Energies of H-bonded DNA base pairs

H-bonded base pairs are stabilized mainly by electrostatic attraction. The high-level ab initio calculations provide reliable data on the energetics of H-bonding which can be used for verification and parameterization of force fields and as a substitution for the missing experimental data. 

Two other important interactions must be considered in the case of protonated pairs the induction interaction and the molecular ion - dipole interaction, i.e., interaction of the charged monomer with the electric field (dipole moment) of the neutral monomer. This interaction is very strong in protonated pairs with a highly polar neutral monomer. For example, the calculated gas-phase complexation energy of the triply-bonded CCH pair is -45 kcal/mol. The molecular ion - dipole interaction leads to protonation of adenine in the (AC)H pair. The strong electric field around cytosine shifts the proton to adenine [32b] despite that for isolated bases protonation of cytosine is preferred. 

It is important to notice that the CCSD(T) procedure provides essentially the same interaction energies as the MP2 procedure for H-bonded pairs [35b]. Basis 

The energetics of planar DNA base pairs [32a,b], trimers[13c], and pairs containing thiobases [59a] evaluated at the MP2 level with medium-sized polarized basis sets and using HF-optimized geometries. AE - HF/6-31G (0.25)//HF/6-31G data, - MP2/6- 

3lG (0.25)//HF/6-31G, AE - Becke3LYP/6-31G (0.25)//HF/6-31G data, AE - AE + deformation energy of monomers. The designation 6-31G (0.25) means that diffuse d-polarization functions with an exponent of 0.25 were used (See refs. [13e,32a,b,59a] for the nomenclature used for the structures). 

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