On the accuracy of density functional theory for iron—sulfur clusters

Abstract

A simple, yet powerful wave function manipulation method was introduced utilizing a generalized ionic fragment approach that allows for systematic mapping of the wave function space for multispin systems with antiferromagnetic coupling. The use of this method was demonstrated for developing ground state electronic wave function for [2Fe-2S] and [Mo-3Fe-4S] clusters. Using well-defined ionic wave functions for ferrous and ferric irons, sulfide, and thiolate fragments, the accuracy of various density functionals and basis sets including effective core potentials were evaluated on a [4Fe-4S] cluster by comparing the calculated geometric and electronic structures with crystallographic data and experimental atomic spin densities from X-ray absorption spectroscopy, respectively. We found that the most reasonable agreement for both geometry and atomic spin densities is obtained by a hybrid functional with 5% HF exchange and 95% density functional exchange supplemented with Perdew's 1986 correlation functional. The basis set seems to saturate only at the triple-level with polarization and diffuse functions. Reasonably preoptimized structures can be obtained by employing computationally less expensive effective core potentials, such as the Stuttgart-Dresden potential with a triple-valence basis set. The extension of the described calibration methodology to other biologically important and more complex iron-sulfur clusters, such as hydrogenase H-cluster and nitrogenase FeMo-co will follow.

Unexpected electron transfer mechanism upon AdoMet cleavage in radical SAM proteins

“…This result can be rationalized by the well known fact that the B3LYP potential used for these QM calculations tends to underestimate the extent of covalency, and, as a consequence, it minimizes orbital overlap, notably in iron sulfur clusters (25). Consequently, we performed additional calculations on the same model with the more delocalized VBP potential implemented in the ADF QM code (26) (see Materials and Methods).…”

“…Along with using the Gaussian-based Jaguar code in the Schrö dinger suite, we ran the Slater-based ADF code (26) (triple-basis sets for all atoms) with the Vosko, Wilk, and Nusair (VWN) LDA functional (37,38) and Becke-Perdew exchange-correlation potential (39,40) (combination referred to as VBP). While the mixed Hartree-Fock/VWN B3LYP potential gives good energetics, the standard 'pure' DFT VBP potential is better in terms of orbital characterization (25,41). Reality (so to speak) lies in between.…”

A novel 1,3,5-triaminocyclohexane-based tripodal ligand forms a unique tetra(pyrazolate)-bridged tricopper(ii) core: solution equilibrium, structure and catecholase activity

“…The basis set employed (def2TZVP 44 ) is larger than needed for the saturation limit as defined earlier. 43,45 The desired spin coupling scheme among the three copper(II) sites in [Cu 3 H -4 L 2 ] 2+ complex was achieved by using the generalized ionic fragment approach (GIFA 46 ). First, the well defined electronic structures of the copper(II) ion and the deprotonated tachpyz ligand were generated at the HF level.…”

Non-innocent ground state electronic structure of a polynuclear copper complex with picolinate bridges

“…All calculations were carried out using Gaussian09 Revision D01 suite of programs [40]. In addition to using the built in initial guess algorithm [28], we have employed the ionic fragment approach [41] to reproducibly construct the initial electronic structure from welldefined ionic fragments such as Cu an average symmetric structure as manifested by the single crystal X-ray diffraction structure.…”