STUDY FOR MOLECULAR DYNAMICS OF PROFLAVIN HYDRATION IN SOLUTION

Abstract

The hydration of a doubly protonated proflavine (C13N3H13) in solution is studied by classical molecular
dynamics. The GROMACS simulation package is used. The topology of the molecules is based on the Amber99
force field, and SPC/E water model is used as solvent. The proflavine behavior is analyzed by the study of the
functions of radial distribution, the establishment of hydrogen bonds between proflavine atoms and surrounding water molecules, and the distributions of frequency of occurrence of hydrogen bonds in water. It is found that the amino groups structure the water that surround them often forming hydrogen bonds, whereas this structure is adapted to that of the solvent. The approximately tetrahedral structure of the water is affected by the presence of proflavine in the first hydration layer (0.25nm) and in two region of the solvent with 0.15 nm of thickness surrounding the proflavine above and below the plane of the rings, where the frequency of occurrence of 4 hydrogen bonds decreases between 25% and 50 %.