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Ring current and electric field effects can considerably influence NMR chemical shifts in biomolecules. Understanding such effects is particularly important for the development of accurate mappings between chemical shifts and the structures of nucleic acids. In this work, we first analyzed the Pople and the Haigh-Mallion models in terms of their ability to describe nitrogen base conjugated ring effects. We then created a database (DiBaseRNA) of three-dimensional arrangements of RNA base pairs from X-ray structures, calculated the corresponding chemical shifts via a hybrid density functional theory approach and used the results to parametrize the ring current and electric field effects in RNA bases. Next, we studied the coupling of the electric field and ring current effects for different inter-ring arrangements found in RNA bases using linear model fitting, with joint electric field and ring current, as well as only electric field and only ring current approximations. Taken together, our results provide a characterization of the interdependence of ring current and electric field geometric factors, which is shown to be especially important for the chemical shifts of non-hydrogen atoms in RNA bases.

Original publication

DOI

10.1021/jp3057306

Type

Journal article

Journal

J Phys Chem B

Publication Date

21/02/2013

Volume

117

Pages

1989 - 1998

Keywords

Crystallography, X-Ray, Databases, Factual, Electricity, Hydrogen Bonding, Magnetic Resonance Spectroscopy, Models, Molecular, Nitrogen, Nucleic Acid Conformation, RNA, Software