Geometry of the phosphate group and its interactions with metal cations in crystals and ab initio calculations

The phosphate geometry was studied in crystal environment by analyzing 178 crystal structures and in vacuo by ab initio calculations of (di)hydrogen and dimethyl phosphates and a diphosphate model system, CH3OP(O-2)O(CH2)(3)OP(O-2)OCH3 (diPh), at the MP2 and HF levels. Since charge determines the phosphate stereochemistry, uncharged, -1, and -2 phosphates were analyzed separately. The P=O and O=P=O bonding parameters depend only on charge and the number of carbon substituents while the remaining parameters depend also on substituent type; the largest sensitivity was observed for the C-O and C-O-P parameters. An acceptable agreement between the crystal and ab initio geometries was obtained only when basis sets contained polarization functions and a model system included a counterion (Na+). In uncharged and -1 phosphates, the C-O-P-O(-C) torsion angles prefer the +/-sc regions. These phosphates substituted by cyclic C-sp3 noncyclic C-sp3, or C-ar carbons have characteristic torsion distributions. Conclusion from both analysis of crystal data and from theoretical calculations is that the internal phosphate geometry is sensitive to a counterion position as well as to values of the C-O-P-O(-C) torsion angles. Most metal cations interact directly with the charged oxygens in -1 phosphates while in many -2 phosphates, this interaction is mediated by water molecules. The distributions of Na+ around -1 and -2 phosphates are localized into two principal sites which Lie outside the O=P=O plane and interact with only one of the charged oxygens. In contrast, theoretically predicted positions are located symmetrically between the charged oxygens in the O=P=O plane. The cation positions around dimethyl phosphate and a model diPh compound mimicking the B-DNA backbone were virtually identical. The discrepancy between these theoretical positions and the sites derived from the crystal data was significantly reduced by incorporation of a single water molecule into the theoretical model. Therefore, both cations and polar particles, particularly water molecules, should be considered when properties of the phosphate group are described.