Molecular Dynamics Simulation Study of Liquid Waters and its Properties

Abstract

This thesis focuses on Molecular Dynamics (MD) simulation study of liquid water modeled by TIP4P/2005 potential. Structure and dynamics of liquid modeled by this potential is discussed over a wide range of temperatures and at three pressures – 1, 1000 and 10000 bar. We also discuss the results from analysis of liquid water structure and dynamics under the influence of static electric fields of magnitude 0.1, 0.4 and 1.0 V/nm. Chapter 1 provides an overview of the literature which is relevant for this work. Section 1.1 discusses the stable and metastable regions of liquid water and section 1.2 discusses the important bulk thermodynamic properties of liquid water. Structural studies are presented in section 1.3. Both experimental and simulation studies of the structure is surveyed here. Section 1.4 illustrate the dynamic studies of liquid water. Studies on hydrogen bond network with emphasis on donor-acceptor asymmetry is discussed in section 1.5. Structure of high pressure liquid water is reported in section 1.6 and section 1.7 presents the literature data available on studies of liquid water under the influence of electric field. Chapter 2 focuses on relevant computational methods employed in this work. We performed Molecular Dynamics (MD) simulation of TIP4P/2005 water potential at several state points under isothermal-isobaric ensemble. Overview of this chapter is given in section 2.1. Model system and the interaction potential is discussed in section 2.2. System size studied, surface effects, periodic boundary conditions, minimum image convention and long-range interaction is discussed in section 2.3. Basics of MD simulations is reported in section 2.4. In section 2.5, we discuss the isothermal-isobaric ensemble which is used for all our simulations. We performed all the MD simulations using GROMACS package, the details of which is presented in section 2.6. Section 2.7 discusses the importance of equilibration of a system and the reproducibility of results. Finally, in section 2.8, we mention the visualization and graph plotting tools used in this work with the summary of computational methodology in section 2.9. Chapter 3 discusses the local structure of liquid water from ambient to supercooled condition. Section 3.1 provides an overview of this chapter. Section 3.2 discusses all the relevant conditions employed during the simulation for the structural studies. All the structural metrics namely, orientational order parameters, fraction of differently coordinated water and most importantly radial distribution functions are reported in section 3.3. Within the first shell, water molecules are primarily 4 coordinated with some percentage of 5 coordinated water also. As liquid water cools, fraction of 4 coordinated water increases and that of 5 coordinated water decreases. Consequently, with cooling oxygen and hydrogen orientations become more ordered. In 4 coordinated water system, oxygen on one hand becomes more tetrahedrally ordered and hydrogen on the other hand prefers to stay in out-of-plane orientation with decrease in temperature. In addition, we also note that oxygen and hydrogen in cooled liquid water shows structural similarity with hexagonal ice. Conclusions from this study is summarised in section 3.4. Chapter 4 presents the dynamics of liquid water. Dynamics of water molecules is perhaps more important than the structure, since whatever structure we report has to be dynamically stable. Overview of this study is reported in section 4.1. Specifics of simulation condition and analysis is presented in section 4.2. Section 4.3 reports all different dynamical analysis performed in this study. Here, we first report the auto correlation functions for all the structural metrics studied in the previous chapter. Along with these, we also report the auto-correlation functions of oxygen/hydrogen velocities and molecular dipole moments. We then analyse the activation energies of the various dynamical processes performing Arrhenius fits on the relaxations. Thereafter, the Fourier Transform spectra obtained from all the ACFs are reported and discussed in detail.