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The dynamics of pigment-pigment and pigment-protein interactions inlight-harvesting complexes is studied with a novel approach which combinesmolecular dynamics (MD) simulations with quantum chemistry (QC) calculations.The MD simulations of an LH-II complex, solvated and embedded in a lipidbilayer at physiological conditions (with total system size of 87,055 atoms)revealed a pathway of a water molecule into the B800 binding site, as well asincreased dimerization within the B850 BChl ring, as compared to thedimerization found for the crystal structure. The fluctuations of pigment (B850BChl) excitation energies, as a function of time, were determined via ab initioQC calculations based on the geometries that emerged from the MD simulations.  From the results of these calculations we constructed a time-dependentHamiltonian of the B850 exciton system from which we determined the linearabsorption spectrum. Finally, a polaron model is introduced to describe quantummechanically both the excitonic and vibrational (phonon) degrees of freedom.The exciton-phonon coupling that enters into the polaron model, and thecorresponding phonon spectral function are derived from the MD/QC simulations.It is demonstrated that, in the framework of the polaron model, the absorptionspectrum of the B850 excitons can be calculated from the autocorrelationfunction of the excitation energies of individual BChls, which is readilyavailable from the combined MD/QC simulations. The obtained result is in goodagreement with the experimentally measured absorption spectrum.

Excitons in a photosynthetic light-harvesting system: A combined molecular dynamics, quantum chemistry, and polaron model study