The interactions of alkyl substituted imidazolium bis(trifluoromethanolsulfonyl)imide protic ionic liquids (PILs) HCnImNTf2 (n = 0-12) were studied using vibrational spectroscopy (FT-IR/ATR and FT-Raman) and differential scanning calorimetry (DSC). The effect of alkyl substituent length (n = 0-12) and temperature on the relative magnitude of the different interactions is elucidated. For short carbon alkyl chains (n < 3), the PIL structure is affected from intramolecular interaction caused from the induction effect (+I) due to the chain substituent of the imidazolium ring, while for PILs with n > 3 the van der Waals forces between the chains and π-π interaction between neighboring imidazolium rings become important. The tendency of reducing the melting point and increasing glass transition values with the lengthening of the alkyl chain was also noticed as a result the increasing contribution of the van der Waals forces to the overall interactions. Finally, we also show that the conformational isomerism of the anion (expressed by ΔHeq) is a good indicator of the relative magnitude of the interactions. When Coulombic interactions are predominant, the trans conformer is the most probable, while when other type of interactions (HB, vdW, etc.) become important the cis conformer is favored.