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Fast Generation of Broken-Symmetry States in a Large System Including Multiple Iron-Sulfur Assemblies: Investigation of QM/MM Energies, Clusters Charges, and Spin Populations

Greco, Claudio; Fantucci, Piercarlo; Ryde, Ulf LU and de Gioia, Luca (2011) In International Journal of Quantum Chemistry 111(14). p.3949-3960
Abstract
A density functional theory study is presented regarding the energetics and the Mulliken population analyses of a quantum mechanical/molecular mechanical (QM/MM) system including multiple iron-sulfur clusters in the QM region. The [FeFe]-hydrogenase from Desulfovibrio desulfuricans was studied, and both the active site (an Fe6S6 assembly generally referred to as the H-cluster) and an ancillary Fe4S4 site were treated at the BP86-RI/TZVP level. The antiferromagnetic coupling that characterizes both sites was modeled using the broken-symmetry (BS) approach. For such a QM system, 36 different BS couplings can be defined, depending on the localization of spin excess on the various spin centers. All the BS states were obtained by means of an... (More)
A density functional theory study is presented regarding the energetics and the Mulliken population analyses of a quantum mechanical/molecular mechanical (QM/MM) system including multiple iron-sulfur clusters in the QM region. The [FeFe]-hydrogenase from Desulfovibrio desulfuricans was studied, and both the active site (an Fe6S6 assembly generally referred to as the H-cluster) and an ancillary Fe4S4 site were treated at the BP86-RI/TZVP level. The antiferromagnetic coupling that characterizes both sites was modeled using the broken-symmetry (BS) approach. For such a QM system, 36 different BS couplings can be defined, depending on the localization of spin excess on the various spin centers. All the BS states were obtained by means of an effective and simple method for spin localization, that is here described and compared with more sophisticated approaches already available in literature. The variation of the QM/MM energy among the various geometry-optimized protein models was found to be less than 25 kJ mol(-1). This energy variation almost doubles if no geometry optimization is performed. A detailed analysis of the additive nature of these variations in QM/MM energy is reported. The Mulliken charges show very small variations among the 36 BS states, whereas the Mulliken spin populations were found to be somewhat more variable. The relevance of such variations is discussed in light of the available Mossbauer and Electron Paramagnetic Resonance (EPR) spectroscopic data for the enzyme. Finally, the influence of the basis set on the spin populations, charges, and structural parameters of the models was investigated, by means of QM/MM computations on the same system at the BP86-RI/SVP level. (C) 2010 Wiley Periodicals, Inc. Int J Quantum Chem 111: 3949-3960, 2011 (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
metalloproteins, broken-symmetry approach, antiferromagnetic coupling, QM/MM, iron-sulfur clusters
in
International Journal of Quantum Chemistry
volume
111
issue
14
pages
3949 - 3960
publisher
John Wiley & Sons
external identifiers
  • wos:000295366300051
  • scopus:79951917749
ISSN
0020-7608
DOI
10.1002/qua.22849
language
English
LU publication?
yes
id
8db8c856-5a89-4d49-9b30-1fa34bc031e5 (old id 2179433)
date added to LUP
2011-10-25 10:25:41
date last changed
2017-09-24 03:22:11
@article{8db8c856-5a89-4d49-9b30-1fa34bc031e5,
  abstract     = {A density functional theory study is presented regarding the energetics and the Mulliken population analyses of a quantum mechanical/molecular mechanical (QM/MM) system including multiple iron-sulfur clusters in the QM region. The [FeFe]-hydrogenase from Desulfovibrio desulfuricans was studied, and both the active site (an Fe6S6 assembly generally referred to as the H-cluster) and an ancillary Fe4S4 site were treated at the BP86-RI/TZVP level. The antiferromagnetic coupling that characterizes both sites was modeled using the broken-symmetry (BS) approach. For such a QM system, 36 different BS couplings can be defined, depending on the localization of spin excess on the various spin centers. All the BS states were obtained by means of an effective and simple method for spin localization, that is here described and compared with more sophisticated approaches already available in literature. The variation of the QM/MM energy among the various geometry-optimized protein models was found to be less than 25 kJ mol(-1). This energy variation almost doubles if no geometry optimization is performed. A detailed analysis of the additive nature of these variations in QM/MM energy is reported. The Mulliken charges show very small variations among the 36 BS states, whereas the Mulliken spin populations were found to be somewhat more variable. The relevance of such variations is discussed in light of the available Mossbauer and Electron Paramagnetic Resonance (EPR) spectroscopic data for the enzyme. Finally, the influence of the basis set on the spin populations, charges, and structural parameters of the models was investigated, by means of QM/MM computations on the same system at the BP86-RI/SVP level. (C) 2010 Wiley Periodicals, Inc. Int J Quantum Chem 111: 3949-3960, 2011},
  author       = {Greco, Claudio and Fantucci, Piercarlo and Ryde, Ulf and de Gioia, Luca},
  issn         = {0020-7608},
  keyword      = {metalloproteins,broken-symmetry approach,antiferromagnetic coupling,QM/MM,iron-sulfur clusters},
  language     = {eng},
  number       = {14},
  pages        = {3949--3960},
  publisher    = {John Wiley & Sons},
  series       = {International Journal of Quantum Chemistry},
  title        = {Fast Generation of Broken-Symmetry States in a Large System Including Multiple Iron-Sulfur Assemblies: Investigation of QM/MM Energies, Clusters Charges, and Spin Populations},
  url          = {http://dx.doi.org/10.1002/qua.22849},
  volume       = {111},
  year         = {2011},
}