Chapter 4: Electron and Molecular Dynamics Simulations with Polarizable Embedding

This chapter describes methodologies to simulate the dynamics of large molecular systems after perturbation of their electron clouds by an external stimulus. The methodology is based on Auxiliary Density Functional Theory, as introduced in Chapter 1, and adapted to time-dependent problems. We review the basic physical equations of Real-Time Time-Dependent ADFT (RT-TD-ADFT), emphasizing the use of the Magnus propagator that permits numerical simulations of electron dynamics. The coupling of RT-TD-ADFT to classical nuclear dynamics within the mean-field Ehrenfest approach is further introduced for mixed quantum–classical simulations. We then introduce a Quantum Mechanics/Molecular Mechanics approach with a polarizable force field (QM/MMpol) and its coupling to RT-TD-ADFT. This methodology permits electron dynamics simulations in large molecular systems such as those encountered in biology or materials science. The computational performance of the methodology is benchmarked on the modern Jean Zay supercomputer hosted at IDRIS, France. The final section is dedicated to some illustrative applications of RT-TD-ADFT to photochemistry and radiation chemistry problems. We show how the absorption spectra of molecules can be simulated using RT-TD-ADFT and how they compare to Linear-Response TD-ADFT calculations. We then consider the collision of a high-energy charged alpha particle with a DNA–protein complex. Attosecond charge migrations resulting from this initial perturbation are investigated using RT-TD-ADFT simulations.