Projets par an
Résumé
The off-resonance and resonant Raman spectra have been simulated for models of fluorescent protein chromophores, those of the green fluorescent protein (GFP, called FP1) and of DsRed (called FP2), which presents a longer πconjugated path, with the aim of providing a systematic investigation of structural but also computational aspects. These were performed at the (time-dependent) density functional theory [(TD)DFT] level. The off-resonance intensities have been calculated from the derivatives of the frequency-dependent polarizability with respect to the normal coordinates while the resonant ones have been evaluated using Huang−Rhys factors determined from the gradients of the excitation energies with respect to the normal coordinates. When applied with the M05 meta-GGA exchange-correlation functional, this simple computational scheme can reproduce most of the experimental Raman signatures of FP1 in its protonated and deprotonated forms, the differences of vibrational signatures of the cis (Z) and trans (E) isomers, as well as their changes as a function of the excitation wavelength. On the other hand, testing the predictions made for FP2 would require new experimental work. It was also observed that simulations with methods that inadequately predict the resonant Raman spectra could nevertheless produce a UV−vis absorption spectrum that is quite similar to the one obtained with better methods, once realistic peak broadening has been applied.
langue originale | Anglais |
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Pages (de - à) | 3414-3424 |
Nombre de pages | 11 |
journal | The Journal of Physical Chemistry. B, Condensed matter, materials, surfaces, interfaces & biophysical |
Volume | 126 |
Numéro de publication | 18 |
Les DOIs | |
Etat de la publication | Publié - 12 mai 2022 |
Financement
V.L. thanks the Fund for Scientific Research (F.R.S.-FNRS) for his Research Associate position. The calculations were performed on the computing facilities of the Consortium des \u00C9quipements de Calcul Intensif (C\u00C9CI, http://www.ceci-hpc. be), and particularly those of the Technological Platform on High-Performance Computing of the University of Namur, for which we gratefully acknowledge the financial support of the FNRS-FRFC, of the Walloon Region, and of the University of Namur (Conventions No. 2.5020.11, GEQ U.G006.15, 1610468, and RW/GEQ2016).
Bailleurs de fonds | Numéro du bailleur de fonds |
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FNRS‐FRFC, of the Walloon Region | |
Fonds De La Recherche Scientifique - FNRS | |
Université de Namur | 1610468, 2.5020.11, RW/GEQ2016, GEQ U.G006.15 |
Empreinte digitale
Examiner les sujets de recherche de « TDDFT Investigation of the Raman and Resonant Raman Spectra of Fluorescent Protein Chromophore Models ». Ensemble, ils forment une empreinte digitale unique.Projets
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CÉCI – Consortium des Équipements de Calcul Intensif
CHAMPAGNE, B. (Responsable du Projet), Lazzaroni, R. (Responsable du Projet), Geuzaine , C. (Co-investigateur), Chatelain, P. (Co-investigateur) & Knaepen, B. (Co-investigateur)
1/01/18 → 31/12/22
Projet: Recherche
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consortium des équipements de calcul intensif
Champagne, B. (Co-investigateur)
1/01/11 → 31/12/22
Projet: Recherche
Équipement
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Plateforme Technologique Calcul Intensif
Champagne, B. (!!Manager)
Plateforme technologique Calcul intensifEquipement/installations: Plateforme technolgique