All-atom molecular dynamics simulations combined with ab initio calculations are used to study the thermodynamic properties and microscopic structure of four ionic liquids (ILs) based on the imidazolium cation with different alkyl side branches, ([bmmim]+, 1-butyl-2,3-dimethylimidazolium; [bmim]+, 1-butyl-3-methylimidazolium; [apmim]+, 1-(3-aminopropyl)-3-methylimidazolium; [mim]+, 1-methylimidazolium), paired with the [(CF3SO2)(2)N]-, bis(trifluoromethanesulfonyl)imide anion, in the temperature range of (298 to 600) K. We observed the highest value of the molar internal energy, enthalpy of vaporization, and cohesive energy density for the amine-functionalized [apmim][Tf2N] ionic liquid. Structural analysis shows that the amine functionalization of the end of the alkyl side chain of imidazolium cation does not significantly affect the organization of [Tf2N]- around [apmim]+, but additional NH2 groups lead to short-range cationcation structural correlations between neighboring [apmim]+. The C-2 methylation extensively affects preferential out-of-plane face-to-face locations of [Tf2N]- around [bmmim]+ and also the cationcation distributions. [mim][Tf2N] has the highest simulated density and better packing efficiency of liquid phase in comparison with other studied ILs. The strongest first shell probability density region of [mim](+) neighbors above and below the imidazolium ring of the reference cation represents better pi-pi stacking in the liquid phase of this ionic liquid. The presented results determine the role of the cation structure on the properties of this family of ILs. Good agreement was achieved between simulation results of the bulk phase and quantum calculations which are performed to determine the optimized structure of isolated ion pairs in chosen configurations and the strength of cationanion interactions.