Parallelized integral-direct CIS(D) calculations with multilayer fragment molecular orbital scheme

Mochizuki, Yuji; Tanaka, Kiyoshi; Yamashita, Katsumi; Ishikawa, Takeshi; Nakano, Tatsuya; Amari, Shinji; Segawa, Katsunori; Murase, Tadashi; Tokiwa, Hiroaki; Sakurai, Minoru

doi:10.1007/s00214-006-0181-6

Cited by 77 publications

(63 citation statements)

References 50 publications

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“…53 Mochizuki et al calculated this system in gas phase by MLFMO-CI, and they obtained the excitation energy of PYP as 4.28 eV by MLFMO-CIS, and as 3.29 eV by MLFMO-CIS(D) using the 6-31G basis set. 28,29 In our previous study, 31 we calculated this system in gas phase at the LC-BLYP/6-31G* level of theory using FMO2-TDDFT and obtained the excitation energy as 3.124 eV. The PYP structure was obtained 31 by optimizing the chromophore geometry with B3LYP/6-31(þ)G* and inserting it to the experimental geometry of PYP.…”

Section: Pyp In Aqueous Solutionmentioning

confidence: 99%

“…26 For excited state treatments of FMO, Mochizuki et al combined multilayer FMO (MLFMO 27 ) with configuration interaction singles (CIS) and singles þ the second order perturbative doubles correction (CIS(D)). 28,29 In their MLFMO-CI method, CI calculation is performed on a single fragment of interest after determining the electronic densities of all fragments self-consistently. As an application of MLFMO-CI, they applied MLFMO-CI to the excitation of the photoactive yellow protein (PYP).…”

Section: Introductionmentioning

confidence: 99%

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Polarizable continuum model with the fragment molecular orbital‐based time‐dependent density functional theory

2008

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The polarizable continuum model (PCM) for describing the solvent effect was combined with the fragment molecular orbital-based time-dependent density functional theory (TDDFT). Several levels of the many-body expansion were implemented, and the importance of the many-body contributions to the singlet-excited states was discussed. To calibrate the accuracy, we performed a number of the model calculations using our method and the regular TDDFT in solution, applying them to phenol and polypeptides at the long-range corrected BLYP/6-31G* level. It was found that for systems up to 192 atoms the largest error in the excitation energy was 0.006 eV (vs. the regular TDDFT/PCM of the full system). The solvent shifts and the conformer effects were discussed, and the scaling was found to be nearly linear. Finally, we applied our method to the lowest singlet excitation of the photoactive yellow protein (PYP) in aqueous solution and determined the excitation energy to be in reasonable agreement with experiment. The excitation energy analysis provided the contributions of individual residues, and the main factors as well as their solvent shifts were determined.

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Section: Pyp In Aqueous Solutionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Polarizable continuum model with the fragment molecular orbital‐based time‐dependent density functional theory

2008

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“…Without the pair corrections from Equation (18), the excitation energy was 3.433 eV and thus significantly higher. Related studies with a CIS- [247] or CIS(D)-based MLFMO approach [248] resulted in an excitation energy of 4.28 eV. Additional work on PYP is presented, for example in the CASPT2/MM study on the color-tuning mechanism of the protein environment in ref.…”

Section: Pypmentioning

confidence: 97%

Subsystem‐Based Theoretical Spectroscopy of Biomolecules and Biomolecular Assemblies

Neugebauer

2009

ChemPhysChem

123

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The absorption properties of chromophores in biomolecular systems are subject to several fine-tuning mechanisms. Specific interactions with the surrounding protein environment often lead to significant changes in the excitation energies, but bulk dielectric effects can also play an important role. Moreover, strong excitonic interactions can occur in systems with several chromophores at close distances. For interpretation purposes, it is often desirable to distinguish different types of environmental effects, such as geometrical, electrostatic, polarization, and response (or differential polarization) effects. Methods that can be applied for theoretical analyses of such effects are reviewed herein, ranging from continuum and point-charge models to explicit quantum chemical subsystem methods for environmental effects. Connections to physical model theories are also outlined. Prototypical applications to optical spectra and excited states of fluorescent proteins, biomolecular photoreceptors, and photosynthetic protein complexes are discussed.

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“…A tendency of CIS to overestimate excitation energies is compensated for by CIS(D) in which the orbital relaxation energy for an excited state of interest as well as the differential correlation energy from the ground state correlated at the MP2 level (Head-Gordon et al, 1994). Both CIS and CIS(D) have been introduced to multilayer FMO (MFMO; Fedorov et al, 2005) in ABINIT-MP (Mochizuki et al, 2005a(Mochizuki et al, , 2007a. Very recently, Mochizuki implemented the parallelized FMO3-CIS gradient calculation, based on the efficient formulations with Fock-like contractions (Foresman et al, 1992).…”

Section: Configuration Interaction Singles (Cis)mentioning

confidence: 99%

Recent Advances in Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD) Simulations

Komeiji¹,

Mochizuki²,

Nakano³

et al. 2012

Molecular Dynamics - Theoretical Developments and Applications in Nanotechnology and Energy

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Parallelized integral-direct CIS(D) calculations with multilayer fragment molecular orbital scheme

Cited by 77 publications

References 50 publications

Polarizable continuum model with the fragment molecular orbital‐based time‐dependent density functional theory

Polarizable continuum model with the fragment molecular orbital‐based time‐dependent density functional theory

Subsystem‐Based Theoretical Spectroscopy of Biomolecules and Biomolecular Assemblies

Recent Advances in Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD) Simulations

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