Molecular complexes of nucleosides and nucleotides with a monomeric cationic porphyrin and some of its metal derivatives

Abstract

Tetrakis(4-7V-methylpyridyl)porphine (H2TMpyP) and a number of its metal derivatives interact extensively with mononucleotides and mononucleosides in aqueous solution. The complexes formed are of a stacking-type involving extensive overlap of the -systems of the porphyrin and purine or pyrimidine bases. Coulombic attractions help stabilize the complexes but there is no evidence for ligation of the bases to axial sites of the metalloporphyrins. Stability constants determined via NMR and spectrophotometric titrations are larger for purine bases than pyrimidines with a given porphyrin derivative. More dramatic influences on stability result from changing porphyrins. Porphyrins having no axial ligands (e.g., metal-free copper(II), palladium(II), and nickel(II) derivatives) or one axial ligand (Zn(II)) produce much larger interactions with a given nucleotide or nucleoside than do metalloporphyrins having two axial ligands (e.g., Mn(III), Fe(III), or Co(III)). The kinetics of the interaction of H2TMpyP with 2'-deoxyadenosine S'-monophosphate (dAMP) were studied via the laser raman temperature-jump method. The measured rate constants are consistent with a simple stacking model for the interaction.

Structures of Metalloporphyrin–Oligomer Multianions: Cofacial versus Coplanar Motifs as Resolved by Ion Mobility Spectrometry

“…Planar side-byside structures ( Figure 6, structure III) can be ruled out both on the of basis of their collision cross section (TM-CCS 691 Å 2 , more than 200 Å 2 above the experimental value) as well as their relative energy (1.7 eV above structure I). To summarize, it is clear that [(MTPPS) 3 + 8Na] 4− consists of a an H-aggregatelike face-to-face stack of three porphyrins.…”

“…We obtained two charge states of the trimers in sufficient intensity to determine their collision cross sections: [(MTPPS) 3 + 8Na] 4− and [(MTPPS) 3 + 7Na] 5− .…”

“…[(MTPPS) 3 + 8Na] 4− . For the quadruply charged trimer we measure a CCS of 477 Å 2 for M = Zn, 479 Å 2 for M = Cu, and 484 Å 2 for M = Pd; again these are identical within the experimental uncertainty.…”

“…It is interesting to compare these values with the CCS for the quintuply charged dimers (see above)they are basically the same, although the trimers consists of 275 atoms instead of 181 atoms for the dimer. Obviously, the geometry of [(MTPPS) 3 + 8Na] 4− must be very compact. Given available computational resources, the trimers are too large for DFT calculations with the TZVPP basis set (which is necessary to minimize basis set superposition errors, see above).…”

“…Given available computational resources, the trimers are too large for DFT calculations with the TZVPP basis set (which is necessary to minimize basis set superposition errors, see above). Therefore, on the basis of our experience with the dimers we rely on PM7 to provide reasonable candidate structures for [(ZnTPPS) 3 + 8Na] 4− . The most favorable structure that we obtain is a face-to-face stack of the three porphyrins.…”