Showing papers by "Serge Pérez published in 2004"

A hydration study of (1→4) and (1→6) linked α‐glucans by comparative 10 ns molecular dynamics simulations and 500‐MHz NMR

Abstract: The hydration behavior of two model disaccharides, methyl-α-D-maltoside (1) and methyl-α-D-isomaltoside (2), has been investigated by a comparative 10 ns molecular dynamics study. The detailed hydration of the two disaccharides was described using three force fields especially developed for modeling of carbohydrates in explicit solvent. To validate the theoretical results the two compounds were synthesized and subjected to 500 MHz NMR spectroscopy, including pulsed field gradient diffusion measurements (1: 4.0 · 10−6 cm2 · s−1; 2: 4.2 · 10−6 cm2 · s−1). In short, the older CHARMM-based force field exhibited a more structured carbohydrate–water interaction leading to better agreement with the diffusional properties of the two compounds, whereas especially the α-(1→6) linkage and the primary hydroxyl groups were inaccurately modeled. In contrast, the new generation of the CHARMM-based force field (CSFF) and the most recent version of the AMBER-based force field (GLYCAM-2000a) exhibited less structured carbohydrate–water interactions with the result that the diffusional properties of the two disaccharides were underestimated, whereas the simulations of the α-(1→6) linkage and the primary hydroxyl groups were significantly improved and in excellent agreement with homo- and heteronuclear coupling constants. The difference between the two classes of force field (more structured and less structured carbohydrate–water interaction) was underlined by calculation of the isotropic hydration as calculated by radial pair distributions. At one extreme, the radial O…O pair distribution function yielded a peak density of 2.3 times the bulk density in the first hydration shell when using the older CHARMM force field, whereas the maximum density observed in the GLYCAM force field was calculated to be 1.0, at the other extreme. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 573–586, 2004

Hydration of the Amylopectin Branch Point. Evidence of Restricted Conformational Diversity of the α-(1→6) Linkage

Abstract: The hydration behavior of a model compound for the amylopectin branch point, methyl 6'-alpha-maltosyl-alpha-maltotrioside, was investigated by combining molecular dynamics simulations in explicit water, 500 MHz NMR spectroscopy, including pulsed field gradient diffusion measurements, and exploratory multivariate data analysis. In comparison with results on a tetrasaccharide analogue, the study reveals that the conformational diversity of the three-bond alpha-(1-->6) linkage becomes quite limited in aqueous solution upon the addition of a fifth glucose residue that elongates the alpha-(1-->6) branch. This investigation reveals two plausible starch branch point structures, one that permits the formation of double helices and one that is adapted for interconnection of double helices. The apparent rigidity of the former is explained by the presence of water pockets/bridges in the vicinity of the branch point that lock the pentasaccharide structure into one conformational family that is able to accommodate the creation of the double-helical amylopectin structure.

(4R,9S)-4-Hydroxymethyl-3,8-dioxa-1,6-diazaspiro[4.4]nonane-2,7-dithione monohydrate

Abstract: The title compound, C6H8N2O3S2·H2O, was synthesized from l-erythrulose and the structure of the enantiopure (4R,9S) diastereo­isomer has been determined. The structure is a hydrate and the water mol­ecules establish a hydrogen-bond network that involves the hydroxy­methyl group as well as one N and one S atom.