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Elucidating the role of structural fluctuations, intermolecular & vibronic interactions in the spectroscopic response of a bacteriophytochrome

Abstract

We present the first comprehensive multiscale computational investigation of Resonance Raman (RR), absorption and Circular Dichroism (CD) spectra of the resting state of the dimeric phytochrome of Deinococcus radiodurans. The spectra are simulated in all their components, namely the energy position and the lineshapes of both the far-red and the blue bands. To achieve such a goal, we have combined a 4.5 microsecond MD simulation of the solvated dimeric phytochrome with a hybrid quantum mechanics/molecular mechanics (QM/MM) model, which accounts for both electrostatic and mutual polarization effects between the QM and the MM subsystems. From simulations, we find a transient H-bond network within the binding pocket of the chromophore that, unexpectedly, do not significantly affect the absorption and CD spectra. In parallel, we characterize the vibrations which are more strongly coupled to the excitation confirming the important role of the hydrogen-out-of-plane mode of the vinyl C-H in between C and D rings together with the expected C=C stretching of the double bond involved in the photoisomerization

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Article information


Submitted
22 Jan 2020
Accepted
21 Mar 2020
First published
23 Mar 2020

Phys. Chem. Chem. Phys., 2020, Accepted Manuscript
Article type
Paper

Elucidating the role of structural fluctuations, intermolecular & vibronic interactions in the spectroscopic response of a bacteriophytochrome

V. Macaluso, L. Cupellini, G. Salvadori, F. Lipparini and B. Mennucci, Phys. Chem. Chem. Phys., 2020, Accepted Manuscript , DOI: 10.1039/D0CP00372G

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