The effect of fluorine substitution on the proton transfer barrier (ΔEPT) of malonaldehyde (1) has been investigated with the aid of density functional theory (DFT) calculations carried out at the B3LYP/ cc-pVTZ level of theory. The results indicate that fluorine substitution in 1 increases the energy barrier for intramolecular proton transfer, which correlates linearly with both the HB distance and the O-H bond stretching frequency. The origin of this structure-energy correlation was investigated by performing a topological analysis of the electron density with Bader's theory of atoms in molecules (AIM). AIM theory indicates that H-by-F substitution in 1 has the effect to decrease the electron density of its intramolecular HB. This implies that conjugation effects are operative within the enolone fragment of 1.