Reactions of the HCN-tetramer with aldehydes

The HCN-tetramer, a 'classic' of the prebiotic chemistry of HCN, is shown to undergo a remarkable reaction with acetaldehyde in slightly basic or neutral aqueous solution at room temperature. The reaction consists in an aldolization-type C,C-bond formation, accompanied by a (presumably aldehyde-catalyzed) hydration of one of the two nitrile groups and the formation of two cyclic aminal-type groupings, each of the latter incorporating an additional molecule of the aldehyde. Should this so far unexplored type of chemistry of the HCN-tetramer prove to have some generality, the finding might add a new dimension to the potential etiological relevance of this HCN-oligomer.     

New Insights into the Characterization of ‘Insoluble Black HCN Polymers’

The data presented here provide a novel contribution to the understanding of the structural features of HCN polymers and could be useful in further development of models for prebiotic chemistry. The interpretation of spectroscopic and analytical data, along with previous results reported by other authors, allowed us to propose a mechanism for the aqueous polymerization of HCN from its primary and simplest isolated oligomer, the diaminomaleonitrile (DAMN) tetramer. We suggest that ‘insoluble black HCN polymers’ are formed by an unsaturated complex matrix, which retains a significant amount of H₂O and important bioorganic compounds or their precursors. This polymeric matrix can be formed by various motifs of imidazoles and cyclic amides, among others. The robust formation of HCN polymers assayed under several conditions seems to explain the plausible ubiquity of these complex substances in space.     

Metabolism and motility in prebiotic structures

Easily accessible, primitive chemical structures produced by self-assembly of hydrophobic substances into oil droplets may result in self-moving agents able to sense their environment and move to avoid equilibrium. These structures would constitute very primitive examples of life on the Earth, even more primitive than simple bilayer vesicle structures. A few examples of simple chemical systems are presented that self-organize to produce oil droplets capable of movement, environment remodelling and primitive chemotaxis. These chemical agents are powered by an internal chemical reaction based on the hydrolysis of an oleic anhydride precursor or on the hydrolysis of hydrogen cyanide (HCN) polymer, a plausible prebiotic chemistry. Results are presented on both the behaviour of such droplets and the surface-active properties of HCN polymer products. Such motile agents would be capable of finding resources while escaping equilibrium and sustaining themselves through an internal metabolism, thus providing a working chemical model for a possible origin of life.     

New insights into the characterization of 'insoluble black HCN polymers'

The data presented here provide a novel contribution to the understanding of the structural features of HCN polymers and could be useful in further development of models for prebiotic chemistry. The interpretation of spectroscopic and analytical data, along with previous results reported by other authors, allowed us to propose a mechanism for the aqueous polymerization of HCN from its primary and simplest isolated oligomer, the diaminomaleonitrile (DAMN) tetramer. We suggest that 'insoluble black HCN polymers' are formed by an unsaturated complex matrix, which retains a significant amount of H(2) O and important bioorganic compounds or their precursors. This polymeric matrix can be formed by various motifs of imidazoles and cyclic amides, among others. The robust formation of HCN polymers assayed under several conditions seems to explain the plausible ubiquity of these complex substances in space.     

Detection of Macromolecular Fractions in HCN Polymers Using Electrophoretic and Ultrafiltration Techniques

Elucidating the origin of life involves synthetic as well as analytical challenges. Herein, for the first time, we describe the use of gel electrophoresis and ultrafiltration to fractionate HCN polymers. Since the first prebiotic synthesis of adenine by Oró, HCN polymers have gained much interest in studies on the origins of life due to the identification of biomonomers and related compounds within them. Here, we demonstrate that macromolecular fractions with electrophoretic mobility can also be detected within HCN polymers. The migration of polymers under the influence of an electric field depends not only on their sizes (one‐dimensional electrophoresis) but also their different isoelectric points (two‐dimensional electrophoresis, 2‐DE). The same behaviour was observed for several macromolecular fractions detected in HCN polymers. Macromolecular fractions with apparent molecular weights as high as 250 kDa were detected by tricine‐SDS gel electrophoresis. Cationic macromolecular fractions with apparent molecular weights as high as 140 kDa were also detected by 2‐DE. The HCN polymers synthesized were fractionated by ultrafiltration. As a result, the molecular weight distributions of the macromolecular fractions detected in the HCN polymers directly depended on the synthetic conditions used to produce these polymers. The implications of these results for prebiotic chemistry will be discussed.     

Hcn and Hnc in Comets C/2000 Wm1 (Linear) and C/2002 C1 (Ikeya-Zhang)

Comets have been suggested as a possibly significant source of organic molecules to the early Earth. Hydrogen cyanide (HCN) is important in models of prebiotic chemistry, but may be difficult to form in the early terrestrial environment, while hydrogen isocyanide (HNC) is a `classical' tracer of interstellar ion-molecule chemistry. We have observed both HCN and HNC in 2 recent comets, bringing the number of comets with published measurements of the HNC/HCN abundance ratio to 6. The HNC/HCN ratio in comet Ikeya-Zhang appears to increase with decreasing heliocentric distance, as was previously observed for comet Hale-Bopp, indicating that the HNC is produced at least in part by processes in the cometary coma (atmosphere) and is not simply a constituent of the nuclear ices. Both comets C/2000 WM1 (Linear) and C/2002 C1 (Ikeya-Zhang) exhibit values of the HNC/HCN ratio that appear to be too large (0.09–0.19) tobe matched by current models of coma chemistry. Cometary HNC maybe a photodissociation product of organic grains or large organic polymers stored in the nucleus. We have also set a limit on the emission from the NO radical in comet WM1.     

The Cold Origin of Life: B. Implications Based on Pyrimidines and Purines Produced From Frozen Ammonium Cyanide Solutions

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.     

Infrared laser photolysis: A new tool for the study of prebiotic chemistry

Infrared laser induced dielectric breakdown and multiphoton absorption experiments on CH₄/NH₃ atmospheres are described. It is found that HCN, a central intermediate in prebiotic chemistry, is a principle product. This, combined with the fact that dielectric breakdown appears to have much in common with ordinary electric sparks, suggests that the laser could be a useful tool in studies of prebiotic chemistry. Several possible experiments in this vein are suggested.     

Quantum chemical study of the thermodynamics,kinetics of formation and bonding of H2CN relevance to prebiotic chemistry

Using the Iterative Extended Huckel Theory (IEHT), energy-conformation studies have been carried out for H₂CN (I),trans-HCNH (IIA), andcis-HCNH (IIB), three possible isomers formed by addition of a hydrogen atom to hydrogen cyanide. Calculations show that the order of decreasing thermodynamic stability is I≫IIA>IIB. Additionally, from calculated energies along simulated reaction pathways, the formation of I from HCN+H appears to be kinetically favored over IIA. Calculated properties of the minimum energy conformers of I and IIA are described and the potential role of H₂CN (I) as a reactive intermediate in prebiotic organic synthesis and its possible relevance to interstellar organic chemistry are discussed.     

Prospects of a Computational Origin of Life Endeavor

While the last century brought an exquisite understanding of the molecular basis of life, very little is known about the detailed chemical mechanisms that afforded the emergence of life on early earth. There is a broad agreement that the problem lies in the realm of chemistry, and likely resides in the formation and mutual interactions of carbon-based molecules in aqueous medium. Yet, present-day experimental approaches can only capture the synthesis and behavior of a few molecule types at a time. On the other hand, experimental simulations of prebiotic syntheses, as well as chemical analyses of carbonaceous meteorites, suggest that the early prebiotic hydrosphere contained many thousands of different compounds. The present paper explores the idea that given the limitations of test-tube approaches with regards to such a 'random chemistry' scenario, an alternative mode of analysis should be pursued. It is argued that as computational tools for the reconstruction of molecular interactions improve rapidly, it may soon become possible to perform adequate computer-based simulations of prebiotic evolution. We thus propose to launch a computational origin of life endeavor (http://ool.weizmann.ac.il/CORE), involving computer simulations of realistic complex prebiotic chemical networks. In the present paper we provide specific examples, based on a novel algorithmic approach, which constitutes a hybrid of molecular dynamics and stochastic chemistry. As one potential solution for the immense hardware requirements dictated by this approach, we have begun to implement an idle CPU harvesting scheme, under the title ool@home.     

The prebiotic role of adenine: A critical analysis

Adenine plays an essential role in replication in all known living systems today, and is prominent in many other aspects of biochemistry. It occurs among the products of oligomerization of HCN. These circumstances have stimulated the idea that adenine was a component in a replication system that was present at the start of life. Such replicators have included not only RNA, but also a number of simpler RNA-like alternatives which utilize a simpler backbone.Despite these encouraging indicators, a consideration of the chemical properties of adenine reveals reasons that disfavor its participation in such a role. These properties include the following: (1) Adenine synthesis requires HCN concentrations of at least 0.01 M. Such concentrations would be expected only in unique circumstances on the early Earth. Adenine yields are low in prebiotic simulations, and if a subsequent high-temperature hydrolysis step is omitted, the reported yield does not represent adenine itself, but 8-substituted adenines and other derivatives. (2) Adenine is susceptibile to hydrolysis (the half life for deamination at 37 °C, pH 7, is about 80 years), and to reaction with a variety of simple electrophiles, forming a multiplicity of products. Its accumulation would not be expected over a geological time scale, and its regioselective incorporation into a replicator appears implausible. (3) The adenine-uracil interaction, which involves two hydrogen bonds (rather than three, as in guanine-cytosine pairing) is weak and nonspecific. Pairing of adenine with many other partners has been observed with monomers, synthetic oligonucleotides and in RNA. The hydrogen-bonding properties of adenine appear inadequate for it to function in any specific recognition scheme under the chaotic conditions of a prebiotic soup.New and fundamental discoveries in the chemistry of adenine would be needed to reverse this perception. An alternative and attractive possibility is that some other replicator preceeded RNA (or RNA-like substances) in the origin of life.     

Role of Ferrocyanides in the Prebiotic Synthesis of α-Amino Acids

We investigated the synthesis of α-amino acids under possible prebiotic terrestrial conditions in the presence of dissolved iron (II) in a simulated prebiotic ocean. An aerosol-liquid cycle with a prebiotic atmosphere is shown to produce amino acids via Strecker synthesis with relatively high yields. However, in the presence of iron, the HCN was captured in the form of a ferrocyanide, partially inhibiting the formation of amino acids. We showed how HCN captured as Prussian Blue (or another complex compound) may, in turn, have served as the HCN source when exposed to UV radiation, allowing for the sustained production of amino acids in conjunction with the production of oxyhydroxides that precipitate as by-products. We conclude that ferrocyanides and related compounds may have played a significant role as intermediate products in the prebiotic formation of amino acids and oxyhydroxides, such as those that are found in iron-containing soils and that the aerosol cycle of the primitive ocean may have enhanced the yield of the amino acid production.     

Quantum-mechanical treatment of the electronic structure and geometry of hydrogen cyanide dimer

Experiments used to develop theories of chemical evolution seem to indicate that hydrogen cyanide, HCN, was an important molecule in prebiotic synthesis. In particular, polymerization products of hydrogen cyanide have been found to yield polypeptides upon hydrolysis. The proposed key intermediate in prebiotic synthesis is the aminocyanocarbene isomer of the dimer, either as a 1,3 biradical or as a dipolar singlet structure. Since this molecule has never been successfully isolated and characterized, a quantum mechanical study of various structures of the dieter is carried out using the INDO method. The results indicate that the lowest energy isomer is the iminoacetonitrile, with the aminocyanocarbene being next lowest. The triplet and singlet energy surfaces of the aminocyanocarbene intersect, so that for some geometries the singlet is lower in energy than the triplet, for others the reverse is true. The minima of both surfaces correspond to the linear configuration, with slightly different bond lengths. The triplet state minimum is 8·8 kcal/mol lower in energy than the singlet minimum. The calculated spin density distribution for the ground state of the carbene can be qualitatively described as a 1,3 biradical, in agreement with the early proposal of Kliss &; Matthews. The charge distribution of the singlet at its minimum energy geometry was also calculated. We found the charge separation to be less than that proposed for the dipolar structure of Moser et al. These calculations indicate that while the lowest energy isomer is the iminoacetonitrile, the aminocyanocarbene, the lowest-energy triplet, does have the appropriate spin distribution in its ground state for the biradical polymerization proposed in the theory of chemical evolution of Kliss &; Matthews. Experiments are suggested to determine the nature of the HCN polymerization mechanism, especially in the gas phase. By application of standard techniques used in polymer science, the nature of the gas phase polymerization of HCN can be determined, and the role of such reactions in chemical evolution can be better understood.     

Impact constraints on the environment for chemical evolution and the continuity of life

The Moon and the Earth were bombarded heavily by planetesimals and asteroids that were capable of interfering with chemical evolution and the origin of life. In this paper, we explore the frequency of giant terrestrial impacts able to stop prebiotic chemistry in the probable regions of chemical evolution. The limited time available between impacts disruptive to prebiotic chemistry at the time of the oldest evidence of life suggests the need for a rapid process for chemical evolution of life. The classical hypothesis for the origin of life through the slow accumulation of prebiotic reactants in the primordial soup in the entire ocean may not be consistent with constraints imposed by the impact history of Earth. On the other hand, rapid chemical evolution in cloud systems and lakes or other shallow evaporating water bodies would have been possible because reactants could have been concentrated and polymerized rapidly in this environment. Thus, life probably could have originated near the surface between frequent surface sterilizing impacts. There may not have been continuity of life depending on sunlight because there is evidence that life, existing as early as 3.8 Gyr ago, may have been destroyed by giant impacts. The first such organisms on Earth where probably not the ancestors of present life.     

Acceleration of HCN oligomerization by formaldehyde and related compounds: Implications for prebiotic syntheses

Summary Formaldehyde and other simple carbonyl compounds are known to react rapidly with HCN in aqueous solution to produce the corresponding cyanohydrin compounds. We have observed that these cyanohydrins markedly accelerate the rate of HCN oligomeri-zation, both in homogeneous solution as well as in the frozen state. These results, for which a tentative mechanism is suggested, significantly extend the possible range of conditions for HCN oligomerization on the prebiotic Earth.     

Prebiotic synthesis of histidine

Summary The prebiotic formation of histidine (His) has been accomplished experimentally by the reacton of erythrose with formamidine followed by a Strecker synthesis. In the first step of this reaction sequence, the formation of imidazole-4-acetaldehyde took place by the condensation of erythrose and formamidine, two compounds that are known to be formed under prebiotic conditions. In a second step, the imidazole-4-acetaldehyde was converted to His, without isolation of the reaction products by adding HCN and ammonia to the reaction mixture. LC, HPLC, thermospray liquid chromatography-mass spectrometry, and tandem mass spectrometry were used to identify the product, which was obtained in a yield of 3.5% based on the ratio of His/erythrose. This is a new chemical synthesis of one of the basic amino acids which has not been synthesized prebiotically until now.     

Aminomalononitrile: Some new data of prebiotic interest

Malonic nitriles are of great interest in prebiotic chemistry, because of the various organic reactions they can give in aqueous solutions. Among those, aminomalononitrile (AMN) plays a key role, as the trimer of HCN. In order to determine some of the thermodynamical data (pKA),...) and kinetic data relating to AMN in water, kinetic studies of the behaviour of AMN in aqueous solutions has been carried out at various pH.The preliminary results are reported concerning the determination of:Acid-base dissociation constants and U.V. andabsorption coefficients     

Dust in the universe: Implications for terrestrial prebiotic chemistry

In the present review we analyze the available literature on the distribution of dust in the Universe, methods of its observation and determination of the chemical composition, and the roles for terrestrial prebiotic chemistry. The most plausible natural sources of dust on the Earth in the prebiotic era are sedimentation of interplanetary dust, meteoritic and cometary impacts, volcanic eruptions, and soil microparticulates; the interplanetary medium being among the most powerful supplier of the dust matter. Two fundamental roles of dust particles for the origins of life are considered: (1) catalytic formation of prebiotic compounds; and (2) delivery of organic matter to the Earth by space dust particles. Due to the fact that there is only approximate information on the chemical composition and properties of interstellar, circumstellar, and major part of interplanetary dust, even the simulating experiments are difficult to perform. Until these gaps are filled, it seems reasonable to focus efforts of the scientists dealing with dust-driven catalytic formation of prebiotically important compounds on the volcanic and meteoritic/cometary impact environments.     

Chemical markers of prebiotic chemistry in hydrothermal systems.

The goal of this chapter is to suggest some organic compounds which may be indicative of prebiotic processes in hydrothermal systems or laboratory simulations of them. While the exact processes which led to the origins of life are not known, studies of life's origins of the past forty years have uncovered a plethora of potential precursor molecules. Some of these same molecules were probably present in hydrothermal systems if chemical processes there had a role in the origins of life. The types of molecules formed in primitive Earth simulation experiments and observed in the interstellar medium, on comets and meteorites will be reviewed in Section 2 of this chapter. Some reactions involving these molecules which may have been important in prebiotic syntheses will be outlined. Since near- to supercritical water is found in hydrothermal systems, its properties and aspects of organic chemistry in supercritical water at high temperature and pressure will be discussed in Section 3. Fischer-Tropsch type (FTT) reactions, which are a potential source of the building blocks of biological molecules in hydrothermal systems, are discussed in Section 4. In the concluding section, Section 5, the possible formation in hydrothermal systems of organic molecules that are believed to have been important for the origins of life is discussed.     

Utilization of cofactors expands metabolism in a new RNA world

RNA has been hypothesized to have preceded proteins as the major catalysts of the biosphere, yet there are only a very limited number of chemical reactions that are known to be catalyzed by modern RNA. Cofactors are used by the majority of protein enzymes to supply additional functional groups to the active site. RNA should also be able to utilize some of these same cofactors to extend its own catalytic potential. We describe here how it could be possible to use selection — amplification from a population of random RNA to obtain a coenzyme A mediated RNA transacylase. Exploitation of some of the sulphur chemistry mediated by coenzyme A could have significantly expanded a prebiotic RNA directed metabolism.