Chapter 6 - Computer Simulations of Photobiological Processes: The Effect of the Protein Environment

Abstract

Organisms have evolved a wide variety of mechanisms to utilize and respond to light. In many cases, the biological response is mediated by structural changes that follow photon absorption. These reactions typically occur at femto- to picosecond timescales. As the relevant time and spatial resolutions are notoriously hard to access experimentally, Molecular dynamics simulations are the method of choice to study such ultrafast processes. In this chapter we review the theoretical concepts of photochemical reactions and present a practical simulation scheme for simulating photochemical reactions in biomolecular systems. In our scheme, a multiconfigurational quantum mechanical description is used to model the electronic rearrangement for those parts of the system that are involved in the absorption. For the remainder, typically consisting of the apoprotein and the solvent, a simple forcefield model suffices. The interactions in the systems are thus computed within a hybrid quantum/classical framework. Forces are calculated on-the-fly, and a diabatic surface-hopping procedure is used to model the excited state decay. The validity of this approach is demonstrated by recent MD simulations on photobiological systems that we also review in this chapter. In addition to providing quantities that are experimentally accessible, such as structural intermediates, fluorescence lifetimes, quantum yields, and spectra, the simulations have also provided information that is much more difficult to measure experimentally, such as reaction mechanisms and the influence of individual amino acid residues