Theory of chemical bonds in metalloenzymes III: Full geometry optimization and vibration analysis of ferredoxin-type [2Fe-2S] cluster

• Published in: International journal of quantum chemistry Vol. 107; no. 1; pp. 116 - 133
• Main Authors: Shoji, Mitsuo, Koizumi, Kenichi, Taniguchi, Takeshi, Kitagawa, Yasutaka, Yamanaka, Shusuke, Okumura, Mitsutaka, Yamaguchi, Kizashi
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 2007
• Subjects: density functional theory; double exchange; exchange interaction; ferredoxin; iron-sulfur protein; mixed valence; natural orbital analysis; vibration analysis
• ISSN: 0020-7608; 1097-461X
• DOI: 10.1002/qua.21016

The nature of chemical bonds in a ferredoxin‐type [2Fe–2S] cluster has been investigated on the basis of natural orbitals and several bond indices developed in Parts I and II of this study. The broken‐symmetry hybrid density functional theory (BS‐HDFT) with spin projection approach has been applied to elucidate the natural orbitals and occupation numbers for a model compound [Fe2S2(SCH3)4] (1), which is used to calculate the indices. The molecular structure, vibration frequencies, electronic structures, and magnetic properties in both oxidized and reduced forms of 1 have been calculated and compared with the experimental values. The optimized molecular structures after approximate spin projection have been in good agreement with experimental data. The structure changes upon one‐electron reduction have been slight (<0.1 Å) and only limited around one side of the Fe atom. Raman and infrared (IR) spectra have been calculated, and their vibration modes have been assigned using the bridging 34S isotope substitution. Their magnetic properties have been examined in terms of spin Hamiltonians that contain exchange interactions and double exchange interactions. The BS‐HDFT methods have provided the magnetic parameters; i.e., effective exchange integral (J) values and valence delocalization (B) values, which agree with the experimental results. It is found that large charge transfer (CT) from the bridging sulfur to the iron atoms has led to the strong antiferromagnetic interactions between iron atoms. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007