Calculation of 13C chemical shifts in RNA nucleosides: Structure-13C chemical shift relationships

Paolo Rossi, Gerard S. Harbison

Research output: Contribution to journalArticle

36 Citations (Scopus)

Abstract

Isotropic 13C chemical shifts of the ribose sugar in model RNA nucleosides are calculated using SCF and DFT-GIAO ab initio methods for different combinations of ribose sugar pucker, exocyclic torsion angle, and glycosidic torsion angle. Idealized conformations were obtained using structures that were fully optimized by ab initio DFT methods starting with averaged parameters from a collection of crystallographic data. Solid-state coordinates of accurate crystal or neutron diffraction structures were also examined directly without optimization. The resulting 13C chemical shifts for the two sets of calculations are then compared. The GIAO-DFT method overestimates the shifts by an average of 5 ppm while the GIAO-SCF underestimates the shifts by the same amount. However, in the majority of cases the errors appear to be systematic, as the slope of a plot of calculated vs experimental shifts is very close to unity, with minimal scatter. The values of the 13C NMR shifts of the ribose sugar are therefore sufficiently precise to allow for statistical separation of sugar puckering modes and exocyclic torsion angle conformers, based on the canonical equation model formulated in a previous paper.

Original languageEnglish (US)
Pages (from-to)1-8
Number of pages8
JournalJournal of Magnetic Resonance
Volume151
Issue number1
DOIs
StatePublished - Jan 1 2001

Fingerprint

nucleosides
Ribose
Chemical shift
sugars
Nucleosides
ribose
Sugars
chemical equilibrium
Discrete Fourier transforms
Torsional stress
RNA
torsion
shift
Neutron Diffraction
self consistent fields
Neutron diffraction
neutron diffraction
Conformations
unity
plots

Keywords

  • Chemical shift
  • Conformation
  • Nucleotide
  • RNA
  • Sugar pucker
  • ab initio

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Nuclear and High Energy Physics
  • Condensed Matter Physics

Cite this

Calculation of 13C chemical shifts in RNA nucleosides : Structure-13C chemical shift relationships. / Rossi, Paolo; Harbison, Gerard S.

In: Journal of Magnetic Resonance, Vol. 151, No. 1, 01.01.2001, p. 1-8.

Research output: Contribution to journalArticle

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