PNNL

Abstract

Non-equilibrium 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 ~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 (~3.3 ps total simulation time), where the accessible phase space is not fully sampled, provide a basis set 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 non-equilibrium chemical phenomena. These effects are well-captured using the described AIMD-based single molecule Raman spectral simulations.