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

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 Mössbauer 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. © 2010 Wiley Periodicals, Inc.