NMR and DFT analysis of trisaccharide from heparin repeating sequence
| Autor: | Miloš Hricovíni, Olga L. Malkina, Pierre-Alexandre Driguez |
|---|---|
| Rok vydání: | 2014 |
| Předmět: |
Coupling constant
Magnetic Resonance Spectroscopy Molecular Structure Chemistry Heparin Sodium Water Hydrogen Bonding Nuclear magnetic resonance spectroscopy Surfaces Coatings and Films Crystallography Molecular geometry Models Chemical Computational chemistry Intramolecular force Materials Chemistry Solvents Molecule Density functional theory Molecular orbital Physical and Theoretical Chemistry Protons Conformational isomerism Trisaccharides |
| Zdroj: | The journal of physical chemistry. B. 118(41) |
| ISSN: | 1520-5207 |
| Popis: | NMR and density functional theory (DFT) have afforded detailed information on the molecular geometry and spin-spin coupling constants of a trisaccharide from the heparin repeating-sequence. The fully optimized molecular structures of two trisaccharide conformations (differing from each other in the form of the central iduronic acid residue) were obtained using the B3LYP/6-311+G(d,p) level of theory in the presence of solvent, the latter included as either explicit water molecules or via a continuum solvent model. NMR spin-spin coupling constants were also computed using various basis sets and functionals and then compared with measured experimental values. Optimized structures for both conformers showed differences in geometry at the glycosidic linkages and in the formation of intramolecular hydrogen bonds. Three-bond proton-proton coupling constants ((3)JH-C-C-H), based on fully optimized geometry computed using the B3LYP/6-311+G(d,p)/UFF level of theory and hydrated with 57 water molecules, showed that the best agreement with experiment was obtained with the 6-311+G(d,p) basis set and a weighted average of 55:45 ((1)C4:(2)S0) of the IdoA2S forms. Other basis sets, DGDZVP and TZVP, also gave acceptable data for most coupling constants, with DGDZVP outperforming the TZVP. Detailed analysis of Fermi-contact contributions to (3)JH-C-C-H showed that important contributions arise from oxygen at both glycosidic linkages, as well as from oxygen atoms on the neighboring monosaccharide units. Their contribution to the Fermi term cannot be neglected and must be taken into account for a correct description of coupling constants. The analysis also showed that the magnitude of paramagnetic (PSO) and diamagnetic (DSO) spin-orbit contributions is comparable to the magnitude of the Fermi-contact contribution in some coupling constants in the IdoA2S residue. Calculations of the localized molecular orbital contributions to the DSO terms from separate conformational residues showed that the contribution from adjacent residues is not negligible and can be important for the spin-spin coupling constants between protons located close to the geometrical center of the molecule. These contributions should be taken into account when interpreting DSO terms in spin-spin coupling constants especially in large molecules. |
| Databáze: | OpenAIRE |
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