Theoretical calculations were carried out for studying the tautomeric protonation of N-methyl piperazine as a prototype six-member aliphatic ring containing a secondary and a tertiary nitrogen atom. The protonation was investigated in three solvents: water, acetonitrile, and dichloromethane. Calculations were performed up to the B3LYP/aug-cc-pvtz and QCISD(T)/CBS levels by applying the IEF-PCM polarizable continuum dielectric solvent model. Relative solvation free energies also were calculated upon explicit solvent models by utilizing the free-energy perturbation theory as implemented in Monte Carlo simulations.The relative free energy for the N-methyl piperazine tautomer protonated at the secondary (NMps) rather than at the tertiary (NMpt) nitrogen was calculated at a ratio of 47/53 in infinitely dilute aqueous solution. The ratio further decreases in lower polarity solvents. In contrast, NMR experiments suggest that the protonation takes place primarily at the secondary nitrogen in 0.37 molar aqueous solution with NMps/NMpt = 80/20. The NMps tautomer is exclusive in dichloromethane at the same concentration. The discrepancy between theory and experiment was resolved by considering association equilibria in parallel with the protonation for the solute. As a result, the theoretically predicted tautomer ratios were obtained in close agreement with the experimental values. The NMps tautomer could form a preferable dimeric structure, where one or two chloride anion(s) is/are in hydrogen bonds with protons of the associating monomers.The calculations suggest that the proton relocation may take place by solvent assistance in water or along an intramolecular proton jump in the twist-boat conformation. The predicted activation free energy was about 10 kcal/mol on the basis of variable temperature NMR experiments in DCM.

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