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The chemical and physical properties of imidazolium-based ionic liquids are determined by the interactions between the counter-ions. The C(2) position plays an important role in these interactions, as it represents the predominant site for interionic hydrogen bonding. This study shows that the directional hydrogen bonds between highly symmetrical anions (iodide, tetrafluoroborate, hexafluorophosphate) and the C(2)-H group of the 1-methyl-3-propylimidazolium cation determine the molecular and macroscopic behavior in terms of the thermal properties. Upon replacing the C(2) proton by a methyl group, the anion repositions itself at the C(4)/(5) moiety, where it forms a new hydrogen bond, apparently with only one of the two CH groups. In addition, the larger the anion is in diameter, the more likely it will establish further interactions with other parts of the cation, such as the propyl chain.