The small planarization barriers for the amino group in the nucleic acid bases

The amino group in the nucleic acid bases frequently interacts with other bases or with other molecular systems. Thus any nonplanarity of the amino group may affect the molecular recognition of nucleic acids. Ab initio Hartree-Fock (HF) and second-order Moller-Plesset perturbation (MP2) levels of theory have been used to obtain the equilibrium geometries of the C-l and C-s structures for five common nucleic acid bases. The energy barriers between the C-l and C-s structures have also been predicted. A series of correlation consistent basis sets up to cc-pCVQZ and aug-cc-pVQZ has been used to systematically study the dependence of the amino group nonplanarity. The equilibrium geometries of the nucleic acid bases with an amino group, including adenine, guanine, and cytosine, are examined carefully. At the MP2 level of theory, larger basis sets decrease the extent of nonplanarity of the amino group, but the decrease slows down when the QZ basis sets are used, demonstrating the intrinsic property of nonplanarity for guanine. For adenine and cytosine the situation is less clear; as the HF limit is approached, these two structures become planar. Addition of core correlation effects or diffuse functions further decreases the degree of nucleic acid base nonplanarity, in comparison to the original cc-pVXZ (X=D, T, and Q) basis sets. The aug-cc-pVXZ basis shows smaller degrees of nonplanarity than the cc-pCVXZ sets. The aug-cc-pVXZ basis is less size dependent than the cc-pVXZ and cc-pCVXZ sets in the prediction of the amino-group-related bond angles and dihedral angles and energy barriers for adenine, guanine, and cytosine. The cc-pCVQZ and aug-cc-pVQZ MP2 results may be regarded as benchmark predictions for the five common bases. The predicted classical barriers to planarization are 0.02 (adenine), 0.74 (guanine), and 0.03(cytosine) kcal mol(-1). (c) 2006 American Institute of Physics.