Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA.
Department of Chemistry, Stanford University, Stanford, California 94305, USA.
J Chem Phys. 2018 Jul 14;149(2):024107. doi: 10.1063/1.5025517.
Many physical phenomena must be accounted for to accurately model solution-phase optical spectral line shapes, from the sampling of chromophore-solvent configurations to the electronic-vibrational transitions leading to vibronic fine structure. Here we thoroughly explore the role of nuclear quantum effects, direct and indirect solvent effects, and vibronic effects in the computation of the optical spectrum of the aqueously solvated anionic chromophores of green fluorescent protein and photoactive yellow protein. By analyzing the chromophore and solvent configurations, the distributions of vertical excitation energies, the absorption spectra computed within the ensemble approach, and the absorption spectra computed within the ensemble plus zero-temperature Franck-Condon approach, we show how solvent, nuclear quantum effects, and vibronic transitions alter the optical absorption spectra. We find that including nuclear quantum effects in the sampling of chromophore-solvent configurations using ab initio path integral molecular dynamics simulations leads to improved spectral shapes through three mechanisms. The three mechanisms that lead to line shape broadening and a better description of the high-energy tail are softening of heavy atom bonds in the chromophore that couple to the optically bright state, widening the distribution of vertical excitation energies from more diverse solvation environments, and redistributing spectral weight from the 0-0 vibronic transition to higher energy vibronic transitions when computing the Franck-Condon spectrum in a frozen solvent pocket. The absorption spectra computed using the combined ensemble plus zero-temperature Franck-Condon approach yield significant improvements in spectral shape and width compared to the spectra computed with the ensemble approach. Using the combined approach with configurations sampled from path integral molecular dynamics trajectories presents a significant step forward in accurately modeling the absorption spectra of aqueously solvated chromophores.
许多物理现象都必须加以考虑，才能准确地模拟溶液相光学光谱线形状，从发色团-溶剂构象的采样到导致振子精细结构的电子-振动跃迁。在这里，我们彻底探讨了核量子效应、直接和间接溶剂效应以及振子效应在计算绿色荧光蛋白和光活性黄色蛋白水合阴离子发色团的光学光谱中的作用。通过分析发色团和溶剂构象、垂直激发能的分布、在系综方法内计算的吸收光谱以及在系综加零温 Franck-Condon 方法内计算的吸收光谱，我们展示了溶剂、核量子效应和振子跃迁如何改变光学吸收光谱。我们发现，通过从头计算路径积分分子动力学模拟在发色团-溶剂构象的采样中包含核量子效应，通过三种机制导致光谱形状得到改善。导致谱线展宽和更好地描述高能尾部的三种机制是：发色团中与光强态耦合的重原子键软化，来自更多不同溶剂环境的垂直激发能分布变宽，以及在计算冻结溶剂口袋中的 Franck-Condon 光谱时，将光谱权重从 0-0 振子跃迁重新分配到更高能量的振子跃迁。与使用系综方法计算的光谱相比，使用组合系综加零温 Franck-Condon 方法计算的吸收光谱在谱形和宽度上都有显著改善。使用与路径积分分子动力学轨迹采样的组合方法代表了在准确模拟水合发色团吸收光谱方面向前迈出的重要一步。
