Mechanical Stretching of Nature Inspired Linear and\nBranched Polysaccharide Motifs through Steered Molecular Dynamics

A variety\nof 10 polysaccharide motifs comprising naturally inspired\nsequences of monosaccharide building blocks are studied to understand\nthe inter-relation between their structural and mechanical behaviors.\nEquilibrium and steered molecular dynamics (SMD) simulations are employed\nto investigate the stress–strain relationships and the associated\nconformational flips of the pyranose moieties along the polysaccharide\nchains. The presence of a variety of glycosidic linkages connecting\nthe diverse monosaccharide units along with chain-branching in some\ncases induce wide diversity in the carbohydrate-Ramachandran plots\nof the glycosidic dihedrals. Similar variations are observed in the\nCremer–Pople ring puckering patterns across the polysaccharide\nvariants. The work further provides a comparison between the experimentally\nobtained atomic force microscopic data of mechanical stretching for\nsome polysaccharides with the stress–strain curves generated\nfrom our SMD simulations. Out of all the systems studied, pectin having\nan axial–axial orientation of the glycosidic linkage showed\nmaximum stretching potential, while acetan-M, with an equatorial–equatorial\ndisposition of the glycosidic bond, stretched the least. The experimental\nYoung’s modulus of the corresponding natural polysaccharides\ncould be reasonably compared to the values obtained from our simulation\nmodels. Force distribution analysis is done to understand the propagation\nof punctual stress in the polysaccharides under SMD conditions. Changes\nin local electrophilicity or nucleophilicity of atomic centers in\npuckered pyranose rings are estimated through the condensed Fukui\nfunctions. All of this information can help understand the physical\nbehavior and chemical reactivity of complex polysaccharides in a complicated\nmilieu of electronic and steric effects experienced by them.