Unraveling the similarity of the photoabsorption of deprotonated p-coumaric acid in the gas phase and within the photoactive yellow protein

Rocha‐Rinza, Tomás; Sneskov, Kristian; Christiansen, Ove; Ryde, Ulf; Kongsted, Jacob

doi:10.1039/c0cp01075h

Cited by 39 publications

(59 citation statements)

References 37 publications

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“…The vertical excitation energy of pCA − has been profusely studied with a vast variety of theoretical methods. 22,24,26,29 Our results are in line with the value (2.98 eV) published by Zuev et al 24 using a similar level of calculation (SS-CASPT2/ANO-RCC-VTZP). For the methylate compounds, Gromov et al 26 reported CC2/cc-pVDZ and EOM-CCSD/cc-pVDZ transition energies of 3.27 and 3.35 eV for pCMe − and 3.10 and 3.17 eV for pCTMe − .…”

Section: ■ Resultssupporting

confidence: 95%

Substituent and Solvent Effects on the UV–vis Absorption Spectrum of the Photoactive Yellow Protein Chromophore

et al. 2015

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Solvent effects on the UV-vis absorption spectra and molecular properties of four models of the photoactive yellow protein (PYP) chromophore have been studied with ASEP/MD, a sequential quantum mechanics/molecular mechanics method. The anionic trans-p-coumaric acid (pCA(-)), thioacid (pCTA(-)), methyl ester (pCMe(-)), and methyl thioester (pCTMe(-)) derivatives have been studied in gas phase and in water solution. We analyze the modifications introduced by the substitution of sulfur by oxygen atoms and hydrogen by methyl in the coumaryl tail. We have found some differences in the absorption spectra of oxy and thio derivatives that could shed light on the different photoisomerization paths followed by these compounds. In solution, the spectrum substantially changes with respect to that obtained in the gas phase. The n → π1* state is destabilized by a polar solvent like water, and it becomes the third excited state in solution displaying an important blue shift. Now, the π → π1* and π → π2* states mix, and we find contributions from both transitions in S1 and S2. The presence of the sulfur atom modulates the solvent effect and the first two excited states become practically degenerate for pCA(-) and pCMe(-) but moderately well-separated for pCTA(-) and pCTMe(-).

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Section: ■ Resultssupporting

confidence: 95%

Substituent and Solvent Effects on the UV–vis Absorption Spectrum of the Photoactive Yellow Protein Chromophore

et al. 2015

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“…The excitation energy with the largest oscillator strength (1.04) in the lowlying excited states for DP model is 3.28 eV using the present ONI-OM (TDDFT:Amber) model. This is in good agreement with the previous theoretical study by QM/MM calculation with CAM-B3LYP [11], i.e. 3.34 eV for the excitation energy with 1.101 for the oscillator strength.…”

Section: Excitation Energiessupporting

confidence: 93%

“…Several theoretical studies on PYP have been reported so far [9][10][11]. In these studies, the contribution from neighboring residues was discussed to clarify the protein environmental effect to the spectral shift.…”

Section: Introductionmentioning

confidence: 97%

A theoretical study on the electronic structure of PYP chromophore in low barrier hydrogen bonding model

Hirano

Sato

2013

Chemical Physics

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Keywords:Photoactive yellow protein (PYP) Low barrier hydrogen bond (LBHB) ONIOM a b s t r a c t Yamaguchi et al. have recently identified positions of hydrogen and deuterium atoms in photoactive yellow protein (PYP) using high-resolution neutron scattering. They reported that the hydrogen bond between the PYP chromophore and Glu46 was not a short ionic hydrogen bond (SIHB) but a low barrier hydrogen bond (LBHB). Furthermore, it was suggested that Arg52 close to the chromophore was deprotonated. In the present study, we investigate the electronic structure of the chromophore in PYP under the condition of protonated or deprotonated Arg52. By analyzing the potential energy curve along the proton migration between Glu46 and the chromophore, we find that a LBHB can be seen only when Arg52 is deprotonated.

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“…The method has previously been used to compute the excitation of the PYP chromophore with the inclusion of the side chains of some of the nearby residues in the QM region. 65–68 …”

Section: Introductionmentioning

confidence: 99%

Electronic Absorption Spectra from MM and ab Initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein

Isborn

Götz

Walker

et al. 2012

J. Chem. Theory Comput.

202

287

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We describe a new interface of the GPU parallelized TeraChem electronic structure package and the Amber molecular dynamics package for quantum mechanical (QM) and mixed QM and molecular mechanical (MM) molecular dynamics simulations. This QM/MM interface is used for computation of the absorption spectra of the photoactive yellow protein (PYP) chromophore in vacuum, aqueous solution, and protein environments. The computed excitation energies of PYP require a very large QM region (hundreds of atoms) covalently bonded to the chromophore in order to achieve agreement with calculations that treat the entire protein quantum mechanically. We also show that 40 or more surrounding water molecules must be included in the QM region in order to obtain converged excitation energies of the solvated PYP chromophore. These results indicate that large QM regions (with hundreds of atoms) are a necessity in QM/MM calculations.

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Unraveling the similarity of the photoabsorption of deprotonated p-coumaric acid in the gas phase and within the photoactive yellow protein

Cited by 39 publications

References 37 publications

Substituent and Solvent Effects on the UV–vis Absorption Spectrum of the Photoactive Yellow Protein Chromophore

Substituent and Solvent Effects on the UV–vis Absorption Spectrum of the Photoactive Yellow Protein Chromophore

A theoretical study on the electronic structure of PYP chromophore in low barrier hydrogen bonding model

Electronic Absorption Spectra from MM and ab Initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein

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