The interactions of Mg2+and Ca2+binding toadenine, cytosine, guanine, and thymine at various bindingsites were studied by a high-level quantum chemicalmethod and ABEEMrp/MM fluctuating charge model. Thegeometries and binding energies of M2+-bases complexeswere determined at CCSD(T)/6-311++G(2d,2p)//MP2/6-311++G(2d,2p) level of theory, with the basis setsuperposition error corrections for the binding energy calculations. In comparison with the ab initio results, anaccurate classical metal cation–base interaction potentialwas constructed and parameterized in terms of ABEEMrp/MM model. It is revealed that Mg2+/Ca2+prefers to bindwith bases at the bidentate position (between two nitrogenatoms or oxygen and nitrogen atoms in purine andpyrimidine), where the binding energy is the largest.Moreover, the distance between M2+and the base increases from Mg2+to Ca2+, while the binding energy ofMg2+–base is greater than that of Ca2+-base. TheABEEMrp/MM potential gives reasonable geometries andbinding energies compared with the present quantumchemical calculations, and the overall percentage RMSDsare 1.4 and 1.6% for geometries and binding energies,respectively. Furthermore, the transferability of theparameters of the new potential is validated by investigation of Mg2+/Ca2+binding to tautomer of bases, and
results from our potential also show quite good consistencywith those of MP2/6-311++G(2d,2p)//B3LYP/6-311++G(d,p) method, with the overall percentageRMSDs of 2.2 and 4.7% for geometries and bindingenergies, respectively. This work will serve as a basis forfurther investigations of the mechanisms of cation effectson the structure and property of nucleic acids
