Effect of Chromophore Potential Model on the Description of Exciton–Phonon Interactions

Abstract

System-bath interactions in nonadiabatic simulations are often depicted by first performing molecular dynamics calculations and then by evaluating excitation energies at the trajectory snapshots. Usually, molecular mechanics models and quantum chemical calculations are used in a mixed manner toward a trade-off between efficiency and accuracy. Here we investigate how this mixing scheme affects that depiction by using various potential energy surfaces (PESs) of coumarin-153 chromophore, with the help of interpolated PESs that can closely match the accuracies of quantum chemical calculations. We find that although spectral densities are computed only with second stage data the PES characteristics during the first sampling stage can still prevail in the densities, with limited influences on related reorganization energies. Our results suggest that using the mixed scheme can be acceptable when dynamics is mainly governed by the integrated effect of all phonon modes, but care must be taken for understanding detailed effects from individual modes.

Successes & challenges in the atomistic modeling of light-harvesting and its photoregulation

“…While protein force fields are rather accurate in describing the structural fluctuations of the peptide environment, they are not optimized to faithfully reproduce the internal coordinates of the pigments. As a result, the energy fluctuations estimated on such MM potentials can be exaggerated, leading to a systematic overestimation of the SD intensities [89], or to an inaccurate distribution of SD intensities along the frequency spectrum [85,90,91]. It has been shown that the MD-based approach is very sensitive to the parameters of the force field, whereas the details of the QM method for excited-state calculations are less important [87,36].…”

“…Several groups have sought to overcome the force-field issue and to refine the MD sampling of nuclear fluctuations, for example, by computing the trajectories using multiscale QM/MM molecular dynamics [93,94,95,96], which combines the ability of MD to account for the environment with the accuracy of the quantum chemical potentials. Another way to refine the MD description, keeping the computational cost adequately low, is by developing ad-hoc force-fields for the pigments, specifically aimed at reproducing excitation properties, [72,73] or by using potentials interpolated from quantum chemical data [91,97].…”

Electronic energy transfer in biomacromolecules

“…This approach is not always feasible, given the dimensions of biological chromophores and the long time window requested by the sampling (vide supra). A compromise solution can be the development of ad‐hoc force fields for the chromophores, specifically targeted to the description of excitation properties, possibly employing PESs directly interpolated from quantum chemical data …”

“…A compromise solution can be the development of ad-hoc force fields for the chromophores, specifically targeted to the description of excitation properties, 122,123 possibly employing PESs directly interpolated from quantum chemical data. 117,124 An alternative approach to SD calculations is the normal-mode analysis proposed by Lee et al 114 and applied to FMO, phycobiliprotein complexes, 125 and the LH2 system of purple bacteria. 126 Such an approach is based on the analytical expression of e C 00 ω ð Þ when the ground and excited state PESs are described by the same harmonic potential, but with shifted equilibrium position:…”

Interpolation for molecular dynamics simulations: from ions in gas phase to proteins in solution

“…With the many trajectories, of course, statistically meaningful analyses could be performed. [26] For example, the electrostatic interactions between the twisting chromophore and neighboring protein residues were analyzed The dominant twisting pathway of the blue fluorescent protein chromophore in its emissive state. The potential along this twisting pathway is highly anharmonic and interpolation performed quite well in describing this surface characteristic.…”