A DFT study on the mechanism of phosphodiester cleavage mediated by monozinc complexes.
Density functional theory (DFT), Tao-Perdew-Staroverov-Scuseria (TPSS), is employed to study the reaction mechanism for the zinc-mediated phosphodiester cleavage reaction. The calculations indicate a general base catalysis mechanism. The flexibility of Zn(II) ion's coordination number (5 and 6) as well as the formation of hydrogen bonds between the coordinating water and the ester are responsible for the trapping (namely, coordinating to the Zn complexes) of the phosphodiester. The hydrogen bonds, between the water, the ester, and the nitrogen-ligand, tris(6-amino-2-pyridylmethyl)amine, not only stabilize the key five-coordinated phosphorus intermediates with a trigonal pyramidal PO5 unit but also lower the energy barriers for the proton transfer within the complexes by gaining stronger solvation energies.
Fan
Yubo
Y
Department of Chemistry, Texas A & M University, College Station, Texas 77843-3255, USA.
Gao
Yi Qin
YQ
D002384:Catalysis; D002413:Cations, Divalent / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D004952:Esters / Q000737:chemistry; D006878:Hydroxides / Q000737:chemistry; D008956:Models, Chemical; D009942:Organometallic Compounds / Q000737:chemistry*; D010756:Phosphoric Acids / Q000737:chemistry*; D011522:Protons; D011725:Pyridines / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D014867:Water / Q000737:chemistry
D002413:Cations, Divalent; D004952:Esters; D006878:Hydroxides; D009942:Organometallic Compounds; D010756:Phosphoric Acids; D011522:Protons; D011725:Pyridines; C518745:aqua(tri(6-aminopyridin-2-yl)amine)zinc(II); C518746:aqua(tri(pyridin-2-yl)amine)zinc(II); D014867:Water; D012313:RNA; D004247:DNA; C031356:hydroxide ion; C030242:phosphoric acid