Stacking of nucleic acid bases: optimization of the computational approach—the case of adenine dimers

Abstract

Stacking interactions play an important role in stabilizing DNA and RNA secondary structure. To select a computational level to study the stacking interactions, both energy and geometric criteria, as well as the time necessary to optimize the system, should be taken into account. In this work, an attempt was made to find the most optimal level of theory describing the stacking interactions in adenine dimers. The obtained results have shown that for this purpose, wB97XD/6-311G(p,d), wB97XD/aug-cc-pvdz, or B97D3/aug-cc-pvdz should be used. What is more, geometry of the most preferable arrangements of molecules was also pointed out, ensuring an optimal starting system for further analyses.