Supramolecular networks via hydrogen bonding and stacking interactions for adenosine 5′-diphosphate. Synthesis and crystal structure of diaqua(2,2′∶6′,2″-terpyridine)copper(II) [adenosine 5′-diphosphato(3–)](2,2′∶6′,2″-terpyridine)cuprate(II) adenosine 5′-diphosphate(1–) hexadecahydrate and density functional geometry optimization analysis of copper(II)- and zinc(II)-pyrophosphate complexes

Abstract

Single crystal X-ray diffraction showed that crystals of [Cu(TERPY)(H₂O)₂][Cu(TERPY)(ADP)][H₂ADP]·16H₂O [TERPY = 2,2′∶6′∶2″-terpyridine; ADP = adenosine 5′-diphosphate(3-)] belong to the triclinic system, space group P1 (no. 1) and contain free nucleotide molecules, nucleotide molecules linked to the metal centre of Cu(TERPY)²⁺ units, [Cu(TERPY)(H₂O)₂]²⁺ complexes and free water molecules. The molecules of free nucleotide, [Cu(TERPY)(ADP)]^– and [Cu(TERPY)(H₂O)₂]²⁺ >are clustered together and interact via the phosphate moieties and the >Cu(H₂O)₂²⁺ group. An extensive web of hydrogen bonds holds the three molecules oriented in such a way that the most hydrophobic regions (TERPY) occupy the perimeter of a pocket which contains the pyrophosphate systems. Stacking interactions between the adenine rings and the TERPY ligands stabilize the supramolecular aggregates. Owing to the high content of cocrystallized water molecules the nucleotides have an environment similar to the aqueous phase. The analysis of the Fourier-difference map and of the geometrical parameters of the molecules is consistent with a model in which the free nucleotide molecule is protonated at N(1) and phosphate(β), whereas the copper-bound nucleotide molecule is fully deprotonated as regards the N(1) and phosphate oxygen atoms. The phosphate(β) of the copper-bound nucleotide behaves as a better ligand than phosphate(α) [Cu–O, 1.919(8) and 2.244(10) Å, respectively]. The chelation to the metal of the pyrophosphate moiety causes a lengthening of 0.040(9) Å of the P(β)–OP bond with respect to P(α)–OP. A density functional analysis at the B3LYP/LANL2DZ level was carried out on P₂O₇^4–, HP₂O₇^3–, [Cu(O,O-PO₄)]^–, [Cu{O(α),O(β)-P₂O₇}]^2–, [Zn{O(α),O(β)-P₂O₇}]^2–, [Zn{O(α),O(β)-HP₂O₇}(H₂O)(OH)]^2–, [Cu{O(α),O(β)-HP₂O₇}(NH₃)₃]^– and [Zn{O(α),O(β)-HP₂O₇}(NH₃)₂]^–·NH₃. The computational procedure was able to reproduce the overall conformation (bond and torsion angles) of the pyrophosphate group as well as the structure of the co-ordination ring found in the solid state. The computed fully optimized structure for [Cu{O(α),O(β)-P₂O₇}]^2– has a Cu–O bond distance of 1.837 Å and the co-ordination ring has a boat-envelope conformation, in agreement with the experimental structure found for the metal-bound nucleotide molecule.