Intramolecular Basis Set Superposition Error Effects on the Planarity of DNA and RNA Nucleobases

Molecules of utmost importance like DNA and RNA nucleobases are predicted to be nonplanar by a typical ab initio method, such as second order Møller-Plesset perturbation theory (MP2) combined with standard Pople's basis sets. Similarly to the case of other planar aromatic systems, these pitfalls can be explained in terms of intramolecular basis set superposition error (BSSE) effects, induced by local basis set deficiencies. We demonstrate that conventional BSSE correction techniques such as the Counterpoise method can account for this wrong behavior and provide proper correction whenever spurious results occur, mainly in case of thymine, uracil and guanine but also to lower extent for adenine and cytosine. We also show that special care must be taken when assessing the BSSE by means of ghost-orbital calculations for strongly overlapping fragments. Often molecular orbitals in the isolated fragment calculation have a different orientation as in the ghost-orbital calculation. This can lead to bogus derivatives of the CP-correction term, essential to account for geometry and vibrational BSSE effects.