Abstract
Glycine at the interface of a pyrite surface (001) FeS2, and bulk water at high pressure and temperature conditions relevant to the “iron-sulfur world” scenario of the origin of life is investigated by theoretical means. Car-Parrinello molecular dynamics is used in order to study the desorption process of the zwitterionic form of this amino acid using two different adsorption modes, where either only one or both oxygens of the carboxylate group are anchored to surface iron atoms. It is found that the formation of stabilizing hydrogen bonds plays a key role in the detachment process, leading to longer retention times for the bidentate adsorption mode. In addition, the chemical reactivity of this heterogeneous system is probed by calculating the Fukui functions as site-specific reactivity indices. The most prominent targets for both nucleophilic and electrophilic reactions to occur are surface atoms, whereas the reactivity of glycine is only slightly affected upon anchoring.
Article PDF
Similar content being viewed by others
References
Bada, J. L. and Lazcano, A.: 2002, Origin of Life-Some Like It Hot, But Not the First Biomolecules, Science 296(5575), 1982–1983.
Bada, J. L. and Lazcano, A.: 2003. Prebiotic Soup-Revisiting the Miller Experiment, Science 300(5620), 745–746.
Bebie, J., Schoonen, M. A. A., Fuhrman, M. and Strongin, D. R.: 1998, Surface Charge Development on Transition Metal Sulfides: An electrokinetic study, Geochim. Cosmochim. Acta. 62(4), 633–642.
Becke, A. D.: 1988, Density-Functional Exchange-Energy Approximation with Correct Asymptotic-behavior, Phys. Rev. A 38(6), 3098–3100.
Bernal, J. D. ed.: 1951, The Physical Basis of Life. Routledge and Kegan Paul Ltd., London. See in particular pp. 33.
Boehme, C. and Marx, D.: 2003, Glycine on a Wet Pyrite Surface at Extreme Conditions, J. Am. Chem. Soc. (Communication to the Editor) 125, 13362–13363.
Car, R. and Parrinello, M.: 1985, Unified Approach for Molecular-Dynamics and Density-Functional Theory, Phys. Rev. Lett. 55(22), 2471–2474.
Chattaraj, P. K.: 2001, Chemical Reactivity and Selectivity: Local HSAB Principle Versus Frontier Orbital Theory, J. Phys. Chem. A 105(2), 511–513.
Chermette, H.: 1999, Chemical Reactivity Indexes in Density Functional Theory, J. Comput. Chem. 20(1), 129–154.
Cody, G. D.: 2004, Transition Metal Sulfides and the Origins of Metabolism, Annu. Rev. Planet. Sci. 32, 569–599.
Cody, G. D., Boctor, N. Z., Brandes, J. A., Filley, T. R., Hazen, R. M. and Yoder, H. S. J.: 2004, Assaying the Catalytic Potential of Transition Metal Sulfides for Abiotic Carbon Fixation, Geochim. Cosmochim. Acta. 68(10), 2185–2196.
de Duve, C. and Miller, S. L.: 1991, 2-Dimensional Life, Proc. Natl. Acad. Sci. USA 88(22), 10014–10017.
de Leeuw, N. H., Parker, S. C., Sithole, H. M. and Ngoepe, P. E.: 2000, Modeling the Surface Structure and Reactivity of Pyrite: Introducing a Potential Model for FeS2, J. Phys. Chem. B 104(33), 7969–7976.
Deamer, D. W. and Fleischaker, G. R. (eds.): 1994, Origins of Life. Bartlett Publishers, Boston.
Dörr, M., KäBbohrer, J., Grunert, R., Kreisel, G., Brand, W. A., Werner, R. A., Geilmann, H., Apfel, C., Robl, C. and Weigand, W.: 2003, A Possible Prebiotic Formation of Ammonia from Dinitrogen on Iron Sulfide Surfaces, Angew. Chem. Int. Ed. 42, 1540–1543.
Fry, I.: 2000, The Emergence of Life on Earth, Rutgers UP, New Brunswick.
Hartwigsen, C., Goedecker, S. and Hutter, J.: 1998, Relativistic Separable Dual-Space Gaussian Pseudopotentials from H to Rn. Phys. Rev. B 58(7), 3641–3662.
Hazen, R. M.: 2001, Life's Rocky Start, Scientifc American, April: 76–85.
Huber, C., Eisenreich, W., Hecht, S. and Wächtershäuser, G.: 2003, A Possible Primordial Peptide Cycle, Science 301(5635), 938–940.
Huber, C. and Wächtershäuser, G.: 1998, Peptides by Activation of Amino Acids with CO on (Ni, Fe)S Surfaces: Implications for the Origin of Life, Science 281(5377), 670–672.
Laasonen, K., Pasquarello, A., Car, R., Lee, C. and Vanderbilt, D.: 1993, Car-Parrinello Molecular-Dynamics with Vanderbilt Ultrasoft Pseudopotentials, Phys. Rev. B 47(16), 10142–10143.
Langel, W. and Menken, L.: 2003, Simulation of the Interface Between Titanium Oxide and Amino Acids in Solution by First Principles MD, Surf. Sci. 538, 1–9.
Leung, K. and Rempe, S. B.: 2005, Ab Initio Molecular Dynamics Study of Glycine Intramolecular Proton Transfer in Water, J. Chem. Phys. 122, 184506, 1–12.
Marx, D. and Hutter, J.: 2000, Ab initio molecular dynamics: Theory and implementation, in Grotendorst, J. (ed.), Modern Methods and Algorithms of Quantum Chemistry, pp. 301–449, NIC, Jülich. for downloads see http://www.theochem.rub.de/go/cprev.html.
Miller, S. L.: 1953, A Production of Amino Acids Under Possible Primitive Earth Conditions, Science 117, 528–592.
Nilsson, A. and Pettersson, L. G. M.: 2004, Chemical Bonding on Surfaces Probed by X-ray Emission Spectroscopy and Density Functional Theory, Surf. Sci. Rep. 55, 49–167.
Ortmann, F., Schmidt, W. G. and Bechstedt, F.: 2005, Attracted by Long-Range Electron Correlation: Adenine on Graphite, Phys. Rev. Lett. 95, 186101–1-186101–4.
Parr, R. G. and Yang, W.: 1989, Density-Functional Theory of Atoms and Molecules, Oxford University Press, New York.
Perdew, J. P.: 1986, Density-Functional Approximation for the Correlation-Energy of the Inhomogeneous Electron-Gas, Phys. Rev. B 33(12), 8822–8824.
Perdew, J. P., Burke, K. and Ernzerhof, M.: 1996, Generalized Gradient Approximation Made Simple, Phys. Rev. Lett. 77(18), 3865–3868. Erratum: 1997, 78, 1396.
Philpott, M. R., Goliney, I. Y. and Lin, T. T.: 2004, Molecular Dynamics Simulation of Water in a Contact with an Iron Pyrite FeS2 Surface, J. Chem. Phys. 120(4), 1943–1950.
Preuss, M., Schmidt, W. G. and Bechstedt, F.: 2005, Coulombic Amino Group-Metal Bonding: Adsorption of Adenine on Cu(110), Phys. Rev. Lett. 94, 236102–1-236102–4.
Saladino, R., Crestini, C., Ciambecchini, U., Ciciriello, F., Costanzo, G. and Di Mauro, E.: 2004, Synthesis and Degradation of Nucleobases and Nucleic Acids by Formamide in the Presence of Montmorillonites, Chem. Bio. Chem. 5, 1558–1556.
Severin, K.: 2000, Hot Stones or Cold Soup? Angew. Chem. Int. Ed. 39, 3589–3590.
Stevens, E. D., DeLucia, M. L. and Coppens, P.: 1980, Experimental-Observation of the Effect of Crystal-Field Splitting on the Electron-Density Distribution of Iron Pyrite. Inorg. Chem. 19(4), 813–820.
Stirling, A., Bernasconi, M. and Parrinello, M.: 2003a, Ab Initio Simulation of H2S Adsorption on the (100) Surface of Pyrite. J. Chem. Phys. 119, 4934–4939.
Stirling, A., Bernasconi, M. and Parrinello, M.: 2003b, Ab Initio Simulation of Water Interaction with the (100) Surface of Pyrite, J. Chem. Phys. 118, 8917–8926.
CPMD (2004): Hutter J. et al., Copyright: IBM Corp 1990–2004, MPI für Festkörperforschung Stuttgart 1997–2001.
Vanderbilt, D.: 1990, Soft Self-Consistent Pseudopotentials in a Generalized Eigenvalue Formalism, Phys. Rev. B 41(11), 7892–7895.
von Kiedrowski, G.: 1996, Origins of life–Primordial soup or crêpes? Nature 381, 20–21.
Vuilleumier, R. and Sprik, M.: 2001, Electronic Properties of Hard and Soft Ions in Solution: Aqueous Na+ and Ag+ Compared, J. Chem. Phys. 115(8), 3454–3468.
Wächtershäuser, G.: 1988a, Before Enzymes and Templates – Theory of Surface Metabolism, Microbiol. Rev. 52(4), 452–484.
Wächtershäuser, G.: 1988b, Pyrite Formation, the 1st Energy-Source for Life – A Hypothesis, Syst. Appl. Microbiol. 10(3), 207–210.
Wächtershäuser, G.: 1990, Evolution of the 1st Metabolic Cycles, Proc. Natl. Acad. Sci. USA 87(1), 200–204.
Wächtershäuser, G.: 1992, Groundworks for an Evolutionary Biochemistry – The Iron Sulfur World, Prog. Biophys. Mol. Biol. 58(2), 85–201.
Wächtershäuser, G.: 1994, Life in a Ligand Sphere, Proc. Natl. Acad. Sci. USA 91(10), 4283–4287.
Wächtershäuser, G.: 1998, Thermophiles, p. 47. Taylor and Francis, Philadelphia.
Wächtershäuser, G.: 2002, Discussing the Origin of Life (comment), Science 298, 748–748.
Will, G., Lauterjung, J., Schmitz, H. and Hinze, E.: 1984, High Pressure in Science and Technology, Elsevier, New York.
Yang, W., Parr, R. G. and Pucci, R.: 1984, Electron-Density, Kohn-Sham Frontier Orbitals, and Fukui Functions, J. Chem. Phys. 81(6), 2862–2863.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Pollet, R., Boehme, C. & Marx, D. AB INITIO Simulations of Desorption and Reactivity of Glycine at a Water-Pyrite Interface at “Iron-Sulfur World” Prebiotic Conditions. Orig Life Evol Biosph 36, 363–379 (2006). https://doi.org/10.1007/s11084-006-9010-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11084-006-9010-0