A retention study on perfluorophenyl silicabased stationary phase was undertaken for some organic
compounds containing different polar functionalities. The dependence of the retention factor on the content of organic modifier (acetonitrile, or methanol) in mobile phase was fitted by polynomial equations. The only exception was observed for adenine, which showed a sigmoidal dependence for the retention factor versus organic modifier content. The extrapolated values of retention factor for water as mobile phase (log kw) from these dependences were well correlated with octanol–water partition constants (log Kow), excepting the values for hexachlorocyclohexane isomers and adenine. Temperature dependences of the retention factor obeyed the van’t Hoff equation with thermodynamic parameters similar to those obtained in reversed phase on C8 or C18 stationary phases, excepting two statines whose dependences of ln k on the reciprocal value of absolute column temperature were nonlinear. Again, adenine had an atypical behavior with decrease in the retention factor with the increase in column temperature, due to possible tautomeric equilibria of this compound in presence of water, in accordance with theoretical models reported by literature. Charge modeling with MarvinSketch package program revealed charged centers from analyte molecule that could interact differently with charge centers from stationary phase.