Classes and Molecular Structures

This chapter presents the molecular structures and some photophysical parameters of over 700 fluorescent dye labels and stains that have high brightness in aqueous solutions. It presents following three most important photophysical parameters, from a practical point-of-view: excitation or absorption maximum, Stokes shift, and molecular brightness. Atom numbering is an important issue for fluoresceins, rhodamines, and rhodols, which have the ortho -carboxyl group and therefore exist in an equilibrium between the open form and the lactone form. Rhodamines is the largest class, containing over 50 bright and photorobust fluorescent dyes. Pyronines are characterized by the presence of the three-ring xanthene and one iminium group bound to carbon 3 and one amino group bound to 6. This is exactly like rhodamines, but without the pendant aryl group bound to carbon 9. Sulforhodamines are rhodamines that contain an ortho -sulfonate in place of the ortho -carboxylate.