Title: Towards Elucidating Structure–Spectra Relationships in Rhamnogalacturonan II: Computational Protocols for Accurate 13C and 1H Shifts for Apiose and Its Borate Esters

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 ¹ H and ¹³ C 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 predictionsmore » and can correctly reproduce the ordering of the ¹³ C shifts and yield predictions that are, on average, within 1.50 ppm for ¹³ C and 0.12 ppm for ¹ H shifts for apio–borate compounds.« less

Authors:

Bharadwaj, Vivek S.; Westawker, Luke P.; Crowley, Michael F.

Publication Date:

Mon Jan 24 00:00:00 EST 2022

Research Org.:

National Renewable Energy Lab. (NREL), Golden, CO (United States)

Sponsoring Org.:

USDOE Office of Science (SC), Basic Energy Sciences (BES)

OSTI Identifier:

1841599

Alternate Identifier(s):

OSTI ID: 1846750

Report Number(s):

NREL/JA-2800-78883
Journal ID: ISSN 2296-889X; 756219

Grant/Contract Number:  

AC36-08GO28308

Resource Type:

Published Article

Journal Name:

Frontiers in Molecular Biosciences

Additional Journal Information:

Journal Name: Frontiers in Molecular Biosciences Journal Volume: 8; Journal ID: ISSN 2296-889X

Publisher:

Frontiers Media SA

Country of Publication:

Switzerland

Language:

English

Subject:

BASIC BIOLOGICAL SCIENCES,BIOMASS FUELS; apiose; borate ester; carbohydrates; DFT; NMR chemical shifts; rhamnogalacturonan-II; solvation; quantum chemistry; gauge invariance approach