Glycine and alanine synthesis from formaldehyde and hydroxylamine in the field of ultrasound waves

High intensity ultrasound waves coupled with other form of energy obviously were initiators of pre-biochemical reactions; these reactions occurred in the water masses of the primordial Earth.Essential biological substances like formaldehyde, ammonia, hydrocyanic acid, and amino acids compounds similar to carbohydrates by their properties were synthesized in the field of ultrasound waves in model experiments.The main partners of these reactions are water and gases of reductional atmosphere: hydrogen, carbon monoxide, methane, nitrogen and argon.Formation of amino acids takes place in aqueous solutions of formaldehyde and hydroxylamine. The sonication yielded alanine and glycine, 2.0×10^–7 and 1.8×10^–7 molecules per 100 eV respectively.     

Gaseous disinfection of Cryptosporidium parvum oocysts.

Purified oocysts of Cryptosporidium parvum suspended in approximately 400 microliters of phosphate-buffered saline or deionized water in microcentrifuge tubes were exposed at 21 to 23 degrees C for 24 h to a saturated atmosphere of ammonia, carbon monoxide, ethylene oxide, formaldehyde, or methyl bromide gas. Controls were exposed to air. Oocysts in each tube were then rinsed and resuspended in fresh, deionized water, and 1 million oocysts exposed to each gas were orally administered to each of three to six neonatal BALB/c mice in replicate groups. Histologic sections of ileum, cecum, and colon tissues taken from each mouse 72 h after oral administration of oocysts were examined microscopically to determine if infection had been established. All 15 mice given oocysts exposed to carbon monoxide had numerous developmental stages of cryptosporidium in all three intestinal segments. Of 10 mice given oocysts exposed to formaldehyde, 6 had a few developmental stages of cryptosporidium in the ileum. No mice given oocysts exposed to ammonia, ethylene oxide, or methyl bromide were found to be infected. These findings indicate the efficacy of these low-molecular-weight gases (ammonia, ethylene oxide, and methyl bromide) as potential disinfectants for C. parvum oocysts where soil, rooms, buildings, tools, or instruments might be contaminated.     

The influence of prebiotic-type organic molecules on the crystallization of Al and Mg hydroxides

It is now well accepted that clays could have concentrated prebiotic organic molecules, protected them from UV radiation, and served as templates and catalysts in their prebiotic evolution. A complementary question is: How did prebiotic organics in the oceans, in ground water, or in hydrothermal solutions affect the formation and inorganic evolution of oxides, hydroxides, and clay minerals? In this study predominantly amorphous Al oxyhydroxides (Al gels) and crystalline Mg hydroxyoxides were synthesized, and then crystallized and recrystallized respectively, to Al and Mg hydroxides via wet and dry (w/d) cycling using both water and organic solutions. The products that resulted were examined using IR spectroscopy and X-ray diffraction (XRD). XRD scans of the products formed by w/d cycling of the Al gels with either water or 0.1 M aqueous solutions of methanol or formaldehyde showed that bayerite (α Al₂O₃) was the major phase formed. The acetonitrile treated sample exhibited the most defined XRD peaks, and no crystalline phase could be observed by XRD of the 0.1 M formamide solution treated sample. Cycling the Mg hydroxyoxide with water, or 0.1 M solutions of methanol, formamide, formaldehyde, or acetonitrile resulted in the formation of brucite (Mg(OH)₂) (in varying amounts) and of three unidentified phases. One unidentified phase, ‘phase II’, was observed in the formaldehyde cycled sample (and tentatively identified in the methanol and formamide cycled samples), ‘phase III’ in the formamide and formaldehyde cycled sample, and ‘phase IV’ in only the formaldehyde. XRD peaks with a spacing of approximately 11.5 Å (assigned to phase III) suggest intercalation of formamide and formaldehyde into the interlayer spaces of the brucite. Phosphate treatment, prior to w/d cycling with water, and also with the above mentioned organics, while totally preventing subsequent formation of any crystalline Al hydroxide, enhanced the formation of Mg phases, shown by XRD data. Formation of brucite was impeded only by w/d cycling using concentrated methanol solution, but even these effects were reversible. The XRD scans of the products resulting from the aqueous and organic solution cycling treatments of the Mg starting materials showed peaks due to brucite and three unidentified phases. Only the brucite is evident in oriented sample XRD scans of the Mg starting material when treated with methanol, formamide, and acetonitrile. In random powder sample XRD scans of the Mg starting material treated with: 1) methanol — the unidentified phase II is evident, 2) formamide — phase II and III are seen, and 3) formaldehyde — phases II, III, and IV are evident.     

Prebiotic Amino Acid Thioester Synthesis: Thiol-Dependent Amino Acid Synthesis from Formose Substrates (Formaldehyde and Glycolaldehyde) and Ammonia

Formaldehyde and glycolaldehyde (substrates of the formose autocatalytic cycle) were shown to react with ammonia yielding alanine and homoserine under mild aqueous conditions in the presence of thiol catalysts. Since similar reactions carried out without ammonia yielded -hydroxy acid thioesters (Weber, 1984a, b), the thiol-dependent synthesis of alanine and homoserine is presumed to occur via amino acid thioesters – intermediates capable of forming peptides (Weber and Orgel 1979). A pH 5.2 solution of 20 mM formaldehyde, 20 mM glycolaldehyde, 20 mM ammonium chloride, 23 mM 3-mercaptopropionic acid, and 23 mM acetic acid that reacted for 35 days at 40°C yielded (based on initial formaldehyde) 1.8% alanine and 0.08% homoserine. In the absence of thiol catalyst, the synthesis of alanine and homoserine was negligible. Alanine synthesis required both formaldehyde and glycolaldehyde, but homoserine synthesis required only glycolaldehyde. At 25 days the efficiency of alanine synthesis calculated from the ratio of alanine synthesized to formaldehyde reacted was 2.1%, and the yield (based on initial formaldehyde) of triose and tetrose intermediates involved in alanine and homoserine synthesis was 0.3 and 2.1%, respectively. Alanine synthesis was also seen in similar reactions containing only 10 mM each of aldehyde substrates, ammonia, and thiol. The prebiotic significance of these reactions that use the formose reaction to generate sugar intermediates that are converted to reactive amino acid thioesters is discussed.     

Sugar-Driven Prebiotic Synthesis of Ammonia from Nitrite

Reaction of 3–5 carbon sugars, glycolaldehyde, and α-ketoaldehydes with nitrite under mild anaerobic aqueous conditions yielded ammonia, an essential substrate for the synthesis of nitrogen-containing molecules during abiogenesis. Under the same conditions, ammonia synthesis was not driven by formaldehyde, glyoxylate, 2-deoxyribose, and glucose, a result indicating that the reduction process requires an organic reductant containing either an accessible α-hydroxycarbonyl group or an α-dicarbonyl group. Small amounts of aqueous Fe⁺³ catalyzed the sugar-driven synthesis of ammonia. The glyceraldehyde concentration dependence of ammonia synthesis, and control studies of ammonia’s reaction with glyceraldehyde, indicated that ammonia formation is accompanied by incorporation of part of the synthesized ammonia into sugar-derived organic products. The ability of sugars to drive the synthesis of ammonia is considered important to abiogenesis because it provides a way to generate photochemically unstable ammonia at sites of sugar-based origin-of-life processes from nitrite, a plausible prebiotic nitrogen species.     

N-Carbamoyl Amino Acid Solid–Gas Nitrosation by NO/NO x : A New Route to Oligopeptides via α-Amino Acid N-Carboxyanhydride. Prebiotic Implications

α-N-Carbamoyl amino acid (CAA), whose conditions of formation in a prebiotic hydrosphere have been described previously (Taillades et al. 1998), could have been an important intermediate in prebiotic peptide synthesis through reaction with atmospheric NO _x . Nitrosation of solid CAA (glycine or valine derivative) by a 4/1 NO/O₂ gaseous mixture (1 atm) yields N-carboxyanhydride (NCA) quantitatively in less than 1 h at room temperature. The crude solid NCA undergoes quantitative oligomerization (from trimer to nonamer under the conditions we used) when treated with a (bi)carbonate aqueous buffer at pH 9. We therefore suggest that part of the prebiotic amino acid activation/polymerization process may have taken place in a dry phase (``drying-lagoon' scenario). Received: 23 June 1998 / Accepted: 7 December 1998     

Enhanced Synthesis of Alkyl Amino Acids in Miller’s 1958 H<Subscript>2</Subscript>S Experiment

Stanley Miller’s 1958 H₂S-containing experiment, which included a simulated prebiotic atmosphere of methane (CH₄), ammonia (NH₃), carbon dioxide (CO₂), and hydrogen sulfide (H₂S) produced several alkyl amino acids, including the α-, β-, and γ-isomers of aminobutyric acid (ABA) in greater relative yields than had previously been reported from his spark discharge experiments. In the presence of H₂S, aspartic and glutamic acids could yield alkyl amino acids via the formation of thioimide intermediates. Radical chemistry initiated by passing H₂S through a spark discharge could have also enhanced alkyl amino acid synthesis by generating alkyl radicals that can help form the aldehyde and ketone precursors to these amino acids. We propose mechanisms that may have influenced the synthesis of certain amino acids in localized environments rich in H₂S and lightning discharges, similar to conditions near volcanic systems on the early Earth, thus contributing to the prebiotic chemical inventory of the primordial Earth.     

Bolide impacts and the oxidation state of carbon in the Earth's early atmosphere

A one-dimensional photochemical model was used to examine the effect of bolide impacts on the oxidation state of Earth's primitive atmosphere. The impact rate should have been high prior to 3.8 Ga before present, based on evidence derived from the Moon. Impacts of comets or carbonaceous asteroids should have enhanced the atmospheric CO/CO₂ ratio by bringing in CO ice and/or organic carbon that can be oxidized to CO in the impact plume. Ordinary chondritic impactors would contain elemental iron that could have reacted with ambient CO₂ to give CO. Nitric oxide (NO) should also have been produced by reaction between ambient CO₂ and N₂ in the hot impact plumes. High NO concentrations increase the atmospheric CO/CO₂ ratio by increasing the rainout rate of oxidized gases. According to the model, atmospheric CO/CO₂ ratios of unity or greater are possible during the first several hundred million years of Earth's history, provided that dissolved CO was not rapidly oxidized to bicarbonate in the ocean. Specifically, high atmospheric CO/CO₂ ratios are possible if either: (1) the climate was cool (like today's climate), so that hydration of dissolved CO to formate was slow, or (2) the formate formed from CO was efficiently converted into volatile, reduced carbon compounds, such as methane. A high atmospheric CO/CO₂ ratio may have helped to facilitate prebiotic synthesis by enhancing the production rates of hydrogen cyanide and formaldehyde. Formaldehyde may have been produced even more efficiently by photochemical reduction of bicarbonate and formate in Fe⁺⁺-rich surface waters.     

Formation and stability of complex organic compounds in space environments.

Complex organic compounds have been found in extraterrestrial bodies such as meteorites and comets. We confirmed the formation of complex organic compounds that contained amino acid precursors from a mixture of carbon monoxide (or methanol), ammonia and water by radiation or UV. Molecular weights of the complex organics were several thousands. Stability of the complex precursors was studied. When free amino acids were irradiated with gamma rays or synchrotron radiation, they easily decomposed. The complex precursors were, however, much more stable than free amino acid against irradiation. We propose to examine the formation and alteration of amino acid precursors in space by using exposed facility of ISS.     

Prebiotic ribose synthesis: A critical analysis

The discovery of catalytic ability in RNA has given fresh impetus to speculations that RNA played a critical role in the origin of life. This question must rest on the plausibility of prebiotic oligonucleotide synthesis, rather than on the properties of the final product. Many cliams have been published to support the idea that the components of RNA were readily available on the prebiotic earth. In this article, the literature cited in support of the prebiotic availability of one subunit, D-ribose, is reviewed to determine whether it justifies the claim.Polymerization of formaldehyde (the formose reaction) has been the single reaction cited for prebiotic ribose synthesis. It has been conducted with different catalysts: numerous basic substances, neutral clays and heat, and various types of radiation. Ribose has been identified (yields are uncertain, but unlikely to be greater than 1%) in reactions run with concentrated (0.15 M or greater) formaldehyde. It has been claimed in reactions run at lower concentration, but characterization has been inadequate, and experimental details have not been provided.The complex sugar mixture produced in the formose reaction is rapidly destroyed under the reaction conditions. Nitrogenous substances (needed for prebiotic base synthesis) would interfere with the formose reaction by reacting with formaldehyde, the intermediates, and sugar products in undesirable ways.The evidence that is currently available does not support the availability of ribose on the prebiotic earth, except perhaps for brief periods of time, in low concentration as part of a complex mixture, and under conditions unsuitable for nucleoside synthesis.     

Photochemical synthesis of biomolecules under anoxic conditions

We report the long-wavelength UV anoxic photosynthesis of uracil, various sugars (including deoxyribose and glycoaldehyde), amino acids, and other organic photoproducts. These reactions occur in mixtures of water, calcium carbonate, formaldehyde and hydrazine. Our data demonstrate that under several sets of conditions biomolecules can be formed in variety and abundance from reduced compounds (formaldehyde and hydrazine) derived from anoxic dinitrogen/carbon dioxide environments. The formaldehyde concentrations were varied from 10 mM to 0.005 mM, and the hydrazine concentrations were varied from 1 mM to 0.01 mM. The highest of these reactant concentrations were 500 and 6 times greater than those reported for earlier experiments upon the synthesis of these precursors from CO₂ or N₂, while the lowest of reactant concentrations employed here were 0.5 (formaldehyde) and 0.006 (hydrazine). Product yields were greatest when the hydrazine/formaldehyde ratio was 1, and when the reactant concentrations were low. These data suggest that organic products can be formed in variety from those amounts of formaldehyde and hydrazine precursors which are themselves formed under anoxic UV photochemical conditions. Hence these various reactions would seem to have prebiotic relevance. The UV 254 nm photon flux employed was 100 times higher than unattenuated solar flux. Durations of UV exposure were 24 hrs and 72 hrs. No experiments have been addressed to the possibility of UV flux dependency.     

Diketopiperazine-mediated peptide formation in aqueous solution

Though diketopiperazines (DKP) are formed in most experiments concerning the prebiotic peptide formation, the molecules have not been paid attention in the studies of chemical evolution. We have found that triglycine, tetraglycine or pentaglycine are formed in aqueous solution of glycine anhydride (DKP) and glycine, diglycine or triglycine, respectively. A reaction of alanine with DKP resulted in the formation of glycylglycylalanine under the same conditions. These results indicate that the formation of the peptide bonds proceeds through the nucleophilic attack of an amino group of the amino acids or the oligoglycines on the DKP accompanied by the ring-opening.The formation of glycine anhydride, di-, tri- and tetraglycine was also observed in a mixed aqueous solution of urea and glycine in an open system to allow the evaporation of ammonia. A probable pathway is proposed for prebiotic peptide formation through diketopiperazine on the primitive Earth.     

Pyrolysis experiment of simulated exogenous complex organics synthesized from the gas mixtures of CO, NH3, and H2O by 3 MeV proton irradiation.

High molecular weight organic matter synthesized from mixtures of carbon monoxide, ammonia and water gases similar to those found in the interstellar medium were irradiated with a 3 MeV proton beam and analyzed by Curie point pyrolysis with detection by gas chromatograph and mass spectrometer (Pyr-GC-MS). A wide variety of organic compounds, not only a number of amide compounds, but also heterocyclic and polycyclic aromatic hydrocarbons (PAHs), were detected among the products of the pyrolysis. The present data shows that primary and primitive organic matter serving as precursors to bioorganic compounds such as amino acids, nucleic acid bases and sugar might have been formed in a gaseous mixture of similar composition to that of the interstellar dust environment.     

Formation of proteinoid microspheres under simulated prebiotic atmospheres and individual gases.

The formation of microspheres from acidic and basic proteinoids was attempted under simulated prebiotic atmospheres and constituent gases thereof. Both types of proteinoid yielded microspheres under carbon dioxide, carbon monoxide, methane, hydrogen sulfide, hydrogen, nitrogen, and oxygen (tested separately) and also under nitrogen-carbon dioxide atmospheres; higher proportions of carbon dioxide resulted in fewer spheres from basic proteinoid. Neither type of proteinoid formed spheres on 10-minute exposure to ammonia or methane-hydrogen-ammonia atmospheres. (Brief exposure resulted in spheres from basic proteinoid.) The effects, both qualitative and quantitative, were indicated by control experiments to be due to pH, rather than to the specific gas (or ion). The results suggest that the proteinoid microsphere model for protocells is applicable under a variety of possible prebiotic atmospheres, with some restrictions imposed by pH.     

Survivability and reactivity of glycine and alanine in early oceans: effects of meteorite impacts

Prebiotic oceans might have contained abundant amino acids, and were subjected to meteorite impacts, especially during the late heavy bombardment. It is so far unknown how meteorite impacts affected amino acids in the early oceans. Impact experiments were performed under the conditions where glycine was synthesized from carbon, ammonia, and water, using aqueous solutions containing ¹³C-labeled glycine and alanine. Selected amino acids and amines in samples were analyzed with liquid chromatography-mass spectrometry (LC/MS). In particular, the ¹³C-labeled reaction products were analyzed to distinguish between run products and contaminants. The results revealed that both amino acids survived partially in the early ocean through meteorite impacts, that part of glycine changed into alanine, and that large amounts of methylamine and ethylamine were formed. Fast decarboxylation was confirmed to occur during such impact processes. Furthermore, the formation of n-butylamine, detected only in the samples recovered from the solutions with additional nitrogen and carbon sources of ammonia and benzene, suggests that chemical reactions to form new biomolecules can proceed through marine impacts. Methylamine and ethylamine from glycine and alanine increased considerably in the presence of hematite rather than olivine under similar impact conditions. These results also suggest that amino acids present in early oceans can contribute further to impact-induced reactions, implying that impact energy plays a potential role in the prebiotic formation of various biomolecules, although the reactions are complicated and depend upon the chemical environments as well.     

Aqueous Synthesis of Peptide Thioesters from Amino Acids and a Thiol Using 1,1′-Carbonyldiimidazole

A new method was developed for the synthesis of peptide thioesters from free amino acids and thiols in water. This one-pot simple method involves two steps: (1) activation in water of an amino acid presumably as its N-carboxyanhydride (NCA) using 1,1′-carbonyldiimidazole (CDI), and (2) subsequent condensation of the activated amino acid-NCA in the presence of a thiol. With this method citrulline peptide thioesters containing up to 10 amino acid residues were prepared in a single reaction. This aqueous synthetic method provides a simple way to prepare peptide thioesters for studies of peptide replication involving ligation of peptide thioesters on peptide templates. The relevance of peptide replication to the origin-of-life process is supported by previous studies showing that amino acid thioesters (peptide thioester precursors) can be synthesized under prebiotic conditions by reaction of small sugars with ammonia and a thiol.     

Purification and characterization of ferredoxin from Peptostreptococcus productus (strain Marburg)

Ferredoxin was purified to apparent homogeneity from cell extracts of the homoacetogen Peptostreptococcus productus (strain Marburg). The yield was 70 g ferredoxin per g wet cells of P. productus. The UV-vis spectrum exhibited characteristics of a typical clostridial ferredoxin spectrum with a molar extinction coefficient ₃₈₅ of 30000 M^-1 cm^-1 and an A₃₈₅/A₂₈₀ ratio of 0.76. The molecular weight M_r was near 5700 as calculated from the amino acid composition. The protein contained per mol 9.9 mol iron, 8.2 mol acid-labile sulfide, and near 7 mol cysteine indicating the presence of two 4 Fe/4 S clusters. The redox potential was determined to be-410 mV. The purified ferredoxin was reduced with carbon monoxide by the carbon monoxide dehydrogenase from crude extracts and by the partially enriched enzyme of P. productus.     

The Use of Ascorbate as an Oxidation Inhibitor in Prebiotic Amino Acid Synthesis: A Cautionary Note

It is generally thought that the terrestrial atmosphere at the time of the origin of life was CO₂-rich and that organic compounds such as amino acids would not have been efficiently formed abiotically under such conditions. It has been pointed out, however, that the previously reported low yields of amino acids may have been partially due to oxidation by nitrite/nitrate during acid hydrolysis. Specifically, the yield of amino acids was found to have increased significantly (by a factor of several hundred) after acid hydrolysis with ascorbic acid as an oxidation inhibitor. However, it has not been shown that CO₂ was the carbon source for the formation of the amino acids detected after acid hydrolysis with ascorbic acid. We therefore reinvestigated the prebiotic synthesis of amino acids in a CO₂-rich atmosphere using an isotope labeling experiment. Herein, we report that ascorbic acid does not behave as an appropriate oxidation inhibitor, because it contributes amino acid contaminants as a consequence of its reactions with the nitrogen containing species and formic acid produced during the spark discharge experiment. Thus, amino acids are not efficiently formed from a CO₂-rich atmosphere under the conditions studied.     

A radical solution for the biosynthesis of the H-cluster of hydrogenase

Fe-only or FeFe hydrogenases, as they have more recently been termed, possess a uniquely organometallic enzyme active site, termed the H-cluster, where the electronic properties of an iron-sulfur cluster are tuned with distinctly non-biological ligands, carbon monoxide and cyanide. Recently, it was discovered that radical S-adenosylmethionine enzymes were involved in active hydrogenase expression. In the current work, we present a mechanistic scheme for hydrogenase H-cluster biosynthesis in which both carbon monoxide and cyanide ligands can be derived from the decomposition of a glycine radical. The ideas presented have broader implications in the context of the prebiotic origin of amino acids.     

The Reactions of Methanimine and Cyanogen with Carbon Monoxide in Prebiotic Molecular Evolution on Earth

A primeval atmosphere is proposedcontaining simple molecules such as formaldehyde, ammonia, carbon monoxide, cyanogen andhydrogen cyanide, which have been detected in space. Chemical reactions aredescribed for the formation ofaziridine-2-one and di-azirine-3-one derivatives aspotential precursors for the original synthesesis of amino-acids, proteins, pyrimidines,purines, nicotinamide and flavin. The reactions have been shown to be kinetically feasiblefrom the overall enthalpy changes in the ZKE approximation at the MP2/6-31G^* level.