Nucleotides, the basic building block of DNA and RNA molecules, are composed of a nucleobase, a five-membered sugar ring, and a phosphate group. The sugar ring (either ribose in RNA or deoxyribose in DNA) forms the flexible link between the nucleobase and phosphate backbone, and the pucker of this ring plays an important role in nucleotide structure and function.  We present benchmark quantum data at the MP2 level for the 2D potential energy surface for DNA and RNA sugars in torsion space. Thesehigh-level surfaces are compared with those obtained from empirical MM and combined QM/MM potentials. We explore the use of a 2D correction that allows coupling of endocyclic torsions, based on the high-level reference potentials, for use in molecular simulations.

Modeling sugar pseudorotation in simulations of DNA and RNA nucleotides

245th National Meeting (2013)

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