Modeling the absorption lineshape of embedded systems from molecular dynamics: A tutorial review

In this tutorial review, we focus on a multiscale method to compute the electronic absorption line shape of molecular dyes embedded in a biological environment. To treat the coupling of the electronic excitations with the nuclear degrees of freedom of the system, we use the spectral density (SD) of the exciton-phonon coupling computed from a Born-Oppenheimer molecular dynamics, which takes into account the effect of the biological environment on the dye's nuclear and electronic degrees of freedom. The theoretical basis of the approach is given, as well as a comprehensive description of the computational protocol for the extraction of the energy gap autocorrelation function evaluating the electronic excitation along the classical trajectory. Furthermore a benchmark application from a recently published study is presented as an example of how the derived SD can be used in computational spectroscopy to accurately simulate the absorption lineshape, including both vibronic and temperature effects.