Dichotomous Disorder versus Excitonic Splitting of the B800 Band of Allochromatium vinosum

Computational elucidations on the role of vibrations in energy transfer processes of photosynthetic complexes

Coupling between pigment excitations and nuclear movements in photosynthetic complexes is known to modulate the excitation energy transfer (EET) efficiencies. Toward providing microscopic information, researchers often apply simulation techniques and investigate how vibrations are involved in EET processes. Here, reports on such roles of nuclear movements are discussed from a theory perspective. While vibrations naturally present random thermal fluctuations that can affect energy transferring characteristics, they can also be intertwined with exciton structures and create more specific non-adiabatic energy transfer pathways. For reliable simulations, a bath model that accurately mimics a given molecular system is required. Methods for obtaining such a model in combination with quantum chemical electronic structure calculations and molecular dynamics trajectory simulations are discussed. Various quantum dynamics simulation tools that can handle pigment-to-pigment energy transfers together with their vibrational characters are also touched on. Behaviors of molecular vibrations often deviate from ideality, especially when all-atom details are included, which practically forces us to treat them classically. We conclude this perspective by considering some recent reports that suggest that classical descriptions of bath effects with all-atom details may still produce valuable information for analyzing sophisticated contributions by vibrations to EET processes.

Efficiently Transplanting Potential Energy Interpolation Database between Two Systems: Bacteriochlorophyll Case with FMO and LH2 Complexes

Generating a reliable potential energy surface (PES) is an important issue for studying the dynamics of any system with computational simulations. Interpolation mechanics/molecular mechanics (IM/MM) based on a PES interpolation scheme is a useful tool in that regard as it provides an accuracy of a quantum chemistry (QC) level while maintaining its computational cost comparable to conventional MM force fields. Despite this benefit, constructing the database for interpolation itself is still challenging and time-consuming. Here, we present a method with which we can construct the IM database of one system based on a preexisting data set for another related system. We adopt the case of constructing bacteriochlorophyll PESs for the light-harvesting 2 (LH2) complex by utilizing already available IM database for the BChls from the Fenna-Matthews-Olson (FMO) complex. In this method, the IM database from FMO is first transplanted to LH2 by considering BChl displacement vectors that take into account the geometry differences induced by the protein scaffolds. From this transplanted primitive database entries, a relatively small number of effective ones are selected by a survival process based on a genetic algorithm such that the IM energies evaluated at geometries in a conveniently collected prediction set can closely match with the reference QC energies. The selection process is expedited by using two different levels of basis sets for the QC calculations. To demonstrate the utility of the PES thus constructed, we carry out 1 ns of IM/MM dynamics simulations with the finally optimized BChl database for LH2. Indeed, the energy profiles of the snapshots are found to be closely matching with the reference QC calculation data, with only ∼0.07 eV of errors in the ground- and excited-state energies and ∼0.008 eV of errors in the transition energies. We also show that properly selecting data points is actually quite important for generating an IM PES toward performing molecular dynamics simulations.

Simulating Fluorescence-Detected Two-Dimensional Electronic Spectroscopy of Multichromophoric Systems

We present a theory for modeling fluorescence-detected two-dimensional electronic spectroscopy of multichromophoric systems. The theory is tested by comparison of the predicted spectra of the light-harvesting complex LH2 with experimental data. A qualitative explanation of the strong cross-peaks as compared to conventional two-dimensional electronic spectra is given. The strong cross-peaks are attributed to the clean ground-state signal that is revealed when the annihilation of exciton pairs created on the same LH2 complex cancels oppositely signed signals from the doubly excited state. This annihilation process occurs much faster than the nonradiative relaxation. Furthermore, the line shape difference is attributed to slow dynamics, exciton delocalization within the bands, and intraband exciton-exciton annihilation. This is in line with existing theories presented for model systems. We further propose the use of time-resolved fluorescence-detected two-dimensional spectroscopy to study state-resolved exciton-exciton annihilation.