Abstract
Using a molecular dynamics simulation method, hydrogen bonds in aqueous glycerol solutions with different concentrations has been studied. The H.O distance was chosen as the basic definition of hydrogen bonds and the necessity of O.O distance, O-H.O angle and H-O.O angle was then analyzed. Results showed that O.O distance was not necessary in the hydrogen bonding definition when H.O distance was involved and O-H.O angle was a complementary geometrical constraint more strict than H-O.O angle. The mean numbers of hydrogen bonds per molecule (water and glycerol) and per atom (oxygen and hydrogen) and percentages of molecules and atoms with n hydrogen bonds have been reported and compared for different hydrogen bonding definitions. Definitions had a significant effect on hydrogen bonding analysis and the results for glycerol molecules were more sensitive to O-H.O angle and H-O.O angle than that for water molecules.
Highlights
Glycerol has been chosen as a cryoprotectant agent (CPA) in this study for its capabilities in the long term preservation of cells and proteins and it is considered as one of the best cryoprotectant solvents [1]
The geometry of a hydrogen bond O-H...O involves an O...O distance, an H...O hydrogen bond length, an O-H covalent bond length, an O-H...O hydrogen bond angle, an H-O...O angle and an O...O...H angle, five of which are related with hydrogen bonds except the O-H covalent bond length which is determined by the chosen water model
The purpose of the study is to evaluate the effect of geometrical criteria on hydrogen bonds analysis in aqueous glycerol solutions including the mean numbers of hydrogen bonds per water and the percentages of water with n hydrogen bonds fn (n=0,1,2,...)
Summary
Glycerol has been chosen as a cryoprotectant agent (CPA) in this study for its capabilities in the long term preservation of cells and proteins and it is considered as one of the best cryoprotectant solvents [1]. There is an enormous amount of literature related to the investigation of hydrogen bonding in glycerol [5,6,7,8,9,10,11,12]. Two criteria are often used for determining the hydrogen bonds, i.e., by energy and by geometry. A pair of molecules is defined as hydrogen bonded when the interaction energy is less than the threshold value [26]. The hydrogen bond is determined by the relative configuration of the two molecules [5,7,8,10,11]. The geometry of a hydrogen bond O-H...O involves an O...O distance, an H...O hydrogen bond length, an O-H covalent bond length, an O-H...O hydrogen bond angle, an H-O...O angle and an O...O...H angle, five of which are related with hydrogen bonds except the O-H covalent bond length which is determined by the chosen water model
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