Hydrogen bonding in imidazole plays a key role it proton conduction and rotation of an imidazole molecule in the process results in the cleavage of hydrogen bonds between molecules. In the present work, we characterize proton transport and rotation, energy barriers in imidazole chains by density functional theory: Our calculations show that propagation of an excess proton along the chain requires crossing of energy barriers, lower than 1 kcal/mol. The presence of the proton has stronger effect on the immediate neighboring imidazole molecules, and the effect is negligible after two molecules. The subsequent rotation of all imidazole molecules after the transfer of first proton is essential to allow the transfer the second proton. The presence of an excess proton in the chain leads to cleavage of hydrogen bonds and the rotation of neighboring imidazole molecule. Further;, rotation of one imidazole molecule results in rotation of all molecules in the chain. The calculated rotational energy barriers in two-, three-, and four-imidazole-molecule chains are 8.0, 17.1, and 20.0 kcal; respectively, and are equivalent to the number of hydrogen bonds broken in the process. The rotational barrier is higher than the proton transport barrier along the hydrogen bond and, thus, is the rate-determining step of proton conduction.