Quantum dynamics of electronic excitations in biomolecular chromophores:   role of the protein environment and solvent
  We consider continuum dielectric models as minimal models to understand the effect of a surrounding globular protein and solvent on the quantum dynamics of electronic excitations in a biological chromophore. We derive expressions for the frequency dependent spectral density which describes the coupling of the electronic levels in the chromophore to its environment. The magnitude and frequency dependence of the spectral density determines whether or not the quantum dynamics is coherent or incoherent, and thus whether on not one can observe quantum interference effects such as Rabi oscillations. We find the contributions to the spectral density from each component of the chromophore environment: the bulk solvent, protein, and water bound to the protein. The relative importance of each component to the quantum dynamics of the chromophore is determined by the dynamics' time scale. Our results provide a natural explanation and model for the different time scales observed in the spectral density extracted from the solvation dynamics probed by ultra-fast laser spectroscopy techniques such as the dynamic Stokes shift and three pulse photon echo spectroscopy. Our results are used to define under what conditions the dynamics of the excited chromophore is dominated by the surrounding protein and when it is dominated by dielectric fluctuations in the solvent. We show that even when the chromophore is shielded from the solvent by the protein ultra-fast solvation can be dominated by the solvent. We suggest that the ultra-fast solvation recently seen in some biological chromophores should not necessarily be assigned to ultra-fast protein dynamics. Spectral densities estimated from our continuum models and extracted from experiment suggest that most quantum dynamics of electronic excitations is incoherent. 
Joel Gilmore and Ross H. McKenzie