A Molecular Perspective on the Dynamics and Entropy of Solvation Shell Water

Abstract

The dynamic and thermodynamic properties of water remains an active area of research due to its significance in the biological processes. Although the pure water properties have been extensively studied through experimental and theoretical methods, water in the solvation shell represents a more realistic and complex scenario for naturally occurring water molecules. Using all-atom molecular dynamics simulations, the dynamics (diffusion coefficients and mean residence times) and thermodynamics of water molecules (entropy) in the solvation shell and bulk water have been investigated in my thesis. With the help of 360 different correlation functions, we showed that the key factor that governs the dynamics of water in a particular DNA groove is the position along the DNA. Extending this study to DNA in hydrated ionic liquid (IL) systems, we showed how the dynamics of water in these hydrated IL solutions causes significant changes in the dynamics of IL cations near different DNA base pairs. In thermodynamics, we investigated the entropy of individual water molecules around different cations and anions. After establishing the reliability of our method by showing the correlation with experimental solvation entropy, we discussed how cations and anions affect solvation shell water differently. We also show a significant contribution of entropy change in the solvation shell originates from the second solvation shell. Finally, we investigated the relation between dynamics and thermodynamics by studying water in the supercooled state. We could show that at the temperature where the dynamical transition takes place in water, the thermodynamic behavior of water (i.e., entropy) also changes. Further, our results provide new insights on the effect of structural polymorphism (high and low-density liquid) and fragile to strong crossover transition on water entropic behavior in its pure state. When the study is extended to the solvation shells of ions, the results correlate the structural polymorphism to the freezing behavior of water. Overall, the study aims to enrich the understanding of solvation shell water in addition to complementing previously known phenomena.