Theoretical Simulations Of Conformational Changes Of Oligosaccharide Molecules In Green Solvents

Carbohydrates are the most abundant organic compounds in nature,with a high degree of diversity.In the past decades,the structure,synthesis and biological function of carbohydrates have attracted intensive interests.Despite the progress made in the experimental works,molecular simulations are highly desired to provide the detailed information of molecular structure and inter-/intramolecular interactions of the systems relating the carbohydrates.In this paper,by use of both quantum mechanics calculations and molecular dynamics simulation,we studied the conformation,solvent effect,biological function and mechanism of dissolution of some oligosaccharide molecules in various media.The main research results are outlined as follows:1.Conformational Dynamics and Polarization Effect of ?,?-Trehalose in a Vacuum and in Aqueous and Salt SolutionsTrehalose is a nonreducing disaccharide,which could maintain cell viability and biological activity in a series of extreme environments,such as drought or extremely high or low temperatures.Conformational changes of ?,?-trehalose in a vacuum,water,and 0-20 wt%NaCl solutions were investigated by means of molecular dynamics simulations at different levels of density functional theory and with fixed-charge nonpolarizable and variable-charge polarizable force fields,respectively.The relative thermodynamic stability of trehalose is enhanced by the formation of intercycle and/or intracycle hydrogen bonds,but some thermodynamically unfavorable structures can be sampled in the DFT-based ab initio molecular dynamics simulation.The polarization effects of polar trehalose molecule in aqueous and NaCl solutions were studied by a series of molecular dynamics simulations with both the conventional nonpolarizable and polarizable force field models.In the polarizable model,the partial charges of trehalose were updated every 2 ps using DFT calculations and fused with the other force field parameters for the energy calculation and molecular dynamics simulation.Around the trehalose,water molecules located in an asymmetry model and trehalose has a stronger tendency to bind with water molecules than Na+ and Cl-ions.When the trehalose concentration is increased from 3.26 to 6.31 wt%in salt aqueous solution,the two trehalose molecules periodically approach each other in a nearly anhydrate state and leave a way to keep the favorable hydration structure with the mean trehalose-trehalose distance of 8.6 A.The similarity between the solvated dimer packing styles(shoulder-by-shoulder or head-to-head)and crystal stacking can be used to make an extrapolation to higher sugar concentrations and to rationalize the bioprotection function of trehalose in high salt concentration.2.Self-aggregation of Trehalose in the Mixed Solvents of 1,3-dimethylimidazolium Ionic Liquid and waterConformational variations of solvated trehaloses in binary mixtures of 1,3-dialkylimidazolium([Cimim]Cl)ionic liquids and trehalose as well as ternary mixtures of trehalose,[Cimim]Cl and water have been studied by MD simulations with and without polarizable force fields.The interaction energy between anion Cl-and water is stronger than that between water itself in the[Cimim]Cl-water mixtures.Isolated water clusters were found in the binary[Cimim]Cl-water mixtures with 60.0 and 75.0%mole fraction of water,but a continuous water network appears when the concentration of the mixture increases to 99.9%.In the case of binary mixtures of trehalose and[Cimim]Cl,both non-polarizable and polarizable models demonstrated that the pyranose rings of trehalose displayed chair conformations.MD simulations with polarization model could sample larger conformation space than that with non-polarizable model.A self-aggregation behaviour of trehalose was found in the ternary trehalose-[Cimim]Cl-water mixtures,which can be rationalized by the stronger non-bonded interaction energy between trehalose molecules and anion Cl-than that between trehalose molecule and water.3.Polarization Effects on the Cellulose Dissolution in Ionic Liquids:MD Simulations with Polarization Model and Integrated Tempering Enhanced Sampling MethodConformation of cellulose with various degree of polymerization of n= 1?12 in ionic liquid[C1mim]Cl and the intermolecular interaction between them were studied by means of MD simulations with fixed-charge and charge variable polarizable force fields,respectively.The integrated tempering enhanced sampling method was also employed in the simulations in order to improve the sampling efficiency.Cellulose undergoes significant conformational changes from a gaseous right-hand helical twist along the long axis to a flexible conformation in ionic liquid.The intermolecular interactions between cellulose and ionic liquid were studied by both infrared spectrum measurements and theoretical simulations.Designated by their puckering parameters,the pyranose rings of cellulose oligomers are mainly arranged in a chair conformation.With the increase in the degree of polymerization of cellulose,the boat and skew-boat conformations of cellulose appear in the MD simulations,especially in the simulations with polarization model.The number and population of hydrogen bonds between the cellulose and the chloride anions show that chloride anion is prone to form HBs whenever it approaches to the hydroxyl groups of cellulose and,thus,each hydroxyl group is fully hydrogen bonded to the chloride anion.MD simulations with polarization model presented more abundant conformations than that with non-polarization model.The application of the enhanced sampling method further enlarged the conformational spaces could be visited by facilitating the system escaping from the local minima.It was found that the electrostatics interactions between the cellulose and ionic liquid contribute more to the total interaction energies than the van der Waals interactions.Although the interaction energy between the cellulose and anion is about 2.9 times than that between the cellulose and cation,the role of cation is non-negligible.In contrast,the interaction energy between the cellulose and water is too weak to dissolve cellulose in water.