Simple inorganic salts, such as NaCl melt at very high temperature. Salts with organic cations, referred to as “ionic liquids” (ILs) open a new window for the liquid state at moderate temperature. These salts are liquid at or near room temperature. Molecular Dynamics (MD) simulation is one of the principal and powerful methods in the theoretical chemistry to explore the relationship between microstructure and macroscopic properties of ILs. In this computer simulation, 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 simulation is used to determine for some structural and dynamic properties of two Amino Acids ionic liquids; Tetrabutylphosphonium Alanine,[TBP][ Ala ] and Tetrabutylphosphonium Glycine,[TBP][Gly]. These ILs show lower viscosities, higher decomposition and efficiency than most of other ionic liquids. AMBER-based force field is used to determine the model of these ILs. This force field is developed by Zhou et al at 2007 [Zhou.G, Liu.X, Yu.G, He.H, J.Phys.Chem.111(2007)7078-7084]. DL_POLY program (version 2.18) is used to perform this simulation with using a time step of 0.001ps and R cutoff =15?. An important check for the accuracy of our simulation and selected model is density. Our predicted densities from our proposed force field are in proper agreement with experimental data. Microstructure properties of [TBP][ Ala ] and [TBP][Gly] have been investigated by looking at the Radial Distribution Function (RDF) plots for the cation-cation, anion-anion and cation-anion atomic sites of two ILs. Finally, traort properties such as Mean Square Displacement (MSD) and Diffusion Coefficient (D) of cation and anion of these ILs are also studied. We have also evaluated qualitatively the effect of extra –CH 2 - groups on these properties.