Paper Citing NAMD - Abstract
Humeres, Eduardo; Mascayano, Carolina; Riadi, Gonzalo; Gonzalez-Nilo, Fernando
Molecular dynamics simulation of the aqueous solvation shell of cellulose and xanthate ester derivatives
JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, 19:896-901, DEC 2006
MD simulations of a pentasaccharide having D-glucopyranoside residues connected by (1 -> 4)-beta glycosidic linkages, as a model of cellulose solvated in water, were carried out comparing the solvation of the hydroxyl group at C-2 of the central ring of the pentamer and that of a single glucopyranose ring. MD simulations of 10 nsec were carried under NPT and periodic boundary conditions at 298 K and 1 atm. Explicit solvent (TIP3) and the force field CHARMM27 (modified for xanthate ester derivatives) were used in the molecular dynamics simulations. RDF calculations with respect to O-2 of the central ring of the pentamer showed a well structured first solvation shell followed by secondary shells. When comparing the simulations of the pentamer to a single glucopyranose ring, it was observed that the solvation of O-2 was lower for one repetitive unit, indicating that the pentamer had a stronger H-bond structure of water around O-2 due to the cooperative effect of the neighboring residues. When the O-2 of the central ring of the pentamer was substituted by a p-nitrobenzylxanthate moiety (pentXNB) there was a strong decrease in the hydration of the substituted O-2 but the carbon and the sulfur of the thiocarbonyl group were clearly hydrated compared to the sulfur bridge. The global minimum energy conformation showed the p-nitrobenzyl group folded over the neighboring glucose ring. However, the simulations showed that the XNB group oscillates over the pentamer in periods of ca. 3000 psec. Copyright (c) 2006 John Wiley & Sons, Ltd.
