Ionic liquids (ILs) are a group of organic salts. While, salts do not melt below 800 ?C, most of ILs remain liquid at room temperature. ILs show negligible vapor pressures, high thermal stabilities and ionic conductivities, and a wide temperature range in the liquid state. Molecular dynamics (MD) simulation is a reliable approach to explore the relationship between microstructures and macroscopic properties of ionic liquids. MD is a form of computer simulation wherein atoms and molecules are allowed to interact for a period of time under known laws of physics, giving a view of the motion of the atoms. In this thesis, MD is used for the simulations of two Amino acid ionic liquids systems. A refined force filed based on the AMBER force field reported by Zhou et al. [Zhou, G., Liu, X., Yu, G., He, H, J. Phys. Chem . 111 (2007) 7078-7084] was set up for two [P(C 4 ) 4 ][AA] ILs composed of tetrabutylphosphonium, [P(C 4 ) 4 ] + , cation with aspartic acid, [Asp] - , and glutamic acid, [Glu] - , as the amino acid anions. The MD simulations were performed with the DL_POLY program (version 2.18) using a time step of 0.001 ps and R cutoff = 13 ?. The NPT Hoover ensemble was used for P = 1 atm and T = 321.85 K to calculate the structural properties and NVE ensemble was used to calculate the dynamical properties of two systems. Each system was equilibrated initially by several runs (~ 15 runs each of length is 10 6 steps). our predicted densities from our proposed force field are in proper agreement with the experimental data at 298.15 K. and they haven’t more than %3 error. we have analyzed the dihedral angle probability of butyl side chains in the tetrabutylphosphonium cation. We have prepared a Rasmol box to show different interactions of our systems (anionic-cationic and polar-nonpolar). And Finally, we have studied the effect of different structure of our anionic systems with one extra -CH 2 - group on mean square displacement (MSD), and diffusion coefficient qualitatively.
