Abstract
On ancient Earth, environmental conditions favored prebiotic chemical reactions. In the Archean, some molecules with conjugated rings might have been synthesized, displaying structural stability in the Archean in the presence of ionizing radiation and hydration–dehydration events. Additionally, it is suggested that on ancient Earth, calcite was a common mineral promoting organic compound synthesis. In the present work a study of the interaction of amino acid mixtures with the (104) surface of calcite is presented. Our preliminary results show the abiotic synthesis of alloxazine (a flavin with relevant photochemical properties). Computer simulations were performed in HyperChem 8.0.1. by means of MM+ molecular mechanics and PM3 semi-empirical methods, in 27 possible amino acid trimers of alanine, glycine and lysine. Alloxazine formation is possible by the gamma irradiation of amino acids. The computer simulations show that trimers GGG and GGA promote the further transformation from diketopiperazines (DKP’s) and KGK to alloxazine. The computer simulations with free radicals are not stable when alloxazine is interacting with the calcite surface. Experiments in anoxygenic environments with hydration–dehydration events in gamma irradiated samples allow the abiotic formation of flavins, DKP’s and a heterocycle compound with possible relevance in prebiotic chemistry.
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References
Bada JL (2002) ORIGIN OF LIFE: some like it hot, but not the first biomolecules. Science 296:1982–1983. https://doi.org/10.1126/science.1069487
Becker M (2013) Astrochemistry: the issue of molecular complexity in astrophysical environments. Bull Soc R Sci Liège 82:33–94
Cherubini C, Ursini O (2015) Amino acids chemical stability submitted to solid state irradiation: the case study of leucine, isoleucine and valine. SpringerPlus. https://doi.org/10.1186/s40064-015-1332-9
Cooper G, Reed C, Nguyen D et al (2011) Detection and formation scenario of citric acid, pyruvic acid, and other possible metabolism precursors in carbonaceous meteorites. Proc Natl Acad Sci USA 108:14015–14020. https://doi.org/10.1073/pnas.1105715108
Cresswell RM, Wood HCS (1960) 928. The biosynthesis of pteridines. Part I. The synthesis of riboflavin. J Chem Soc 4:768. https://doi.org/10.1039/jr9600004768
Cronin JR, Pizzarello S (1983) Amino acids in meteorites. Adv Space Res 3:5–18. https://doi.org/10.1016/0273-1177(83)90036-4
De Graaf RM, Visscher J, Xu Y et al (1998) Mineral catalysis of a potentially prebiotic aldol condensation. J Mol Evol 47:501–507. https://doi.org/10.1007/PL00006406
de la Cruz-López A, del Ángel-Meraz E, Colín-García M et al (2017) Ultraviolet irradiation of glycine in presence of pyrite as a model of chemical evolution: an experimental and molecular modelling approach. Int J Astrobiol 16:237–243. https://doi.org/10.1017/S1473550416000161
Domagal-Goldman SD, Wright KE, Adamala K et al (2016) The Astrobiology Primer v2.0. Astrobiology 16:561–653. https://doi.org/10.1089/ast.2015.1460
Erastova V, Degiacomi MT, Fraser DG, Greenwell HC (2017) Mineral surface chemistry control for origin of prebiotic peptides. Nat Commun. https://doi.org/10.1038/s41467-017-02248-y
Harada K, Fox SW (1958) The thermal condensation of glutamic acid and glycine to linear peptides. J Am Chem Soc 80:2694–2697. https://doi.org/10.1021/ja01544a027
Hazen RM, Sverjensky DA (2010) Mineral surfaces, geochemical complexities, and the origins of life. Cold Spring Harb Perspect Biol 2:a002162. https://doi.org/10.1101/cshperspect.a002162
Heinz B, Ried W (1981) The formation of chromophores through amino acid thermolysis and their possible role as prebiotic photoreceptors. Biosystems 14:33–40. https://doi.org/10.1016/0303-2647(81)90019-8
Heinz B, Ried W, Dose K (1979) Thermal generation of pteridines and flavines from amino acid mixtures. Angew Chem Int Ed Engl 18:478–483. https://doi.org/10.1002/anie.197904781
Heredia A, van der Strate HJ, Delgadillo I et al (2008) Analysis of organo-silica interactions during valve formation in synchronously growing cells of the diatom Navicula pelliculosa. ChemBioChem 9:573–584. https://doi.org/10.1002/cbic.200700313
Jeilani YA, Fearce C, Nguyen MT (2015) Acetylene as an essential building block for prebiotic formation of pyrimidine bases on Titan. Phys Chem Chem Phys 17(37):24294–24303. https://doi.org/10.1039/C5CP03247D
Kasting JF (2002) Life and the evolution of earth’s atmosphere. Science 296:1066–1068. https://doi.org/10.1126/science.1071184
Kasting JF, Howard MT (2006) Atmospheric composition and climate on the early Earth. Philos Trans R Soc B 361:1733–1742. https://doi.org/10.1098/rstb.2006.1902
Kazansky LP (2016) DFT and PM3 calculated charges on atoms in heterocyclic molecules and XPS. Corros Sci 112:724–727. https://doi.org/10.1016/j.corsci.2016.09.003
Kikuchi O, Nakajima H, Horikoshi K, Takahashi O (1993) Rapid evaluation of molecular electrostatic potential maps by simple analytical functions. Extension to compounds containing π electron systems. J Mol Struct THEOCHEM 285:57–69. https://doi.org/10.1016/0166-1280(93)87019-A
Linstrom P (1997) NIST Chemistry WebBook, NIST Standard Reference Database 69
Marshall-Bowman K, Ohara S, Sverjensky DA et al (2010) Catalytic peptide hydrolysis by mineral surface: implications for prebiotic chemistry. Geochim Cosmochim Acta 74:5852–5861. https://doi.org/10.1016/j.gca.2010.07.009
Michaelian K, Simeonov A (2015) Fundamental molecules of life are pigments which arose and co-evolved as a response to the thermodynamic imperative of dissipating the prevailing solar spectrum. Biogeosciences 12:4913–4937. https://doi.org/10.5194/bg-12-4913-2015
Mosqueira FG, Ramos-Bernal S, Negrón-Mendoza A (2008) Prebiotic thermal polymerization of crystals of amino acids via the diketopiperazine reaction. Biosystems 91:195–200. https://doi.org/10.1016/j.biosystems.2007.09.001
Nagayama M, Takaoka O, Inomata K, Yamagata Y (1990) Diketopiperazine-mediated peptide formation in aqueous solution. Orig Life Evol Biosph 20:249–257. https://doi.org/10.1007/BF01808107
Negron-Mendoza A, Ramos-Bernal S, Mosqueira FG (2005) Synthesis in prebiotic clay environments induced by radiation. Int J Astrobiol 3:295–300. https://doi.org/10.1017/S1473550405002193
Oró J, Kimball AP (1961) Synthesis of purines under possible primitive earth conditions. I. Adenine from hydrogen cyanide. Arch Biochem Biophys 94:217–227. https://doi.org/10.1016/0003-9861(61)90033-9
Redondo P, Martínez H, Cimas Á, Barrientos C, Largo A (2013) Computational study of peptide bond formation in the gas phase through ion–molecule reactions. Phys Chem Chem Phys 15(31):13005–13012. https://doi.org/10.1039/c3cp51535d
Rodriguez-Garcia M, Surman AJ, Cooper GJT et al (2015) Formation of oligopeptides in high yield under simple programmable conditions. Nat Commun. https://doi.org/10.1038/ncomms9385
Schoonen M, Smirnov A, Cohn C (2004) A perspective on the role of minerals in prebiotic synthesis. AMBIO J Hum Environ 33:539–551. https://doi.org/10.1579/0044-7447-33.8.539
Tayyari SF, Milani-Nejad F (2000) Vibrational assignment of acetylacetone. Spectrochim Acta A 56:2679–2691. https://doi.org/10.1016/S1386-1425(00)00304-8
Towe KM (1981) Environmental conditions surrounding the origin and early Archean evolution of life: a hypothesis. Precambrian Res 16:1–10. https://doi.org/10.1016/0301-9268(81)90002-4
Varsányi G, Szöke S (1969) Vibrational spectra of benzene derivatives. Academic, Cambridge
Waddell TG, Henderson BS, Morris RT et al (1987) Chemical evolution of the citric acid cycle: sunlight photolysis of α-ketoglutaric acid. Orig Life Evol Biosph 17:149–153. https://doi.org/10.1007/BF01808242
Wiberg KB, Hammer JD, Castejon H et al (1999) Conformational studies in the cyclohexane series. 1. Experimental and computational investigation of methyl, ethyl, isopropyl, and tert-butylcyclohexanes. J Org Chem 64:2085–2095. https://doi.org/10.1021/jo990056f
Yoneda F, Sakuma Y, Ichiba M, Shinomura K (1972) Syntheses of isoalloxazines. A new synthesis of riboflavin. Chem Pharm Bull (Tokyo) 20:1832–1834. https://doi.org/10.1248/cpb.20.1832
Zhong L, Lu Y, Li H et al (2018) High-performance aqueous sodium-ion batteries with hydrogel electrolyte and alloxazine/CMK-3 anode. ACS Sustain Chem Eng 6:7761–7768. https://doi.org/10.1021/acssuschemeng.8b00663
Acknowledgements
Bach. (in Chem.) Ms. Claudia Consuelo Camargo Raya, M. in Sci. Isabel Mejía Luna (Departamento de Física, Facultad de Ciencias, UNAM) M. in Sci. Benjamín Leal Acevedo, Tech. Francisco García Flores y Tech. Acad. Mr. José Rangel (AH) to PAPIIT Project RN210119. We also thank M. in Sc. Audra Patterson for the edition and English version of this manuscript and to M. in Sc. Luciano Díaz González, Martín Cruz Villafañe, Luis Miguel Valdez Pérez, Ing. Juan Eduardo Murrieta León, Antonio Ramírez Fernández, Mat. Enrique Palacios Boneta for their technical assistance. We acknowledge the relevant work from the Reviewers for the clear improvement of our manuscript.
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Mendoza-Torres, E., Cruz-Catañeda, J., Negrón-Mendoza, A. et al. Computer and Experimental Simulation of Alloxazine Synthesis from Gamma Irradiation of Amino Acids on Iceland Spar: A Prebiotic Chemistry Perspective. J Mol Evol 88, 284–291 (2020). https://doi.org/10.1007/s00239-020-09933-5
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DOI: https://doi.org/10.1007/s00239-020-09933-5