Novel Approach to Excited-State Calculations of Large Molecules Based on Divide-and-Conquer Method: Application to Photoactive Yellow Protein

Yoshikawa, Takeshi; Kobayashi, Masato; Fujii, Atsuhiko; Nakai, Hiromi

doi:10.1021/jp401819d

Cited by 38 publications

(33 citation statements)

References 61 publications

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“…Some fragmentation QM approaches have been proposed for calculations of the excited-state properties of large systems, including the generalized energy-based fragmentation (GEBF) approach developed by Li and coworkers ( Li et al, 2016 ), the divide-and-conquer (D and C) method of Nakai and coworkers ( Yoshikawa et al, 2013 ), the extension of the binary-interaction method ( Hirata et al, 2005 ) of Hirata et al, and the fragment molecular orbital (FMO) method of Kitaura and coworkers ( Chiba et al, 2007 ; Nakata et al, 2014 ). Recently, the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method was developed to calculate the excited-state properties of molecular crystals ( Liu et al, 2019 ; Zhang et al, 2020 ) and fluorescent proteins ( Jin et al, 2020 ) by our group.…”

Section: Introductionmentioning

confidence: 99%

Fragment-Based Quantum Mechanical Calculation of Excited-State Properties of Fluorescent RNAs

Chenfei

Wang

2021

Front. Chem.

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Fluorescent RNA aptamers have been successfully applied to track and tag RNA in a biological system. However, it is still challenging to predict the excited-state properties of the RNA aptamer–fluorophore complex with the traditional electronic structure methods due to expensive computational costs. In this study, an accurate and efficient fragmentation quantum mechanical (QM) approach of the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) scheme was applied for calculations of excited-state properties of the RNA aptamer–fluorophore complex. In this method, the excited-state properties were first calculated with one-body fragment quantum mechanics/molecular mechanics (QM/MM) calculation (the excited-state properties of the fluorophore) and then corrected with a series of two-body fragment QM calculations for accounting for the QM effects from the RNA on the excited-state properties of the fluorophore. The performance of the EE-GMFCC on prediction of the absolute excitation energies, the corresponding transition electric dipole moment (TEDM), and atomic forces at both the TD-HF and TD-DFT levels was tested using the Mango-II RNA aptamer system as a model system. The results demonstrate that the calculated excited-state properties by EE-GMFCC are in excellent agreement with the traditional full-system time-dependent ab initio calculations. Moreover, the EE-GMFCC method is capable of providing an accurate prediction of the relative conformational excited-state energies for different configurations of the Mango-II RNA aptamer system extracted from the molecular dynamics (MD) simulations. The fragmentation method further provides a straightforward approach to decompose the excitation energy contribution per ribonucleotide around the fluorophore and then reveals the influence of the local chemical environment on the fluorophore. The applications of EE-GMFCC in calculations of excitation energies for other RNA aptamer–fluorophore complexes demonstrate that the EE-GMFCC method is a general approach for accurate and efficient calculations of excited-state properties of fluorescent RNAs.

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Section: Introductionmentioning

confidence: 99%

Fragment-Based Quantum Mechanical Calculation of Excited-State Properties of Fluorescent RNAs

Chenfei

Wang

2021

Front. Chem.

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“…[73][74][75][76] It is not surprising that the above fragment-based methods can also be used to describe low-lying excited states that are localized in a small region of the system. [77][78][79][80][81][82][83][84][85][86][87][88][89] Low-lying delocalized excited states (excitons or transitions between delocalized orbitals) can be accessed either by linear combinations of local states [90][91][92][93][94][95][96] or by enlarged buffer regions. 97 Short-range charge transfer (CT) effects can also be accounted for deliberately to improve those states dominated by local excitations.…”

Section: Introductionmentioning

confidence: 99%

iOI: an Iterative Orbital Interaction Approach for Solving the Self-Consistent Field Problem

Wang

Liu

2021

Preprint

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An iterative orbital interaction (iOI) approach is proposed to solve, in a bottomup fashion, the self-consistent field problem in quantum chemistry. While it belongs grossly to the family of fragment-based quantum chemical methods, iOI is distinctive in that (1) it divides and conquers not only the energy but also the wave function, and that (2) the subsystems sizes are automatically determined by successively merging neighboring small subsystems until they are just enough for converging the wave function to a given accuracy. Orthonormal occupied and virtual localized molecular orbitals are obtained in a natural manner, which can be used for all post-SCF purposes.

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“…The divide‐and‐conquer (DC) scheme is one of the linear‐scaling methods originally proposed by Yang and Lee . Our group has developed the DC‐based HF, post‐HF theories, their gradient calculations, and excited‐state properties . Recently, quantum mechanical molecular dynamics (QM‐MD) simulations for tens of thousands atoms in the ground states have been accomplished by applying the DC method to the density‐functional tight‐binding (DFTB) method, which is an approximation to DFT with the concept of adopting up to two‐center terms for parameterized integrals and repulsive potential.…”

Section: Introductionmentioning

confidence: 99%

GPU‐Accelerated Large‐Scale Excited‐State Simulation Based on Divide‐and‐Conquer Time‐Dependent Density‐Functional Tight‐Binding

et al. 2019

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The present study implemented the divide-and-conquer timedependent density-functional tight-binding (DC-TDDFTB) code on a graphical processing unit (GPU). The DC method, which is a linear-scaling scheme, divides a total system into several fragments. By separately solving local equations in individual fragments, the DC method could reduce slow central processing unit (CPU)-GPU memory access, as well as computational cost, and avoid shortfalls of GPU memory. Numerical applications confirmed that the present code on GPU significantly accelerated the TDDFTB calculations, while maintaining accuracy. Furthermore, the DC-TDDFTB simulation of 2-acetylindan-1,3-dione displays excitedstate intramolecular proton transfer and provides reasonable absorption and fluorescence energies with the corresponding experimental values.

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Novel Approach to Excited-State Calculations of Large Molecules Based on Divide-and-Conquer Method: Application to Photoactive Yellow Protein

Cited by 38 publications

References 61 publications

Fragment-Based Quantum Mechanical Calculation of Excited-State Properties of Fluorescent RNAs

Fragment-Based Quantum Mechanical Calculation of Excited-State Properties of Fluorescent RNAs

iOI: an Iterative Orbital Interaction Approach for Solving the Self-Consistent Field Problem

GPU‐Accelerated Large‐Scale Excited‐State Simulation Based on Divide‐and‐Conquer Time‐Dependent Density‐Functional Tight‐Binding

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