TIME SERIES ANALYSIS OF MOLECULAR DYNAMICS TRAJECTORIES

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The photosynthetic unit (PSU) is located in the intracytoplasmic membrane of purple bacteria and consists of two types of pigment-protein complexes: the photosynthetic reaction center (RC) and light-harvesting complexes (LHs). The LHs capture sunlight and transfer the excitation energy to the RC where it initiates a charge separation process. We have constructed an atomic model of the entire bacterial PSU* consisting of an LH-I-RC complex surrounded by an array of LH-Is through a combination of x-ray crystallography, electron microscopy and molecular modeling [66-70]. This accomplishment opens the door to both spectroscopic and theoretical studies of the pathways of excitation transfer and of the underlying transfer mechanisms in the bacterial photosynthetic membrane. The excitation transfer pathway can be divided into two steps: intramolecular excitation transfer between pigments within a pigment-protein complex, and intermolecular excitation transfer between different pigment-protein complexes. Within a light-harvesting complex, photons can be absorbed either by carotenoids that instantly transfer their excitation energy to bacteriochlorophylls (BChls), or by BChls themselves. We calculated the couplings between various electronic excitations of carotenoids and BChls through the Pariser-Parr-Pople self-consistent field/CI description of their electronic states, thereby identifying the most probable pathway and dominant mechanism of the excitation transfer between carotenoids and BChls [71]. Excitation transfer between different light-harvesting complexes occurs through the interactions of rings of BChls. The ring-shaped BChl aggregates in LHs were found by quantum chemical and effective Hamiltonian calculations to display coherent excited state properties that are optimal for excitation transfer [70, 72, 73]. On the basis of the effective Hamiltonian description we have determined the excitation transfer rates LH-II . LH-I . RC for the PSU of Rb. sphaeroides [68, 70, 72], which are in good agreement with spectroscopic measurements. Our quantum calculations have also shed light on the role of the accessory BChls as mediators of excitation transfer from LH-I BChls to the RC special pair.