<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msub><mml:mi>S</mml:mi><mml:mn>1</mml:mn></mml:msub></mml:math>and<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msub><mml:mi>S</mml:mi><mml:mn>2</mml:mn></mml:msub></mml:math>Excited States of Gas-Phase Schiff-Base Retinal Chromophores

Nielsen, Ingolf; Lammich, Lutz; Andersen, Lars H.

doi:10.1103/physrevlett.96.018304

Cited by 107 publications

(98 citation statements)

References 27 publications

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“…55 One would thus expect a similar overestimation for the excitation energy in the protein. However, the computed value for the protein environment lies 0.07 eV below the experimental value.…”

Section: Comparison To Experimentsmentioning

confidence: 99%

Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems

Send¹,

Kaila²,

Sundholm³

2011

The Journal of Chemical Physics

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We investigate how the reduction of the virtual space affects coupled-cluster excitation energies at the approximate singles and doubles coupled-cluster level (CC2). In this reduced-virtual-space (RVS) approach, all virtual orbitals above a certain energy threshold are omitted in the correlation calculation. The effects of the RVS approach are assessed by calculations on the two lowest excitation energies of 11 biochromophores using different sizes of the virtual space. Our set of biochromophores consists of common model systems for the chromophores of the photoactive yellow protein, the green fluorescent protein, and rhodopsin. The RVS calculations show that most of the high-lying virtual orbitals can be neglected without significantly affecting the accuracy of the obtained excitation energies. Omitting all virtual orbitals above 50 eV in the correlation calculation introduces errors in the excitation energies that are smaller than 0.1 eV. By using a RVS energy threshold of 50 eV, the CC2 calculations using triple-ζ basis sets (TZVP) on protonated Schiff base retinal are accelerated by a factor of 6. We demonstrate the applicability of the RVS approach by performing CC2/TZVP calculations on the lowest singlet excitation energy of a rhodopsin model consisting of 165 atoms using RVS thresholds between 20 eV and 120 eV. The calculations on the rhodopsin model show that the RVS errors determined in the gas-phase are a very good approximation to the RVS errors in the protein environment. The RVS approach thus renders purely quantum mechanical treatments of chromophores in protein environments feasible and offers an ab initio alternative to quantum mechanics/molecular mechanics separation schemes.

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Section: Comparison To Experimentsmentioning

confidence: 99%

Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems

Send¹,

Kaila²,

Sundholm³

2011

The Journal of Chemical Physics

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“…pCAand pCA 2-. Electrospray ionization (ESI) is routinely used to produce gas-phase compounds, including PYP chromophores, 8 retinal chromophores, 3,9 and tyrosine. 58,59 Most of these species, such as pCA and tyrosine, have more than one acidic site, so the structure produced in electrospray technique is unclear.…”

Section: Iva Neutral Pyp Chromophoresmentioning

confidence: 99%

“…Recent measurements of the optical absorption of chromophores in the gas phase provide an experimental benchmark for theoretical methods. [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.…”

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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“…9,10 In the fully dark-adapted (dark) state of rhodopsin, an 11-cis-retinal is attached via a protonated Schiff base (PSB) linkage to the ε-amino group of Lys296 in the binding pocket of the seven α-helical trans-membrane opsin protein. The opsin protein environment attenuates the absorption maximum of the retinal PSB, leading to an absorption maximum of 498 nm for the dark state rhodopsin, compared to 610 nm for isolated 11-cis retinal PSB in the gas phase, 11 and 450 nm for all-trans retinal PSB in…”

Section: Introductionmentioning

confidence: 99%

Three-Layer ONIOM Studies of the Dark State of Rhodopsin: The Protonation State of Glu181

Hall

Vreven²,

Frisch³

et al. 2008

Journal of Molecular Biology

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S1andS2Excited States of Gas-Phase Schiff-Base Retinal Chromophores

Cited by 107 publications

References 27 publications

Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems

Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems

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

Three-Layer ONIOM Studies of the Dark State of Rhodopsin: The Protonation State of Glu181

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