The modeling of the absorption lineshape for embedded molecules through a polarizable QM/MM approach†,Photochemical & Photobiological Sciences

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The modeling of the absorption lineshape for embedded molecules through a polarizable QM/MM approach†
Photochemical & Photobiological Sciences ( IF 2.7 ) Pub Date : 2018-03-05 00:00:00 , DOI: 10.1039/c8pp00033f
Daniele Loco _{1,

2,

3,

4} , Sandro Jurinovich _{1,

2,

3,

4} , Lorenzo Cupellini _{1,

2,

3,

4} , Maximilian F. S. J. Menger _{1,

2,

3,

4} , Benedetta Mennucci _{1,

2,

3,

4}

Affiliation

We present a computational strategy to simulate the absorption lineshape of a molecule embedded in a complex environment by using a polarizable QM/MM approach. This strategy is presented in two alternative formulations, one based on a molecular dynamics simulation of the structural fluctuations of the system and the other using normal modes and harmonic frequencies calculated on optimized geometries. The comparison for the case of a chromophore within a strongly inhomogeneous and structured environment, namely the intercalation pocket of DNA, shows that the MD-based approach is able to reproduce the experimental spectral bandshape. In contrast, the static approach overestimates the vibronic coupling, resulting in a much broader band.

中文翻译：

通过可极化的QM / MM方法对嵌入分子的吸收线形进行建模†

我们提出了一种计算策略，通过使用可极化的QM / MM方法来模拟嵌入复杂环境中的分子的吸收线形。可以用两种替代方法来表示该策略，一种是基于对系统结构波动的分子动力学模拟，另一种是使用法线模和在优化的几何结构上计算出的谐波频率。在强不均匀和结构化的环境（即DNA的插入口袋）中对发色团的情况进行的比较表明，基于MD的方法能够重现实验光谱的谱带形状。相反，静态方法高估了振动耦合，从而产生了更宽的频带。

更新日期：2018-03-05

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