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

Citations Over TimeTop 10% of 2014 papers

Abstract

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.

Related Papers

• → A global potential energy surface for the H2 + OH ↔ H2O + H reaction using neural networks(2013)180 cited
• → Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes(2008)90 cited
• → Mode specificity in the OH + CHD3 reaction: Reduced-dimensional quantum and quasi-classical studies on an ab initio based full-dimensional potential energy surface(2016)18 cited
• → Quantal study of the exchange reaction for N+N2 using an ab initio potential energy surface(2003)78 cited
• → A global 12-dimensional ab initio potential energy surface and dynamical studies for the SiH4+H→SiH3+H2 reaction(2006)10 cited