Photo-Active Biological Molecular Materials: From Photoinduced Dynamics to Transient Electronic Spectroscopies

We present an overview of a methodology for the simulation of the photo-response of biological (macro)molecules, designed around a Quantum Mechanics / Molecular Mechanics (QM/MM) subtractive scheme. The resulting simulation workflow, that goes from the characterization of the photo-active system to the modeling of (transient) electronic spectroscopies is implemented in the software COBRAMM, but is completely general and can be used in the framework of any specific QM/MM implementation. COBRAMM is a smart interface to existing state-of-the-art theoretical chemistry codes, combining different levels of description and different algorithms to realize tailored problem-driven computations. The power of this approach is illustrated by reviewing the studies of two fundamental problems involving biological light-sensitive molecules. First, we will consider the photodynamics of the retinal molecule, the pigment of rhodopsin, a visual receptor protein contained in the rod cells of the retina. Retinal, with its light-induced isomerization, triggers a cascade of events leading to the production of the nerve impulse. Then, we will review some studies focusing on the interaction of DNA systems with ultraviolet (UV) light, a problem that has become one of the benchmark for the development of nonlinear spectroscopy, because of the ultrashort excited state lifetimes that arise from very efficient radiationless excited state decay and consent self-protection of DNA against UV damage