Theoretical Characterization of the Spectral Density of the Water-Soluble Chlorophyll-Binding Protein from Combined Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulations

Rosnik, Andreana M.; Curutchet, Carles

doi:10.1021/acs.jctc.5b00891

Cited by 64 publications

(89 citation statements)

References 64 publications

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“…The low frequency part (or backgound) is the combination [63] of three log-normal functions with with S 1 = 0.39, S 2 = 0.23, S 3 = 0.23, σ 1 = 0.4, σ 2 = 0.25, σ 3 = 0.2, ω 1 = 26cm −1 , ω 2 = 51cm −1 , ω 3 = 85cm −1 . The three Lorentzian peaks have all the same width γ k = γ = 5cm −1 , and are centered in Ω 1 = 181cm −1 , Ω 2 = 221cm −1 , Ω 3 = 240cm −1 and have weights g 1 = 0.0173, g 2 = 0.0246, g 3 = 0.0182.…”

Section: E Wscp Spectral Densitymentioning

confidence: 99%

Efficient Simulation of Finite-Temperature Open Quantum Systems

et al. 2019

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Chain-mapping techniques in combination with the time-dependent density matrix renormalization group are a powerful tool for the simulation of open-system quantum dynamics. For finite-temperature environments, however, this approach suffers from an unfavorable algorithmic scaling with increasing temperature. We prove that the system dynamics under thermal environments can be non-perturbatively described by temperature-dependent system-environmental couplings with the initial environment state being in its pure vacuum state, instead of a mixed thermal state. As a consequence, as long as the initial system state is pure, the global system-environment state remains pure at all times. The resulting speedup and relaxed memory requirements of this approach enable the efficient simulation of open quantum systems interacting with highly structured environments in any temperature range, with applications extending from quantum thermodynamics to quantum effects in mesoscopic systems.

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Section: E Wscp Spectral Densitymentioning

confidence: 99%

Efficient Simulation of Finite-Temperature Open Quantum Systems

et al. 2019

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“…It was argued that a mismatch in equilibrium position between the FF and QM PESs leads to exaggeratedly large (or small) fluctuations in the excitation energies, inevitably leading to unphysical SDs. [46][47][48][49][50] Likewise, a mismatch in the frequencies and corresponding normal modes leads to wrong positions for the SD peaks, and to a redistribution of the peak intensities. 51 Here we review an ensemble-based approach that aims to solve this issue, using as test case the Thiazole Orange (TO) intercalated in a short DNA double helix previously investigated by some of the authors.…”

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confidence: 99%

Modeling the absorption lineshape of embedded systems from molecular dynamics: A tutorial review

Loco

Cupellini

2018

Int J of Quantum Chemistry

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In this tutorial review, we focus on a multiscale method to compute the electronic absorption line shape of molecular dyes embedded in a biological environment. To treat the coupling of the electronic excitations with the nuclear degrees of freedom of the system, we use the spectral density (SD) of the exciton-phonon coupling computed from a Born-Oppenheimer molecular dynamics, which takes into account the effect of the biological environment on the dye's nuclear and electronic degrees of freedom. The theoretical basis of the approach is given, as well as a comprehensive description of the computational protocol for the extraction of the energy gap autocorrelation function evaluating the electronic excitation along the classical trajectory. Furthermore a benchmark application from a recently published study is presented as an example of how the derived SD can be used in computational spectroscopy to accurately simulate the absorption lineshape, including both vibronic and temperature effects. K E Y W O R D S absorption lineshape, spectral density, QM/MM molecular dynamics 1 | INTRODUCTIONThe accurate modeling of electronic absorption spectra is a fundamental tool to understand and complement experimental data. Experimental and computational techniques are widely used to identify molecular species and to predict environment effects on the molecular response and photochemistry.From a computational point of view, many different approaches have been exploited in theoretical spectroscopy. [1][2][3][4] The most basic one applied to the simulation of absorption spectra, is based on the computation of the excitation energies of a dye in the ground-state equilibrium geometry, including, if necessary, the solvent effects with an implicit model 5-8 or within an atomistic approach. 9-16 These vertical excitation energies are then compared to the maxima of the corresponding experimental absorption bands. This approach is commonly used, even to benchmark the level of theory for excited-state simulations against experiments. 17 However, comparison of vertical excitation energies can easily become inadequate when accurate estimations of the absorption spectrum are needed. 1 The coupling of electronic transitions to nuclear degrees of freedom (DOFs), for example, generates a characteristic vibronic progression, and can result in an asymmetrical lineshape even when the vibronic structure is hidden in homogeneous and inhomogeneous broadening. 18 Other factors, such as the configurations sampled by the chromophore and the finite lifetime of the excited state, contribute to the spectral shape.For molecules in condensed phase, peaks positions and intensities in the absorption spectra are also affected by the interactions with the inhomogeneous environment, owing to the many different configurations that the solvent adopts around the molecule. The resulting spectra are thus broadened by the many possible solvatochromic shifts.A method able to reproduce both peak positions and line shapes would be of crucial importance to the computatio...

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“…In any case, a full understanding of the energy transfer process is only possible with a correct description of the interaction between the chromophores and their fluctuating protein environment. A lot of effort has been devoted to this subject recently (7)(8)(9)(10)(11)(12)(13)(14)(15)(16). The environment affects both site energies and couplings and is a constant source of noise; this has a smearing effect on experimental spectra and poses great challenges to theoretical treatments.…”

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confidence: 99%

Macrocycle ring deformation as the secondary design principle for light-harvesting complexes

Vico

Anda

Osipov

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

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Natural light-harvesting is performed by pigment-protein complexes, which collect and funnel the solar energy at the start of photosynthesis. The identity and arrangement of pigments largely define the absorption spectrum of the antenna complex, which is further regulated by a palette of structural factors. Small alterations are induced by pigment-protein interactions. In light-harvesting systems 2 and 3 from , the pigments are arranged identically, yet the former has an absorption peak at 850 nm that is blue-shifted to 820 nm in the latter. While the shift has previously been attributed to the removal of hydrogen bonds, which brings changes in the acetyl moiety of the bacteriochlorophyll, recent work has shown that other mechanisms are also present. Using computational and modeling tools on the corresponding crystal structures, we reach a different conclusion: The most critical factor for the shift is the curvature of the macrocycle ring. The bending of the planar part of the pigment is identified as the second-most important design principle for the function of pigment-protein complexes-a finding that can inspire the design of novel artificial systems.

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Theoretical Characterization of the Spectral Density of the Water-Soluble Chlorophyll-Binding Protein from Combined Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulations

Cited by 64 publications

References 64 publications

Efficient Simulation of Finite-Temperature Open Quantum Systems

Efficient Simulation of Finite-Temperature Open Quantum Systems

Modeling the absorption lineshape of embedded systems from molecular dynamics: A tutorial review

Macrocycle ring deformation as the secondary design principle for light-harvesting complexes

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