Influence of Site-Dependent Pigment–Protein Interactions on Excitation Energy Transfer in Photosynthetic Light Harvesting

Abstract

A site-dependent spectral density system-bath model of the Fenna-Matthews-Olsen (FMO) pigment-protein complex is developed using results from ground-state molecular mechanics simulations together with a partial charge difference model for how the long-range contributions to the chromophore excitation energies fluctuate with environmental configuration. A discussion of how best to consistently process the chromophore excitation energy fluctuation correlation functions calculated in these classical simulations to obtain reliable site-dependent spectral densities is presented. The calculations reveal that chromophores that are close to the protein-water interface can experience strongly dissipative environmental interactions characterized by reorganization energies that can be as much as 2-3 times those of chromophores that are buried deep in the hydrophobic protein scaffolding. Using a linearized density matrix quantum propagation method, we demonstrate that the inhomogeneous system-bath model obtained from our site-dependent spectral density calculations gives results consistent with experimental dissipation and dephasing rates. Moreover, we show that this model can simultaneously enhance the energy-transfer rate and extend the decoherence time. Finally, we explore the influence of initially exciting different chromophores and mutating local environments on energy transfer through the network. These studies suggest that different pathways, selected by varying initial photoexcitation, can exhibit significantly different relaxation times depending on whether the energy-transfer path involves chromophores at the protein-solvent interface or if all chromophores in the pathway are buried in the protein.

Photosynthetic pigment-protein complexes as highly connected networks: implications for robust energy transport

“…Furthermore, we also note that the role of localized baths, where a different set of bath modes is employed for each chromophore site, has also been investigated recently by Coker and co-workers [43], with initial results from such Hamiltonians indicating that site-dependent vibrational modes can have a significant impact on the EET dynamics. Finally, while the form of the harmonic bath potential is perhaps oversimplified, we note that this approximation is essential in the derivation and implementation of several computational approaches for modelling EET dynamics (see below).…”

Effect of Chromophore Potential Model on the Description of Exciton–Phonon Interactions

“…It was also shown that the temperature-independent nature of the spectral density can be properly reproduced with this expression. 29,30 As previously described, we employed a series of different potential surfaces for MD simulations: PES-i g , PES-1, PES-2, and PES-3. During the second stage of the gap energy calculations, the same set of surfaces can still be adopted.…”

Optimization of energy transport in the Fenna-Matthews-Olson complex via site-varying pigment-protein interactions

“…In fact, recent computational chemistry calculations have shown, for instance in the case of the Fenna-Matthews-Olson (FMO) complex of the green sulfur bacteria, that site variations of spectral density can be significant [1][2][3] . Obviously, in biological systems, traits showing some degree of heterogeneity are expected, and in many cases, it is simply random.…”