Fluorescence Spectroscopy and Stokes Shift

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RYANDTRAVERS
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This is a question on fluorescence spectroscopy so physics/chemistry. What causes a large Stokes shift in the spectra? I know what causes the shift in wavelength, i.e., a relaxation of vibrational states before de-excitation to the ground state, but what actually causes a (very) large Stokes shift and what can it tell you about the organic molecule?
 
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Stokes shifts in fluorescent molecules are caused by thermal relaxation and depend on not just the fluorophore but also the chemical environment. Stokes shifts for quantum dots appears to involve a different mechanism, but I'm not expert enough to elaborate. There are some results on designing a Stokes shift:

http://pubs.acs.org/doi/abs/10.1021/jp404170w
http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=4472661&abstractAccess=no&userType=inst
http://www.sciencedirect.com/science/article/pii/S1010603010003631