by analysis. The extrapolated limit of detection provided by the valine biomarker was approximately 4 x 10(3) cells per sample. Products of an NH(4)CN polymerization that simulate a prebiotic synthesis were also successfully isolated via sublimation and analyzed. Adenine and alanine/serine were detected with no additional sample cleanup at 120 +/- 13 microM and 4.1 +/- 1 microM, respectively, corresponding to a reaction yield of 0.04% and 0.0003%, respectively. This study demonstrates that the MOA provides sensitive detection and analysis of low levels of a wide variety of amine-containing organic compounds from both biological and abiotic sources.