A molecular modeling kit provides a system for molecular modeling that represents exclusion between resonance structures in a molecule and permits their rotation, providing an informative tool for describing resonance in a classroom or other learning environment. The kit includes atom modeling components and bond connector components that are connected together to form models of molecules. The atom modeling components or the bond connector components include a mechanical exclusion feature that prevents simultaneous connection of two bond connector components to represent two pi-bonds formed with a single atom in a single plane.