Photophysical properties have been measured for five merocyanine dyes having (i) different alkyl substituents on the thiobarbiturate subunit [i.e. ethyl (butyl Merocyanine 540), or hexyl], (ii) the sulfonate group replaced with a methyl group, or (iii) the benzoxazole residue replaced with 1,2-naphthoxazole, and for one of the corresponding oxonol derivatives. Neither the nature of the alkyl group nor the absence of the sulfonate group exert any significant effect on the photophysical properties of the dyes in ethanol solution at 22 °C. However, extending the size of the benzoxazole residue increases fluorescence and triplet yields and decreases the yield for photoisomerization. A detailed two-dimensional NMR analysis of one of the dyes has shown that the ground state exists exclusively in an all-trans conformation while FTIR indicates hydrogen bonding between the thiobarbiturate subunit and the polymethine bridge. Using this structural information, the energetics and mechanics of the isomerization processes are discussed. It is further shown that these structural modifications affect the efficacy with which the dyes kill leukemic cells under illumination due to pronounced changes in lipophilicity.