Abstract
After a review of the current status of density functional theory (DFT) for spin-polarized and spin-coupled systems, we focus on the resting states and intermediates of redox-active metalloenzymes and electron transfer proteins, showing how comparisons of DFT-calculated spectroscopic parameters with experiment and evaluation of related energies and geometries provide important information. The topics we examine include (1) models for the active-site structure of methane monooxygenase intermediate Q and ribonucleotide reductase intermediate X; (2) the coupling of electron transfer to proton transfer in manganese superoxide dismutase, with implications for reaction kinetics; (3) redox, pK a, and electronic structure issues in the Rieske iron–sulfur protein, including their connection to coupled electron/proton transfer, and an analysis of how partial electron delocalization strongly alters the electron paramagnetic resonance spectrum; (4) the connection between protein-induced structural distortion and the electronic structure of oxidized high-potential 4Fe4S proteins with implications for cluster reactivity; (5) an analysis of cluster assembly and central-atom insertion into the FeMo cofactor center of nitrogenase based on DFT structural and redox potential calculations.
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Notes
We warn the reader at this point that the terms “electron exchange”, or “electron exchange potential,” or “exchange hole” have different meanings in HF and DFT methods because these methods are constructed from different starting points. There is a fairly close correspondence for atoms, but not for molecules, and these differences are important.
Abbreviations
- ADF:
-
Amsterdam Density Functional
- BP:
-
Becke 1988–Perdew 1986
- BS:
-
Broken symmetry
- B86:
-
Becke 1986
- B88:
-
Becke 1988
- COSMO:
-
Conductor-like screening model
- DFT:
-
Density functional theory
- ENDOR:
-
Electron–nuclear double resonance
- ESEEM:
-
Electron spin echo envelope modulation
- EXAFS:
-
Extended X-ray absorption fine structure
- GGA:
-
Generalized gradient approximation
- G96:
-
Gill 1996
- HF:
-
Hartree–Fock
- HIPIP:
-
High-potential 4Fe4S protein
- LSDA:
-
Local spin density approximation
- MCD:
-
Magnetic circular dichroism
- MM:
-
Molecular mechanics
- MMOH:
-
Methane monooxygenase
- PW91:
-
Perdew–Wang 1991
- QM:
-
Quantum mechanics
- RNR:
-
Ribonucleotide reductase
- RSCP:
-
Resonance spin crossover pair
- SCF:
-
Self-consistent field
- SOD:
-
Superoxide dismutase
- VWN:
-
Vosko–Wilk–Nusair
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Acknowledgements
We want to thank all the former group members who contributed to some of the research reported here, particularly T. Lovell, R. Torres, F. Himo, J. Li, T. Liu, G.M. Ullmann, L. Hunsicker-Wang, J.-M. Mouesca, C.L. Fisher, R. Konecny, X.-G. Zhao, S. Sinnecker, and my collaborators D.A. Case, J.A. Fee, and D. Bashford. We thank V. Roberts, J.A. Fee, and V. Pelmenschikov for their critical reading and comments on the manuscript. This work was funded by NIH grants GM43278 and GM39914.
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Noodleman, L., Han, WG. Structure, redox, pK a, spin. A golden tetrad for understanding metalloenzyme energetics and reaction pathways. J Biol Inorg Chem 11, 674–694 (2006). https://doi.org/10.1007/s00775-006-0136-3
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DOI: https://doi.org/10.1007/s00775-006-0136-3