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Updated: Aug 12, 2026

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides
Published on: November 21, 2013
Recognition through self-assembly. A quadruply-hydrogen-bonded, strapped porphyrin cleft that binds dipyridyl
Xue-Bin Shao1, Xi-Kui Jiang, Xin Zhao
1Shanghai Institute of Organic Chemistry (SIOC), Chinese Academy of Sciences, 354 Fenglin Lu, Shanghai 200032, China.
Abstract:
Quadruply-hydrogen-bonded porphyrin homodimer Zn1.Zn1 has been designed, assembled, and evaluated as a supramolecular cleft-featured receptor for its ability to bind dipyridyl guests in chloroform-d. Monomer Zn1 consists of a 2-ureidopyrimidin-4(1H)-one unit, which was initially reported by Meijer et al., and a zinc porphyrin unit. The zinc porphyrin is strapped with an additional aliphatic chain for controlling the atropisomerization of porphyrin. The 2-ureidopyrimidin-4(1H)-one unit dimerizes exclusively in chloroform even at the dilute concentration of 10(-)(4) M, while the two "strapped" zinc porphyrin units of the homodimer provide additional binding sites for selective guest recognition. (1)H NMR studies indicate that the new homodimer Zn1.Zn1 adopts an S-type conformation due to strong donor-acceptor interaction between the electron-rich porphyrin units and the electron-deficient 2-ureidopyrimidin-4(1H)-one unit. (1)H NMR, UV-vis, and vapor pressure osmometry investigations reveal that Zn1.Zn1 could function as a new generation of assembled supramolecular cleft, to be able to not only efficiently bind linear dipyridyl molecules 14-17, resulting in the formation of stable termolecular complexes, with K(aasoc) values ranging from 3.8 x 10(6) to 8.9 x 10(7) M(-)(1), but also strongly complex a hydrogen-bond-assembled [2]rotaxane, 18, which consists of a rigid fumaramide thread and a pyridine-incorporated tetraamide cyclophane, with K(aasoc) = 1.2 x 10(4) M(-)(1). (1)H NMR competition experiments reveal that complexation to the dipyriyl guests also promotes the stability of the quadruply-hydrogen-bonded dimeric receptor.
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