Excitons in a photosynthetic light-harvesting system: A combined molecular dynamics, quantum chemistry, and polaron model study - art. no. 031919
Excitons in a photosynthetic light-harvesting system: A combined molecular dynamics, quantum chemistry, and polaron model study - art. no. 031919
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DOI：
10.1103/physreve.65.031919
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发表时间：
2002-03-01
影响因子：
2.4
通讯作者：
Schulten, K
中科院分区：
文献类型：
--
作者：
Damjanovic, A;Kosztin, I;Schulten, K
采用分子动力学模拟、量子化学计算和极化子模型分析相结合的方法，研究了捕光复合物中色素-色素和色素-蛋白质相互作用的动力学。在87 055个原子组成的系统上进行了捕光（LH）复合物的分子动力学模拟，该系统由包埋在脂质双层中的Rhodocellum molischianum的LH-II复合物和适当的水层包围。对于每16 B850细菌叶绿素（BChls），我们进行了400从头量子化学计算的几何形状出现的分子动力学模拟，确定作为时间的函数的色素激发能的波动。从这些计算的结果中，我们构建了一个依赖于时间的哈密顿量的B850激子系统，我们确定在线性响应理论的吸收光谱。最后，我们引入了一个极化子模型来描述激子和耦合声子的量子力学自由度。从分子动力学和量子化学模拟中导出了极化子模型中的激子-声子耦合以及相应的声子谱函数。该模型预测，激子在B850 BChl环离域超过五个颜料在室温下。此外，极化子模型允许计算的吸收和圆二色性光谱的B850激子从单独的BChls，这是很容易从组合的分子动力学和量子化学模拟的激发能的自相关函数的唯一知识。所得结果与实验测得的吸收光谱和圆二色光谱符合得很好。
The dynamics of pigment-pigment and pigment-protein interactions in light-harvesting complexes is studied with an approach that combines molecular dynamics simulations with quantum chemistry calculations and a polaron model analysis. The molecular dynamics simulation of light-harvesting (LH) complexes was performed on an 87 055 atom system comprised of a LH-II complex of Rhodospirillum molischianum embedded in a lipid bilayer and surrounded with appropriate water layers. For each of the 16 B850 bacteriochlorophylls (BChls), we performed 400 ab initio quantum chemistry calculations on geometries that emerged from the molecular dynamical simulations, determining the fluctuations of pigment excitation energies as a function of time. From the results of these calculations we construct a time-dependent Hamiltonian of the B850 exciton system from which we determine within linear response theory the absorption spectrum. Finally, a polaron model is introduced to describe both the excitonic and coupled phonon degrees of freedom by quantum mechanics. The exciton-phonon coupling that enters into the polaron model, and the corresponding phonon spectral function, are derived from the molecular dynamics and quantum chemistry simulations. The model predicts that excitons in the B850 BChl ring are delocalized over five pigments at room temperature. Also, the polaron model permits the calculation of the absorption and circular dichroism spectra of the B850 excitons from the sole knowledge of the autocorrelation function of the excitation energies of individual BChls, which is readily available from the combined molecular dynamics and quantum chemistry simulations. The obtained results are found to be in good agreement with the experimentally measured absorption and circular dichroism spectra.