  Spectral properties of chromophores are used to probe complex biological
processes in vitro and in vivo, yet how the environment tunes their optical
properties is far from being fully understood. Here we present a method to
calculate such properties on large scale systems, like biologically relevant
molecules in aqueous solution. Our approach is based on many body perturbation
theory combined with quantum-mechanics/molecular-mechanics (QM/MM) approach. We
show here how to include quasi-particle and excitonic effects for the
calculation of optical absorption spectra in a QM/MM scheme. We apply this
scheme, together with the well established TDDFT approach, to indole in water
solution. Our calculations show that the solvent induces a redshift in the main
spectral peak of indole, in quantitative agreement with the experiments and
point to the importance of performing averages over molecular dynamics
configurations for calculating optical properties.
