Adenosine 5'-triphosphate (ATP) is an essential energy carrier in mammalian and other cells, and its hydrolysis to the diphosphate (ADP) in the presence of metal cations (e.g., Mg2+ or Ca2+) is one of the most prevalent biochemical reactions. We describe here density functional (DF) calculations on closely related systems and compare the results with other calculations and available experimental data: Na(H2O)(n)(+), Mg(H2O)(n)(2+) Ca(H2O)(n)(2+) clusters (n = 1, 4-7), the crystalline pyrophosphates Mg2P2O7-6H(2)O and alpha-CaNa(2)P(2)O(7)(.)4H(2)O, and crystalline Na(2)ATP(.)3H(2)O. The last of these comprises asymmetric units of ATP dimers (monomers A and B) in a double-protonated state H-2(ATp)(2-). The calculated structures agree well with available measurements and provide additional information, including the location of the H atoms. Analysis of the dipole moments of individual ATP monomers and their dimers shows that the crystal comprises blocks of opposing dipoles. Replacing one Na+ ion with Mg2+ or Ca 21 results in a significant elongation of the terminal bridgin P-O bond. The calculations provide benchmarks for the use of DF methods in ATP systems and are used in the companion paper to study the hydrolysis of ATP at the active site of the protein actin.