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

Abstract

The dynamics of pigment-pigment and pigment-protein interactions in light-harvesting complexes is studied with a novel approach that combines molecular dynamics simulations with quantum chemistry calculations and a polaron model analysis. The molecular dynamics simulation of lightharvesting complexes was performed on an 87,055 atom system comprised of an LH-II complex of Rhodospirillum molischianum embedded in a lipid bilayer and surrounded with appropriate water layers. The simulation provided information about the extent and timescales of geometrical deformations of pigment and protein residues at physiological temperatures, revealing also a pathway of a water molecule into the B800 binding site, as well as increased dimerization within the B850 BChl ring, as compared to the dimerization found for the crystal structure. For each of the 16 B850 BChls we performed 400 ab initio quantum chemistry calculations on geometries that emerged from the molecular dynamical simulations, determining the fluctuations of pigment excitation energies as a function of time. From the results of these calculations we construct a time-dependent Hamiltonian of the B850 exciton system from which we determine within linear response theory the absorption spectrum. Finally, a polaron model is introduced to describe both the excitonic and coupled phonon degrees of freedom by quantum mechanics. The exciton-phonon coupling that enters into the polaron model, and the corresponding phonon spectral function are derived from the molecular dynamics and quantum chemistry simulations. The model predicts that excitons in the B850 bacteriochlorophyll ring are delocalized over five pigments at room temperature. Also, the polaron model permits the calculation of the absorption spectrum of the B850 excitons from the sole knowledge of the autocorrelation function of the excitation energies of individual BChls, which is readily available from the combined molecular dynamics and quantum chemistry simulations. The obtained result is found to be in good agreement with the experimentally measured absorption spectrum. PACS number(s): 87.15. Aa, 87.15.Mi, 87.16.Ac

Theoretical characterization of excitation energy transfer in chlorosome light-harvesting antennae from green sulfur bacteria

“…We use MD simulations to generate R(t) and TDDFT excited-state calculations to obtain ǫ(R), which is consistent with the models proposed previously [35][36][37][38][39] Thus, in contrast to many studies based on a quantum master equation, this approach can describe the system-bath coupling in complete atomistic detail.…”

“…However, for natural light-harvesting structures an intermediate strength interaction between the electronic excitations and the high-frequency BChl vibrational modes of the range of 1600 − 2000 cm −1 has been suggested [79][80][81]. In order to account for this effect polaron models have been proposed [35,82,83]. In general, a strong coupling between the exciton and vibrations renormalizes the exciton energy and also reduces its mobility.…”

“…A similar approach has been previously applied to small lightharvesting systems such as the FMO complex [37][38][39] and light-harvesting complexes II (LHII) of purple bacteria [35,36]. For a large number of BChls present in the chlorosome, it is computationally unfeasible to calculate site energies of all pigment molecules along an MD trajectory.…”

“…The absorption and CD spectra were calculated from the exciton propagation by using the following expressions [35,39]:…”

Coherent Dynamics of Mixed Frenkel and Charge-Transfer Excitons in Dinaphtho[2,3-b:2′3′-f]thieno[3,2-b]-thiophene Thin Films: The Importance of Hole Delocalization

“…Both of them are calculated from a spectral density j n (ω) for the nth diabatic state [62,65]. The spectral densities [66,67] have been obtained by combing molecular dynamics simulations for the DNTT crystal with excited-state calculations using time-dependent density functional theory at B3LYP/6-31G* level. The details for calculating spectral densities are presented in the Appendix B.…”