<p>In order to compare the effects of different transition metals on the metal–organic frameworks with different linkers, the structures, electronic, and magnetic properties of the H₂BCPP-M, H₄TCPP-M, TPyP-M, and DPyDFP-M clusters have been investigated using density functional theory. The results revealed that only the Sc atoms deviated from the center planes of these clusters. The H₂BCPP-Sc, H₄TCPP-Sc, TPyP-Sc, and DPyDFP-Sc clusters exhibited the largest dipole magnitudes. The H₂BCPP-Ni, H₄TCPP-Ni, TPyP-Ni, and DPyDFP-Ni clusters were found to be the most suitable for synthesis. The Sc atoms in the H₂BCPP-Sc, H₄TCPP-Sc, TPyP-Sc, and DPyDFP-Sc clusters had the highest Hirshfeld charge values. The Mülliken spin densities of the TM atoms in the H₂BCPP-M, H₄TCPP-M, TPyP-M, and DPyDFP-M clusters decreased to zero, except for Mn (-3.450 |e|) in the H₂BCPP-M clusters, Cr (3.675 |e|) and Mn (−3.457 |e|) in the H₄TCPP-M clusters, and Cr (3.679 |e|) in the DPyDFP-M clusters.</p>