Deuterolysis of amino acid precursors: evidence for hydrogen cyanide polymers as protein ancestors

Chemistry of Abiotic Nucleotide Synthesis

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

Hypercondensation of an amino acid: synthesis and characterization of a black glycine polymer

A granular material was obtained by thermal polymerization of glycine at 200 °C. It has been named "thermomelanoid" because of its strikingly deep-black color. The polymerization process is mainly a dehydration condensation leading to conventional amide bonds, and also CC double bonds that are formed from CO and CH2 groups ("hypercondensation"). Spectroscopic data, in particular from (13) C and (15) N solid-state cross-polarization magic angle spinning (CP-MAS) NMR spectra, suggest that the black color is due to (cross-)conjugated CC, CO, and NH groups. Small glycine peptides, especially triglycine, appear to be key intermediates in the formation of the thermomelanoid. This has been concluded by comparing the thermal behavior of glyn homopeptides (n=2-6) and glycine. The glycine polymerization was accompanied by the formation of small amounts of byproducts. Notably, a few percent of alanine and aspartic acid could be detected in the polymer. By using (13) C-labeled glycine, it was shown that these two amino acids formed through a common pathway, namely CαCα bond formation between glycine molecules. The thermomelanoid is hydrolyzed by strong acids and bases at room temperature, forming brown solutions.

Photochirogenesis: photochemical models on the absolute asymmetric formation of amino acids in interstellar space

Proteins of all living organisms including plants, animals, and humans are made up of amino acid monomers that show identical stereochemical L-configuration. Hypotheses for the origin of this symmetry breaking in biomolecules include the absolute asymmetric photochemistry model by which interstellar ultraviolet (UV) circularly polarized light (CPL) induces an enantiomeric excess in chiral organic molecules in the interstellar/circumstellar media. This scenario is supported by a) the detection of amino acids in the organic residues of UV-photo-processed interstellar ice analogues, b) the occurrence of L-enantiomer-enriched amino acids in carbonaceous meteorites, and c) the observation of CPL of the same helicity over large distance scales in the massive star-forming region of Orion. These topics are of high importance in topical biophysical research and will be discussed in this review. Further evidence that amino acids and other molecules of prebiotic interest are asymmetrically formed in space comes from studies on the enantioselective photolysis of amino acids by UV-CPL. Also, experiments have been performed on the absolute asymmetric photochemical synthesis of enantiomer-enriched amino acids from mixtures of astrophysically relevant achiral precursor molecules using UV-circularly polarized photons. Both approaches are based on circular dichroic transitions of amino acids that will be highlighted here as well. These results have strong implications on our current understanding of how life's precursor molecules were possibly built and how life selected the left-handed form of proteinogenic amino acids.

HCN polymers characterized by solid state NMR: chains and sheets formed in the neat liquid

Hydrogen cyanide polymerizes readily under a variety of conditions and significant prebiotic roles have been suggested for these polymers due to the abundance of HCN in universe. However, the structures of HCN polymers have been more speculative than grounded in experimental data. Here we show that (13)C and (15)N solid state NMR spectra of polymers formed in neat HCN are inconsistent with the previously proposed structures and suggest instead that the polymers are formed by simple monomer addition, first in head-to-tail fashion to form linear, conjugated chains, and then laterally to form saturated two-dimensional networks. This interpretation of the NMR spectra finds support in other information about the polymerization of neat HCN, including the presence of free radicals. As expected from the literature, formation of the HCN tetramer, diaminomaleonitrile, is also observed, but only when the reaction is catalyzed exclusively by base and then in crystalline form.

Hydrogen cyanide polymers connect cosmochemistry and biochemistry

To understand the origin of protein/nucleic acid based life as we know it on Earth, we must “follow” the nitrogen. Because of its unique hydrogen bonding characteristics, nitrogen is the key element in catalytic and/or informational proteins and nucleic acids essential to cell function and reproduction. We present evidence that HCN is the original source of prebiotic protein and nucleobase nitrogen. We also present chemically rational models supporting the radical hypothesis that the polymerization of HCN yields ab initio mundi prebiotic protein and polynucleobase macromolecules of sufficient size and complexity to allow the spontaneous generation of pre-RNA World biopolymers capable of catalysis and information transfer.

Hydrogen cyanide polymers, comets and the origin of life

Hydrogen cyanide polymers--heterogeneous solids ranging in colour from yellow to orange to brown to black--could be major components of the dark matter observed on many bodies of the outer solar system including asteroids, moons, planets and, especially, comets. The presence on cometary nuclei of frozen volatiles such as methane, ammonia and water subjected to high energy sources makes them attractive sites for the ready formation and condensed-phase polymerization of hydrogen cyanide. This could account for the dark crust observed on Comet Halley in 1986 by the Vega and Giotto missions. Dust emanating from its nucleus would arise partly from HCN polymers as suggested by the Giotto detection of free hydrogen cyanide, CN radicals, solid particles consisting only of H, C and N, or only of H, C, N, O, and nitrogen-containing organic compounds. Further evidence for cometary HCN polymers could be expected from in situ analysis of the ejected material from Comet Tempel 1 after collision with the impactor probe from the two-stage Deep Impact mission on July 4, 2005. Even more revealing will be actual samples of dust collected from the coma of Comet Wild 2 by the Stardust mission, due to return to Earth in January 2006 for analyses which we have predicted will detect these polymers and related compounds. In situ results have already shown that nitriles and polymers of hydrogen cyanide are probable components of the cometary dust that struck the Cometary and Interstellar Dust Analyzer of the Stardust spacecraft as it approached Comet Wild 2 on January 2, 2004. Preliminary evidence (January 2005) obtained by the Huygens probe of the ongoing Cassini-Huygens mission to Saturn and its satellites indicates the presence of nitrogen-containing organic compounds in the refractory organic cores of the aerosols that give rise to the orange haze high in the atmosphere of Titan, Saturn's largest moon. Our continuing investigations suggest that HCN polymers are basically of two types: ladder structures with conjugated -C=N- bonds and polyamidines readily converted by water to polypeptides. Thermochemolysis GC-MS studies show that cleavage products of the polymer include alpha-amino acids, nitrogen heterocycles such as purines and pyrimidines, and provide evidence for peptide linkages. Hydrogen cyanide polymers are a plausible link between cosmochemistry and the origin of informational macromolecules. Implications for prebiotic chemistry are profound. Following persistent bolide bombardment, primitive Earth may have been covered by water and carbonaceous compounds, particularly HCN polymers which would have supplied essential components for establishing protein/nucleic acid life.

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.

Hydrogen cyanide polymers from the impact of comet P/Shoemaker-Levy 9 on Jupiter

Hydrogen cyanide polymers--heterogeneous solids ranging in color from yellow to orange to brown to black--may be among the organic macromolecules most readily formed within the Solar System. The non-volatile black crust of comet Halley, for example, as well as the extensive orange-brown streaks in the atmosphere of Jupiter, might consist largely of such polymers synthesized from HCN formed by photolysis of methane and ammonia. Laboratory studies of these ubiquitous compounds point to the presence of polyamidine structures synthesized directly from hydrogen cyanide. These would be converted by water to polypeptides which can be further hydrolyzed to alpha-amino acids. Other polymers and multimers with ladder structures derived from HCN would also be present and might well be the source of the many nitrogen heterocycles, adenine included, detected by thermochemolytic analysis. The dark brown color arising from the impacts of comet P/Shoemaker-Levy 9 on Jupiter could therefore be mainly caused by the presence of HCN polymers, whether originally present, deposited by the impactor or synthesized from freshly formed HCN. Spectroscopic detection of these predicted macromolecules and their hydrolytic and pyrolytic by-products would strengthen significantly the hypothesis that cyanide polymerization is a preferred pathway for prebiotic and extraterrestrial chemistry.

Organic analysis of hydrogen cyanide polymers: prebiotic and extraterrestrial chemistry

Hydrogen cyanide polymerizes readily to a black solid from which a yellow-brown powder can be extracted by water and further hydrolyzed to alpha-amino acids. These macromolecules could be major components of the dark matter observed on many bodies in the outer solar system, including comets and asteroids. Primitive Earth might therefore have been covered with HCN polymers through bolide bombardment or be terrestrial synthesis. Several instrumental methods were used for the separation and identification of these intriguing polymeric materials, including photoacoustic Fourier transform infrared spectroscopy, supercritical fluid extraction chromatography and pyrolysis mass spectrometry. Our integrated analytical approach revealed fragmentation patterns and chemical functionalities consistent with the presence of polymeric peptide precursors both in HCN polymers and in the Murchison meteorite.

Hydrogen cyanide polymers on comets

The original presence on cometary nuclei of frozen volatiles such as methane, ammonia and water makes them ideal sites for the formation and condensed-phase polymerization of hydrogen cyanide. We propose that the non-volatile black crust of comet Halley consists largely of such polymers. Dust emanating from Halley's nucleus, contributing to the coma and tail, would also arise partly from these solids. Indeed, secondary species such as CN have been widely detected, as well as HCN itself and particles consisting only of H, C and N. Our continuing investigations suggest that the yellow-orange-brown-black polymers are of two types: ladder structures with conjugated -C=N- bonds, and polyamidines readily converted by water to polypeptides. These easily formed macromolecules could be major components of the dark matter observed on the giant planets Jupiter and Saturn, as well as on outer solar system bodies such as asteroids, moons and other comets. Implications for prebiotic chemistry are profound. Primitive Earth may have been covered by HCN polymers either through cometary bombardment or by terrestrial happenings of the kind that brought about the black crust of Halley. The resulting proteinaceous matrix could have promoted the molecular interactions leading to the emergence of life.

CH4/NH3/H2O spark tholin: chemical analysis and interaction with Jovian aqueous clouds

The organic solid (tholin) produced by spark discharge in a CH4 + NH3 + H2O atmosphere is investigated, along with the separable components of its water-soluble fraction. The chemistry of this material serves as a provisional model for the interaction of Jovian organic heteropolymers with the deep aqueous clouds of Jupiter. Intact (unhydrolyzed) tholin is resolved into four chemically distinct fractions by high-pressure liquid chromatography (HPLC). Gel filtration chromatography reveals abundant components at molecular weights approximately or equal to 600-700 and 200-300 Da. Gas chromatography/mass spectrometry of derivatized hydrolysis products of unfractionated tholin shows about 10% by mass protein and nonprotein amino acids, chiefly glycine, alanine, aspartic acid, beta-alanine, and beta-aminobutyric acid, and 12% by mass other organic acids and hydroxy acids. The stereospecificity of alanine is investigated and shown to be racemic. The four principal HPLC fractions yield distinctly different proportions of amino acids. Chemical tests show that small peptides or organic molecules containing multiple amino acid precursors are a possibility in the intact tholins, but substantial quantities of large peptides are not indicated. Candidate 700-Da molecules have a central unsaturated, hydrocarbon- and nitrile-rich core, linked by acid-labile (ester or amide) bonds to amino acid and carboxylic acid side groups. The core is probably not HCN "polymer." The concentration of amino acids from tholin hydrolysis in the lower aqueous clouds of Jupiter, about 0.1 micromole, is enough to maintain small populations of terrestrial microorganisms even if the amino acids must serve as the sole carbon source.

Heteropolypeptides on Titan?

Since hydrogen cyanide is a component of Titan's hazy atmosphere, HCN polymers might also be present by way of a low energy pathway leading initially to the synthesis of polyaminomalonitrile. Subsequent reactions of HCN with the activated nitrile groups of this HCN homopolymer would then yield heteropolyamidines, readily converted to heteropolypeptides following contact with frozen water on the surface of Titan. Similar HCN polymers in the reducing atmospheres of Jupiter and Saturn could be major contributors to the yellow-brown-orange appearance of these giant planets. Any detection of such HCN chemistry by the Voyager missions or the pending Galileo probe would constitute evidence for the hypothesis that heteropolypeptides on the primitive Earth were synthesized directly from hydrogen cyanide and water without the intervening formation of alpha-amino acids.

Origin of life: consideration of alternatives to proteins and nucleic acids

Starting with relatively simple, non-hydrolyzable compounds in aqueous solution, entirely spontaneous condensations give rise to polymers that contain purines, pyrimidines, amino acids, coenzymes, lipid components and even phosphate. The presence of certain lipid micelles allows significant product formation at millimolar substrate concentrations. The first step involves formation of a Michael adduct from alpha-beta-unsaturated carbonyl compounds and various nucleophiles. Polymerization of these adducts occurs via sequential Knoevenagel condensations. All reactions take place readily at temperatures below 45 degrees. The polymers can act as macromolecular catalysts as evidenced by hydrolytic activity. The purines and pyrimidines in the polymers appear to be capable of both base pairing and stacking interactions with ribonucleic acids. Specific examples of potential alternatives to base pairing are presented. These results are discussed from the standpoint of the spontaneous development of reproducing molecules. Proteins and nucleic acids may be evolutionary developments which have displaced earlier biopolymers.

Synthesis of protein, nucleosides and other organic compounds from cyanamide and potassium nitrite under possible primitive earth conditions

The mixing of cyanamide and KNO2 produced changes from white solids to yellow liquid and then to orange solid. The gases cyanogen and ammonia were formed. No external energy was used. The reactions were carried out with a small amount of O2. The presence of proteins in the reaction product formed 13 months after the mixing was indicated by the positive reactions of the cyanamide-KNO2 reaction product with ninhydrin, microbiuret, and Folin reagent; the ultraviolet absorption at about 280 nm; the yield of 24% of 15 amino acids; and molecular weight measurements of more than 160,000. The presence of nucleosides, nucleic acid bases, hydrocarbons, and organic esters in the reaction product formed 2 months after the mixing was indicated by ultraviolet absorption at about 260 nm, and the results of ligand-exchange chromatography, paper chromatography, infrared analysis, mass spectral analysis, and NMR spectroscopy. Possible cyanamide-mediated dehydration reactions and mechanisms are discussed.