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Electronic landscape of the P-cluster of nitrogenase as revealed through many-electron quantum wavefunction simulations

Nature Chemistry volume 11, pages 1026–1033 (2019)Cite this article

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Abstract

The electronic structure of the nitrogenase metal cofactors is central to nitrogen fixation. However, the P-cluster and FeMo cofactor, each containing eight Fe atoms, have eluded detailed characterization of their electronic properties. We report on the low-energy electronic states of the P-cluster in three oxidation states through exhaustive many-electron wavefunction simulations enabled by new theoretical methods. The energy scales of orbital and spin excitations overlap, yielding a dense spectrum with features that we trace to the underlying atomic states and recouplings. The clusters exist in superpositions of spin configurations with non-classical spin correlations, complicating interpretation of magnetic spectroscopies, whereas the charges are mostly localized from reorganization of the cluster and its surroundings. On oxidation, the opening of the P-cluster substantially increases the density of states, which is intriguing given its proposed role in electron transfer. These results demonstrate that many-electron simulations stand to provide new insights into the electronic structure of the nitrogenase cofactors.

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Fig. 1: Structural models and computational strategy.
Fig. 2: Conceptual framework for the electronic states of the P-cluster.
Fig. 3: The states of the PN and synthetic clusters.
Fig. 4: The states of the oxidized P-clusters.
Fig. 5: A state correlation diagram showing the relationships between spin isomers in the low-lying electronic states of the P-cluster.

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Data availability

The authors declare that all the data that support the findings of this study are available in the paper and its Supplementary Information, and/or from the authors on reasonable request.

Code availability

The spin-projected and spin-adapted DMRG codes used in this work are available from GitHub repositories (https://github.com/zhendongli2008/zmpo_dmrg and http://sanshar.github.io/Block).

References

  1. Beinert, H., Holm, R. H. & Münck, E. Iron–sulfur clusters: nature’s modular, multipurpose structures. Science 277, 653–659 (1997).

    Article  CAS  PubMed  Google Scholar 

  2. Howard, J. B. & Rees, D. C. Structural basis of biological nitrogen fixation. Chem. Rev. 96, 2965–2982 (1996).

    CAS  PubMed  Google Scholar 

  3. Rees, D. C. & Howard, J. B. The interface between the biological and inorganic worlds: iron–sulfur metalloclusters. Science 300, 929–931 (2003).

    Article  CAS  PubMed  Google Scholar 

  4. Hoffman, B. M., Lukoyanov, D., Yang, Z.-Y., Dean, D. R. & Seefeldt, L. C. Mechanism of nitrogen fixation by nitrogenase: the next stage. Chem. Rev. 114, 4041–4062 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Spatzal, T. et al. Evidence for interstitial carbon in nitrogenase FeMo cofactor. Science 334, 940–940 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Lancaster, K. M. et al. X-ray emission spectroscopy evidences a central carbon in the nitrogenase iron–molybdenum cofactor. Science 334, 974–977 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Sharma, S., Sivalingam, K., Neese, F. & Chan, G. K.-L. Low-energy spectrum of iron–sulfur clusters directly from many-particle quantum mechanics. Nat. Chem. 6, 927–933 (2014).

    Article  CAS  PubMed  Google Scholar 

  8. Chan, J. M., Christiansen, J., Dean, D. R. & Seefeldt, L. C. Spectroscopic evidence for changes in the redox state of the nitrogenase P-cluster during turnover. Biochemistry 38, 5779–5785 (1999).

    Article  CAS  PubMed  Google Scholar 

  9. Danyal, K., Dean, D. R., Hoffman, B. M. & Seefeldt, L. C. Electron transfer within nitrogenase: evidence for a deficit-spending mechanism. Biochemistry 50, 9255–9263 (2011).

    Article  CAS  PubMed  Google Scholar 

  10. Seefeldt, L. C. et al. Energy transduction in nitrogenase. Acc. Chem. Res. 51, 2179–2186 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Bolin, J. T., Campobasso, N., Muchmore, S. W., Morgan, T. V. & Mortenson, L. E. in Molybdenum Enzymes, Cofactors and Model Systems (eds Stiefel, E., Coucouvanis, D. & Newton, W. E.) Ch. 12, 186–195 (American Chemical Society, 1993).

  12. Peters, J. W. et al. Redox-dependent structural changes in the nitrogenase P-cluster. Biochemistry 36, 1181–1187 (1997).

    Article  CAS  PubMed  Google Scholar 

  13. Keable, S. M. et al. Structural characterization of the P1+ intermediate state of the P-cluster of nitrogenase. J. Biol. Chem. 293, 9629–9635 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Cao, L., Börner, M. C., Bergmann, J., Caldararu, O. & Ryde, U. Geometry and electronic structure of the P-cluster in nitrogenase studied by combined quantum mechanical and molecular mechanical calculations and quantum refinement. Inorg. Chem. 58, 9672–9690 (2019).

  15. Lanzilotta, W. N., Christiansen, J., Dean, D. R. & Seefeldt, L. C. Evidence for coupled electron and proton transfer in the [8Fe-7S] cluster of nitrogenase. Biochemistry 37, 11376–11384 (1998).

    Article  CAS  PubMed  Google Scholar 

  16. Noodleman, L., Norman, J. G. Jr, Osborne, J. H., Aizman, A. & Case, D. A. Models for ferredoxins: electronic structures of iron-sulfur clusters with one, two, and four iron atoms. J. Am. Chem. Soc. 107, 3418–3426 (1985).

    Article  CAS  Google Scholar 

  17. Noodleman, L. & Davidson, E. R. Ligand spin polarization and antiferromagnetic coupling in transition metal dimers. Chem. Phys. 109, 131–143 (1986).

    Article  Google Scholar 

  18. Yamaguchi, K., Fueno, T., Ueyama, N., Nakamura, A. & Ozaki, M. Antiferromagnetic spin couplings between iron ions in iron–sulfur clusters. A localized picture by the spin vector model. Chem. Phys. Lett. 164, 210–216 (1989).

    Article  CAS  Google Scholar 

  19. Shoji, M. et al. Theory of chemical bonds in metalloenzymes V: hybrid-DFT studies of the inorganic [8Fe-7S] core. Int. J. Quantum Chem. 106, 3288–3302 (2006).

    Article  CAS  Google Scholar 

  20. Schollwöck, U. The density-matrix renormalization group in the age of matrix product states. Ann. Phys. 326, 96–192 (2011).

    Article  CAS  Google Scholar 

  21. White, S. R. & Martin, R. L. Ab initio quantum chemistry using the density matrix renormalization group. J. Chem. Phys. 110, 4127–4130 (1999).

    Article  CAS  Google Scholar 

  22. Chan, G. K.-L. & Sharma, S. The density matrix renormalization group in quantum chemistry. Annu. Rev. Phys. Chem. 62, 465–481 (2011).

    Article  CAS  PubMed  Google Scholar 

  23. Anderson, P. W. & Hasegawa, H. Considerations on double exchange. Phys. Rev. 100, 675 (1955).

    Article  CAS  Google Scholar 

  24. Ohki, Y., Sunada, Y., Honda, M., Katada, M. & Tatsumi, K. Synthesis of the P-cluster inorganic core of nitrogenases. J. Am. Chem. Soc. 125, 4052–4053 (2003).

    Article  CAS  PubMed  Google Scholar 

  25. Coucouvanis, D. et al. Tetrahedral complexes containing the Fe(ii)S4 core. The syntheses, ground-state electronic structures and crystal and molecular structures of the bis(tetraphenylphosphonium)tetrakis (thiophenolato)ferrate(ii) and bis(tetrapheny lphosphonium) bis(dithiosquarato)ferrate(ii) complexes. An analog for the active site in reduced rubredoxins (Rdred). J. Am. Chem. Soc. 103, 3350–3362 (1981).

    Article  CAS  Google Scholar 

  26. Noodleman, L. Exchange coupling and resonance delocalization in reduced iron–sulfur [Fe4S4]+ and iron-selenium [Fe4Se4]+ clusters. 1. Basic theory of spin-state energies and EPR and hyperfine properties. Inorg. Chem. 30, 246–256 (1991).

    Article  CAS  Google Scholar 

  27. Watt, G. D. & Reddy, K. Formation of an all ferrous Fe4S4 cluster in the iron protein component of Azotobacter vinelandii nitrogenase. J. Inorg. Biochem. 53, 281–294 (1994).

    Article  CAS  Google Scholar 

  28. Angove, H. C., Yoo, S. J., Burgess, B. K. & Münck, E. Mössbauer and EPR evidence for an all-ferrous Fe4S4 cluster with S = 4 in the Fe protein of nitrogenase. J. Am. Chem. Soc. 119, 8730–8731 (1997).

    Article  CAS  Google Scholar 

  29. Rupnik, K. et al. Nonenzymatic synthesis of the P-cluster in the nitrogenase MoFe protein: evidence of the involvement of all-ferrous [Fe4S4]0 intermediates. Biochemistry 53, 1108–1116 (2014).

    Article  CAS  PubMed  Google Scholar 

  30. Tittsworth, R. C. & Hales, B. J. Detection of EPR signals assigned to the 1-equiv-oxidized P-clusters of the nitrogenase MoFe-protein from Azotobacter vinelandii. J. Am. Chem. Soc. 115, 9763–9767 (1993).

    Article  CAS  Google Scholar 

  31. Surerus, K. K. et al. Mössbauer and integer-spin EPR of the oxidized P-clusters of nitrogenase: POX is a non-Kramers system with a nearly degenerate ground doublet. J. Am. Chem. Soc. 114, 8579–8590 (1992).

    Article  CAS  Google Scholar 

  32. Owens, C. P., Katz, F. E., Carter, C. H., Oswald, V. F. & Tezcan, F. A. Tyrosine-coordinated P-cluster in G. diazotrophicus nitrogenase: evidence for the importance of O-based ligands in conformationally gated electron transfer. J. Am. Chem. Soc. 138, 10124–10127 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Shomura, Y., Yoon, K.-S., Nishihara, H. & Higuchi, Y. Structural basis for a [4Fe-3S] cluster in the oxygen-tolerant membrane-bound [NiFe]-hydrogenase. Nature 479, 253 (2011).

    Article  CAS  PubMed  Google Scholar 

  34. Fritsch, J. et al. The crystal structure of an oxygen-tolerant hydrogenase uncovers a novel iron–sulphur centre. Nature 479, 249 (2011).

    Article  CAS  PubMed  Google Scholar 

  35. Volbeda, A. et al. X-ray crystallographic and computational studies of the O2-tolerant [NiFe]-hydrogenase 1 from Escherichia coli. Proc. Natl Acad. Sci. U S A 109, 5305–5310 (2012).

  36. Tabrizi, S. G., Pelmenschikov, V., Noodleman, L. & Kaupp, M. The Mössbauer parameters of the proximal cluster of membrane-bound hydrogenase revisited: a density functional theory study. J. Chem. Theory Comput. 12, 174–187 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Noodleman, L. & Han, W.-G. Structure, redox, pK a, spin. A golden tetrad for understanding metalloenzyme energetics and reaction pathways. J. Biol. Inorg. Chem. 11, 674–694 (2006).

    Article  CAS  PubMed  Google Scholar 

  38. Lovell, T., Li, J., Liu, T., Case, D. A. & Noodleman, L. FeMo cofactor of nitrogenase: a density functional study of states MN, MOX, MR, and MI. J. Am. Chem. Soc. 123, 12392–12410 (2001).

    Article  CAS  PubMed  Google Scholar 

  39. Dance, I. Electronic dimensions of FeMo-co, the active site of nitrogenase, and its catalytic intermediates. Inorg. Chem. 50, 178–192 (2010).

    Article  CAS  PubMed  Google Scholar 

  40. Siegbahn, P. E. Model calculations suggest that the central carbon in the FeMo-cofactor of nitrogenase becomes protonated in the process of nitrogen fixation. J. Am. Chem. Soc. 138, 10485–10495 (2016).

    Article  CAS  PubMed  Google Scholar 

  41. Bjornsson, R., Neese, F. & DeBeer, S. Revisiting the Mössbauer isomer shifts of the FeMoco cluster of nitrogenase and the cofactor charge. Inorg. Chem. 56, 1470–1477 (2017).

    Article  CAS  PubMed  Google Scholar 

  42. Cao, L. & Ryde, U. Influence of the protein and DFT method on the broken-symmetry and spin states in nitrogenase. Int. J. Quantum Chem. 118, e25627 (2018).

    Article  CAS  Google Scholar 

  43. Spatzal, T. et al. Nitrogenase FeMoco investigated by spatially resolved anomalous dispersion refinement. Nat. Commun. 7, 10902 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Rupnik, K. et al. P+ state of nitrogenase P-cluster exhibits electronic structure of a [Fe4S4]+ cluster. J. Am. Chem. Soc. 134, 13749–13754 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Mouesca, J.-M., Noodleman, L. & Case, D. Analysis of the 57Fe hyperfine coupling constants and spin states in nitrogenase P-clusters. Inorg. Chem. 33, 4819–4830 (1994).

    Article  CAS  Google Scholar 

  46. Mouesca, J.-M., Noodleman, L., Case, D. & Lamotte, B. Spin densities and spin coupling in iron–sulfur clusters: a new analysis of hyperfine coupling constants. Inorg. Chem. 34, 4347–4359 (1995).

    Article  CAS  Google Scholar 

  47. Huynh, B. et al. Nitrogenase XII. Mössbauer studies of the MoFe protein from Clostridium pasteurianum W5. Biochim. Biophys. Acta Protein Struct. 623, 124–138 (1980).

    Article  CAS  Google Scholar 

  48. Li, Z. & Chan, G. K.-L. Spin-projected matrix product states: versatile tool for strongly correlated systems. J. Chem. Theory Comput. 13, 2681–2695 (2017).

    Article  CAS  PubMed  Google Scholar 

  49. Sharma, S. & Chan, G. K.-L. Spin-adapted density matrix renormalization group algorithms for quantum chemistry. J. Chem. Phys. 136, 124121 (2012).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This work was supported by the US National Science Foundation through grant no. NSF-CHE 1665333. The BLOCK and PySCF codes used in the calculations were developed by additional support from the US National Science Foundation through grant no. NSF-SSI 1657286. G.K.-L.C. is a Simons Investigator in Physics.

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  1. Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA

    Zhendong Li, Sheng Guo, Qiming Sun & Garnet Kin-Lic Chan

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  1. Zhendong Li
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  2. Sheng Guo
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Contributions

Z.L. and G.K.-L.C. designed the study and wrote the manuscript. Z.L. performed the calculations. S.G. contributed to interfacing SP-MPS to SA-MPS used in the BLOCK code. Q.S. contributed to interfacing the PySCF code with COSMO. All authors contributed to the discussion of the results.

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Correspondence to Zhendong Li or Garnet Kin-Lic Chan.

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Li, Z., Guo, S., Sun, Q. et al. Electronic landscape of the P-cluster of nitrogenase as revealed through many-electron quantum wavefunction simulations. Nat. Chem. 11, 1026–1033 (2019). https://doi.org/10.1038/s41557-019-0337-3

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