Abstract
In this chapter, it is shown how in silico modeling by quantum mechanical methods provides structures and energetic as well as mechanistic reaction details relevant to prebiotic chemistry. In particular, reactions of astrobiochemical interest and processes related to the polymerization of amino acids on the rocks are dealt with, in which the role of naturally occurring inorganic surfaces (icy particles and silica-based materials, respectively) as catalysts is highlighted.
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Abbatt JPD (2003) Interactions of atmospheric trace gases with ice surfaces: adsorption and reaction. Chem Rev 103:4783–4800
Basiuk VA, Gromovoy TY, Golovaty VG, Glukhoy AM (1990–1991) Mechanisms of amino acid polycondensation on silica and alumina surfaces. Orig Life Evol Biosph 20:483–498
Belloche A, Menten KM, Comito C, Müller HSP, Schilke P, Ott J, Thorwirth S, Hieret C (2008) Detection of amino acetonitrile in Sgr B2(N). Astron Astrophys 482:179–196
Bernal JD (1949) The physical basis of life. Proc Phys Soc B 62:597–618
Bernstein MP, Dworkin JP, Sandford SA, Cooper GW, Allamandola LJ (2002) Racemic amino acids from the ultraviolet photolysis of interstellar ice analogues. Nature 416:401–403
Bolis V, Fubini B, Marchese L, Martra G, Costa D (1991) Hydrophilic and hydrophobic sites on dehydrated crystalline and amorphous silicas. J Chem Soc Faraday Trans 87:497–505
Brack A (2007) From interstellar amino acids to prebiotic catalytic peptides: a review. Chem Biodivers 4:665–679
Cleaves HJ, Chalmers JH, Lazcano A, Miller SL, Bada JL (2008) A reassessment of prebiotic organic synthesis in neutral planetary atmospheres. Orig Life Evol Biosph 38:105–115
Cody GD, Boctor NZ, Filley TR, Hazen RM, Scott JH, Sharma A, Yoder HS Jr (2000) Primordial carbonylated iron-sulfur compounds and the synthesis of pyruvate. Science 289:1337–1340
Dovesi R, Orlando R, Civalleri B, Roetti C, Saunders VR, Zicovich-Wilson CM (2005) CRYSTAL: a computational tool for the ab initio study of the electronic properties of crystals. Z Kristallogr 220:571–573
Elsila JE, Glavin DP, Dworkin JP (2009) Cometary glycine detected in samples returned by Stardust. Meteorit Planet Sci 44:1323–1330
Ferris JP (2006) Montmorillonite-catalysed formation of RNA oligomers: the possible role of catalysis in the origins of life. Phil Trans R Soc B 361:1777–1786
Ferris JP, Hill-Jr AR, Liu R, Orgel LE (1996) Synthesis of long prebiotic oligomers on mineral surfaces. Nature 381:59–61
Grimme S (2006) Semiempirical GGA-type density functional constructed with a long-range dispersion correction. J Comput Chem 27:1787–1799
Hafner J (2008) Ab-initio simulations of materials using VASP: density-functional theory and beyond. J Comput Chem 29:2044–2078
Hazen R (2005) Genesis: the scientific quest for life’s origins. Joseph Henry Press, Wahington, DC
Huber C, Wächtershäuser G (1998) Peptides by activation of amino acids with CO on (Ni, Fe)S surfaces: implications for the origin of life. Science 281:670–672
Jones PA, Cunningham MR, Godfrey PD, Cragg DM (2007) A search for biomolecules in Sagittarius B2 (LMH) with the Australia Telescope Compact Array. Mon Not R Astron Soc 372:579–589
Koch DM, Toubin C, Peslherbe GH, Hynes JT (2008) A theoretical study of the formation of the aminoacetonitrile precursor of glycine on icy grain mantles in the interstellar medium. J Phys Chem C 112:2972–2980
Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157:105–132
Lambert J-F (2008) Adsorption and polymerization of amino acids on mineral surfaces: a review. Orig Life Evol Biosph 38:211–242
Lomenech C, Bery G, Costa D, Stievano L, Lambert JF (2005) Theoretical and experimental study of the adsorption of neutral glycine on silica from the gas phase. Chemphyschem 6:1061–1070
Miller SL (1953) A production of amino acids under possible primitive Earth conditions. Science 117:528–529
Miller SL (1955) Production of some organic compounds under possible primitive Earth conditions. J Am Chem Soc 77:2351–2666
Miyakawa S, Yamanashi H, Kobayashi K, Cleaves J, Miller SL (2002) Prebiotic synthesis from CO atmospheres: implications for the origins of life. Proc Natl Acad Sci USA 99:14628–14631
Morokuma K (2003) ONIOM and its applications to material chemistry and catalysis. Bull Korean Chem Soc 24:797–801
Morrow BA, Cody IA, Lee LSM (1976) Infrared studies of reactions on oxide surfaces. 7. Mechanism of the adsorption of water and ammonia on dehydroxylated silica. J Phys Chem 80:2761–2767
Muñoz-Caro GM, Meierhenrich UJ, Schutte WA, Barbier B, Segovia AA, Rosenbauer H, Thiemann WH-P, Brack A, Greenberg JM (2002) Amino acids from ultraviolet irradiation of interstellar ice analogues. Nature 416:403–406
Nuevo M, Auger G, Blanot D, d’Hendecourt L (2008) A detailed study of the amino acids produced from the vacuum UV irradiation of interstellar ice analogs. Orig Life Evol Biosph 38:37–56
Orgel LE (1998) Polymerization on the rocks: theoretical introduction. Orig Life Evol Biosph 28:227–234
Orgel LE (2004) Prebiotic chemistry and the origin of the RNA world. Crit Rev Biochem Mol Biol 39:99–123
Oró J (1961) Mechanism of synthesis of adenine from hydrogen cyanide under possible primitive Earth conditions. Nature 191:1193–1194
Pisani C, Busso M, Capecchi G, Casassa S, Dovesi R, Maschio L, Saunders VR, Zicovich-Wilson CM, Schütz M (2005) Local-MP2 electron correlation method for non conducting crystals. J Chem Phys 122:094113
Pizzarello S (2006) The chemistry of life’s origin: a carbonaceous meteorite perspective. Acc Chem Res 39:231–237
Rimola A, Ugliengo P (2008) A quantum mechanical study of the reactivity of (SiO)2-defective silica surfaces. J Chem Phys 128:204702
Rimola A, Ugliengo P (2009) The role of defective silica surfaces in exogenous delivery of prebiotic compounds: clues from first principles calculations. Phys Chem Chem Phys 11:2497–2506
Rimola A, Sodupe M, Tosoni S, Civalleri B, Ugliengo P (2006) Interaction of glycine with isolated hydroxyl groups at the silica surface: first principles B3LYP periodic simulation. Langmuir 22:6593–6604
Rimola A, Sodupe M, Ugliengo P (2007) Aluminosilicate surfaces as promoters for peptide bond formation: an assessment of Bernal’s hypothesis by ab initio methods. J Am Chem Soc 129:8333–8344
Rimola A, Civalleri B, Ugliengo P (2008) Neutral vs. zwitterionic glycine forms at the water/silica interface. Structure, energies and vibrational features from B3LYP periodic simulations. Langmuir 24:14027–14034
Rimola A, Sodupe M, Ugliengo P (2009a) Affinity scale for the interaction of amino acids with silica surfaces. J Phys Chem C 113:5741–5750
Rimola A, Ugliengo P, Sodupe M (2009b) Formation versus hydrolysis of the peptide bond from a quantum-mechanical viewpoint: the role of mineral surfaces and implications for the origin of life. Int J Mol Sci 10:746–760
Rimola A, Sodupe M, Ugliengo P (2010a) Deep-space glycine formation via Strecker-type reactions activated by ice water dust mantles. A computational approach. Phys Chem Chem Phys 12:5285–5294
Rimola A, Zicovich-Wilson CM, Dovesi R, Ugliengo P (2010b) Search and characterization of transition state structures in crystalline systems using valence coordinates. J Chem Theory Comput 6:1341–1350
Saladino R, Neri V, Crestini C, Costanzo G, Graciotti M, Mauro ED (2008) Synthesis and degradation of nucleic acid components by formamide and iron sulfur minerals. J Am Chem Soc 130:15512–15518
Sauer J, Ugliengo P, Garrone E, Saunders VR (1994) Theoretical-study of van der Waals complexes at surface sites in comparison with the experiment. Chem Rev 94:2095–2160
Schopf WJ (1993) Microfossils to the early Archean Apex Chert: new evidence of the antiquity of life. Science 260:640–646
Sherrill CD (2010) Frontier in electronic structure theory. J Chem Phys 132:110902
Smith JV (1998) Biochemical evolution. I. Polymerization on internal, organophilic silica surfaces of dealuminated zeolites and feldspars. Proc Natl Acad Sci 95:3370–3375
Snyder LE, Lovas FJ, Hollis JM, Friedel DN, Jewell PR, Remijan A, Ilyushin VV, Alekseev EA, Dyubko SF (2005) A rigorous attempt to verify interstellar glycine. Astrophys J 619:914–930
Sousa SF, Fernandes PA, Ramos MJ (2007) General performance of density functionals. J Phys Chem A 111:10439–10452
Tosoni S, Tuma C, Sauer J, Civalleri B, Ugliengo P (2007) A comparison between plane wave and Gaussian-type orbital basis sets for hydrogen bonded systems: formic acid as a test case. J Chem Phys 127:154102
Woon DE (2002) Pathways to glycine and other amino acids in ultraviolet-irradiated astrophysical ices determined via quantum chemical modeling. Astrophys J 571:L177–L180
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Rimola, A., Sodupe, M., Ugliengo, P. (2012). Computational Simulations of Prebiotic Processes. In: Seckbach, J. (eds) Genesis - In The Beginning. Cellular Origin, Life in Extreme Habitats and Astrobiology, vol 22. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-2941-4_20
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DOI: https://doi.org/10.1007/978-94-007-2941-4_20
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