title: Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods.
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 benchmarkab initiogas-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 theab initiopuckering 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 theab initiotransition state is reproduced when the B-spline correction is used.
authors.affiliation: Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University , 174 Frelinghuysen Road, Piscataway, New Jersey 08854-8076, United States ; Scientific Computation, University of Minnesota , 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States.
authors.forename: Ming
authors.initials: M
authors.lastname: Huang
authors.affiliation: Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University , 174 Frelinghuysen Road, Piscataway, New Jersey 08854-8076, United States.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Giese
authors.affiliation: Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University , 174 Frelinghuysen Road, Piscataway, New Jersey 08854-8076, United States.
authors.forename: Tai-Sung
authors.initials: TS
authors.lastname: Lee
authors.affiliation: Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University , 174 Frelinghuysen Road, Piscataway, New Jersey 08854-8076, United States.
authors.forename: Darrin M
authors.initials: DM
authors.lastname: York