DFT Fea3–O/O–O Vibrational Frequency Calculations over Catalytic Reaction Cycle States in the Dinuclear Center of Cytochrome c Oxidase

• Published in: Inorganic chemistry 2019-10, Vol.58 (20), p.13933-13944
• Main Authors: Du, Wen-Ge Han, Götz, Andreas W, Noodleman, Louis
• Format: Article
• Language: English
• ISSN: 0020-1669; 1520-510X
• DOI: 10.1021/acs.inorgchem.9b01840

Density functional vibrational frequency calculations have been performed on eight geometry optimized cytochrome c oxidase (CcO) dinuclear center (DNC) reaction cycle intermediates and on the oxymyoglobin (oxyMb) active site. The calculated Fe–O and O–O stretching modes and their frequency shifts along the reaction cycle have been compared with the available resonance Raman (rR) measurements. The calculations support the proposal that in state A[Fea3 3+–O2 –• ···CuB +] of CcO, O2 binds with Fea3 2+ in a similar bent end-on geometry to that in oxyMb. The calculations show that the observed 20 cm–1 shift of the Fea3–O stretching mode from the P R to F state is caused by the protonation of the OH – ligand on CuB 2+ (P R [Fea3 4+O2– ···HO – –CuB 2+] → F[Fea3 4+O2– ···H2O–CuB 2+]), and that the H2O ligand is still on the CuB 2+ site in the rR identified F[Fea3 4+O2– ···H2O–CuB 2+] state. Further, the observed rR band at 356 cm–1 between states P R and F is likely an O–Fea3–porphyrin bending mode. The observed 450 cm–1 low Fea3–O frequency mode for the O H active oxidized state has been reproduced by our calculations on a nearly symmetrically bridged Fea3 3+–OH–CuB 2+ structure with a relatively long Fea3–O distance near 2 Å. Based on Badger’s rule, the calculated Fea3–O distances correlate well with the calculated ν Fe–O –2/3 (ν Fe–O is the Fea3–O stretching frequency) with correlation coefficient R = 0.973.