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Factors affecting the computation of the 13 C shielding in disaccharides
Author(s) -
Garay Pablo G.,
Martin Osvaldo A.,
Scheraga Harold A.,
Vila Jorge A.
Publication year - 2014
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.23697
Subject(s) - glycosidic bond , disaccharide , chemistry , glycan , density functional theory , computational chemistry , anomer , carbohydrate conformation , molecular dynamics , computation , molecule , stereochemistry , crystallography , nuclear magnetic resonance spectroscopy , glycoprotein , organic chemistry , mathematics , algorithm , biochemistry , enzyme
Knowledge of the three‐dimensional structures of glycans and glycoproteins is useful for a full understanding of molecular processes in which glycans are involved, such as antigen‐recognition and virus infection, to name a few. Among the ubiquitous nuclei in glycan molecules, the 13 C nucleus is an attractive candidate for computation of theoretical chemical shifts at the quantum chemical level of theory to validate and determine glycan structures. For this purpose, it is important to determine, first, which carbons can be used as probes to sense conformational changes and, second, all factors that affect the computation of the shielding, at the density functional theory (DFT) level of theory, of those carbons. To answer such questions, we performed a series of analyses on low‐energy conformations, obtained by sampling the glycosidic torsional angles ( ϕ , ψ ) every 10°, of 12 disaccharides. Our results provide evidence that: (i) the carbons that participate in the glycosidic linkage are the most sensitive probes with which to sense conformational changes of disaccharides; (ii) the rotation of the hydroxyl groups closest to the glycosidic linkage significantly affects the computation of the shieldings of the carbons that participate in the glycosidic linkage; (iii) it is not possible to obtain the shieldings of one disaccharide from the computed values of a different disaccharide or from those disaccharides that differ in the anomeric state; and (iv) a proper basis set distribution, a functional, and a step size, with which to sample the conformational space, are necessary to compute shieldings accurately and rapidly. © 2014 Wiley Periodicals, Inc.