High-level ab initio calculations show that the most stable stacking for benzene–cyclohexane is 17% stronger than that for benzene–benzene. However, as these systems are displaced horizontally the benzene–benzene attraction retains its strength. At a displacement of 5.0 Å, the benzene–benzene attraction is still ∼70% of its maximum strength, while benzene–cyclohexane attraction has fallen to ∼40% of its maximum strength. Alternatively, the radius of attraction (>2.0 kcal/mol) for benzene–benzene is 250% larger than that for benzene–cyclohexane. Thus, at relatively large distances aromatic rings can recognize each other, a phenomenon that helps explain their importance in protein folding and supramolecular structures.

The geometry of hydrogen bonds in the crystal structures from the Cambridge Structural Database and calculated data show that water coordination to a metal ion has a remarkable influence on hydrogen bonds. The calculated energies of hydrogen bonds of coordinated water are much stronger, even if the aqua complex is neutral.

Stacking interactions between cyclohexane and benzene were studied in crystal structures from the Cambridge Structural Database and by ab initio calculations. Calculated at the very accurate CCSD(T)/CBS level of theory, the cyclohexane–benzene interaction energy is −3.27 kcal mol⁻¹, which is significantly stronger than the interaction in the benzene dimer (−2.84 kcal mol⁻¹) indicating the importance of aliphatic–aromatic interactions.