Study of Electronic Structures and Pigment–Protein Interactions in the Reaction Center of Thermochromatium tepidum with a Dynamic Environment

Abstract

On the basis of the recently reported X-ray crystal structure of light-harvesting complex 1-reaction center (LH1-RC) complex from Thermochromatium tepidum, we investigate electronic structures and pigment-protein interactions in the RC complex from a theoretical perspective. Hybrid quantum-mechanics/molecular-mechanics methods in combination with molecular dynamics simulations are employed to study environmental effects on excitation energies of RC cofactors with the consideration of a dynamic environment. The environmental effects are found to be essential for electronic structure determination. The special pair, a dimer of bacteriochlorophylls which serves as the primary electron donor in the bacterial RC, is our focus in this work. The first excited state of the special pair is found to have the lowest excitation energy of all molecules in the system, making it the most likely populated site after the excitation transfer. The transition charges from electrostatic potentials and the point dipole approximation have been applied to calculate the electronic coupling between individual pigments and that between the special pair and other pigments. Stronger electronic coupling is obtained between the P molecule and the L branch pigments than that between the P and the pigments in the M branch. Quantum chemical calculations reveal charge transfer characteristics of the first excited state of the special pair. It follows that charge separation takes place along the L branch in the RC. Spectral densities for all the cofactors are also calculated.

Fully Quantum Modeling of Exciton Diffusion in Mesoscale Light Harvesting Systems

“…As shown in Hamiltonian (4), explicit values of ω r q and g r q for individual bath modes are required in a proper description of the coupled exciton-phonon dynamics. Typically, these parameters are obtained by discretizing the bath spectral densities, which can be established from QM/MM calculations [53,71], or from fitting the fluorescence line-narrowing spectra [72,73] of the target system. It has been found that different methods can produce totally different spectral densities.…”

“…It has been found that different methods can produce totally different spectral densities. For instance, in spectral densities calculated by MD simulations of some photosynthetic systems, several high frequency (∼1670 cm −1 ) modes are found to couple strongly to the electronic transitions [53,71]. On the other hand, the spectral density obtained by fitting the fluorescence line-narrowing spectra of the B777 complex includes some low frequency modes strongly coupled to the excitons [73].…”

“…The excitonic coupling strength between the BChla α (BChla β) molecules in two neighboring dimers is -52 cm −1 (-31 cm −1 ) [33]. The coupling strengths between the other pairs of pigments are estimated with the transition charges from the electrostatic potentials method [71,93,94]. Shown in Table A1 is the exciton Hamiltonian of a B850 ring used in our simulations.…”

Gaussian Process Regression for Absorption Spectra Analysis of Molecular Dimers

“…Using these transition charges and the molecular structures of the dimers, as given in Ref. [21], we then evaluated the interaction V using the Transition Charges from Electrostatic Potentials (TrEsp) method, which has been widely applied to accurately evaluate inter-molecular couplings [35][36][37][38] 1 . The angle α is also estimated directly from the given dimer structures (for details see section IV of the Supplementary Material.…”

Analysis of Photosynthetic Systems and Their Applications with Mathematical and Computational Models

“…The multiple excited states observed in the FMO complex are also due to the presence of different BChls in different local environments of the protein. While still debated, the possibility of existence of the long-lived quantum coherence also motivates to intensify the computational studies in different directions including the study of the excitation properties using different types of computational techniques [4,11,13,20,71,94,[132][133][134][135][136][137][138][139][140][141][142].…”