Uracil synthesis via HCN oligomerization

Chapter 4: A Geological and Chemical Context for the Origins of Life on Early Earth

Within the first billion years of Earth's history, the planet transformed from a hot, barren, and inhospitable landscape to an environment conducive to the emergence and persistence of life. This chapter will review the state of knowledge concerning early Earth's (Hadean/Eoarchean) geochemical environment, including the origin and composition of the planet's moon, crust, oceans, atmosphere, and organic content. It will also discuss abiotic geochemical cycling of the CHONPS elements and how these species could have been converted to biologically relevant building blocks, polymers, and chemical networks. Proposed environments for abiogenesis events are also described and evaluated. An understanding of the geochemical processes under which life may have emerged can better inform our assessment of the habitability of other worlds, the potential complexity that abiotic chemistry can achieve (which has implications for putative biosignatures), and the possibility for biochemistries that are vastly different from those on Earth.

The Prebiotic Kitchen: A Guide to Composing Prebiotic Soup Recipes to Test Origins of Life Hypotheses

“Prebiotic soup” often features in discussions of origins of life research, both as a theoretical concept when discussing abiological pathways to modern biochemical building blocks and, more recently, as a feedstock in prebiotic chemistry experiments focused on discovering emergent, systems-level processes such as polymerization, encapsulation, and evolution. However, until now, little systematic analysis has gone into the design of well-justified prebiotic mixtures, which are needed to facilitate experimental replicability and comparison among researchers. This paper explores principles that should be considered in choosing chemical mixtures for prebiotic chemistry experiments by reviewing the natural environmental conditions that might have created such mixtures and then suggests reasonable guidelines for designing recipes. We discuss both “assembled” mixtures, which are made by mixing reagent grade chemicals, and “synthesized” mixtures, which are generated directly from diversity-generating primary prebiotic syntheses. We discuss different practical concerns including how to navigate the tremendous uncertainty in the chemistry of the early Earth and how to balance the desire for using prebiotically realistic mixtures with experimental tractability and replicability. Examples of two assembled mixtures, one based on materials likely delivered by carbonaceous meteorites and one based on spark discharge synthesis, are presented to illustrate these challenges. We explore alternative procedures for making synthesized mixtures using recursive chemical reaction systems whose outputs attempt to mimic atmospheric and geochemical synthesis. Other experimental conditions such as pH and ionic strength are also considered. We argue that developing a handful of standardized prebiotic recipes may facilitate coordination among researchers and enable the identification of the most promising mechanisms by which complex prebiotic mixtures were “tamed” during the origin of life to give rise to key living processes such as self-propagation, information processing, and adaptive evolution. We end by advocating for the development of a public prebiotic chemistry database containing experimental methods (including soup recipes), results, and analytical pipelines for analyzing complex prebiotic mixtures.

A Comprehensive Review of HCN-Derived Polymers

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

The Nitrogen Heterocycle Content of Meteorites and Their Significance for the Origin of Life

Carbonaceous chondrites are very primitive meteorites that are rich in carbon. They contain many soluble organic compounds, including nitrogen heterocycles. These play a crucial role in present-day living organisms as they are components of the genetic material and of the co-factors of enzymes. This review outlines the nitrogen heterocycle content of carbonaceous meteorites. The potential mechanisms of formation of these molecules are also described. Measurements of the compound-specific carbon and hydrogen isotopic compositions are mentioned as a way of establishing the origin of the nitrogen heterocycles detected in meteorites.

Orotidine-Containing RNA: Implications for the Hierarchical Selection (Systems Chemistry Emergence) of RNA

The prebiotic synthesis of canonical nucleobases from HCN is a cornerstone for the RNA world hypothesis. However, their role in the primordial pathways to RNA is still debated. The very same process starting from HCN also gives rise to orotic acid, which (via orotidine) plays a crucial role in extant biology in the de novo synthesis of uridine and cytidine, the informational base-pairs in RNA. However, orotidine itself is absent in RNA. Given the prebiotic and biological relevance of orotic acid vis-à-vis uracil, we investigated orotidine-containing RNA oligonucleotides and show that they have severely compromised base-pairing properties. While not unexpected, these results suggest that the emergence of extant RNA cannot just be a consequence of the plausible prebiotic formation of its chemical constituents/building blocks. In combination with other investigations on alternative prebiotic nucleobases, sugars, and linkers, these findings imply that the selection of the components of extant RNA occurred at a higher hierarchical level of an oligomer/polymer based on its functional properties-pointing to a systems chemistry emergence of RNA from a library of precursors.

Acetylene as an essential building block for prebiotic formation of pyrimidine bases on Titan

Prebiotic building blocks for the formation of biomolecules are important in understanding the abiotic origin of biomolecules.

Effects of sulfur-deficient defect and water on rearrangements of formamide on pyrite (100) surface

The efficient formation of HCN/HNC from formamide (FM) combining the advantages of water-assistance, self-catalyzed reactions, and the mineral surfaces was investigated. Periodic density functional theory calculations with plane-wave pseudopotential basis sets were performed to study the interaction of FM with pyrite (100) ideal and defect surfaces. Effects of sulfur vacancy defect and water on tautomerization and rearrangement barriers of FM on the (100) surface were evaluated. Calculated results show that FM adsorbs more strongly on the defect surface than on the ideal surface, with the lowest adsorption energy on the defect surface being -22 kcal/mol. The energy barriers for rearrangements of FM on these two surfaces being close to each other suggests that the adsorptions on the surfaces have small effects on the energy barriers. The energy barriers for formimic acid isomer formations are 44.5 and 46.0 kcal/mol, and those of aminohydroxymethylene formations are 72.6 and 71.9 kcal/mol on the ideal and defect surfaces, respectively. A reduction of ∼30 kcal/mol in tautomerization energy barriers is observed in water-assisted process on the defect surface. Because this reduction is close to that of the gas-phase reactions, the catalytic effect is clearly due to the presence of water molecule instead of the interaction with the surface. In this case, the pyrite surfaces with the ability to accumulate reactive species only play the role of connecting bridges between the two steps of the proposed reaction mechanism: the water-assisted rearrangement and the self-catalyzed dehydration.

Simple Organics and Biomonomers Identified in HCN Polymers: An Overview

Hydrogen cyanide (HCN) is a ubiquitous molecule in the Universe. It is a compound that is easily produced in significant yields in prebiotic simulation experiments using a reducing atmosphere. HCN can spontaneously polymerise under a wide set of experimental conditions. It has even been proposed that HCN polymers could be present in objects such as asteroids, moons, planets and, in particular, comets. Moreover, it has been suggested that these polymers could play an important role in the origin of life. In this review, the simple organics and biomonomers that have been detected in HCN polymers, the analytical techniques and procedures that have been used to detect and characterise these molecules and an exhaustive classification of the experimental/environmental conditions that favour the formation of HCN polymers are summarised. Nucleobases, amino acids, carboxylic acids, cofactor derivatives and other compounds have been identified in HCN polymers. The great molecular diversity found in HCN polymers encourages their placement at the central core of a plausible protobiological system.

Mineral-organic interfacial processes: potential roles in the origins 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.

Prebiotic chemistry in eutectic solutions at the water-ice matrix

A crystalline ice matrix at subzero temperatures can maintain a liquid phase where organic solutes and salts concentrate to form eutectic solutions. This concentration effect converts the confined reactant solutions in the ice matrix, sometimes making condensation and polymerisation reactions occur more favourably. These reactions occur at significantly high rates from a prebiotic chemistry standpoint, and the labile products can be protected from degradation. The experimental study of the synthesis of nitrogen heterocycles at the ice-water system showed the efficiency of this scenario and could explain the origin of nucleobases in the inner Solar System bodies, including meteorites and extra-terrestrial ices, and on the early Earth. The same conditions can also favour the condensation of monomers to form ribonucleic acid and peptides. Together with the synthesis of these monomers, the ice world (i.e., the chemical evolution in the range between the freezing point of water and the limit of stability of liquid brines, 273 to 210 K) is an under-explored experimental model in prebiotic chemistry.

The effects of borate minerals on the synthesis of nucleic acid bases, amino acids and biogenic carboxylic acids from formamide

The thermal condensation of formamide in the presence of mineral borates is reported. The products afforded are precursors of nucleic acids, amino acids derivatives and carboxylic acids. The efficiency and the selectivity of the reaction was studied in relation to the elemental composition of the 18 minerals analyzed. The possibility of synthesizing at the same time building blocks of both genetic and metabolic apparatuses, along with the production of amino acids, highlights the interest of the formamide/borate system in prebiotic chemistry.

Formation of nucleobases from formamide in the presence of iron oxides: implication in chemical evolution and origin of life

Simple compounds like HCN, which have one C and one N, are proposed as the probable precursors for biomonomers. Formamide, a hydrolysis product of HCN, is known as the precursor of various biologically important compounds, for example, nucleobases (purines and pyrimidines). In this paper, we report our results on the synthesis of nucleobases, adenine, cytosine, purine, 9-(hydroxyacetyl) purine, and 4(3H)-pyrimidinone from formamide, using iron oxide (hematite) and oxide hydroxides (goethite and akaganeite) as a catalyst. Goethite and hematite produced purine in higher yield. The products formed were characterized by high-performance liquid chromatography and electrospray ionization mass spectrometry techniques. Results of our study reveal that iron oxides might have worked as efficient prebiotic catalysts.

Adsorption of thymine and uracil on 1:1 clay mineral surfaces: comprehensive ab initio study on influence of sodium cation and water

This computational study performed using the density functional theory shows that hydrated and non-hydrated tetrahedral and octahedral kaolinite mineral surfaces in the presence of a cation adsorb the nucleic acid bases thymine and uracil well. Differences in the structure and chemistry of specific clay mineral surfaces led to a variety of DNA bases adsorption mechanisms. The energetically most predisposed positions for an adsorbate molecule on the mineral surface were revealed. The target molecule binding with the surface can be characterized as physisorption, which occurs mainly due to a cation-molecular oxygen interaction, with hydrogen bonds providing an additional stabilization. The adsorption strength is proportional to the number of intermolecular interactions formed between the target molecule and the surface. From the Atoms in Molecules analysis and comparison of binding energy values of studied systems it is concluded that the sorption activity of kaolinite minerals for thymine and uracil depends on various factors, among which are the structure and accessibility of the organic compounds. The adsorption is governed mostly by the surface type, its properties and presence of cation, which cause a selective binding of the nucleobase. Adsorbate stabilization on the mineral surface increases only slightly with explicit addition of water. Comparison of activity of different studied kaolinite mineral models reveals the following order for stabilization: octahedral-Na-water > octahedral-Na > tetrahedral-Na > tetrahedral-Na-water. Further investigation of the electrostatic potentials helps understanding of the adsorption process and confirmation of the active sites on the kaolinite mineral surfaces. Based on the conclusions that clay mineral affinity for DNA and RNA bases can vary due to different structural and chemical properties of the surface, a hypothesis on possible role of clays in the origin of life was made.

Uracil-catalyzed synthesis of acetyl phosphate: a photochemical driver for protometabolism

Progress toward a protometabolism (the earliest energy storage networks) has been severely hindered by a shortage of driver reactions, which could have harnessed solar photons or coupled electron sources/sinks on the primordial Earth. Here, it is reported for the first time that thioacetate can be converted into a known metabolite, acetyl phosphate, by ultraviolet light and in aqueous solution at neutral pH. Of more compelling importance, the synthesis is catalyzed by uracil, which suggests that a genetic component may have also facilitated the emergence of metabolic pathways. The chemistry of acetyl phosphate has been extensively studied, and it is known to be a precursor of phosphate esters, pyrophosphate and possibly longer inorganic chains. Moreover, its bifunctional reactivity (as either an acetyl or phosphoryl donor) would have been integral for the first metabolic cycles.

The effects of ferrous and other ions on the abiotic formation of biomolecules using aqueous aerosols and spark discharges

It has been postulated that the oceans on early Earth had a salinity of 1.5 to 2 times the modern value and a pH between 4 and 10. Moreover, the presence of the banded iron formations shows that Fe(+2) was present in significant concentrations in the primitive oceans. Assuming the hypotheses above, in this work we explore the effects of Fe(+2) and other ions in the generation of biomolecules in prebiotic simulation experiments using spark discharges and aqueous aerosols. These aerosols have been prepared using different sources of Fe(+2), such as FeS, FeCl(2) and FeCO(3), and other salts (alkaline and alkaline earth chlorides and sodium bicarbonate at pH = 5.8). In all these experiments, we observed the formation of some amino acids, carboxylic acids and heterocycles, involved in biological processes. An interesting consequence of the presence of soluble Fe(+2) was the formation of Prussian Blue, Fe(4)[Fe(CN)(6)](3), which has been suggested as a possible reservoir of HCN in the initial prebiotic conditions on the Earth.

On a Hypothetical Generational Relationship between HCN and Constituents of the Reductive Citric Acid Cycle

Encouraged by observations made on the course of reactions the HCN-tetramer can undergo with acetaldehyde, I delineate a constitutional and potentially generational relationship between HCN and those constituents of the reductive citric acid cycle that are direct precursors of amino acids in contemporary metabolism. In this context, the robustness postulate of classical prebiotic chemistry is questioned, and, by an analysis of the (hypothetical) reaction-tree of a stepwise hydrolysis of the HCN-tetramer, it is shown how such a non-robust chemical reaction platform could harbor the potential for the emergence of autocatalytic cycles. It is concluded that the chemistry of HCN should be revisited by focussing on its non-robust parts in order to demonstrate its full potential as one of the possible roots of prebiotic self-organizing chemical processes.

Pyrimidine as constituent of natural biologically active compounds

This review describes the various manifestations of the pyrimidine system (alkylated, glycosylated, benzo-annelated.). These comprise pyrimidine nucleosides as well as alkaloids and antibiotics--some of them have been discovered and isolated from natural sources already long time ago, others have been reported very recently. A short overview on pyrimidine syntheses (prebiotic synthesis, biosynthesis, and metabolism) is given. The biological activities of most of the pyrimidine analogs are briefly described, and, in some cases, syntheses are formulated.

Montmorillonite-catalysed formation of RNA oligomers: the possible role of catalysis in the origins of life

Large deposits of montmorillonite are present on the Earth today and it is believed to have been present at the time of the origin of life and has recently been detected on Mars. It is formed by aqueous weathering of volcanic ash. It catalyses the formation of oligomers of RNA that contain monomer units from 2 to 30-50. Oligomers of this length are formed because this catalyst controls the structure of the oligomers formed and does not generate all possible isomers. Evidence of sequence-, regio- and homochiral selectivity in these oligomers has been obtained. Postulates on the role of selective versus specific catalysts on the origins of life are discussed. An introduction to the origin of life is given with an emphasis on reaction conditions based on the recent data obtained from zircons 4.0-4.5Ga.

The cold origin of life: A. Implications based on the hydrolytic stabilities of hydrogen cyanide and formamide

It has been suggested that hydrogen cyanide (HCN) would not have been present in sufficient concentration to polymerize in the primitive ocean to produce nucleic acid bases and amino acids. We have measured the hydrolysis rates of HCN and formamide over the range of 30-150 degrees C and pH 0-14, and estimated the steady state concentrations in the primitive ocean. At 100 degrees C and pH 8, the steady state concentration of HCN and formamide were calculated to be 7 x 10(-13) M and 1 x 10(-15) M, respectively. Thus, it seems unlikely that HCN could have polymerized in a warm primitive ocean. It is suggested that eutectic freezing might have been required to have concentrated HCN sufficiantly for it to polymerize. If the HCN polymerization was important for the origin of life, some regions of the primitive earth might have been frozen.

The cold origin of life: B. Implications based on pyrimidines and purines produced from frozen ammonium cyanide solutions

A wide variety of pyrimidines and purines were identified as products of a dilute frozen ammonium cyanide solution that had been held at -78 degrees C for 27 years. This demonstrates that both pyrimidines and purines could have been produced on the primitive earth in a short time by eutectic concentration of HCN, even though the concentration of HCN in the primitive ocean may have been low. We suggest that eutectic freezing is the most plausible demonstrated mechanism by which HCN polymerizations could have produced biologically important prebiotic compounds.

The reactions of nitrogen heterocycles with acrolein: scope and prebiotic significance

It has been suggested that life began with a self-replicating RNA molecule. However, after much research into the prebiotic synthesis of RNA, the difficulties encountered have lead some to hypothesize that RNA was preceded by a simpler molecule, one more easily synthesized prebiotically. Many of the proposed alternative molecules are based on acrolein, since it reacts readily with nucleophiles, such as the nucleobases, via Michael addition and is readily synthesized from formaldehyde and acetaldehyde. Reports regarding the reactions of nucleobases with concentrated acrolein solutions suggest that this is a plausible reaction mechanism, though there are also reports that the "incorrect" isomers are obtained. The scope and kinetics of the reaction of acrolein with various nitrogen heterocycles are reported here. Reactions of pyrimidines often give N(1) adducts as the major products. Reactions of purines often give N(9) adducts in good yield. The reactions are rapid under neutral to slightly alkaline conditions, and proceed at low temperatures and dilutions. The implications of these findings for the origin of life are discussed.

Catalysis and prebiotic RNA synthesis

The essential role of catalysis for the origins of life is discussed. The status of the prebiotic synthesis of 2',5'- and 3',5'-linked oligomers of RNA is reviewed. Examples of the role of metal ion and mineral catalysis in RNA oligomer formation are discussed.

Prebiotic synthesis of orotic acid parallel to the biosynthetic pathway

By heating an aqueous solution of aspartic acid and urea, carbamylaspartic acid is first formed and then the molecule is cyclized to dihydroorotic acid (DHO) with loss of water. Irradiation of an aqueous solution of DHO with a tungsten lamp yields orotic acid by photo-dehydrogenation of the molecule. This pathway of orotic acid formation is quite similar to that of biosynthesis of the molecule.

Primeval procreative comet pond

It is speculated that life originated in a small, shallow body of water containing concentrated prebiotic organic feedstocks, inorganic compounds, and catalytic agents in a diversity of microenvironments. This pond was formed by an improbable, fortuitous soft-landing of a cometary nucleus, or fragment thereof, on the surface of a suitable planet with an atmosphere in an appropriate thermodynamic state, such as Earth.

Recent progress in the prebiotic chemistry of HCN

This article reports some recent results on the mechanisms of synthesis of biologically important molecules in oligomerizing solutions of HCN. It will also attempt to summarize, as completely as possible, our present state of knowledge concerning the range of products obtained under a variety of conditions in this reaction system.

Search for heterocyclic radiolytic products in aqueous solutions of cyanides

This work is a part of a systematic search for biologically significant compounds which are formed during radiolysis of aqueous solutions of cyano compounds. Aqueous solutions of HCN (0.2M, O2-free, natural pH) were irradiated at 18 Mrad dose of 60Co gammas, and the non-volatile radiolytic products concentrated in a dry residue. An aliquot of the dry residue was hydrolyzed with formic acid and the hydrolyzate selectively absorbed on active charcoal. The bulk of products from the charcoal was passed through a SP Sephadex C-25 column and the fractions analyzed by means of high performance liquid chromatography on a reverse phase column. Tentative assignments are based on retention times in the HPLC procedure and their pH dependence, and the coinjection of standards. The presence of adenine is certain. There is supporting evidence for uracil, thymine and cytosine. Experimental results also strongly support the presence of triazines.

Prebiotic synthesis in atmospheres containing CH4, CO, and CO2. II. Hydrogen cyanide, formaldehyde and ammonia

The electric discharge synthesis of HCN, H2CO, NH3 and urea has been investigated using various mixtures of CH4, CO, CO2, N2, NH3, H2O, and H2. HCN and H2CO were each synthesized in yields as high as 10% from CH4 as a carbon source. Similar yields were obtained from CO when H2/CO greater than 1.0 and from CO2 when H2/CO2 greater than 2.0. At H2/CO2 less than 1.0 the yields fall off drastically. Good yields of NH3 (0.7 to 5%) and fair yields of urea (0.02 to 0.63%) based on nitrogen were also obtained. The directly synthesized NH3 together with the NH3 obtained from the hydrolysis of HCN, nitriles and urea could have been a major source of ammonia in the atmosphere and oceans of the primitive earth. These results show that prebiotic syntheses from HCN and H2CO to give products such as purines and sugars and some amino acids could have occurred in primitive atmospheres containing CO and CO2 provided the H2/CO and H2/CO2 ratios were greater than about 1.0. Methane containing atmospheres give comparable quantities of HCN and H2CO, and are superior in the synthesis of amino acids.

Prebiotic adenine synthesis via HCN oligomerization in ice

Adenine is produced (after hydrolysis) when 0.01 M solutions of HCN are adjusted to pH 9.2 with NH4OH and are frozen at -2 degrees C for 60-100 days. The addition of glycolonitrile (the cyanohydrin of formaldehyde) increases the yield of adenine under these conditions by about five-fold. These results confirm and extend an earlier suggestion that purine synthesis on the prebiotic Earth might have occurred in frozen, dilute solutions of HCN.