Using quantum chemical (QC) calculations at the B3LYP/6-31G(d) level of theory, we investigate for three selected layer–pillar paddle–wheel metal–organic framework materials of composition M2IIL21L2(MII=Zn,Cu;L1=2,3,5,6-tetrafluorobenzene-1,4-dicarboxylate, 2,3,5,6-tetramethylbenzene-1,4-dicarboxylate; L2=1,4-diazabicylco[2.2.2]octane) the preferential orientations and the rotational energy barriers of both layer (L1) and pillar (L2) linkers. The calculations suggest unhindered rotational motion for pillar linker in all compounds studied (ΔEbarrier⩽0.14kcalmol−1). For layer linkers, the energy barriers for the rotation of benzene rings are found to vary significantly, indicating an hindered rotation in the case of the fluorine substituent (ΔEbarrier≈14kcalmol−1), and a static situation in the case of the methyl substituent (ΔEbarrier≈75kcalmol−1). The rotational dynamics are found not to depend on the type of metal ion. AIM analysis indicates that the rotational energy barriers are influenced by C–H⋯F hydrogen-bonding interactions between the dabco and fluorine-substituted linkers.