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Thermodynamic Parameters for Stacking and Hydrogen Bonding of Nucleic Acid Bases in Aqueous Solution: Ab Initio/Langevin Dipoles Study

The potentials of mean force (PMF) for the association of purine, adenine, thymine, guanine, cytosine, and uracil in aqueous solution are investigated using ab initio MP2/6-31G(d-0.25) calculations (diffuse d-polarization functions were used) and Langevin dipoles solvation model. The entropy contributions to the free energies for stacking and hydrogen bonding are approximated using the linear relationship between binding enthalpies and entropies determined here from the available experimental data. This methodology is used to evaluate the dependence of PMF, and the gas-phase and solvation energies on the twist angle (Ω) in a number of undisplaced face-to-back stacking complexes. Further, we characterized the vertical association of the parallel (Ω = 0°) and antiparallel (Ω = 180°) stacked cytosine dimers. The results show large compensation between the gas-phase and solvation energetics and an overall preference of the bases in the undisplaced face-to-back stacked complexes for the twist angles near 30°. ...