Dynamical aspects of supercooled TIP3P–water in the grooves of DNA

Abstract

We investigate by molecular dynamics simulations the mobility of the water located at the DNA minor and major grooves. We employ the TIP3P water model, and our system is analyzed for a range of temperatures 190–300 K. For high temperatures, the water at the grooves shows an Arrhenius behavior similar to that observed in the bulk water. At lower temperatures, a departure from the bulk behavior is observed. This slowing down in the dynamics is compared with the dynamics of the hydrogen of the DNA at the grooves and with the autocorrelation functions of the water hydrogen bonds. Our results indicate that the hydrogen bonds of the water at the minor grooves are highly correlated, which suggests that this is the mechanism for the slow dynamics at this high confinement