Spectral densities and absorption spectra of the core antenna complex CP43 from photosystem II

Abstract

Besides absorbing light, the core antenna complex CP43 of photosystem II is of great importance in transferring excitation energy from the antenna complexes to the reaction center. Excitation energies, spectral densities and linear absorption spectra of the complex have been evaluated by a multiscale approach. In this scheme, quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations are performed employing the parameterized density functional tight binding (DFTB) while the time-dependent long-range-corrected DFTB scheme is applied for the excited state calculations. The obtained average spectral density of the CP43 complex shows a very good agreement with experimental results. Moreover, the excitonic Hamiltonian of the system alongwith the computed site-dependent spectral densities were used to determine the linear absorption. While a Redfield-like approximation has severe shortcomings in dealing with the CP43 complex due to quasi-degenerate states, the non-Markovian full second-order cumulant expansion formalism is able to overcome the drawbacks. Linear absorption spectra were obtained which show a good agreement with the experimental counterparts at different temperatures. This study once more emphasizes that by combining diverse techniques from the areasof molecular dynamics simulations, quantum chemistry and open quantum systems it is possible to obtain first-principle results for photosynthetic complexes which are in accord with experimental findings.

Manifestation of Hydrogen Bonding and Exciton Delocalization on the Absorption and Two-Dimensional Electronic Spectra of Chlorosomes

“…The lower intensity on the blue side of the simulated spectrum may originate from the Q x -band and tails of the Soret band at higher frequencies, which are not accounted for in the present model. Additional contributions to the spectral intensity and broadening could arise due to the coupling of the excitonic states to intramolecular vibrations 55 − 57 or to the charge transfer states. 58 Since these effects are neglected in the current model, they could be a cause for the discrepancy between the simulated and the experimental spectra in the high energy region.…”

Machine Learning Exciton Hamiltonians in Light-Harvesting Complexes

“…Another interesting application to be explored in the future is the ML determination of spectral densities from QM/MM trajectories. 15,64 This approach provides a fast and accurate estimation of excitonic Hamiltonians for an arbitrary number of MD structures. While in this work we focused on Chls a and b in light-harvesting complexes, the remarkable performance on several tests makes our model a promising tool for accelerating calculations also for other protein-embedded chromophores.…”

“…This makes it possible to analyze known mutants as well as providing a rational basis with which mutants can be devised in silico , i.e., by inserting mutations and then rapidly assessing their impact on the exciton properties of the bound pigments. Another interesting application to be explored in the future is the ML determination of spectral densities from QM/MM trajectories. , …”

“…For this reason, it has been classified as a dispersion-like or resonance contribution. 41 Within an induced-dipole formulation of polarizable embedding, this contribution can be written as 16,40 MMPol tr (15) where m runs over the polarizable MM sites, and μ m MMPol (ρ tr ) is the induced dipole on MM atom m due to the transition density ρ tr . As we have shown in our previous work, 30 we can approximate the transition density ρ tr as a set of transition charges {q tr } and estimate the polarization contribution as…”

“…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.…”