Document Type


Original Publication Date


Journal/Book/Conference Title

The Journal of Chemical Physics





DOI of Original Publication



Originally published at http://dx.doi/org/10.1063/1.4817327

Date of Submission

October 2015


Equilibrium thermochemical measurements using an ion mobility drift cell technique have been utilized to investigate the binding energies and entropy changes associated with the stepwise hydration of the biologically significant ions pyrimidine radical cation and protonated pyrimidine. The binding energy of the hydrated pyrimidine radical cation is weaker than that of the proton-bound dimer pyrimidineH+(H2O) consistent with the formation of a weak carbon-based CHδ+··OH2 hydrogen bond (11.9 kcal/mol) and a stronger NH+··OH2 hydrogen bond (15.6 kcal/mol), respectively. Other proton-bound dimers such as pyrimidineH+(CH3OH) and pyrimidineH+(CH3CN) exhibit higher binding energies (18.2 kcal/mol and 22.8 kcal/mol, respectively) due to the higher proton affinities and dipole moments of acetonitrile and methanol as compared towater. The measured collisional cross sections of the proton-bound dimers provide experimental-based support for the DFT calculated structures at the M06-2x/6-311++G (d,p) level. The calculations show that the hydrated pyrimidine radical cation clusters form internally solvated structures in which the water molecules are bonded to the C4N2H4 •+ ion by weak CHδ+··OH2 hydrogen bonds. The hydrated protonated pyrimidine clusters form externally solvatedstructures where the water molecules are bonded to each other and the ion is external to thewater cluster. Dissociative proton transfer reactions C4N2H4 •+(H2O)n−1 + H2O → C4N2H3 • + (H2O)nH+ and C4N2H5 +(H2O)n−1 + H2O → C4N2H4 + (H2O)nH+ are observed for n ≥ 4 where the reactions become thermoneutral or exothermic. The absence of the dissociative proton transfer reaction within the C4N2H5 +(CH3CN)n clusters results from the inability of acetonitrile molecules to form extended hydrogen bonding structures such as those formed by water and methanol due to the presence of the methyl groups which block the extension of hydrogen bonding networks.


Hamid, A. M., Sharma, P., & El-Shall, M. S., et al. Hydration of the pyrimidine radical cation and stepwise solvation of protonated pyrimidine with water, methanol, and acetonitrile. The Journal of Chemical Physics, 139, 084304 (2013). Copyright © 2013 AIP Publishing LLC.

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