Characterization of the Pentacoordinate Sodium Cations in Hydrated Nucleoside 5‘-Phosphates by Solid-State 23Na NMR and Quantum Mechanical Calculations

Abstract

We report a solid-state 23Na NMR study for the sodium cations in four hydrated disodium salts of nucleoside 5‘-phosphates: 2‘-deoxycytidine 5‘-monophosphate (dCMP), 2‘-deoxyguanosine 5‘-monophosphate (dGMP), 2‘-deoxyuridine 5‘-monophosphate (dUMP), and adenosine 5‘-triphosphate (ATP). Using one- and two-dimensional solid-state NMR techniques, we were able to detect all crystallographically distinct Na+ ions in each of the Na−nucleotide systems. A total of 12 Na sites were fully characterized, among which four exhibit unusual penta-coordination geometry. The present study provides the first reliable solid-state 23Na NMR characterization for the pentacoordinate Na+ ions in nucleoside 5‘-phosphates. Spectral assignment was achieved on the basis of quantum mechanical electric-field-gradient (EFG) calculations at the restricted Hartree−Fock level with a 6-31G(d) basis set. The pentacoordinate Na+ ion found in [d(TG4T)]4 by high-resolution X-ray crystallography was modeled by using an isolated guanine quartet together with a central Na+ ion and an axial water molecule. Quantum mechanical calculations suggest that the 23Na quadrupole coupling constant for this square-pyramidal Na site is large (ca. 3 MHz), providing a possible explanation for the previous failure in detecting this type of Na+ ions by solid-state 23Na NMR.