Exploring the interstitial atom in the FeMo cofactor of nitrogenase: insights from QM and QM/MM calculations

The Journal of Physical Chemistry. B
Hujun XieZexing Cao

Abstract

Density functional theory and combined quantum mechanics and molecular mechanics (QM/MM) calculations have been used to explore structural features of the FeMo cofactor with an interstitial atom X (X = N, C, or O) and its interactions with CO and N 2. Predicted frequencies of the metal-bound CO, QM/MM-optimized geometries, and calculated redox potentials of the FeMo cofactor with different central ligands show that the oxygen atom is the candidate for the interstitial atom. Calculations on the interactions of the FeMo cofactor with CO and N 2 reveal that there is a remarkable dependence of the binding energy on the binding site and the interstitial atom. Generally, the Fe2 site of the FeMo cofactor has stronger interactions with CO and N 2 than Fe6, and both the Fe2 and Fe6 sites in the N-centered and O-centered clusters of the FeMo cofactor can effectively bind N 2 while the coordination of N 2 to the Fe6 site of the C-centered active cluster is unfavorable energetically. Present results indicate that the protein environment is important for computational characterization of the structure of the FeMo cofactor and properties of the metal-bound CO and N 2 are sensitive to the interstitial atom.

References

Jun 1, 1996·Journal of Molecular Graphics·W Smith, T R Forester
Jun 15, 1992·Physical Review. B, Condensed Matter·J P Perdew, Y Wang
Oct 28, 1996·Physical Review Letters·J P PerdewM Ernzerhof
Sep 28, 2000·Current Opinion in Chemical Biology·D C Rees, J B Howard
Dec 6, 2001·Journal of the American Chemical Society·T LovellL Noodleman
Nov 7, 1996·Chemical Reviews·Barbara K. Burgess, David J. Lowe
Feb 6, 2003·Journal of the American Chemical Society·Berit Hinnemann, Jens K Nørskov
Mar 5, 2003·Chemical Communications : Chem Comm·Ian Dance
May 8, 2003·Journal of the American Chemical Society·Hong-In LeeBrian M Hoffman
Dec 18, 2003·Journal of the American Chemical Society·Johannes SchimplPeter E Blöchl
Feb 11, 2004·Biochemistry·Lance C SeefeldtDennis R Dean
Mar 25, 2004·Journal of the American Chemical Society·Berit Hinnemann, Jens K Nørskov
Jun 8, 2004·The Journal of Biological Chemistry·Robert Y IgarashiLance C Seefeldt
Aug 5, 2004·Journal of the American Chemical Society·Hong-In LeeBrian M Hoffman
Mar 16, 2005·Accounts of Chemical Research·Patricia C Dos SantosDennis R Dean
Jul 14, 2005·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Johannes Kästner, Peter E Blöchl
Aug 4, 2005·Journal of the American Chemical Society·Ian Dance
Oct 19, 2005·The Journal of Chemical Physics·Johannes KästnerPeter E Blöchl
Mar 3, 2006·Current Opinion in Chemical Biology·John W Peters, Robert K Szilagyi
Nov 8, 2006·Proceedings of the National Academy of Sciences of the United States of America·James B Howard, Douglas C Rees
Feb 21, 2007·Journal of the American Chemical Society·Johannes Kästner, Peter E Blöchl
Apr 30, 1998·The Journal of Physical Chemistry. B·A D MacKerellM Karplus

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Citations

Mar 22, 2013·Journal of the American Chemical Society·Jared A WiigMarkus W Ribbe
Jan 18, 2019·Physical Chemistry Chemical Physics : PCCP·Lili Cao, Ulf Ryde
Apr 9, 2020·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Lili Cao, Ulf Ryde
Oct 17, 2013·Chemical Communications : Chem Comm·Ian Dance
Jul 16, 2011·Angewandte Chemie·Deidra L Gerlach, Nicolai Lehnert
Feb 1, 2020·Journal of Chemical Theory and Computation·Lili Cao, Ulf Ryde

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