Analysis of microviscosity and reaction coordinate concepts in isomerization dynamics described by Kramers’ theory

Abstract

Dynamic reaction path analysis based on an intrinsic reaction coordinateIn this work we have studied the isomerization dynamics of a cyanine dye molecule in solution. The viscosity and temperature dependencies of the isomerization rate have been measured in the series of n-alcohols for three different sizes of the isomerizing group. From these measurements we conclude that the shear viscosity of the solvent is not a good measure of the microscopic friction experienced by the isomerizing groups. The friction is varying in a nonhydrodynamic manner with viscosity, which shows that the relative volume of the isomerizing group and solvent molecules ( V p / V s ) is a critical parameter determining the microscopic friction. When the microscopic friction is calculated using a model for molecular rotational relaxation proposed by Dote, Kievelson, and Schwartz [J. Phys. Chern. 85, 2169 ], good fits to Kramers' equation is obtained. Similar models for microscopic rotational and translational friction combined with Kramers' equation also yield an apparent improvement over the hydrodynamic Kramers description. The measurements also show that the non-Kramers behavior of the reaction rates have a more complex origin than the (Vp/v.,) dependence of the microscopic friction, that possibly can be traced back to a more general failure of the hydrodynamic description of friction (frequency dependent friction), or to a temperature and solvent dependence of the potential surface parameters. The results also suggest that the detailed nature of the reaction coordinate plays an important role in determining the detailed viscosity dependence of the isomerization. Thus a reactive motion mainly experiencing rotational friction is much more sensitive to the molecular size and freevolume effects, than is the isomerization controlled by translational friction.6508

Cyanine dyes in biophysical research: the photophysics of polymethine fluorescent dyes in biomolecular environments

“…The lifetime of fluorescence depends strongly on temperature and solvent viscosity because isomerization is an activated process that involves a large molecular motion. Åkesson et al (1991) and Korppitommola et al (1991) independently determined the activation energies of the N→t process in a series of primary alcohols of increasing viscosity from methanol ( E Nt =11·7 kJ/mol), to dodecanol ( E Nt =29·9 kJ/mol). A value of 19 kJ/mol was reported for the succinimidyl ester derivative of Cy3 (Cy3-SE) in a buffer solution (Sanborn et al 2007), and is very similar to the one obtained for diIC 2 (3) in primary alcohols of similar viscosities (Åkesson et al 1991; Korppitommola et al 1991).…”

“…Åkesson et al (1991) and Korppitommola et al (1991) independently determined the activation energies of the N→t process in a series of primary alcohols of increasing viscosity from methanol ( E Nt =11·7 kJ/mol), to dodecanol ( E Nt =29·9 kJ/mol). A value of 19 kJ/mol was reported for the succinimidyl ester derivative of Cy3 (Cy3-SE) in a buffer solution (Sanborn et al 2007), and is very similar to the one obtained for diIC 2 (3) in primary alcohols of similar viscosities (Åkesson et al 1991; Korppitommola et al 1991). Bond rotation leads to the formation of the partially twisted intermediate, which deactivates to the cis or trans ground states with a branching ratio ( k tP : k tN ) of approximately 2:1 for diIC 1 (3) in ethanol (Chibisov et al 1995).…”

Isomerisation dynamics of a thiacarbocyanine dye in different electronic states and in different classes of solvents

“…However, apart of the small values of [37]. This procedure was not so satisfactory with the the barrier frequencies, the relative magnitude of the isomerisation of cyanines in n-alcohols, although the frequencies showed realistic trends when different Kramers fit was clearly improved [38]. Similar imsolute/solvent systems were compared.…”

“…Similar imsolute/solvent systems were compared. Waldeck and provements were also obtained using the free space co-workers have compared the parameters obtained model of Dote, Kivelson and Schwartz [38][39][40].…”

Isomerization and Properties of Isomers of Carbocyanine Dyes

“…In [35], the kinetics of isomerization of molecules of indocarbocyanine dyes with substituents in positions 3 and 3' of various length in solutions of alcohols (methanol-decanol series) was studied. The results indicate, in particular, that the nature of the reaction coordinate plays an important role in determining the dependence of photoisomerization on viscosity.…”