Sonia Jafari - Department of Chemistry, Faculty of Science, University of Kurdistan, Sanandaj, Iran
Ulf RYDE - Department of Theoretical Chemistry, Lund University,Lund, Sweden
MEHDI IRANI - Department of Chemistry, Faculty of Science, University of Kurdistan, Sanandaj, Iran

The accuracy of geometries is important for predicting the electronic properties of molecularsystems using computational methods. A previous investigation has indicated that there exist twolocal minima for [۴Fe–۴S] clusters in proteins when optimized with a density functional theory(DFT) method [۱]. In this work, we performed a detailed study of two distinct local minima for[۴Fe–۴S] clusters in five proteins and two oxidation states, using combined quantum mechanicaland molecular mechanical (QM/MM) methods.The MM part of the QM/MM calculations wasperformed with the Amber software [۲], using the Amber ff۱۴SB force fields. In the QM part,we employed nine different DFT methods, PBE, BP۸۶, BLYP, B۹۷D, TPSS, r۲SCAN, TPSSh,B۳LYP, and B۳LYP*. All the functionals were combined withdef۲-SV(P) or def۲-TZVPDbasissets.The QM system consisted of the Fe and S ions and the directly coordinated Cys groupsmodeled by CH۳CH۲S–, for the whole cluster (cf. Figure ۱).Weindicated that one local minimum(L state) has longer Fe–Fe distances than the other (S state) and that the L state is more stable forall cases studied. Also, our results showed that some DFT methods may only obtain the L state,while others may obtain both states. We recommend r۲SCAN for optimizing [۴Fe-۴S] clusters inproteins, which gives the most accurate structures.

Iron-Sulfur Cluster, Protein, DFT, Geometry, QM/MM