Formation Of Amino Acid Precursors Research Articles

Amino Acid Precursors from a Simulated Lower Atmosphere of Titan: Experiments of Cosmic Ray Energy Source with 13C- and 18O-Stable Isotope Probing Mass Spectrometry

The organic haze of aerosols that shrouds the Saturnian moon Titan has previously been studied by both observations and laboratory simulation experiments. Here we report the abiotic formation of amino acid precursors in complex organic molecules during experimental simulation of the environment near Titan's surface with proton irradiation. Pyrolysis of the organic molecules formed in the simulated Titan atmosphere by proton irradiation at 600°C yielded compounds that contained HCN and NH₃ (m/z = 27 and 17). These experimental results are consistent with the molecular information obtained by pyrolysis gas chromatography/mass spectrometry (pyrolysis GC/MS) of samples collected by the Huygens probe to Titan. Scanning electron microscopy (SEM) and three-dimensional atomic force microscopy (AFM) images of the irradiation products reveal nanometer-scale filaments and globules in complex amorphous structures (approximately 1000 Da). Isotope probing experiments by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) show that oxygen atoms were incorporated into the racemic amino acids by hydrolysis of ¹⁸O-labeled water. We suggest that the amino acid precursors possibly formed after water hydrolysis, as suggested in a previous observational study (C. A. Griffith, T. Owen, T. R. Geballe, J. Rayner, and P. Rannou, Science, 2003, 300, 628). We propose that cosmic rays are a significant and effective energy source for producing complex organics and amino acid precursors in Titan's atmospheric haze.

Radical formation of amino acid precursors in interstellar regions? Ser, Cys and Asp

It is proposed that the glycine precursor NH(2)CH(2)CN may be synthesised in interstellar dust clouds by the radical combination reactions NH(2)˙ + ˙CH(2)CN → NH(2)CH(2)CN (ΔG = -302 kJ mol(-1)) and/or NH(2)CH(2)˙ + ˙CN → NH(2)CH(2)CN (ΔG = -414 kJ mol(-1)). All calculations at the CCSD(T)/aug-cc-pVDZ//B3LYP/6-31+G(d) level of theory. This paper extends that concept to radical/radical coupling reactions to form Ser, Cys and Asp precursor nitriles. The hydrogen abstraction process NH(2)CH(2)CN + HO˙→ NH(2)˙CHCN + H(2)O (ΔG = -130 kJ mol(-1)) is suggested to precede the radical coupling reactions NH(2)˙CHCN + R˙→ NH(2)CHRCN (R˙ = ˙CH(2)OH, ˙CH(2)SH and ˙CH(2)CN) to form nitrile precursors of the amino acids Ser, Cys and Asp. These three reactions are all favourable (ΔG = -240, -227 and -223 kJ mol(-1)). The radical species ˙CH(2)NH(2), ˙CH(2)OH, ˙CH(2)SH and ˙CH(2)CN are shown to be stable for the microsecond timeframe by a combination of theoretical calculations and the experimental mass spectrometric neutralization/reionization procedure.

Reaction mechanisms of thiamin diphosphate enzymes

Thiamin diphosphate (ThDP), the biologically active form of vitamin B1, is an essential cofactor that is involved in numerous metabolic pathways, such as the oxidative and non-oxidative decarboxylation of 2-oxo acids, interketol transfer between sugar phosphates, electron transfer reactions and the formation of amino acid precursors. ThDP consists of a thiazolium nucleus, an aminopyrimidine ring, and a diphosphate moiety that is required to provide tight binding to the target enzyme. The electrophilic nature of the positivelycharged thiazolium ring is key to the stabilization of carbanion states of the cofactor (i.e. the ThDP ylide) and of covalent substrate-ThDP conjugates in terms of a ‘Umpolung – or polarity inversion’ mechanism predestining ThDP as an effective participant in the reversible catalytic cleavage of carbon-carbon bonds of vicinal dicarbonyl or a-hydroxyketone groups, exhibiting a chemical ability not possessed by protein functional groups. The first committed step in all ThDP-dependent enzymes is the deprotonation of the thiazolium C2 and attack of the resulting carbanion on a substrate carbonyl. X-ray crystallographic analysis of ThDP enzymes has demonstrated the cofactor to be bound in the canonical V conformation, with the amino group of the aminopyrimidine and C2 of the thiazolium moiety juxtaposed with respect to hydrogen-bonding distance. A strictly conserved glutamate residue interacts with nitrogen 1 of the aminopyrimidine. The conserved structure of the cofactor binding site, and the observed loss of activity accompanyingmutagenesis of the conserved glutamate or uponuse of ThDP analogs lacking nitrogen 1 or the amino group of the aminopyrimidine, all support a mechanism in which proton removal fromC2 of ThDP is assisted by a catalytic triad consisting of the conserved glutamate, the aminopyrimidine and thiazolium moieties of the cofactor, presumably involving the imino tautomer of the aminopyrimidineas thegeneralbase forprotonabstraction. This minireview series, based on lectures given at an international conference on thiamin held in Wittenberg, Germany, in May 2008, highlights recent advancements in the mechanistic understanding of ThDP-promoted biochemical reactions. Jordan et al. have accumulated spectroscopic evidence for the occurrence and interconversion of the different tautomeric and ionization states of enzymebound ThDP along the pathways of various ThDP enzymes. The data clearly implicate the delicately balanced equilibria of the different cofactor forms on the enzymes’ active sites, such that all of these states are thermodynamically accessible at the pH optimum of a given ThDP enzyme. As outlined above, a glutamate residue interacting with the cofactor aminopyrimidine has hitherto been believed to be vital for tautomerization of the aminopyrimidine and thus chemical activation of ThDP. However, structural and mechanistic studies on the ThDP-dependent enzyme glyoxylate carboligase (GCL), as reviewed by Shaanan and Chipman, have revealed valine as having replaced the expected glutamate. Mechanistic analysis suggested that GCL sacrifices the otherwise strictly conserved mechanism of protein-cofactor activation as a consequence of evolutionary adaption to avoid formation of overlystabilized intermediates as thermodynamic traps. The oxidative decarboxylation of 2-oxo acids such as pyruvate is a key reaction of intermediary metabolism in virtually all organisms and requires ThDP to act in tandem with additional cofactors (e.g. flavins, iron-sulfur cluster, lipoic acid) as redox partners. The review by Tittmann, devoted to the mechanistic analysis of redox reactions of ThDP enzymes, shows how some of these enzymes make use of elegant radical chemistry in an intimate coupling mechanism of oxidation–reduction and the formation of energy-rich metabolites such as acetyl-CoA or acetyl phosphate.

Synthesis of amino acid precursors from simulated interstellar media by high‐energy particles or photons

AbstractExtraterrestrial organic compounds have been considered as important sources for the origin of life on the Earth. In order to study the formation of organic compounds found in extraterrestrial bodies, simulated interstellar media were irradiated with high‐energy particles or photons. Particles used were protons from a Van de Graaff accelerator, protons and helium ions from a cyclotron, electrons from a synchrotron, and heavy ions from the “HIMAC” heavy ion accelerator. Photons used were UV light and soft X‐rays from a synchrotron. Gamma‐ray irradiation was performed by using a 60Co source. Amino acid precursors were formed from a mixture of carbon monoxide (or methodanol), ammonia (or nitrogen), and water by high‐energy particles, gamma rays, or X‐rays. If nitrogen molecule was used as N‐source, amino acid precursors could be formed by high‐energy particles, X‐rays and gamma rays, but not by UV light. When ammonia was used, amino acid precursors were detected in all cases, but energy yields (G‐values) of amino acid precursors by high‐energy particles were much higher than those by UV or X‐rays photons. Possible formation of amino acid precursors in interstellar environments was discussed from the point of view of chemical evolution toward origins of life. © 2008 Wiley Periodicals, Inc. Electron Comm Jpn, 91(3): 15– 21, 2008; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecj.10069

Formation of amino acid precursors with large molecular weight in dense clouds and their relevance to origins of bio-homochirality

AbstractA wide variety of organic compounds have been found in carbonaceous chondrites and comets, which suggests that extraterrestrial organic compounds could have been an important source of the first terrestrial biosphere. In the Greenberg model, these organic compounds in the small bodies were originally formed in interstellar dusts (ISD) in dense clouds by the action of cosmic rays and ultraviolet light. We irradiated a frozen mixture of methanol, ammonia and water with high-energy heavy ions from an accelerator (“HIMAC” in NIRS, Japan) to simulate the action of cosmic rays in dense clouds. Racemic mixtures of amino acids were detected after hydrolysis of the irradiation products. A mixture of carbon monoxide, ammonia and water also gave such complex amino acid precursors with large molecular weights. When such amino acid precursors were irradiated with circular polarized UV light from a synchrotron, enantiomeric excesses were detected. The yield of amino acids was not largely changed between, before, and after CPL-irradiation. The present results suggest that the seed of homochirality of terrestrial amino acids were originally formed in interstellar space.

Synthesis of Amino Acid Precursors from Simulated Interstellar Media by High-Energy Particles or Photons

Extraterrestrial organic compounds have been considered as important sources for the origin of life on the Earth. In order to study the formation of organic compounds found in extraterrestrial bodies, simulated interstellar media were irradiated with high energy particles or photons. Particles used were protons from a van de Graaff accelerator, protons and helium ions from a cyclotron, electrons from a synchrotron, and heavy ions from “HIMAC heavy ion accelerator. Photons used were UV light and soft X-rays from a synchrotron. Gamma-rays irradiation was performed by using a 60Co source. Amino acid precursors were formed from a mixture of carbon monoxide (or methanol), ammonia (or nitrogen) and water by high-energy particles, gamma-rays, or X-rays. If nitrogen molecule was used as N-source, amino acid precursors could be formed by high energy particles, X-rays and gamma-rays, but not by UV light. In the case that ammonia was used, amino acid precursors were detected in all the cases, but energy yields (G-values) of amino acid precursors by high energy particles were much higher than those by UV or X-ray photons. Possible formation of amino acid precursors in interstellar environments was discussed from the point of view of chemical evolution toward origins of life.

Formation of Amino Acid Precursors in the Interstellar Medium. A DFT Study of Some Gas-Phase Reactions Starting with Methylenimine

To evaluate feasibility of the formation of amino acid precursors in dense interstellar clouds from methylenimine, HCN, ·CN radical, water, and ·OH radical, stationary points for four gas-phase reactions have been computed at the B3LYP/6-311++G(d,p) level of theory. All the reactions are exothermic. For the reaction HNCH2 + HC⋮N → H2NCH2C⋮N, three high-energy transition states have been found (energies of ca. 23−33 kcal mol-1 relative to the reactant level) which do not allow this reaction to occur as a purely gas-phase process. The same conclusion has been done for the further glycine amide formation according to the pathway H2NCH2C⋮N + H2O → H2NCH2C(O)NH2, where three transitions states have been obtained as well, one of them having relative energy of ca. 52 kcal mol-1. Reaction HNCH2 + ·C⋮N → H2NC(·)HC⋮N (>70 kcal mol-1 exothermic) exhibits no positive barriers at the theoretical level employed; it is the only one unconditionally feasible in the gas-phase. Despite the fact that for reaction H2NCH2C⋮N + ·OH → H2NC(·)HC(O)NH2 (ca. 60 kcal mol-1 exothermic) four transition states have been found, it might also appear plausible under the interstellar conditions for the following reasons: all the barriers are associated with exclusively proton-transfer processes; only one of them is positive, and three lay below the level of reactants; for the only positive barrier, proton tunneling might facilitate the reaction. Radical products H2NC(·)HCN and H2NC(·)HC(O)NH2 forming in the latter two cases have a free valence at the carbon atom corresponding to α-C atom in the molecules of biological amino acids. Combining them with a vast variety of open-shell interstellar species is suggested as a possible route to diverse amino acid derivatives in dense molecular clouds.

Formation of Organic Compounds in Simulated Interstellar Media with High Energy Particles

Abstract Abiotic formation of amino acid precursors in interstellar dusts (ISDs) by cosmic radiation was quantitatively examined. In order to study the formation of organic compounds in ISDs, ice mixtures of carbon monoxide (or methane), ammonia, and water made in a cryostat at 10 K were irradiated with high energy protons. Irradiated ice products were warmed up to room temperature, while sublimed gases were analyzed with a quadrupole mass spectrometer. Some hydrocarbons and alcohols were detected. Amino acid precursors, which gave amino acids after acid-hydrolysis, were detected in non-volatile products remaining on the substrate at room temperature. G-values of glycine precursors from methanol, ammonia, and water in solid state irradiation were about 6 × 10−4, which was about two orders less than those in gasous state irradiation. The present results suggest that a considerable amount of organic compounds formed in extraterrestrial environments were supplied to the primitive earth before the origin of life.

Formation of amino acid precursors in cometary ice environments by cosmic radiation

Cometary ices are believed to contain water, carbon monoxide, methane and ammonia, and are possible sites for the formation and preservation of organic compounds relating to the origin of life /1/. Cosmic rays, together with ultraviolet light, are among the most effective energy sources for the formation of organic compounds in space. In order to study the possibility of the formation of amino acids in comets or their precursory bodies (interstellar dust grains), several types of ice mixtures made in a cryostat at 10 K (“simulated cometary ices”) were irradiated with high energy protons. After irradiation, the volatile products were analyzed with a quadrupole mass spectrometer, while temperature of the cryostat was raised to room temperature. The non-volatile products remaining in the cryostat at room temperature were collected with water. They were acid-hydrolyzed, and analyzed by ion-exchange chromatography. When an ice mixture of carbon monoxide (or methane), ammonia and water was irradiated, some hydrocarbons were formed, and amino acids such as glycine and alanine were detected in the hydrolyzate. These results suggest the possible formation of “amino acid precursors” (compounds yielding amino acids after hydrolysis) in interstellar dust grains by cosmic radiation. We previously reported that amino acid precursors were formed when simulated primitive planetary atmospheres were irradiated with cosmic ray particles /2/. It will be of great interest to compare the amount of bioorganic compounds that were formed in the primitive earth and that brought by comets to the earth.

The formation of amino acid precursors in the reaction of atomic carbon with water and ammonia at 77 K.

When atomic carbon is condensed on a surface at 77 K containing ammonia and water, glycine, N-methylglycine, alanine, beta-alanine, aspartic acid and serine are generated. It is postulated that these reactions may mimic those which occur when an extraterrestrial carbon atom condenses on a frozen surface coated with water and ammonia and may provide a route to extraterrestrial amino acids. Experiments designed to elucidate the mechanisms of amino acid formation under these conditions have been carried out.

ChemInform Abstract: REACTION OF ATOMIC CARBON WITH AMMONIA. THE MECHANISM OF FORMATION OF AMINO ACID PRECURSORS

Chemischer InformationsdienstVolume 14, Issue 21 Preparative Organic Chemistry ChemInform Abstract: REACTION OF ATOMIC CARBON WITH AMMONIA. THE MECHANISM OF FORMATION OF AMINO ACID PRECURSORS P. B. SHEVLIN, P. B. SHEVLINSearch for more papers by this authorD. W. MCPHERSON, D. W. MCPHERSONSearch for more papers by this authorP. MELIUS, P. MELIUSSearch for more papers by this author P. B. SHEVLIN, P. B. SHEVLINSearch for more papers by this authorD. W. MCPHERSON, D. W. MCPHERSONSearch for more papers by this authorP. MELIUS, P. MELIUSSearch for more papers by this author First published: May 24, 1983 https://doi.org/10.1002/chin.198321120AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume14, Issue21May 24, 1983 RelatedInformation

Reaction of atomic carbon with ammonia. The mechanism of formation of amino acid precursors

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReaction of atomic carbon with ammonia. The mechanism of formation of amino acid precursorsPhilip B. Shevlin, Daniel W. McPherson, and Paul MeliusCite this: J. Am. Chem. Soc. 1983, 105, 3, 488–491Publication Date (Print):February 1, 1983Publication History Published online1 May 2002Published inissue 1 February 1983https://doi.org/10.1021/ja00341a031RIGHTS & PERMISSIONSArticle Views322Altmetric-Citations35LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (533 KB) Get e-Alerts Get e-Alerts

Bildung von Aminosäurevorprodukten in Zeolith X / Formation of Aminoacid Precursors in Zeolithe X

The formation of amino acid precursors through the action of ammonium cyanide on formaldehyde and acetaldehyde absorbed in the cages of zeolithe X has been demonstrated. The significance of this reaction as a model for the prebiological syntheses of amino acids in space is discussed