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Theoretical and NMR-based Conformational Analysis of Phosphodiester-linked Disaccharides
Alexey G Gerbst1, Andrei V Nikolaev2, Dmitry V Yashunsky3
1Laboratory of Glycoconjugate Chemistry, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, 119991, Moscow, Russian Federation. alger@ioc.ac.ru.
Abstract:
The conformational behaviour of three phosphate-bridged dimannosides was studied by means of NMR and computational molecular modelling. First, the conformations of the phosphodiester linker were determined by quantum chemistry methods using dimethyl phosphate as a model. Then, a series of conformations was constructed for each of the studied molecules. Preliminary molecular dynamics (MD) simulations revealed that the inclusion of a cation had a drastic influence on the obtained results. Additionally, triethylammonium had the same effect as sodium as the counter-ion. After that, another series of MD simulations was run. The resulting MD trajectories were used to define the conformations responsible for the observed nuclear Overhauser effects and inter-nuclear coupling.
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