Porous coordination polymers constructed from Zn2+ and isophthalate with linear bipyridyl-type ligands were synthesized. [Zn(ip)(bpb)]n (CID-21; ip=isophthalate, bpb=1,4-bis(4-pyridyl)benzene), [Zn(ip)(bpt)]n (CID-22; bpt=3,6-bis(4-pyridyl)-1,2,4,5-tetrazine), and [Zn(ip)(bpa)]n (CID-23; bpa=1,4-bis(4-pyridyl)acetylene) all have interdigitated structures of layers and similar void volumes (≈27 %). In these compounds, 1D bottleneck-type channels run along the perpendicular direction of the layer stacking and their properties are strongly dominated by the dipyridyl linker ligands. Because of the difference in packing of 2D layers, CID-21 and CID-22 have relatively rigid porous structures, whereas CID-23 has greater flexibility, as indicated by the results of powder X-ray diffraction studies. The micropores of CID-22 surrounded by tetrazine moieties adsorb polar molecules, such as methanol and water. The higher affinity of CID-22 for water than CID-21 is supported by a theoretical study. The 1D channel of CID-23 is wider than that of the other two compounds, which enables the incorporation of aromatic molecules. This is because the shape of the bpa linker ligand generates a wider pore diameter (8.6 Å). Only CID-23 can adsorb a benzene molecule and the isotherm of benzene has a gate-opening-type profile. This offers proof of the guest accommodation process through large structural transformation from a nonporous to a porous structure. The flexibility and restricted pore space of CID-23, at 298 K, allows only benzene, but not cyclohexane, to enter the channels. The porous structure exhibits clear selectivity for these similar guests. The incorporation of an elongated dipyridyl linker ligand in the 2D coordination layers provides a strategy for the design of microporous compounds with different flexibilities, microporous environments, and separation abilities.