Energy-based fragmentation contribution approach for calculating the fluorescence spectrum of biomacromolecules

Yang, Yunfan; Xu, Jianjie; Liu, Yonggang; Liu, Qiangqiang; Guo, Tengxiao; Junhua, Xiao; Hu, Jianbo

doi:10.1016/j.chemphys.2021.111425

Cited by 3 publications

(3 citation statements)

References 47 publications

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“…There is a variety of theoretical methods developed for calculating local − and nonlocal − excited states in large molecular systems. There is an ongoing work to model the excitonic coupling ,− and the effect of environment on it. − Fragment-based methods are naturally conducive to handling the excitonic coupling by treating chromophore as fragments.…”

Section: Introductionmentioning

confidence: 99%

Analysis of Site Energies and Excitonic Couplings: The Role of Symmetry and Polarization

Fedorov

2024

J. Phys. Chem. A

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An excitonic coupling model is developed based on an equation-of-motion coupled cluster combined with the fragment molecular orbital method. The effects of polarization and excitonic coupling on the splitting of quasi-degenerate levels in systems containing multiple chromophores are elucidated on dimers of formaldehyde, water, formic acid, hydrogen fluoride, and carbon monoxide. It is shown that the level structure is mainly determined by the mutual polarization of chromophores and to a lesser extent by the excitonic coupling. The role of symmetry in excitonic coupling in dimers is discussed. The excitonic coupling between all residues in the photoactive yellow protein (PDB: 2PHY) is analyzed.

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Section: Introductionmentioning

confidence: 99%

Analysis of Site Energies and Excitonic Couplings: The Role of Symmetry and Polarization

Fedorov

2024

J. Phys. Chem. A

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“…Excited states are involved in many important processes, such as phosphorescence, luminescence, photochemical reactions, and other light-related phenomena, of which light conversion in solar batteries is of particular importance to sustainable development . Computing excited states is possible with low-scaling methods. − …”

Section: Introductionmentioning

confidence: 99%

Analytic Gradient for Time-Dependent Density Functional Theory Combined with the Fragment Molecular Orbital Method

Nakata

Fedorov

2023

J. Chem. Theory Comput.

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The analytic energy gradient of energy with respect to nuclear coordinates is derived for the fragment molecular orbital (FMO) method combined with time-dependent density functional theory (TDDFT). The response terms arising from the use of a polarizable embedding are derived. The obtained analytic FMO-TDDFT gradient is shown to be accurate in comparison to both numerical FMO-TDDFT and unfragmented TDDFT gradients, at the level of two- and three-body expansions. The gradients are used for geometry optimizations, molecular dynamics, vibrational calculations, and simulations of IR and Raman spectra of excited states. The developed method is used to optimize the geometry of the ground and excited electronic states of the photoactive yellow protein (PDB: 2PHY).

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“…The cost of quantum-mechanical (QM) calculations of properties of molecular systems can be reduced by using fragmentation methods developed for both ground − and excited states. − …”

Section: Introductionmentioning

confidence: 99%

Site-Specific Ionization Potentials and Electron Affinities in Large Molecular Systems at Coupled Cluster Level

Fedorov

2023

J. Phys. Chem. A

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A many-body expansion of ionization potentials and electron affinities is developed based on a combination of the fragment molecular orbital method and equation-of-motion coupled-cluster (EOM-CC). In addition to site-specific values, obtained as one-body properties, pair and triple corrections are added to account for nonlocal EOM-CC contributions of the molecular environment of a chromophore. The developed method is applied to carboxylic acids, alkyl cations, a protein ubiquitin (Protein Data Bank ID 1UBQ), and a nano ribbon of white graphene elucidating the effect of environment on ionization potential and electron affinity.

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Energy-based fragmentation contribution approach for calculating the fluorescence spectrum of biomacromolecules

Cited by 3 publications

References 47 publications

Analysis of Site Energies and Excitonic Couplings: The Role of Symmetry and Polarization

Analysis of Site Energies and Excitonic Couplings: The Role of Symmetry and Polarization

Analytic Gradient for Time-Dependent Density Functional Theory Combined with the Fragment Molecular Orbital Method

Site-Specific Ionization Potentials and Electron Affinities in Large Molecular Systems at Coupled Cluster Level

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