• hydrogen bond;
  • interaction energy;
  • permanent bond dipole moment;
  • induced bond dipole moment;
  • dipole–dipole interaction;
  • polarization

In this article, a polarizable dipole–dipole interaction model is established to estimate the equilibrium hydrogen bond distances and the interaction energies for hydrogen-bonded complexes containing peptide amides and nucleic acid bases. We regard the chemical bonds N[BOND]H, C[DOUBLE BOND]O, and C[BOND]H as bond dipoles. The magnitude of the bond dipole moment varies according to its environment. We apply this polarizable dipole–dipole interaction model to a series of hydrogen-bonded complexes containing the N[BOND]H···O[DOUBLE BOND]C and C[BOND]H···O[DOUBLE BOND]C hydrogen bonds, such as simple amide-amide dimers, base-base dimers, peptide-base dimers, and β-sheet models. We find that a simple two-term function, only containing the permanent dipole–dipole interactions and the van der Waals interactions, can produce the equilibrium hydrogen bond distances compared favorably with those produced by the MP2/6-31G(d) method, whereas the high-quality counterpoise-corrected (CP-corrected) MP2/aug-cc-pVTZ interaction energies for the hydrogen-bonded complexes can be well-reproduced by a four-term function which involves the permanent dipole–dipole interactions, the van der Waals interactions, the polarization contributions, and a corrected term. Based on the calculation results obtained from this polarizable dipole–dipole interaction model, the natures of the hydrogen bonding interactions in these hydrogen-bonded complexes are further discussed. © 2013 Wiley Periodicals, Inc.