Competing hydrogen bonding and acyclic π-stacking between hydrogen-bridged quasi-rings in Z- and E-methyl pyruvate semicarbazone: a quantitative interaction energy analysis

Abstract

The competition between hydrogen bonding and stacking interactions in the solid-state packing of Z- and E-isomers of methyl pyruvate semicarbazone (1-Z and 1-E) is quantitatively analyzed using a combination of X-ray crystallography, density functional theory (DFT), and energy vector diagrams (EVDs). The E-isomer forms dimers stabilized by resonance-assisted hydrogen bonds (RAHBs) with an interaction energy of −70.4 kJ mol⁻¹, which serve as the building units (BUs) of its columnar-layered crystal structure. In contrast, the Z-isomer exhibits weaker RAHBs (−61.7 kJ mol⁻¹) and relies more heavily on dispersion-driven stacking interactions between hydrogen-bridged quasi-rings, resulting in a distinct layered motif. Solution NMR studies confirm intramolecular hydrogen bonding in 1-Z and present evidence of self-association. This work highlights the delicate balance between classical hydrogen bonds and stacking forces in directing crystal packing, with implications for the design of hydrazone-based functional materials.