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The chemical species of bridge oxygen (WB) in active site of urease was examined in terms of a magnetic interaction between Ni(II) ions. The effective exchange integrals (Jab) values between Ni(II) ions were calculated by using three candidates of WB, i.e., H2O, OH− and O2−. The unrestricted hybrid density functional theory (UHDFT) calculations were carried out using the smallest models and realistic models. In the case of the smallest models, the experimental Jab value (−6.3 cm−1) was a middle value of WB = H2O (−2.6 cm−1) and WB = OH− (−11.4 cm−1), while we could not obtain appropriate electronic structure using O2−-bridge model. The Jab became −16.7 cm−1 by using more realistic OH−-bridge model, while one spin density on Ni2 ion was delocalized to Asp360 in case of H2O-bridge model. Natural orbital analyses revealed that the magnetic orbital through Lys-bridge delocalized to Asp360 and it seemed to associate with the spin transfer. From the results, OH−-bridge seemed to be the most possible candidate for the structure of active site in urease. |
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