Stacking and H-bonding patterns of dGpdC and dGpdCpdG: Performance of the M05-2X and M06-2X Minnesota density functionals for the single strand DNA

Abstract

The Minnesota density functionals, M05-2X and M06-2X, were used to predict the structures of the nucleotide oligomers. This study indicates that these functionals are able to reliable predict bases stacked structures in nucleotide oligomers (dGpdC and dGpdCpdG). The obtained results are in excellent agreement with those from the MP2 theory. The electron density distributions between the stacked nucleobases calculated by the Minnesota density functionals are very close to that evaluated by the MP2 method (differences are less than 0.001 au). The M05-2X and M06-2X functionals also appear to provide a reliable description for the intra-strand H-bonding in single strands of DNA.