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Modeling the MoFe Nitrogenase System with Broken Symmetry Density Functional Theory

  • Gregory M. Sandala
  • Louis NoodlemanEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 766)

Abstract

Density functional theory (DFT) represents a unified framework for gaining molecular level insight into molybdenum–iron (MoFe) nitrogenase. However, accurately describing the electronic structure of the spin-polarized and spin-coupled iron–molybdenum cofactor (FeMo-co) where N2 reduction occurs within MoFe nitrogenase is challenging. Therefore, the enhancement of DFT to include broken symmetry (BS-DFT) plus approximate spin projection has proven valuable because it provides a procedure to compute reliable geometries, energies, redox potentials, and quantities relevant to Mössbauer and ENDOR spectroscopies. After describing the theoretical tools necessary to obtain this information, we show by way of examples how BS-DFT is a very powerful partner to experiment. We expect that quantitative quantum chemical theory of this type will play an ever-increasing role in helping to decipher complex bioinorganic systems like those found in MoFe nitrogenase.

Key words

Density functional theory (DFT) broken symmetry spin coupling spin polarization spin projection techniques redox potentials Mössbauer parameters ENDOR hyperfine parameters FeMo cofactor iron–sulfur clusters 

Notes

Acknowledgments

The authors would like to acknowledge the other contributors to our nitrogenase work, whose names appear throughout the reference section. Most recently, Vladimir Pelmenschikov and David A. Case have made substantial contributions. We also gratefully acknowledge financial support by NIH grant GM039914.

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.Department of Molecular BiologyThe Scripps Research InstituteLa JollaUSA

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