An optimized potential function for the calculation of nucleic acid interaction energies I. base stacking

An optimized potential function for base-stacking interactions is constructed. Stacking energies between the complementary pairs of a dimer are calculated as a function of the rotational angle and separation distance. Using several different sets of atomic charges, the electrostatic component in the monopole-monopole approximation (MMA) is compared to the more refined segmented multipole-multipole representation (SMMA); the general features of the stacking minima are found to be correctly reproduced with IEHT or CNDO atomic charges. The electrostatic component is observed to control the location of stacking minima.The MMA, in general, is not a reliable approximation of the SMMA in regions away from minima; however, the MMA is reliable in predicting the location and nature of stacking minima.The attractive part of the Lennard-Jones 6-12 potential is compared to and parameterized against the expressions for the second-order interaction terms composed of multipole-bond polarizability for the polarization energy and transition-dipole bond polariz abilities for approximation of the dispersion energy. The repulsive part of the Lennard-Jones potential is compared to a Kitaygorodski-type repulsive function; changing the exponent from its usual value of 12 to 11.7 gives significantly better agreement with the more refined repulsive function.Stacking minima calculated with the optimized potential method are compared with various perturbation-type treatments. The optimized potential method yields results that compare as well with melting data as do any of the more recent and expensive perturbation methods.