Chapter 6. Computational Spectroscopy and Photophysics in Complex Biological Systems: Towards an In Silico Photobiology

In this chapter we report a selection and critical analysis of the use of molecular modelling and simulations techniques to tackle problems related to the interaction between light and matter in macromolecular systems of biological relevance. After a brief recall of the importance and limitations of hybrid quantum mechanics/molecular mechanics (QM/MM) techniques to include the effects owing to the complex and inhomogeneous environments, we concentrate on the calculation of absorption and emission spectra. We also underline, through an ensemble of specific examples, the necessity of taking into account a proper sampling of the conformational space of the chromophores to include the effects of the thermal and vibrational motion on the optical properties. The same protocols are also applied to the study of circular dichroism spectra, allowing study of the properties of complex aggregates and clearly matching the optical properties with the structure. Finally, we illustrate how modern computational chemistry can allow understanding of the evolution of the excited states, either via an exploration of the potential energy surfaces or by a dynamic approach, and hence solving problems related to their photochemical evolution. We clearly show, through a collection of examples and a pedagogical approach that is suitable for the non-specialist reader, how molecular modelling and simulation can nowadays solve complex problems in complex systems, hence paving the way to the veritable development of in silico photobiology.