Dynamical recrossing, internal friction and memory effects: Investigating model systems and drug-DNA intercalation process

Abstract

Recrossing is a dynamical effect that changes the rate calculated using static energy landscape criteria such as transition state theory. Kramers theory predicted that for spatial diffusion regime, recrossing is directly proportional to the friction felt by the system and thus rate will be inversely proportional to the friction. However for some reactions it was found that the rate did not exhibit an inverse dependence on the viscosity (macroscopic equivalent of friction). Further, addition of a frictional term to the solvent viscosity was found to explain the rate dependence on the viscosity. Consequently, this additional frictional term was coined internal friction since it was thought to arise from the system itself. In this thesis, we show that the non-linear dependence of rate on viscosity does not necessarily imply the presence of internal friction. We demonstrate using a simple model system, a Lennard Jones particle in water medium, that the non-linear dependence of rate on viscosity can stem from memory effects arising from the solvent which can be accounted by Grote-Hynes theory. Secondly, we extended this study to simple systems, a diatomic model and a united atom butane model to understand the interplay between memory effects and internal friction. We demonstrate that the presence of internal friction decreases the rate whereas memory effects increase the rate and thereby conclude that there are no internal friction effects in butane. Finally, we investigate the dynamical recrossing effects in the intercalation of the drug proflavine into DNA. Using numerical methods, we find that there is substantial recrossing in this process. Also, we get the mechanism of the process in great detail which indicate that several variables such as Rise, water number around DNA and drug affect the rate of the process. Furthermore, we show that Grote-Hynes theory is inadequate to estimate recrossing in this complex system owing to the breakdown of parabolic barrier assumption used in the theory. Future investigations are required to whether the process is affected by internal friction or memory friction.