Recent progress in atomistic modeling of light-harvesting complexes: a mini review

Abstract

In this mini review, we focus on recent advances in the atomistic modeling of biological light-harvesting (LH) complexes. Because of their size and sophisticated electronic structures, multiscale methods are required to investigate the dynamical and spectroscopic properties of such complexes. The excitation energies, in this context also known as site energies, excitonic couplings, and spectral densities are key quantities which usually need to be extracted to be able to determine the exciton dynamics and spectroscopic properties. The recently developed multiscale approach based on the numerically efficient density functional tight-binding framework followed by excited state calculations has been shown to be superior to the scheme based on pure classical molecular dynamics simulations. The enhanced approach, which improves the description of the internal vibrational dynamics of the pigment molecules, yields spectral densities in good agreement with the experimental counterparts for various bacterial and plant LH systems. Here, we provide a brief overview of those results and described the theoretical foundation of the multiscale protocol.

Machine Learning Exciton Hamiltonians in Light-Harvesting Complexes

“…A very effective strategy to get through these difficulties is to use classical molecular dynamics (MD) simulations to generate conformational ensembles of LHCs at the desired external conditions, in combination with hybrid quantum mechanics (QM)-classical descriptions of the embedded aggregate. In particular, methods coupling atomistic molecular mechanics (MM) to QM descriptions (QM/MM) have been shown to be successful in describing LHCs. ,− Within QM/MM, the environment interacts with the QM subsystem through electrostatic interactions of a classical nature. In its standard formulation, known as electrostatic embedding QM/MM (EE-QM/MM), each MM atom is assigned a fixed charge (i.e., the charge it has in a classical MM force-field (FF)), and the corresponding set of MM point charges interacts with the electrostatic potential of the QM part.…”

Impact of Spatial Inhomogeneity on Excitation Energy Transport in the Fenna–Matthews–Olson Complex

“…Thus, understanding the mechanisms that allow for the efficient transport of molecular excitation from the point of creation to the reaction center is of fundamental importance. A lot of work has been done in simulating the excitation energy transfer (EET) and characterizing the vibronic couplings. − Early experiments , seemed to provide evidence of quantum beating. Theoretical studies were performed around the same time to shed light on the origins of these long-lived electronic oscillations. − It was hypothesized that this oscillatory dynamics could be the reason behind the efficiency of EET in biosystems.…”

Understanding Primary Charge Separation in the Heliobacterial Reaction Center

“…Snapshots from the resulting trajectories can be used as an input to subsequent TDDFT calculations. In this context, classical force fields may be problematic, e.g., due to the so-called “geometry mismatch problem”. ,− One way to avoid such issues is to perform the BOMD simulations on the basis of DFT. − There is, however, a computational price to pay for this gain in accuracy.…”

“…There are various ways of adapting these methods to larger systems by introducing further levels of approximation. ,,,− Quantum-chemical calculations based on model Hamiltonians efficiently cover the electronic interaction of multiple chromophores. In multiscale approaches the quantum mechanical treatment of a small subsystem (typically a few chromophores) is coupled to the semiclassical, molecular mechanics description of the remaining protein complex, where the interaction with the environment atoms is approximated by empirical force fields.…”