Ground and Excited States of Retinal Schiff Base Chromophores by Multiconfigurational Perturbation Theory

Sekharan, Sivakumar; Weingart, Oliver; Buß, Volker

doi:10.1529/biophysj.106.087122

Cited by 62 publications

(77 citation statements)

References 28 publications

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“…By changing it one can change the excitation energy by up to 0.7 eV. The PBE0/cc-pVDZ bond alternation value is close to the value found for N-methyl-11-cis PSBR obtained by Sekharan et al [48] with the MP2 method. As suggested by Wanko et al [46] the hybrid exchange-correlation functionals like the PBE0 used in the aforementioned work, should provide BLA values very close to those computed at the CASPT2 level of theory.…”

Section: Methods and Modelssupporting

confidence: 84%

Computational Photobiology and Beyond

et al. 2010

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In this paper we review the results of a group of computational studies of the spectroscopy and photochemistry of light-responsive proteins. We focus on the use of quantum mechanics/molecular mechanics protocols based on a multiconfigurational quantum chemical treatment. More specifically, we discuss the use, limitations, and application of the ab initio CASPT2//CASSCF protocol that, presently, constitutes the method of choice for the investigation of excited state organic molecules, most notably, biological chromophores and fluorophores. At the end of this Review we will also see how the computational investigation of the visual photoreceptor rhodopsin is providing the basis for the design of light-driven artificial molecular devices.

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Section: Methods and Modelssupporting

confidence: 84%

Computational Photobiology and Beyond

et al. 2010

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“…For all-trans retinal (Schiff-base terminal = −NH 2 /−NHCH 3 ) in the gas phase, CASPT2 (at CASSCF geometry = 534/545 nm) 22 and TD-B3LYP (this study at B3LYP geometry = 501/509 nm) excitation energies with the 6−31G* basis set agree within 35 nm but differ significantly from an another CASPT2 result with an ANO basis set (at DFTB and MP2 geometries = 606 nm). 21,23 The later reproduce the experimental result of 610 nm. 5 In a CASPT2/AMBER study on bovine Rh, the improvement of the 6−31G* basis set to ANO-S corrects the first excitation energy by 30 nm.…”

Section: Introductionmentioning

confidence: 59%

Spectral Tuning in Visual Pigments: An ONIOM(QM:MM) Study on Bovine Rhodopsin and its Mutants

2008

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We have investigated geometries and excitation energies of bovine rhodopsin and some of its mutants by hybrid quantum mechanical/molecular mechanical (QM/MM) calculations in ONIOM scheme, employing B3LYP and BLYP density functionals as well as DFTB method for the QM part and AMBER force field for the MM part. QM/MM geometries of the protonated Schiff-base 11-cisretinal with B3LYP and DFTB are very similar to each other. TD-B3LYP/MM excitation energy calculations reproduce the experimental absorption maximum of 500 nm in the presence of native rhodopsin environment and predict spectral shifts due to mutations within 10 nm, whereas TD-BLYP/ MM excitation energies have red-shift error of at least 50 nm. In the wild-type rhodopsin, Glu113 shifts the first excitation energy to blue and accounts for most of the shift found. Other amino acids individually contribute to the first excitation energy but their net effect is small. The electronic polarization effect is essential for reproducing experimental bond length alternation along the polyene chain in protonated Schiff-base retinal, which correlates with the computed first excitation energy. It also corrects the excitation energies and spectral shifts in mutants, more effectively for deprotonated Schiff-base retinal than for the protonated form. The protonation state and conformation of mutated residues affect electronic spectrum significantly. The present QM/MM calculations estimate not only the experimental excitation energies but also the source of spectral shifts in mutants.

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“…[3][4][5][6][7][8][9][10] Ab initio calculations for biological chromophores have been performed extensively at various levels of quantum chemistry theory. The methods used include time-dependent density functional theory (TDDFT), 4,6,[11][12][13][14] second-order approximate coupled cluster singles and doubles model (CC2), 15,16 equation of motion coupled cluster theory (EOM-CCSD), 4,5,13,15,17,18 complete active space with secondorder perturbation theory (CASPT2), [18][19][20][21][22] and the augmented version of the multiconfigurational quasi-degenerate perturbation theory (aug-MCQDPT2): 10,23 both accuracy and computational cost progressively increase from TDDFT, through CC2, EOM-CCSD, CASPT2 up to aug-MCQDPT2. Recently quantum Monte Carlo has also been used for evaluating excited states.…”

Section: Introductionmentioning

confidence: 99%

Modeling the Excited States of Biological Chromophores within Many-Body Green’s Function Theory

Rohlfing

Molteni

2009

J. Chem. Theory Comput.

101

121

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First-principle many-body Green's function theory (MBGFT) has been successfully used to describe electronic excitations in many materials, from bulk crystals to nanoparticles. Here we assess its performance for the calculations of the excited states of biological chromophores. MBGFT is based on a set of Green's function equations, whose key ingredients are the electron's self-energy Σ, which is obtained by Hedin's GW approach, and the electron-hole interaction, which is described by the Bethe-Salpeter equation (BSE). The GW approach and the BSE predict orbital energies and excitation energies with high accuracy, respectively. We have calculated the low-lying excited states of a series of model biological chromophores, related to the photoactive yellow protein (PYP), rhodopsin, and the green fluorescent protein (GFP), obtaining a very good agreement with the available experimental and accurate theoretical data; the order of the excited states is also correctly predicted. MBGFT bridges the gap between time-dependent density functional theory and high-level quantum chemistry methods, combining the efficiency of the former with the accuracy of the latter: this makes MBGFT a promising method for studying excitations in complex biological systems.

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Ground and Excited States of Retinal Schiff Base Chromophores by Multiconfigurational Perturbation Theory

Cited by 62 publications

References 28 publications

Computational Photobiology and Beyond

Computational Photobiology and Beyond

Spectral Tuning in Visual Pigments: An ONIOM(QM:MM) Study on Bovine Rhodopsin and its Mutants

Modeling the Excited States of Biological Chromophores within Many-Body Green’s Function Theory

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