Rapid evaluation of the interaction energies for hydrogen-bonded uracil and thymine dimers, trimers and tetramers

Abstract Hydrogen bonds play an important role in the self-assembled processes of nucleic acid bases. The ability to rapidly and accurately evaluate the interaction energy for hydrogen-bonded nucleic acid base pairs and multimers is critical for correctly understanding the mechanism underlying the assembly and modeling the self-assembled processes of nucleic acid bases. In this paper, the polarizable dipole–dipole interaction model is developed and applied to hydrogen-bonded uracil and thymine base dimers, trimers and tetramers. We regard the chemical bonds N H, C H and C O in uracil and thymine as bond dipoles. The magnitude of the bond dipole moment varies according to its environment. The parameters needed are first determined from the training dimers. Then the polarizable dipole–dipole interaction model together with the parameters is applied to a series of hydrogen-bonded uracil and thymine base dimers, trimers and tetramers. The hydrogen bond distances and the interaction energies obtained from the polarizable dipole–dipole interaction model are compared to those obtained from MP2 calculations. The calculation results show that the polarizable dipole–dipole interaction model produces the equilibrium hydrogen bond distances compared well with those yielded by the MP2/6-31G(d) method and produces the interaction energies in good agreement with those yielded by the counterpoised-corrected MP2/6-311++G(3df,2p) method, demonstrating that the polarizable dipole–dipole interaction model is reasonable and useful.