Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods

Neglect
of diatomic differential overlap (NDDO) and self-consistent
density-functional tight-binding (SCC-DFTB) semiempirical models commonly
employed in combined quantum mechanical/molecular mechanical simulations
fail to adequately describe the deoxyribose and ribose sugar ring
puckers. This failure limits the application of these methods to RNA
and DNA systems. In this work, we provide benchmark ab initio gas-phase two-dimensional potential energy scans of the RNA and
DNA sugar puckering. The benchmark calculations are compared with
semiempirical models. Pucker corrections are introduced into the semiempirical
models via B-spline interpolation of the potential energy difference
surface relative to the benchmark data. The corrected semiempirical
models are shown to well reproduce the ab initio puckering
profiles. Furthermore, we demonstrate that the uncorrected semiempirical
models do not usually produce a transition state between the A-form
and B-form sugar puckers, but the ab initio transition
state is reproduced when the B-spline correction is used.