In the present work, we demonstrate the results of a theoretical study concerned with the question how tautomerization and protonation of adenine affect the various properties of adenine-cytosine mismatches. The calculations, in gas phase and in water, are performed at B3LYP/6-311++G(d,p) level. In gas phase, it is observed that any tautomeric form of investigated mismatches is more stabilized when adenine is protonated. As for the neutral mismatches, the mismatches containing amino form of cytosine and imino form of protonated adenine are more stable. The role of aromaticity on the stability of tautomeric forms of mismatches is investigated by NICS(1)ZZ index. The stability of mispairs decreases by going from gas phase to water. It can be explained using dipole moment parameter. The influence of hydrogen bonds on the stability of mismatches is examined by atoms in molecules and natural bond orbital analyses. In addition to geometrical parameters and binding energies, the study of the topological properties of electron charge density aids in better understanding of these mispairs.

The effect of substitution on the strength and nature of CHÁ Á ÁN hydrogen bond in XCCHÁ Á ÁNH 3 (X ¼ F, Cl, Br, OH, H, Me) and NCHÁ Á ÁNH 3 complexes were investigated by quantum chemical calculations. Ab initio calculations were performed using MP2 method with a wide range of basis sets. With tacking into account the BSSE and ZPVE, the values of BEs decrease. Replacement of the nonparticipatory hydrogen atom of HCCH by the electronegative atoms (F, Cl, and Br), lead to the BEs increases. The BE corresponding to the replacement of the nonparticipatory hydrogen atom of HCCH by the OH and CH 3 groups decreases. A far greater enhancement of the interaction energy arises from replacement of HCCH by the more acidic HCN. The natural bond orbital analysis and the Bader's quantum theory of atoms in molecules were also used to elucidate the interaction characteristics of these complexes. The electrostatic nature of H-bond interactions is predicted from QTAIM analysis. In addition, the relationship between the isotropic and anisotropic chemical shifts of the bridging hydrogen and binding energy of complexes as well as electron density at NÁ Á ÁH BCPs were investigated.

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