DNA base stacking: the stacked uracil/uracil and thymine/thymine minima.

The potential energy surfaces of stacked uracil dimer (U/U) and stacked thymine dimer (T/T) have been explored at the counterpoise (CP)-corrected M06-2X/6-31+G(d) level of theory, in the gas phase and in solution (with water and, for U/U, 1,4-dioxane as the solvents) modeled by a continuum solvent using the polarizable continuum model. Potential energy scans were created by rotation of one monomer around its center-of-mass, whereas the other monomer remained still. Both face-to-back (one molecule exactly on top of the other) and face-to-face (one base molecule flipped by 180°) structures were considered. Five or six (dependent on whether CP correction is included or not) stacked uracil dimer minima and six stacked thymine dimer minima were located. A number of transition states on the U/U and T/T potential energy surfaces were likewise identified. The general effect of the continuum solvent is a flattening of the potential energy surface. Comparison of the gas-phase M06-2X/6-31+G(d) U/U interaction energies with estimated CCSD(T)/complete basis set values (where available) show the excellent performance of this functional for stacking energies.