The Transformation by Catalysis of Prebiotic Chemical Systems to Useful Biochemicals: A Perspective Based on IR Spectroscopy of the Primary Chemicals: I. The Synthesis of Peptides by the Condensation of Amino Acids

Volume 6, Issue 1, February 2021     |     PP. 1-20      |     PDF (524 K)    |     Pub. Date: January 28, 2021
DOI: 10.54647/chemistry15165    187 Downloads     6210 Views  

Author(s)

Ragnar Larsson, Dept of Chemical Engineering, University of Lund Box, 124, SE 221 00 Lund, Sweden
Abdul Malek, Technologie DMI 980 Rue Robert Brossard, Quebec, QC J4X 1C9, Canada

Abstract
It is now widely speculated that life originated at the “Black Smokers” of the undersea hydrothermal vents, where conditions exist for the formation of the primary ingredients and their subsequent transformation to higher biotic species such as amino acids, alcohols, etc. Any possible routes for the prebiotic oligomerization of simple compounds like amino acids, necessary for cell formation, has so far not been well understood. However, Leman et al. recently reported that under standard laboratory conditions carbonyl sulfide (COS) can “mediate” the oligomerization of simple amino acids in moderate yield. COS being a well-known volcanic gas points to its possible role in prebiotic peptide formation in the environment of the hydrothermal vents. Based on a previously developed and tested model for selective (vibrational) energy transfer (SET), we show that a COS-catalyzed condensation of -amino-acids can lead to the formation of polypeptides. We also indicate that other agents can act as catalysts of the amino acid condensation, such as Fe(CN)63- and cyanamide (H2N-CN). This is related to the existence of vibrations with a frequency near to that of the critical vibration of the reactant, w (NH2). This wagging vibration occurs at 1048 ± 10 cm−1 (the mean value of Cu and Ni complexes) and, as the vibration of the presumed catalyst lies at 2079 cm−1, one notes that one quantum of the catalyst equals two quanta of the NH2 wagging: 2079 / 2 × 1048 = 0.9919. This is a good indication of a resonance.

Keywords
catalysis; amino acids; polypeptides; vibrational resonance; selective energy transfer (SET), prebiotic reactions; reorganization of orbital patterns (sp3 to sp2)

Cite this paper
Ragnar Larsson, Abdul Malek, The Transformation by Catalysis of Prebiotic Chemical Systems to Useful Biochemicals: A Perspective Based on IR Spectroscopy of the Primary Chemicals: I. The Synthesis of Peptides by the Condensation of Amino Acids , SCIREA Journal of Chemistry. Volume 6, Issue 1, February 2021 | PP. 1-20. 10.54647/chemistry15165

References

[ 1 ] De Duve, C. Vital Dust: Life as a Cosmic Imperative; Basic Books: New York, NY, USA, 1995.
[ 2 ] Oparin, A.I. Origin of Life; Morgolis, T.S., Ed.; Dover Publications, Inc.: New York, NY, USA, 1953.
[ 3 ] Bernal, J.D. The Physical Basis of Life; Routledge & Kegan Paul: London, UK, 1951.
[ 4 ] Danger, G.; Plasson, R.; Pascal, R. Pathways for the formation and evolution of peptides in prebiotic environments. Chem. Soc. Rev. 2012, 41, 5416.
[ 5 ] Holm, N.G.; Andersson, E. Hydrothermal Simulation Experiments as a Tool for Studies of the Origin of Life on Earth and Other Terrestrial Planets: A Review. Astrobiology 2005, 5, 444–460.
[ 6 ] NIST Chemistry WebBook. Available online: http://webbook.nist.gov/chemistry (accessed on 14-11-2014).
[ 7 ] Herzberg, G. Molecular Spectra and Molecular Structure, II. Infrared and Raman Spectra of Polyatomic Molecules; D van Nostrand Company, Inc.: Princeton, NY, USA, 1962.
[ 8 ] Herzberg, G. Spectra of Diatomic Molecules, 2nd ed.; Van Norstrand Co., Inc.: New York, NY, USA, 1950.
[ 9 ] Colín-García, M.; Heredia, A.; Cordero, G.; Camprubí, A.; Negrón-Mendoza, A.; Ortega-Gutiérrez, F.; Beraldi, H.; Ramos-Bernal, S. Hydrothermal vents and prebiotic chemistry: A review. Boletín Soc. Geol. Mex. 2016, 68, 599–620.
[ 10 ] Dodd, M.S.; Papineau, D.; Grenne, T.; Slack, J.F.; Rittner, M.; Pirajno, F.; O’Neil, J.; Little, C.T.S. Evidence for early life in Earth’s oldest hydrothermal vent precipitates. Nature 2017, 543, 60–64.
[ 11 ] Miller, S.L. A Production of Amino Acids Under Possible Primitive Earth Conditions. Science 1953, 117, 528–529.
[ 12 ] Miller, S.L.; Urey, H.C. Organic compound synthesis on the primitive earth. Science 1959, 130, 245–251.
[ 13 ] Larsson, R. A model of selective energy transfer at the active site of the catalyst. J. Mol. Catal. 1989, 55, 70–83.
[ 14 ] Larsson, R. A SET Approach to the Interplay of Catalysts and Reactants. Catalysts 2018, 8, 97.
[ 15 ] Larsson, R. Concluding remarks on the theory of selective energy transfer and exemplification on a zeolite kinetics study. Monatsh. Chem. 2013, 144, 21–28.
[ 16 ] Kittel, C.; Knight, W.D.; Ruderman, M.A. Mechanics, Berkeley Physics Course; McGraw-Hill: New York, NY, USA, 1965; Volume 1, Chapter 7.
[ 17 ] Larsson, R. Propane Dehydrogenation Catalyzed by ZSM-5 Zeolites. A Mechanistic Study Based on the Selective Energy Transfer (SET) Theory. Molecules 2015, 20, 2529–2535.
[ 18 ] Larsson, R. An analysis of ammonia synthesis by the model of Selective Energy Transfer (SET). RSC Adv. 2019, in preparation.
[ 19 ] James, W. Pragmatism; Longmans, Green and Co.: New York, NY, USA, 1955.
[ 20 ] Berzelius, J. Årsberättelse om Framstegen i Physik och Chemie; Royal Swedish Academy of Sciences: Stockholm, Sweden, 1835.
[ 21 ] Ostwald, W. Nobel Lecture; The Royal Swedish Academy of Sciences, Stockholm, Sweden, 1909.
[ 22 ] Leman, L.; Orgel, L.; Ghadiri, M.R. Carbonyl Sulfide-Mediated Prebiotic Formation of Peptides. Science 2004, 306, 283–286.
[ 23 ] Nakamoto, K. Infrared and Raman Spectra of Inorganic and Coordination Compounds, 4th ed.; John Wiley & Sons: New York, NY, USA, 1986; p. 236.
[ 24 ] Wikipedia, https://en.wikipedia.org/wiki/Molecular_vibrationout-of-plane vibrations/Case study/partly. ( accessed. on 23-04-2016 ).
[ 25 ] Huber, C.; Eisenreich, W.; Hecht, S.; Wächtershäuser, G. A Possible Primordial Peptide Cycle. Science 2003, 301, 938–940.
[ 26 ] Huber, C. Peptides by Activation of Amino Acids with CO on (Ni,Fe)S Surfaces: Implications for the Origin of Life. Science 1998, 281, 670–672.
[ 27 ] Parker, E.T.; Zhou, M.; Burton, A.S.; Glavin, D.P.; Dworkin, J.P.; Krishnamurthy, R.; Fernández, F.M.; Bada, J.L. A Plausible Simultaneous Synthesis of Amino Acids and Simple Peptides on the Primordial Earth. Angew. Chem. 2014, 126, 8270–8274.
[ 28 ] Davies, M.; Jones, W.J. The Infrared Spectrum and Structure of Cyanamide and Dimethyl cyanamide. Trans. Farad. Soc. 1958, 54, 1454–1463.
[ 29 ] Rosado, M.T.; Duarte, M.L.T.; Fausto, R. Vibrational spectra of acid and alkaline glycine salts. Vib. Spectrosc. 1998, 16, 35–54.