Structures and stabilities of H-bonded adenine···uracil Watson−Crick (AU WC) and two uracil···uracil nucleic acid base pairs possessing C−H···O contacts (UU7, UU−C) were determined using gradient optimization with inclusion of electron correlation via the second-order Møller−Plesset (MP2) perturbational method with a 6-31G** basis set of atomic orbitals. In the AU WC pair, closest contacts occur between the N6(A) and O4(U), N1(A) and N3(U), and C2(A) and O2(U) atoms:  2.969, 2.836, and 3.568 Å, respectively. For the UU7 pair the closest contact corresponds to O4···N1 and C5···O2 pairs with distances of 2.860 and 3.257 Å, respectively, while in UU−C pair the closest contact was found for O4···N3 and C5···O4 heteroatoms with distances of 2.913 and 3.236 Å, respectively. The nature of all intermolecular contacts in the sense of a conventional H-bonding or improper, blue-shifting H-bonding was determined on the basis of harmonic vibrational analysis, atom-in-molecules (AIM) Bader analysis of electron density, and natural bond orbital analysis (NBO) performed at the MP2/6-31G** level of theory. N−H stretch frequencies of A and U exhibited a red shift and intensity decrease upon formation of AU WC base pair. It unambiguously proves the existence of the N−H···O and O···H−N H-bonds. The frequency shift of the C−H stretching frequency of A upon complex formation is, however, marginal (2 cm-1). Bader AIM analysis and NBO analysis confirmed the existence of N−H···O and O···H−N H-bonds in the AU WC pair but was inconclusive in the case of C−H···O contact. The results thus clearly show that the C2−H2···O2 contact in the AU or AT WC base pair corresponds neither to standard H-bond nor to improper, blue-shifting H-bond. The opposite result, however, has been found for the UU pairs; here the vibrational analysis shows a red shift and intensity increase of both N−H and C−H stretching vibrational frequencies upon the formation of the pair. This is a clear manifestation of the presence of two H-bonds of the N−H···O and O···H−C types. Bader AIM analysis as well as NBO analysis confirmed the existence of both H-bonds.