A theoretical study of molecular conformations and gelation ability of N,N′-dipyridyl urea compounds in ethanol solution: DFT calculations and MD simulations

The molecular conformations and gelation ability of N,N'-bis(4-pyridyl) urea (1) and N,N'-bis(2-pyridyl) urea (3) in ethanol solution were studied through density functional theory (DFT) calculations and molecular dynamics (MD) simulations. DFT calculations demonstrated that compound 1 adopts an energetically more favorable ZZ conformation (1a), which is polarized significantly from the gas phase to ethanol solution. Moreover, the hydrogen-bond donors and acceptors such as carbonyl group, amidogen, and pyridine nitrogen atoms are exposed to molecular lateral sides of compound 1, which is conducive to form fascinating hydrogen bond network structures in multiple directions between gelator molecules and gelling solvents. The intramolecular hydrogen-bonded ZE isomer (3d) is beneficial to the conformational stability, but weakens the gelation property of compound 3 due to steric hindrance. The dimerisation effect further reduces its gelling ability with ethanol molecules. The microscopic solvation structures, including short-range solute-solvent intermolecular interactions were also illustrated through MD simulations from the viewpoint of radial distribution functions, angle probability distribution, three-dimensional spatial distribution functions, and especially solvent coordination number. It demonstrated that the averaged solvent coordination number decreased from 4.56 for compound 1 to 3.08 for compound 3. The dimerisation effect of compound 3 in ethanol solution further reduced the solvent coordination number to 1.32. It is remarkable that by going from 4-pyridyl (1) to 2-pyridyl (3) urea-based derivatives, the gelation ability disappears, in good agreement with experimental phenomena.