Environmental effects on the dynamics in the light-harvesting complexes LH2 and LH3 based on molecular simulations

Mallus, Maria Ilaria; Shakya, Yashoj; Prajapati, Jigneshkumar Dahyabhai; Kleinekathöfer, Ulrich

doi:10.1016/j.chemphys.2018.08.013

“…In most studies, two-dimensional electronic spectra were calculated by using experimental observables to obtain several modeling parameters as e.g., done for LH2 (van der Vegte et al 2015) and Fenna-Matthews-Olson (FMO) complex (Olbrich et al 2011a). Also, the dynamics in the excited states were simulated e.g., for LH2 (van der Vegte et al 2015), LH3 (Mallus et al 2018), and the bacterial reaction center (Vassiliev and Bruce 2006;Zhang et al 2014;Hsieh et al 2019) based on snapshots extracted from MD simulations. From a theoretical point of view, including the protein environment in calculations of electronic states is challenging.…”

Section: Including Electronic Degrees Of Freedom Using Quantum Mechanmentioning

confidence: 99%

Molecular dynamics simulations in photosynthesis

Liguori¹,

Croce²,

Marrink

³

et al. 2020

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Photosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments, lipids, and cofactors that takes place on a large spatio-temporal scale. Molecular dynamics (MD) simulations provide a powerful toolkit to investigate dynamical processes in (bio)molecular ensembles from the (sub)picosecond to the (sub)millisecond regime and from the Å to hundreds of nm length scale. Therefore, MD is well suited to address a variety of questions arising in the field of photosynthesis research. In this review, we provide an introduction to the basic concepts of MD simulations, at atomistic and coarse-grained level of resolution. Furthermore, we discuss applications of MD simulations to model photosynthetic systems of different sizes and complexity and their connection to experimental observables. Finally, we provide a brief glance on which methods provide opportunities to capture phenomena beyond the applicability of classical MD.Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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“…[51][52][53] Classical correlation functions are generally much easier to compute than their quantum counterparts and can, for example, be constructed by calculating vertical excitation energies along an MD trajectory. [23][24][25][26][27]46,[48][49][50] Although the choice of QCF is not unique, 49,52 a commonly used approximation for the energy-gap autocorrelation function C {2} δU (t) is the harmonic QCF, where…”

Section: Quantum Correction Factors (Qcfs)mentioning

confidence: 99%

Nonlinear Spectroscopy in the Condensed Phase: The Role of Duschinsky Rotations and Third Order Cumulant Contributions

Zuehlsdorff

¹

,

Hong²,

Shi³

et al. 2020

Preprint

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First-principles modeling of nonlinear optical spectra in the condensed phase is highly challenging because both environment and vibronic interactions can play a large role in determining spectral shapes and excited state dynamics. Here, we compute two dimensional electronic spectroscopy (2DES) signals based on a cumulant expansion of the energy gap fluctuation operator, with a specific focus on analyzing mode mixing effects introduced by the Duschinsky rotation and the role of the third order term in the cumulant expansion for both model and realistic condensed phase systems. We show that for a harmonic model system, the third order cumulant correction captures effects introduced by a mismatch in curvatures of ground and excited state potential energy surfaces, as well as effects of mode mixing. We also demonstrate that 2DES signals can be accurately reconstructed from purely classical correlation functions using quantum correction factors. We then compute nonlinear optical spectra for the Nile red and Methylene blue chromophores in solution, assessing the third order cumulant contribution for realistic systems. We show that the third order cumulant correction is strongly dependent on the treatment of the solvent environment, revealing the interplay between environmental polarization and the electronic-vibrational coupling.

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“…[20][21][22] However, in many situations, such as in energy transa) Electronic mail: tzuehlsdorff@ucmerced.edu b) Electronic mail: lshi4@ucmerced.edu c) Electronic mail: cisborn@ucmerced.edu fer processes in biological systems, the complex condensed phase environment couples to the excited states of the system to facilitate efficient relaxation. [23][24][25][26][27] Furthermore, in linear spectroscopy, such as in computing absorption spectra in solvated dyes, a fully atomistic representation of the environment is often necessary to correctly describe specific interactions between the chromophore and its surroundings. [28][29][30][31][32][33][34][35][36][37] To capture polarization effects of the electronic excited state, it is often necessary to treat significant parts of the environment quantum mechanically, 28,31,34,35,[38][39][40][41][42] making efficient electronic structure approaches necessary.…”

Section: Introductionmentioning

confidence: 99%

“…Truncation at second order maps the system dynamics onto a fictitious bath of linearly coupled harmonic oscillators, for which linear and nonlinear spectroscopy signals can be computed analytically. 47 The electronic-vibrational coupling in the system is then fully defined by the autocorrelation function of energy gap fluctuations, which can be efficiently obtained in complex condensed phase systems by computing vertical excitation energies along molecular dynamics (MD) trajectories [23][24][25][26][27]46,[48][49][50] and using quantum correction factors (QCF) 49,[51][52][53] to account for nuclear quantum effects.…”

Section: Introductionmentioning

confidence: 99%

Nonlinear Spectroscopy in the Condensed Phase: The Role of Duschinsky Rotations and Third Order Cumulant Contributions

Zuehlsdorff

¹

,

Hong²,

Shi³

et al. 2020

Preprint

0

View full text Add to dashboard Cite

First-principles modeling of nonlinear optical spectra in the condensed phase is highly challenging because both environment and vibronic interactions can play a large role in determining spectral shapes and excited state dynamics. Here, we compute two dimensional electronic spectroscopy (2DES) signals based on a cumulant expansion of the energy gap fluctuation operator, with a specific focus on analyzing mode mixing effects introduced by the Duschinsky rotation and the role of the third order term in the cumulant expansion for both model and realistic condensed phase systems. We show that for a harmonic model system, the third order cumulant correction captures effects introduced by a mismatch in curvatures of ground and excited state potential energy surfaces, as well as effects of mode mixing. We also demonstrate that 2DES signals can be accurately reconstructed from purely classical correlation functions using quantum correction factors. We then compute nonlinear optical spectra for the Nile red and Methylene blue chromophores in solution, assessing the third order cumulant contribution for realistic systems. We show that the third order cumulant correction is strongly dependent on the treatment of the solvent environment, revealing the interplay between environmental polarization and the electronic-vibrational coupling.

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Environmental effects on the dynamics in the light-harvesting complexes LH2 and LH3 based on molecular simulations

Cited by 23 publications

References 91 publications

Molecular dynamics simulations in photosynthesis

Molecular dynamics simulations in photosynthesis

Nonlinear Spectroscopy in the Condensed Phase: The Role of Duschinsky Rotations and Third Order Cumulant Contributions

Nonlinear Spectroscopy in the Condensed Phase: The Role of Duschinsky Rotations and Third Order Cumulant Contributions

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