On the relation of protein dynamics and exciton relaxation in pigment–protein complexes: An estimation of the spectral density and a theory for the calculation of optical spectra

A theory for calculating time– and frequency–domain optical spectra of pigment–protein complexes is presented using a density matrix approach. Non-Markovian effects in the exciton–vibrational coupling are included. A correlation function is deduced from the simulation of 1.6 K fluorescence line narrowing spectra of a monomer pigment–protein complex (B777), and then used to calculate fluorescence line narrowing spectra of a dimer complex (B820). A vibrational sideband of an excitonic transition is obtained, a distinct non-Markovian feature, and agrees well with experiment on B820 complexes. The theory and the above correlation function are used elsewhere to make predictions and compare with data on time–domain pump–probe spectra and frequency–domain linear absorption, circular dichroism and fluorescence spectra of Photosystem II reaction centers.