DNA Base Trimers: Empirical and Quantum Chemical Ab Initio Calculations vs. Experiment in Vacuo

Kabelác, M.; Sherer, E. C.; Cramer, C. J.; Hobza, P.
Chem. Eur. J. 2007, 13, 2067.

A complete scan of the potential energy surfaces for selected DNA base trimers has been performed by a molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The resulting most stable/populated structures were then reoptimized at a correlated ab initio level employing Resolution of the Identity Møller-Plesset second-order perturbation theory (RI-MP2). A systematic study of these trimers at so complete a level of electronic structure theory is presented for the first time. We show that prior experimental and theoretical interpretations were incorrect in assuming that the most stable structures of the methylated trimers correspond to planar systems characterized by cyclic intermolecular hydrogen bonding. We found that stacked structures of two bases with the third base in a T-shape arrangement are the global minima in all of the methylated systems: they are more stable than the cyclic planar structures by about 10 kcal/mol. The different behavior of non-methylated and methylated trimers is also discussed. The high-level geometries and interaction energies computed for the trimers serve also as a reference for the testing of recently developed DFT functionals with respect to their ability to describe correctly the balance between electrostatic and dispersion contributions that binds these trimers together. The recently reported M052X functional with a polarized triple-zeta basis set predicts 11 uracil trimer interaction energies with a root-mean-square error of 2.3 kcal/mol compared to our most highly correlated ab initio level of theory.

To request a copy of this article, send e-mail to the Research Reports Coordinator at the Minnesota Supercomputer Institute (requests@msi.umn.edu). Please provide a mailing address and specify that you would like UMSI report 2007/53.