The newly developed density functional M06-2x was used to predict the structures and stacking interactions of the nucleic acid base dimers of uracil and thymine. This study demonstrates that the M06-2x functional is able to predict stacked structures for the uracil and thymine dimers that are in good agreement with MP2 theory. From the reliable CCSD(T) results, the stacking energies estimated by the DFT M06-2x approach (-9.2 kcal/mol for U: U and -10.8 kcal/mol for T: T) appear consistently better than those evaluated by the MP2 method. The DFT M06-2x functional with the DZP++ basis set appears to provide reliable and reasonable descriptions for the stacked nuclei acid bases. (c) 2008 Elsevier B.V. All rights reserved.