Study On The Ion Or Molecular Recognition Mechanism Of Pyrrole Macrocycles

As a conjugated structure, pyrrole ring can form hydrogen bond with its N-H group. Therefore, the supramolecular recognition behaviors of macrocyclic host compounds including pyrrole ring would be more complex and interesting. The recognition mechanism investigations of these host compounds toward common anions and bioactive small molecules may have special important guiding significance to understand the formation of some supramolecular systems, to design and synthesis of novel host compounds for ionic or molecular guests. In this thesis, calix[4]pyrrole and tetra-phenyl porphyrin derivatives were chosen as the host compounds to study systematically their ionic or molecular recognition mechanisms in the following three sections.1. Theoretical study of calix[4]pyrrole-ion assembly systemsThe density functional theory M06-2X/6-31 G(d,p) methods were performed on the possible assembly systems of calix[4]pyrrole(CP) with halide anions (X-=F-,Cr,Br-) and NH4+-X’ ion-pairs. Geometries, binding energies, natural bond orbital (NBO) analysis, and Multiwfn analysis were presented in detail. The calculated results indicated that the interaction between calix[4]pyrrole and halide anions mainly involved hydrogen bond interactions. Long range van der Waals force and steric effect were determined in CP-Cl- and CP-Br- systems by Multiwfn analysis. As a well known ion-pair receptor. calix[4]pyrrole could form stable complexes with NH4+-X- ion-pairs mainly through H-bonds and the electrostatic interactions between anion and cation as well as the cation-π interaction. The 2:1 assembly complexes of CP and anions or ion-pairs were also considered theoretically for the first time, but it was not the dominant stochiometry relative to the 1:1 ones. The current study further demonstrated that calix[4]pyrrole functions as not only an anion receptor but also a good ion-pair receptor, especially in cases involving fluoride ion. What’s more, we also study on the assembled systems formed by calix[4]pyrrole (CP) and anions with different configurations, such as OH- (C∞v), MO3- (D3h), and C104-(Td),were explored at the M06-2X/6-31+G(d,p) level of theory. The calculated results showed that the anion configuration had a direct effect on the structure of assembly systems no matter the host-guest stoichiometry as 1:1 or 2:1. The larger the steric size and the stronger the electronegativity of an anion was, the more easily the 2:1 complex formed. Considering calix[4]pyrrole as an ion-pair receptor, the interaction between CP and NH4+-X (X=OH-,NO3-, ClO4-) ion-pairs were also investigated in this work. In the assembly systems formed by CP and ion-pairs, the hydrogen-bond interaction between anion and CP weakened due to the ion-pairing of anion and cation as the dominant force. The 1:1 stoichiometric systems of CP and ion-pairs were more advantageous whatever anionic spatial configurations.2. Computational simulation study on the anion recognition properties ofFunctionalized Tetraphenyl porphyrinsThe anion recognitions of tetra-(2-formamido) phenyl porphyrin (APP), tetra-(2-ureido) phenyl porphyrin (UPP), and their zinc derivatives (ZnAPP and ZnUPP) to three anions (Cl-, H2PO4-, CH3COO-) were studied using quantum mechanical calculations (QM) and molecular dynamics simulations (MD). The density functional theory (DFT) calculations at M06-2X/6-3] G(dp) level indicated that the anion recognition ability of ZnAPP was better than that of APP, and the anion selectivity was in the order of Cl-< H2PO4-< CH3COO-. The selectivity trend for ZnUPP and UPP were found to be H2PO4-< Cl-< CH3COO-. The structures, thermodynamic properties, and recognition mechanisms were discussed in detail. The 2 ns MD simulations were then carried out for anion@ZnAPP and anion@ZnUPP complexes in the mixed solvent of DMSO/H2O. The MD simulation results showed that anion@ZnUPP complexes exhibited higher stability than anion@ZnAPP, which was in good agreement with QC results. H-bonds formed between anion and side chain of receptors and zinc coordination bonds with anion contributed significantly to the stability of complexes.3. Recognition properties of bioactive small molecules by functionalized zinc tetra-(2-ureido) phenyl porphyrin derivativeThe molecular dynamics (MD) simulations were carried out for the inclusion complexes of zinc tetra-(2-ureido) phenyl porphyrin derivative (ZnUPP) with some bioactive small molecules (four base pair fragment molecules:adenine, guanine, thymine, cytosine and two amino acid molecules:valine, serine). Based on the stability and interaction analysis of the complexes within 5 ns MD simulation time, we found that the host molecule mainly rely on its side chains and zinc ligand to form interaction with guest molecules, and the weak inter-molecule interactions contribute to the complex stability. The host-guest interaction strength was directly related to the functional groups and the structures of guest molecules. The interaction of pyrimidine substances with host molecule was stronger than that of purine ones, which showed the higher recognition selectivity of ZnUPP towards pyrimidine species relative to purine ones. In the case of valine and serine, the similar interaction strength with ZnUPP and the small selectivity differences were obtained due to the similar interaction functional groups of these two amino acid molecules with host molecule, respectively. Finally, the graphene sheet was also introduced in the host-guest systems to form the ternary supramolecular complex. The MD simulation results indicated that the graphene sheet could stabilize the motion of ZnUPP significantly, and improve the stability of host-guest interactions. These results would provide some theoretical basis for the bioactive small molecule recognition application of porphyrin derivatives and graphene.