Is slow thermal isomerization in viscous solvents understandable with the idea of frequency dependent friction?

Isomerization and Properties of Isomers of Carbocyanine Dyes

One of the important features of polymethine (cyanine) dyes is isomerization about one of C–C bonds of the polymethine chain. In this review, spectral properties of the isomers, photoisomer-ization and thermal back isomerization of carbocyanine dyes, mostly meso-substituted carbocy-anine dyes, are considered. meso-Alkyl-substituted thiacarbocyanine dyes are present in polar solvents mainly as cis isomers and, hence, exhibit no photoisomerization, whereas in nonpolar solvents, in which the dyes are in the trans form, photoisomerization takes place. In contrast, the meso-substituted dyes 3,3′-dimethyl-9-phenylthiacarbocyanine and 3,3′-diethyl-9-(2-hydroxy-4-methoxyphenyl)thiacarbocyanine occur as trans isomers and exhibit photoisomerization in both polar and nonpolar solvents. The behavior of these dyes may be ex-plained by the fact that the phenyl ring of the substituent in their molecules can be twisted at some angle, removing the substituent from the plane of the molecule and reducing its steric ef-fect on the conformation of the trans isomer. In some cases, photoisomerization of cis isomers of meso-substituted carbocyanine dyes is also observed (for some meso-alkyl-substituted dyes com-plexed with DNA and chondroitin-4-sulfate; for 3,3′-diethyl-9-methoxythiacarbocyanine in moderate polarity solvents). The cycle photoisomerization–thermal back isomerization of cya-nine dyes can be used in various systems of information storage and deserves further investiga-tion using modern research methods.

Isomerization and Properties of Isomers of Carbocyanine Dyes

One of the important features of polymethine (cyanine) dyes is isomerization around one of C–C bonds of the polymethine chain. In this review, spectral properties of the isomers, photoisomerization and thermal back isomerization of carbocyanine dyes, mostly meso-substituted carbocyanine dyes, are considered. meso-Alkyl-substituted thiacarbocyanine dyes are present in polar solvents mainly as cis isomers and, hence, exhibit no photoisomerization, whereas in nonpolar solvents, in which the dyes are in the trans form, photoisomerization takes place. In contrast, the meso-substituted dyes 3,3′-dimethyl-9-phenylthiacarbocyanine and 3,3′-diethyl-9-(2-hydroxy-4-methoxyphenyl)thiacarbocyanine occur as trans isomers and exhibit photoisomerization in both polar and nonpolar solvents. The behavior of these dyes may be explained by the fact that the phenyl ring of the substituent in their molecules can be twisted at some angle, removing the substituent from the plane of the molecule and reducing its steric effect on the conformation of the trans isomer. In some cases, photoisomerization of cis isomers of meso-substituted carbocyanine dyes is also observed (for some meso-alkyl-substituted dyes complexed with DNA and chondroitin-4-sulfate; for 3,3′-diethyl-9-methoxythiacarbocyanine in moderate polarity solvents). The cycle photoisomerization–thermal back isomerization of cyanine dyes can be used in various systems of information storage and deserves further investigation using modern research methods.

Dynamic effects of nonequilibrium solvation: Potential and free energy surfaces for Z/E isomerization in solvent-solute coordinates

A novel definition of a solvent coordinate associated with a given reaction is formulated in terms of molecular-dynamic trajectories of the solvent and is applied to discuss the topography of potential energy and free energy surfaces of model liquid phase Z/E isomerization reactions in solvent-solute coordinates. It is shown that the arrangement of the reactant and product valleys on these surfaces can vary from consecutive to parallel, depending on the strength of the solvent-solute interactions.