Molecular Dynamics Simulation of Neocarrabiose 2,4′-Bis(sulfate) and Carrabiose 4′,2-Bis(sulfate) as Building Blocks of ι-Carrageenan in Water

Abstract

Abstract Molecular mechanics and molecular dynamics simulations were performed on two types of disaccharides, neocarrabiose 2,4′-bis(sulfate) and carrabiose 4′,2-bis(sulfate), which are building blocks of ι-carrageenan. Although the conformation and potential-energy surfaces of these disaccharides have been investigated by several researchers, all of them were analyzed using a vacuum calculation. To investigate the conformational behavior of these molecules in water, we performed a molecular dynamics simulation with the presence of explicit water molecules and counter ions around the disaccharides. The trajectories of the glycosidic dihedral angles in the water simulation reproduced the potential-energy surface calculated not with a dielectric constant of 80, but with 1. The electrostatic force was found to act so as to restrict the allowed area of the potential-energy surfaces. The most stable conformation of neocarrabiose 2,4′-bis(sulfate) is φ = 162, ψ = 174. Although the global minimum conformation of carrabiose 4′,2-bis(sulfate) is at A1 (φ = 176° and ψ = −166°), the molecular dynamics simulation in water suggested that the structure, B1 (φ = 164° and ψ = −87°), is more stable than A1 by analyzing the trajectory and the hydrogen bonds with water molecules. This indicates that it is important for the conformational analysis to take into account the solvation effect explicitly. The structure of B1 agrees with that found by an NMR experiment.