Calcium Ion Coordination: A Comparison with That of Beryllium, Magnesium, and Zinc

Abstract

The coordination geometry of divalent calcium ions has been investigated by analyses of the crystal structures of small molecules containing this cation that are found in the Cambridge Structural Database, protein crystal structures in the Protein Databank, and by ab initio molecular orbital calculations on hydrated structures of the form Ca[H 2 O] n 2+ · m H 2 O, in which there are n water molecules in the first coordination shell and m water molecules in the second coordination shell (hydrogen bonded to water molecules in the first shell). Calcium ions in crystal structures generally bind to oxygen atoms in ligands (rather than any other element), and their preferred coordination numbers range from 6 to 8. In protein crystal structures the tendency of calcium to bind water molecules is less than for magnesium (1.5 versus 2.2 water molecules on the average per metal ion site, respectively). The ratio of bidentate to monodentate binding of calcium ions to carboxylate groups is similar for small molecules and protein structures in that no bidentate binding occurs if the coordination number of Ca 2+ is 6, but its occurrence rises to near 20% for coordination numbers 7 and 8. Complexes of the form Ca[H 2 O] 5 2+ ·H 2 O and Ca[H 2 O] 4 2+ ·2H 2 O were found (by ab initio molecular orbital calculations in vacuo ) to be significantly higher in energy than Ca[H 2 O] 6 2+ (by 8.2 and 15.0 kcal/mol, respectively). For Ca 2+ surrounded by seven or eight water molecules, the differences in energy between Ca[H 2 O] 6 2+ ·H 2 O and Ca[H 2 O] 7 2+ and among Ca[H 2 O] 6 2+ ·2H 2 O, Ca[H 2 O] 7 2+ ·H 2 O, and Ca[H 2 O] 8 2+ are extremely small when diffuse functions are included in the basis set. Thus, the net energy penalty for changing the number of water molecules in the first coordination shell between 6 and 8 is small. Molecular orbital calculations also indicate that the effect of a calcium ion on the H−O−H angle to bound water is less (at normal coordination numbers) than that of magnesium, zinc, or beryllium.