Time Domain Simulations of Single Molecule Raman Scattering
Time Domain Simulations of Single Molecule Raman Scattering
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DOI：
10.1021/acs.jpca.8b05912
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发表时间：
2018-09-20
影响因子：
2.9
通讯作者：
El-Khoury, Patrick Z.
中科院分区：
文献类型：
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作者：
Apra, Edoardo;Bhattarai, Ashish;El-Khoury, Patrick Z.
已知非平衡化学现象在单分子显微镜和光谱学中发挥着重要作用。在这里，我们通过基于从头分子动力学 (AIMD) 的拉曼光谱模拟来探索这些效应。我们的目标是分离的芳香硫醇（硫代苯甲腈，TBN）作为原型分子系统。我们首先表明，TBN 的整体平均拉曼光谱中包含的基本特征可以通过对跨越大约 60 ps 的总模拟时间的 18 个短 AIMD 轨迹进行平均来再现。这涉及 B3LYP/def2-TZVP 理论水平的超过 90 000 次极化率计算。然后，我们说明了短轨迹（类似于 3.3 ps 的总模拟时间），其中可访问的相空间未完全采样，为理解在针对单分子的测量中经常观察到的关键特征提供了一个起点。我们的结果表明，除了局部光场和修改的选择规则之外，对单分子拉曼散射的完整理解还需要考虑分子构象灵活性和非平衡化学现象。使用所描述的基于 AIMD 的单分子拉曼光谱模拟可以很好地捕捉到前一种效应。
Nonequilibrium chemical phenomena are known to play an important role in single molecule microscopy and spectroscopy. Herein, we explore these effects through ab initio molecular dynamics (AIMD)-based Raman spectral simulations. We target an isolated aromatic thiol (thiobenzonitrile, TBN) as a prototypical molecular system. We first show that the essential features contained in the ensemble-averaged Raman spectrum of TBN can be reproduced by averaging over 18 short AIMD trajectories spanning a total simulation time of similar to 60 ps. This involved more than 90 000 polarizability calculations at the B3LYP/def2-TZVP level of theory. We then illustrate that the short trajectories (similar to 3.3 ps total simulation time), where the accessible phase space is not fully sampled, provide a starting point for understanding key features that are often observed in measurements targeting single molecules. Our results suggest that a complete understanding of single molecule Raman scattering needs to account for molecular conformational flexibility and nonequilibrium chemical phenomena in addition to local optical fields and modified selection rules. The former effects are well-captured using the described AIMD-based single molecule Raman spectral simulations.