Solution Structure of Mannobioses Unravelled by Means of Raman Optical Activity

Abstract

Structural analysis of carbohydrates is a complicated endeavour, due to the complexity and diversity of the samples at hand. Herein, we apply a combined computational and experimental approach, employing molecular dynamics (MD) and density functional theory (DFT) calculations together with NMR and Raman optical activity (ROA) measurements, in the structural study of three mannobiose disaccharides, consisting of two mannoses with varying glycosidic linkages. The disaccharide structures make up the scaffold of high mannose glycans and are therefore important targets for structural analysis. Based on the MD population analysis and NMR, the major conformers of each mannobiose were identified and used as input for DFT analysis. By systematically varying the solvent models used to describe water interacting with the molecules and applying overlap integral analysis to the resulting calculational ROA spectra, we found that a full quantum mechanical/molecular mechanical approach is required for an optimal calculation of the ROA parameters. Subsequent normal mode analysis of the predicted vibrational modes was attempted in order to identify possible marker bands for glycosidic linkages. However, the normal mode vibrations of the mannobioses are completely delocalised, presumably due to conformational flexibility in these compounds, rendering the identification of isolated marker bands unfeasible.

Simulation of Raman and Raman optical activity of saccharides in solution

“…We were able to recover most of the errors performing full optimization of the sugar while keeping the water molecules frozen (MM_w, i.e. the OPTSOLUTE approach used by the ''Manchester group'' 13,17 ), however, at additional computational cost. Further comparison of hybrid_w and hybrid_fo showed that excessive optimization without any restraints only worsens the results.…”

“…Small basis set 6-31G* was not able to accurately reproduce the spectral features. The widely used rDPS basis set 11,13,[17][18][19][20] (see Table S1 in the ESI †) provides significantly better results at a similar cost to the 6-31G* basis set. Using the 6-311++G** basis set provides further improvement of the results at B2.5Â the performance cost as compared to rDPS.…”

“…8 shows that the 6-31G* basis set is not large enough to reproduce the spectral features, while 6-311++G** is sufficient and it performs almost the same as the much more expensive aug-ccpvtz. The frequently used rDPS basis set 11,13,[17][18][19][20] offers slightly worse performance compared to 6-311++G** at the cost of the B6-31G* basis set.…”

“…The same approach was recently used to study mannobiose disaccharides, where MD simulations, together with NMR spectroscopy, and DFT calculations were combined to produce Raman/ROA spectra. 17 Another study focused on b-xylose showed that at least a 1 nm thick layer of water molecules is needed to model correctly the bulk aqueous environment. 18 Other studies using explicit waters focused on subtle spectral modifications between D-glucose and D-galactose differing only in one chiral center 19 and on a study of D-glucuronic acid and N-acetyl-D-glucosamine.…”

Helical polysaccharides

“…This technique has been used to determine the secondary structure of native and carboxylated agarose gels . Recently, ROA has been applied to dimannosides with different glycosidic linkages …”