Factors governing metal-ligand distances and coordination geometries of metal complexes.
The metal-ligand (M-L) distances play a central role in determining the structure and reactivity of the metal complex and in metal discrimination in proteins. They reflect properties of the metal ion and the ligand during their coordination as well as the environment. However, the variation of the M-L distances as a function of the properties of the metal cation and its donor atoms had not been systematically analyzed, and no public website listing the M-L distances from metal complexes was available. Herein, the distances around 63 different types of metal ions in approximately 200,000 high-resolution crystal structures in the Cambridge Structural Database as well as their preferred coordination geometries have been determined. The dependence of these distances on (i) the donor atom's charge and charge-donating ability, (ii) the donor atom's size, (iii) the metal ion's oxidation state and charge-accepting ability, and (iv) the metal ion's size has also been determined. The concept of ligand coordination number (CN) was introduced to take into account the effect of the number of constituent ligand atoms on the M-L distances in addition to the number of metal-bound ligands. We propose grouping the M-L distances according to both the metal CN and the ligand CN. The mean M-L distance corresponding to a given metal CN and ligand CN was found to be linearly correlated with the metal's ionic radius in going down a main group or in going across the first three rows of the periodic table. The M-L distances as a function of the metal and ligand coordination numbers are available via http://bioit.ibms.sinica.edu.tw/CSD.htm
Kuppuraj
Gopi
G
Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.
Dudev
Minko
M
Lim
Carmay
C
D000465:Algorithms; D001703:Biophysics / Q000379:methods*; D002627:Chemistry, Physical / Q000379:methods; D030562:Databases, Protein; D007477:Ions; D008024:Ligands; D008670:Metals / Q000737:chemistry*; D008962:Models, Theoretical; D010100:Oxygen / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D007477:Ions; D008024:Ligands; D008670:Metals; D011506:Proteins; D010100:Oxygen