Optical Spectra of Cu(II)−Azurin by Hybrid TDDFT-Molecular Dynamics Simulations

The ground state electronic structure of oxidized azurin from Pseudomonas aeruginosa and its optical response
have been investigated by combining hybrid quantum mechanics/molecular mechanics simulations with time-dependent density functional theory. In agreement with experiment, we find that the unpaired electron spin
density is mainly localized on the copper ion. The vertical absorption spectrum in the visible range is well
reproduced, with the central band centered around 2.1 eV. The anisotropic dipolar field due to the extended
α-helix polarizes the metal binding site and is responsible for a shift of the absorption bands by ±0.1−0.2
eV. At 300 K, the bond distances of the copper binding site undergo large fluctuations (∼0.3 Å). It is crucial
to take these thermal fluctuations into account for a faithful description of the optical properties.

本研究结合杂交量子力学/分子力学（hybrid quantum mechanics/molecular mechanics, QM/MM）模拟与含时密度泛函理论（time-dependent density functional theory, TDDFT），对铜绿假单胞菌（Pseudomonas aeruginosa）来源的氧化天青蛋白（azurin）的基态电子结构及其光学响应开展了研究。未成对电子的自旋密度主要定域于铜离子之上，该结果与实验观测一致。可见光范围内的垂直吸收光谱得到了良好重现，其中心吸收带的峰值位于约2.1电子伏特处。延伸α螺旋所产生的各向异性偶极场会使金属结合位点发生极化，进而导致吸收带产生±0.1~0.2电子伏特的位移。在300开尔文温度下，铜结合位点的键长会出现约0.3埃的大幅涨落。若要对该蛋白的光学性质进行准确且贴合实际的描述，必须将这些热涨落纳入考量范畴。