Polarizable Dipole-dipole Interaction Model Including Lone-pair Dipole Moment Treatment

Hydrogen bond plays an important role in the structure and functions of nucleic acids as well as the in the specificity and the structural stability of DNA-protein complexes. Hence, it is important to quickly and acuurately prediction of the structures and interaction energies of the hydrogen-bonded complexes. The polarizable dipole-dipole interaction model has been established in our laboratory and has been successfully used to rapidly and accurately calculate the interaction energies for the N-H…O=C, C-H…O=C and O-H…O hydrogen-bonded complexes. The present paper further develops the model into nucleic acids and DNA-protein complexes that include not only N-H…O=C, C-H…O=C and O-H…O, but also N-H…N and conducts predictions on the bond lengths and interaction energies of the complexes. The specifics of the study are as follows:1. We here not only regard the bonds C=O, C-O, N-H, C-H and O-H as bond dipoles, but also regard the nitrogens with lone-pair electrons of adenine, guanine, and cytosine as lone-pair dipoles. Six base dimers are selected as training dimers to work out the parametres needed.2. The polarizable dipole-dipole interaction model and the parametres are used to predict the equilibrium hydrogen bond distances in base dimers, nulceoside dimers,base-peptide complexes and nucleoside-peptide complexes with different types of hydrogen bonds as well as their interaction energies. The result shows that the equilibrium hydrogen bond distances worked out by the polarizable model satisfactorily compared with the results produced by the MP2/6-31+G(d,p) and B3LYP/6-31+G(d,p) methods. The interaction energies predicted by the polarizable model also well matches the results using MP2/aug-cc-pVTZ(BSSE)?MP2/CBS or CCSD(T)/CBS. Morover, the polarizable model reproduces the CP-corrected MP2/aug-cc-pVTZ interaction potential energy curves satisfactorily. The above results show that the polarizable model is reliable and the parameters determined in this work are reasonable.3. The interactions of the researched hydrogen-bond complexes can be broken down using the polarizable model. Based on the results, the natures of the hydrogen bonding interactions are further discussed. The results show that the sequence of the components in terms of proportions varies with different systems. However, the electrostatic interaction accounts for the most in all cases.4. Comparisons show that DFT-D method and the polarizable model can work out the interaction energies that match those by means of MP2/aug-cc-pVTZ(BSSE)method. Among them, the polarizable model works thousands of times more efficiently than DFT-D and MP2. The larger the system is, the more efficient the computation will be.