Finding unifying principles and concepts to describe large classes of complex molecular materials is no easy task. Seth Olsen has made significant progress in this direction by giving a rigorous quantum chemical justification of a heuristic "colour resonance" theory for methine dyes proposed by Platt almost 60 years ago. Seth has a paper that just appeared in Journal of Chemical Theory and Computation and discusses it on his blog .
A key component of Platt's theory is assigning a "basicity" to the molecular fragments which form the left and right part of the dye. This quantity should be an intrinsic property of the fragment and independent (or at least very weakly dependent on) what other fragment it is combined with the form the methine dye.
The figure below is taken from the supplementary information from Seth's paper. It shows the basicities one deduces for the different fragments (including different protonation states) that can make up fluorescent protein chromophores. Each point corresponds to the basicity one deduces for a specific chromophore. The cluster of points indeed shows the basicity is well defined for each fragment.
Note also how protonation [a change physicists may think of as "small"] can
- produce a large shift in the "basicity"
- give a corresponding large shift in the absorption frequency of the dye
- tune or detune the resonance associated with the dye
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