We have studied the light absorption properties of the p-coumaric acid chromophore in the photoactive yellow protein (PYP) with a hybrid time-dependent density functional theory/molecular mechanics (TDDFT/MM) method. To critically assess the performance of TDDFT for this specific system, we first evaluated in vacuo the excited states of several PYP chromophore models. We then calculated the absorption maximum of the phenolate anion of the thiomethyl-p-coumaric acid (TMpCA) in the protein. Although within the limitations of TDDFT in describing charge-transfer and resonance excited states, we confirm a sizeable red shift in the absorption maximum due to the chemical differences between the free chromophore and that in the protein. The interaction between the chromophore and the protein environment induces a very small spectral shift, in line with experimental evidence. Comparison between the vertical electron detachment energy of the chromophore in vacuo and in the protein reveals that the protein stabilizes the choromophore in the excited states by preventing radical formation.
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