Ab initio Molecular Dynamics Studies of Aspects of the "Iron-Sulfur World Scenario"

• Antragsteller: Professor Dr. Dominik Marx
• Fachliche Zuordnung: Theoretische Chemie: Elektronenstruktur, Dynamik, Simulation
• Förderung: Förderung von 2003 bis 2013
• Projektkennung: Deutsche Forschungsgemeinschaft (DFG) - Projektnummer 5412430

• Erstellungsjahr: 2013

Zusammenfassung der Projektergebnisse

Prebiotic chemistry is a highly speculative field due to the lack of detailed knowledge right at the link between inanimate matter and most primitive forms of life. Various scenarios, often called “Worlds” in the community, have been proposed in order to suggest possible routes for detailed research. Here, the so–called “Iron–Sulfur World” (ISW) proposal has been selected as the basis in order to investigate elementary chemical reactions that might have established a complex reaction network eventually being able to sustain some sort of metabolism. Prebiotic conditions according to the ISW scenario are characterized by the presence of energy–rich iron–sulfur minerals in contact with water at high temperature and pressure conditions such as those met close to deep sea hydrothermal vents. Realizing and controlling such conditions in experiment is a most daunting task, whereas modern computer simulations offer a systematic access by being able to vary temperature, pressure and minerals in a most systematic fashion. Guided by these ideas, a selected set of putative prebiotic reactions has been studied using several model systems together with advanced ab initio molecular dynamics techniques in conjunction with high–performance computing on capability platforms. These efforts resulted in proposing a complete “prebiotic peptide cycle” that leads from amino acids via intermediate activation steps to peptides in an environment of hot–pressurized water in contact with pyrite, which mimicks typical ISW conditions. Aspects of these research results have been covered in the general press, including “Die Welt” and “Neue Zürcher Zeitung”. But iron–sulfur systems do also play a crucial role in extant biology in terms of iron–sulfur proteins. In the second, much more technical part of this proposal [2Fe–2S] clusters embedded in biomatrices have been studied with a particular focus on the coupling of molecular motion and magnetic properties. In order to approximately describe their magnetic properties in dynamical simulations we developed and implemented in the CPMD program package what we call the “extended broken symmetry”(EBS) method in order to approximately treat the antiferromagnetically coupled ground state of such binuclear transition metal complexes. Upon applying the novel method to Anabaena ferredoxin, we found that there exists a hitherto unknown correlation and thus an intimate coupling between the molecular vibrations of the iron–sulfur prosthetic group embedded in the protein matrix and the dynamics of the antiferromagnetic exchange coupling J(t). This so–called “magnetostructural dynamics” has been analyzed in detail using cross–correlation techniques and spectroscopic experiments able to probe these effects have been proposed. It is expected that similar dynamical effects can be observed for magnetic properties other than the antiferromagnetic exchange coupling.

Projektbezogene Publikationen (Auswahl)

• Glycine at the Pyrite–Water Interface: The Role of Surface Defects, J. Am. Chem. Soc. 128, 13815–13826 (2006)
  N. N. Nair, E. Schreiner, and D. Marx
  
• Dynamical magnetostructural properties of Anabaena ferredoxin, Proc. Natl. Acad. Sci. USA 104, 20725–20730 (2007)
  E. Schreiner, N. N. Nair, R. Pollet, V. Staemmler, and D. Marx
  
• Invited Feature Article: Prebiotic Peptide Synthesis on Blue Gene Platforms at “Iron–Sulfur–World” Conditions, inSiDE (Innovatives Supercomputing in Deutschland) 6(2), 30–35 (2008)
  N. N. Nair, E. Schreiner, and D. Mar
  
• Influence of Extreme Thermodynamic Conditions and Pyrite Surfaces on Peptide Synthesis in Aqueous Media, J. Am. Chem. Soc. (Communication) 130, 2768–2770 (2008)
  E. Schreiner, N. N. Nair, and D. Marx
  
• Magnetostructural Dynamics with the Extended Broken Symmetry Formalism: Antiferromagnetic [2Fe–2S] Complexes, J. Chem. Theory Comput. 4, 1174–1188 (2008)
  N. N. Nair, E. Schreiner, R. Pollet, V. Staemmler, and D. Marx
  
• Peptide Synthesis in Aqueous Environments: The Role of Extreme Conditions on Amino Acid Activation, J. Am. Chem. Soc. 130, 14148–14160 (2008)
  N. N. Nair, E. Schreiner, and D. Marx
  
• Peptide Synthesis in Aqueous Environments: The Role of Extreme Conditions on Peptide Bond Formation and Peptide Hydrolysis, J. Am. Chem. Soc. 131, 13668–13675 (2009)
  E. Schreiner, N. N. Nair, and D. Marx
  
• Magnetostructural Dynamics from Hubbard–U Corrected Spin–Projection: [2Fe– 2S] Complex in Ferredoxin, J. Chem. Theory Comput. 6, 569–575 (2010)
  N. N. Nair, J. Ribas–Arino, V. Staemmler, and D. Marx
  
• Revealing the Magnetostructural Dynamics of [2Fe–2S] Ferredoxins from Reduced-Dimensionality Analysis of Antiferromagnetic Exchange Coupling Fluctuations, J. Phys. Chem. B 114, 11612–11619 (2010)
  S. A. Fiethen, V. Staemmler, N. N. Nair, J. Ribas–Arino, E. Schreiner, and D. Marx
  
• Peptide Synthesis in Aqueous Environments: The Role of Extreme Conditions and Pyrite Mineral Surfaces on Formation and Hydrolysis of Peptides, J. Am. Chem. Soc. 133, 8216–8226 (2011)
  E. Schreiner, N. N. Nair, C. Wittekindt, and D. Marx
  
• Constrained spin-density dynamics of an iron-sulfur complex: Ferredoxin cofactor, J. Chem. Phys. 136, 224101-1–8 (2012)
  Md. E. Ali, N. N. Nair, V. Staemmler, and D. Marx
  
• Water confined between sheets of mackinawite FeS minerals, J. Chem. Phys. 137, 054710-1–8 (2012)
  C. Wittekindt and D. Marx
  
• Nanoconfinement effects on hydrated excess protons in layered materials, Nat. Commun. 4, 2349-1–5 (2013)
  D. Munoz–Santiburcio, C. Wittekindt and D. Marx