Towards Elucidating Structure-Spectra Relationships in Rhamnogalacturonan II - Computational Protocols for Accurate 13 C and 1 H Shifts for Apiose and its Borate Esters

Research output: Contribution to journalArticlepeer-review

Abstract

Apiose is a naturally occurring, uncommon branched-chain pentose found in plant cell walls as part of the complex polysaccharide Rhamnogalacturonan II (RG-II). The structural elucidation of the three-dimensional structure of RG-II by nuclear magnetic resonance (NMR) spectroscopy is significantly complicated by the ability of apiose to cross-link via borate ester linkages to form RG-II dimers. Here, we developed a computational approach to gain insight into the structure–spectra relationships of apio–borate complexes in an effort to complement experimental assignments of NMR signals in RG-II. Our protocol involved structure optimizations using density functional theory (DFT) followed by isotropic magnetic shielding constant calculations using the gauge-invariant atomic orbital (GIAO) approach to predict chemical shifts. We evaluated the accuracy of 23 different functional–basis set (FBS) combinations with and without implicit solvation for predicting the experimental 1H and 13C shifts of a methyl apioside and its three borate derivatives. The computed NMR predictions were evaluated on the basis of the overall shift accuracy, relative shift ordering, and the ability to distinguish between dimers and monomers. We demonstrate that the consideration of implicit solvation during geometry optimizations in addition to the magnetic shielding constant calculations greatly increases the accuracy of NMR chemical shift predictions and can correctly reproduce the ordering of the 13C shifts and yield predictions that are, on average, within 1.50 ppm for 13C and 0.12 ppm for 1H shifts for apio–borate compounds.

Original languageAmerican English
Article number756219
Number of pages15
JournalFrontiers in Molecular Biosciences
Volume8
DOIs
StatePublished - 2022

Bibliographical note

Publisher Copyright:
Copyright © 2022 Bharadwaj, Westawker and Crowley.

NREL Publication Number

  • NREL/JA-2800-78883

Keywords

  • H and C
  • Apiose
  • Borate
  • DFT
  • Gauge invariance approach
  • NMR chemical shifts
  • Quantum chemistry
  • Rhamnogalacturonan II

Fingerprint

Dive into the research topics of 'Towards Elucidating Structure-Spectra Relationships in Rhamnogalacturonan II - Computational Protocols for Accurate 13 C and 1 H Shifts for Apiose and its Borate Esters'. Together they form a unique fingerprint.

Cite this