The effect of clays on the oligomerization of HCN

Setting the geological scene for the origin of life and continuing open questions about its emergence

The origin of life is one of the most fundamental questions of humanity. It has been and is still being addressed by a wide range of researchers from different fields, with different approaches and ideas as to how it came about. What is still incomplete is constrained information about the environment and the conditions reigning on the Hadean Earth, particularly on the inorganic ingredients available, and the stability and longevity of the various environments suggested as locations for the emergence of life, as well as on the kinetics and rates of the prebiotic steps leading to life. This contribution reviews our current understanding of the geological scene in which life originated on Earth, zooming in specifically on details regarding the environments and timescales available for prebiotic reactions, with the aim of providing experimenters with more specific constraints. Having set the scene, we evoke the still open questions about the origin of life: did life start organically or in mineralogical form? If organically, what was the origin of the organic constituents of life? What came first, metabolism or replication? What was the time-scale for the emergence of life? We conclude that the way forward for prebiotic chemistry is an approach merging geology and chemistry, i.e., far-from-equilibrium, wet-dry cycling (either subaerial exposure or dehydration through chelation to mineral surfaces) of organic reactions occurring repeatedly and iteratively at mineral surfaces under hydrothermal-like conditions.

Clays and the Origin of Life: The Experiments

There are three groups of scientists dominating the search for the origin of life: the organic chemists (the Soup), the molecular biologists (RNA world), and the inorganic chemists (metabolism and transient-state metal ions), all of which have experimental adjuncts. It is time for Clays and the Origin of Life to have its experimental adjunct. The clay data coming from Mars and carbonaceous chondrites have necessitated a review of the role that clays played in the origin of life on Earth. The data from Mars have suggested that Fe-clays such as nontronite, ferrous saponites, and several other clays were formed on early Mars when it had sufficient water. This raised the question of the possible role that these clays may have played in the origin of life on Mars. This has put clays front and center in the studies on the origin of life not only on Mars but also here on Earth. One of the major questions is: What was the catalytic role of Fe-clays in the origin and development of metabolism here on Earth? First, there is the recent finding of a chiral amino acid (isovaline) that formed on the surface of a clay mineral on several carbonaceous chondrites. This points to the formation of amino acids on the surface of clay minerals on carbonaceous chondrites from simpler molecules, e.g., CO2, NH3, and HCN. Additionally, there is the catalytic role of small organic molecules, such as dicarboxylic acids and amino acids found on carbonaceous chondrites, in the formation of Fe-clays themselves. Amino acids and nucleotides adsorb on clay surfaces on Earth and subsequently polymerize. All of these observations and more must be subjected to strict experimental analysis. This review provides an overview of what has happened and is now happening in the experimental clay world related to the origin of life. The emphasis is on smectite-group clay minerals, such as montmorillonite and nontronite.

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

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

An XPS study of HCN-derived films on pyrite surfaces: a prebiotic chemistry standpoint towards the development of protective coatings

Traditionally, the effect of mineral surfaces on increasing molecular complexity has been considered a major issue in studies about the origin of life. In contrast, herein, the effects of organic films derived from cyanide over an important prebiotic mineral, pyrite, are considered. An XPS spectroscopy study was carried out to understand the surface chemistry of the HCN-derived polymer/pyrite system. As a result, the simulation of a plausible prebiotic alkaline hydrothermal environment led to the identification of an NH4CN-based film with protective corrosion properties that immediately prevented the oxidation of the highly reactive pyrite surface. In addition, the effect of coating with antioxidant properties was preserved over a relatively long time, and the polymeric film was very stable under ambient conditions. These results increase the great potential of HCN polymers for development as a cheap and easily produced new class of multifunctional polymeric materials that also show promising and attractive insights into prebiotic chemistry.

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.

Walking over 4 Gya: Chemical Evolution from Photochemistry to Mineral and Organic Chemistries Leading to an RNA World

Here we overview the chemical evolution of RNA molecules from inorganic material through mineral-mediated RNA formation compatible with the plausible early Earth environments. Pathways from the gas-phase reaction to the formation of nucleotides, activation and oligomerization of nucleotides, seem to be compatible with specific environments. However, how these steps interacted is not clear since the chemical conditions are frequently different and can be incompatible between them; thus the products would have migrated from one place to another, suitable for further chemical evolution. In this review, we summarize certain points to scrutinize the RNA World hypothesis.

Mechanism for the Coupled Photochemistry of Ammonia and Acetylene: Implications for Giant Planets, Comets and Interstellar Organic Synthesis

Laboratory studies provide a fundamental understanding of photochemical processes in planetary atmospheres. Photochemical reactions taking place on giant planets like Jupiter and possibly comets and the interstellar medium are the subject of this research. Reaction pathways are proposed for the coupled photochemistry of NH3 (ammonia) and C2H2 (acetylene) within the context Jupiter's atmosphere. We then extend the discussion to the Great Red Spot, Extra-Solar Giant Planets, Comets and Interstellar Organic Synthesis. Reaction rates in the form of quantum yields were measured for the decomposition of reactants and the formation of products and stable intermediates: HCN (hydrogen cyanide), CH3CN (acetonitrile), CH3CH = N-N = CHCH3 (acetaldazine), CH3CH = N-NH2 (acetaldehyde hydrazone), C2H5NH2 (ethylamine), CH3NH2 (methylamine) and C2H4 (ethene) in the photolysis of NH3/C2H2 mixtures. Some of these compounds, formed in our investigation of pathways for HCN synthesis, were not encountered previously in observational, theoretical or laboratory photochemical studies. The quantum yields obtained allowed for the formulation of a reaction mechanism that attempts to explain the observed results under varying experimental conditions. In general, the results of this work are consistent with the initial observations of Ferris and Ishikawa (1988). However, their proposed reaction pathway which centers on the photolysis of CH3CH = N-N = CHCH3 does not explain all of the results obtained in this study. The formation of CH3CH = N-N = CHCH3 by a radical combination reaction of CH3CH = N• was shown in this work to be inconsistent with other experiments where the CH3CH = N• radical is thought to form but where no CH3CH = N-N = CHCH3 was detected. The importance of the role of H atom abstraction reactions was demonstrated and an alternative pathway for CH3CH = N-N = CHCH3 formation involving nucleophilic reaction between N2H4 and CH3CH = NH is advanced.

Polymer GARD: computer simulation of covalent bond formation in reproducing molecular assemblies

The basic Graded Autocatalysis Replication Domain (GARD) model consists of a repertoire of small molecules, typically amphiphiles, which join and leave a non-covalent micelle-like assembly. Its replication behavior is due to occasional fission, followed by a homeostatic growth process governed by the assembly's composition. Limitations of the basic GARD model are its small finite molecular repertoire and the lack of a clear path from a 'monomer world' towards polymer-based living entities. We have now devised an extension of the model (polymer GARD or P-GARD), where a monomer-based GARD serves as a 'scaffold' for oligomer formation, as a result of internal chemical rules. We tested this concept with computer simulations of a simple case of monovalent monomers, whereby more complex molecules (dimers) are formed internally, in a manner resembling biosynthetic metabolism. We have observed events of dimer 'take-over' - the formation of compositionally stable, replication-prone quasi stationary states (composomes) that have appreciable dimer content. The appearance of novel metabolism-like networks obeys a time-dependent power law, reminiscent of evolution under punctuated equilibrium. A simulation under constant population conditions shows the dynamics of takeover and extinction of different composomes, leading to the generation of different population distributions. The P-GARD model offers a scenario whereby biopolymer formation may be a result of rather than a prerequisite for early life-like processes.

The adsorption and reaction of adenine nucleotides on montmorillonite

The binding of AMP to Zn(2+)-montmorillonite was investigated in the presence of buffers and salts. Good's buffers, piperazine-N,N'-bis(2-ethanesulfonate) [PIPES] and morpholine-N-2-ethanesulfonate [MES], perturbed the exchangeable cations to a lesser extent (only 9% of Zn2+ displaced by 0.2 M buffer) than was observed with imidazole and lutidine buffers or NaCl and KCl salts (up to 80% of Zn2+ displaced). AMP adsorption isotherms measured in the presence of 0.2 M PIPES, MES, or Na2SO4 exhibited normal Langmuir-type behavior. The adsorption coefficient, KL, is 3-fold greater in the presence of HEPES or PIPES than it is in the absence of buffers. Basal spacings measured by X-ray diffraction for Zn(2+)-montmorillonite are 13 and 15 angstroms in the presence of PIPES, while a value of 12.8 angstroms was determined in the absence of PIPES. These data are interpreted in a model in which the adsorption of AMP is mediated by a Zn2+ complex of PIPES in different orientations in the interlamellar region of the montmorillonite. The type of exchangeable cation does not affect the ability of the lattice-bound Fe3+ in the montmorillonite to oxidize diaminomaleonitrile (DAMN). Exchangeable Cu2+ oxidizes DAMN, but exchangeable Fe3+ is nearly ineffective as an oxidant. The addition of DISN to 3'-AMP bound to Zn(2+)-montmorillonite in the presence of 0.2 M PIPES resulted in a higher yield of 2',3'-cAMP than is observed with a comparable concentration of Zn2+, a result which inplicates surface catalysis by the montmorillonite.

The investigation of the HCN derivative diiminosuccinonitrile as a prebiotic condensing agent. The formation of phosphate esters

Diiminosuccinonitrile (DISN) is formed readily by the Fe3+ oxidation of diaminomaleonitrile, a tetramer of HCN. DISN effects the phosphorylation of uridine in 13% yield to a mixture of the isomers of UMP when the reaction is performed in dimethylformamide solution. A 4% yield of the UMP isomers is obtained in neutral aqueous solution using 2 times the DISN concentration and 7 times the phosphate concentration used in DMF. DISN did not effect the conversion of adenosine to AMP or 5'-AMP to 5'-ADP in aqueous solution. The cyclization of 3'-AMP and 3'-UMP to the corresponding 2'-3'-cyclic phosphates proceeds in yields as high as 40-50% at 60 degrees C in pH 6 aqueous solutions in the presence of divalent metal ions. Lower yields of the cyclic phosphate are observed when 2'-AMP is the starting material. Substitution of acetate buffer for imidazole buffer results in a decrease in the yield of cyclic phosphate, the extent of which depends on the metal ion used in the reaction. No 3'5'-cyclic AMP was detected as a reaction product with either 5'-AMP or 3'-AMP as the starting material except for a 2.4% yield from 3'-AMP in the presence of Zn2+. BrCN effects the conversion of 3'-AMP to the 2'-3'-cyclic AMP in 37-65% yield depending on the divalent cation used as catalyst. A mechanism has been proposed for these cyclization reactions and their potential significance to the prebiotic synthesis of ribonucleic acid derivatives is discussed.

Oligomerization reactions of ribonucleotides: the reaction of the 5'-phosphorimidazolide of nucleosides on montmorillonite and other minerals

The reaction of ImpA in the presence of Na+ -montmorillonite 22A or Na+ -Volclay in aqueous, pH 8 solution gives a 50-60% yield of dimers and trimers (pA)2 and (pA)3. The ratio of 3',5'-phosphodiester bond formation is twice as great as 2',5'-bond formation. The reaction requires the presence of Mg2+ and is inhibited by 0.4 M imidazole. N-methylimidazole enhances the rate of the reaction but does not cause major changes in yield or product composition. Higher yields were obtained when Li+ -or Ca2+ -montmorillonites were used in place of Na+ -montmorillonite. Little or no phosphodiester bond formation was observed with Mg2+ - or Al3+ -montmorillonite. Montmorillonites other than 22A and Volclay exhibited little or no catalysis. In addition, little or no catalysis was exhibited in ferrugenous smectite, nontronite, allophane, imogolite or sepiolite. Oligomers were also formed by the reaction of ImpG, 2-methylImpG, ImpC and ImpU in the presence of Na+ -montmorillonite. The pyrimidine nucleotides gave significantly lower yields of oligomers.

Cyanide self-addition, controlled adsorption, and other processes at layered double hydroxides

Layered double hydroxides (LDH) are anion-exchanging materials of the type M(III)-M(II)x(OH)(2x + 2)Y that occur abundantly in nature, and can concentrate, protect, and activate simple organic anionic species of possible relevance to the earliest organisms. We now wish to report progress in the following areas: 1) Internal vs. external uptake of anions. Ferrocyanide does not displace carbonate from synthetic hydrotalcite (Mg:Al LDH carbonate) but is nevertheless taken up on the outside of the particles. In other cases, anion uptake is controlled by specific hydrogen bonding requirements rather than by charge density alone, a feature that can be used to control whether uptake will be both internal and external, or external only. These two findings taken together have important implications for specific catalysis by LDH, since specific hydrogen bonding will affect the individual and relative conformations of substrate anions, and anions occupying space in the interlayer will be under tighter constraints than those adsorbed externally. 2) Specific reactions catalyzed by LDH. We have found that the LDH Mg2Al(OH)6Cl catalyzes the self-addition of cyanide, to give in a one-pot reaction at low concentrations an increased yield of diaminomaleonitrile and in addition, at higher (> or = 0.05 M) concentrations, a purple-pink material that adheres to the LDH. We are investigating whether this reaction also occurs with hydrotalcite itself, what is the minimum effective concentration of cyanide, and what can be learned about the products and how they compare with those reported at high HCN concentrations in the absence of catalyst.

Binding of adenine and adenine-related compounds to the clay montmorillonite and the mineral hydroxylapatite

The first living things may have consisted of no more than RNA or RNA-like molecules bound to the surfaces of mineral particles. A key aspect of this theory is that these mineral particles have binding sites for RNA and its prebiotic precursors. The object of this study is to explore the binding properties of two of the best studied minerals, montmorillonite and hydroxylapatite, for possible precursors of RNA. The list of compounds investigated includes purines, pyrimidines, nucleosides, nucleotides, nucleotide coenzymes, diaminomaleonitrile and aminoimidazole carboxamide. Affinities for hydroxylapatite are dominated by ionic interactions between negatively charged small molecules and positively charged sites in the mineral. Binding to montmorillonite presents a more complex picture. These clay particles have a high affinity for organic ring structures which is augmented if they are positively charged. This binding probably takes place on the negatively charged faces of these sheet-like clay particles. Additional binding sites on the edges of these sheets have a moderate affinity for negatively charged molecules. Small molecules that bind to these minerals sometimes bind independently to sites on the minerals and sometimes bind cooperatively with favorable interactions between the bound molecules.

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.

Montmorillonite: a multifunctional mineral catalyst for the prebiological formation of phosphate esters

Reaction of diiminosuccinonitrile (DISN) with 3'-AMP in the presence of alkali- and alkaline earth-montmorillonites results in the formation of 2',3'-cAMP in aqueous solution. Little or no 2', 3'-cAMP is produced when metal ion concentrations equivalent to that of the metal ion associated with the homoionic clays are used instead of mobntmorillionite. Yields comparable to those obtained with DISN are obtained when diaminomaleonitrile (DAMN) is used in place of DISN as the condensing agent. DAMN, a compound which is more stable than DISN in aqueous solution, is oxidized to DISN on the surface of the clay by Fe+3 in the clay lattice. DISN, the true condensing agent, is thus generated in the presence of the bound 3'-AMP on the montmorillonite surface. The montmorillonite catalyzes the DISN-mediated formation of 2', 3'-cAMP and this product, which binds much less strongly than does the 3'-AMP, is desorbed from the clay surface. This research established that the montmorillonite performs four different functions in its role as catalyst: (1) Binding one of the substrate molecules (3'-AMP) (2) Activating the second substrate (DAMN) (3) Catalyzing the formation of 2', 3'-cAMP (4) Releasing the reaction product so another substrate molecules can bind to the montmorillonite.

Syntheses with isotopically labelled carbon. Methyl iodide, formaldehyde and cyanide

Many of the uniquely labelled synthetic precursors currently employed in the design of sophisticated radiolabelled compounds have their origins in the field of hot atom chemistry. Particularly, the development during the past few years of automated, on-line synthetic procedures which combine the nuclear reaction, hot atom and classical chemistry, and rapid purification methods has allowed the incorporation of useful radionuclides into suitable compounds of chemical and biochemical interest. The application of isotopically labelled methyl iodide, formaldehyde, and cyanide anion as synthetic intermediates in research involving human physiology and nuclear medicine, as well as their contributions to other scientific methodology, is reviewed.

The prebiotic chemistry of nucleotides

Diiminosuccinonitrile (DISN), formed by the oxidation of diaminomaleonitrile (DAMN), has been investigated as a potential prebiotic phosphorylating agent. DISN effects the cyclization of 3'-adenosine monophosphate to adenosine 2', 3'-cyclic phosphate in up to 39% yield. The mechanism of this reaction was investigated. The DISN-mediated phosphorylation of uridine to uridine monophosphate does not proceed efficiently in aqueous solution. The reaction of DISN with uridine-5'-phosphate and uridine results in the formation of 2,2'-anhydronucleotides and 2,2'-anhydronucleosides respectively, and other reaction products resulting from an initial reaction at the 2'- and 3'- hydroxyl groups. The clay mineral catalysis of the cyclization of adenosine-3'-phosphate was investigated using homoionic montmorillonites.

Prebiotic synthesis and reactions of nucleosides and nucleotides

Diiminosuccinonitrile (DISN) has been investigated as a potential prebiotic phosphorylating agent. It is formed readily by the oxidation of diaminomaleonitrile (DAMN), a tetramer of HCN. DISN effects the cyclization of 3'-adenosine monophosphate to adenosine 2',3'-cyclic phosphace in up to 40% yield. The DISN-mediated phosphorylation of uridine to uridine mono-phosphate does not proceed efficiently in aqueous solution. The reaction of DISN and BrCN with uridine-5'-phosphate and uridine results in the formation of 2,2'-anhydronucleotides and 2,2'-anhydronucleosides respectively, and other reaction products resulting from an initial reaction at the 2'- and 3'-hydroxyl groups. The clay mineral catalysis of the cyclization of adenosine-3'-phosphate was investigated using homoionic montmorillonites.

Clay and the origin of life

Research concerning the possible role of clay in chemical evolution is reviewed. The probable importance of clays in the origin of life is assessed.

Clays in prebiological chemistry

In this review an attempt is made to highlight the structures and properties of clay that may contribute to a better understanding of the role of clays in chemical evolution. The adsorption of organic molecules on clays has been demonstrated, as has the synthesis of bioorganic monomers in the presence of clays. For instance, amino acids (glycine, aspartic acid, threonine, alanine and others) as well as purines and pyrimidines, have been obtained from CO and NH3 in the presence of clays at relatively high temperatures (250-325 degrees C). Carbohydrates are also easily derived from formaldehyde at relatively low temperatures (approximately equal to 80 degrees C). The oligomerization of biochemical monomers, mediated by clays has also been shown to result in the formation of polymer molecules basic to life. For instance the condensation of amino acyl adenylates at room temperature in the presence of montmorillonite is known to yield polypeptides in discrete ranges of molecular weights with degrees of polymerization up to 56. Clays have also been found to affect the condensation of mononucleotides to oligonucleotides. Although the role of clays in the origin or metabolic pathways has not been demonstrated, it is possible that clays may have played a cooperative role with catalytic peptides in an intermediate stage of prebiological chemistry preceding the emergence of life on this planet.