The Cornell et al. empirical potential (Cornell et al., J Am Chem Soc 1995, 117, 5197) was modified by the introduction of nonplanarity of the amino group in guanine, adenine, and cytosine. Reparameterization was performed for 12 bond parameters of the amino group (three valence angles (C-N-H(1), C-N-H(2), and H(1)-N-H(2)) and the improper dihedral angle at nitrogen, four dihedral angles (X-C-N-H(1), Y-C-N-H(2), X-X-C-N, Y-Y-C-N), three valence angles (X-C-N, Y-C-N, X-C-Y), and the improper dihedral angle at the adjacent carbon), and was based on correlated ab initio potential energy surfaces. Calculations were performed using the resolution of identity MP2 (RIMP2) method with SVP (3s2p1d/2s1p), TZVP (5s3p1d/3s1p), TZVPP (5s3p2d1f/3s2p1d), and augTZVPP (6s4p3d2f/4s3p2d) basis sets. Results obtained on the latter two levels are practically identical with the literature reference data [MP2/6-311++G(2df,p)] and the RIMP2/augTZVPP data can be considered a new reference set. The potential energy surface used for reparameterization was evaluated at the RIMP2/SVP level because respective geometry as well as energy data were close to the reference ones, and the computational time was very favorable. The modified potential was tested for 19 H-bonded and eight stacked nucleic acid base pairs. Interaction energies as well as geometries were described by the modified potential considerably better than by the original one and significant improvement resulted in the description of the nonplanar H-bonded and stacked complexes.

J Heyrovský Institute of Physical Chemistry Academy of Sciences of the Czech Republic 182 23 Prague 8 Czech Republic

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Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs