Theory of chemical bonds in metalloenzymes IV: Hybrid‐DFT study of Rieske‐type [2Fe2S] clusters

Abstract

ABSTRACT:The Rieske-type [2FeO2S] cores of electron-transfer (ET) proteins in the mitochondrial respiratory chain have unusual properties, such as redox potentials and spectroscopy. In this study, part IV of a series, the inherent molecular structures and characteristic electronic structures of the Rieske-type [2FeO2S] clusters are investigated using broken-symmetry hybrid density functional theory (BS-HDFT). Geometry optimizations for the oxidized and reduced states were performed and their characteristic vibrational modes are assigned. Magnetic properties are investigated using model Hamiltonians to describe the electron delocalization and the unsymmetric property. The parameters of the model Hamiltonian, such as exchange coupling J, valence delocalization B, and potential energy difference ⌬, are evaluated from the BS-HDFT calculations. The valence localization and excitation energy (⌬E) of the Rieske-type [2FeO2S] cluster are discussed. The chemical bond nature is characterized by chemical indices from natural orbital analysis. Our theoretical results are reasonably consistent with experimental results.

Distinguishing Protonation States of Histidine Ligands to the Oxidized Rieske Iron–Sulfur Cluster through 15N Vibrational Frequency Shifts

“…[44] Vibrational frequencies were also calculated for 15 Ni sotopic substitutions within the imidazole rings of the structures described in Figure 2. Three sets of isotopics ubstitutions were performed:1 )both nitrogen atoms within both protonated imidazole ligands were substituted, 2) both nitrogen atoms within ad eprotonated imidazole were substituted when the second imidazole remained protonated, and 3) both nitrogen atoms within the protonated imidazole were substituted, whereas the second imidazole was deprotonated.…”

Quantum Electron Tunneling in Respiratory Complex I

“…Spin-orbit coupling is also expected to be not too much smaller than k B T in these systems, and will further lift the 2 S +1 degeneracy of these states to give more than 100 different spin states. All relevant vibrations (Fe-S stretch, ring breathing, ring deformation, etc) of a Fe/S cluster calculated with BS-DFT have frequencies in 200–400 cm −1 , which corresponds to the time scale of 80–160 fs 26–27 , and therefore the time scale of the resulting mixing is expected to be 6 to 8 orders of magnitude faster than that of the slowest electron transfer.…”

Theory of chemical bonds in metalloenzymes. XVII. Symmetry breaking in manganese cluster structures and chameleonic mechanisms for the OO bond formation of water splitting reaction

“…Thus, symmetry and broken symmetry play an important role for characterization of cluster structures of multinuclear iron-sulfur complexes in chemistry and biology. These are closely related to homolytic and heterolytic bond cleavages (or formations) in chemical reaction as discussed previously [3,4,[22][23][24][25]26]. SCHEME 1.…”

“…Interestingly, the D 2 symmetry is broken in the case of Rieske-type 2Fe-2S cluster (C) due to the different ligand field [24]. Similarly, the T d symmetry is also broken in 4Fe-4S cluster of aconitase (D) [1].…”

“…In this series of papers [22][23][24], we have examined several iron-sulfur clusters that play important roles in electron transfers and several chemical reactions. The binuclear iron-sulfur (2Fe-2S; A) and tetranuclear iron-sulfur (4Fe-4S; B) clusters have D 2 and T d symmetries, respectively, as shown in Scheme 3.…”