Persistent hole-burning spectra of protonated acridine, 9-aminoacridine and proflavine doped in polyvinyl alcohol films have been studied to examine how the functional group affects chromophore-glass interactions. Proton transfer between the chromophore and the matrix upon electronic excitation is proposed to be the mechanism for the hole burned spectra of the three molecules studied. The high resolution of the spectrum of 9-aminoacridine is attributed to reduction of the electron-phonon coupling strength when substituting an amino group to the C(9) position of acridine. However, when substituting two amino groups to the C(3) and C(6) positions of acridine, significant increase of the electron-phonon coupling strength decreases the spectral resolution of proflavine.