The influence of chromophore structure on the protonation constant of the Photoactive Yellow Protein chromophore is explored with isolated para-coumaric acid (pCA) and thiomethyl-para-coumaric acid model chromophores in solution. pH titration coupled with visible absorption spectra of the trans and photogenerated cis conformer of isolated pCA demonstrates that the isomerization of the chromophore increases the pK a of the phenolate group by 0.6 units (to 10.1 ± 0.22). Formation of the pCA

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... ter reduces the pK a of the phenolic group by 0.3 units (from 9.5 ± 0.15 to 9.2 ± 0.16). Unfortunately, a macroscopic cis-TMpCA population was not achieved via photoexcitation. Both trends were explained with electronic structure calculations including a Natural Bond Orbital analysis that resolves that the pK a upshift for the cis configuration is attributed to increased Columbic repulsion between the coumaryl tail and the phenolate moieties. This structurally induced pK a upshift after isomerization is argued to aid in the protonation of the chromophore within the PYP protein environment and the subsequent propagation of the photocycle response and in vivo photo-activity.