Figure 1
An example illustrating the importance of correct bond orders for structure interpretation is one of the sandwich structures present in the PDB. Both cyclopentadienyl rings must be planar with a nominal charge of −1. All C atoms on these rings must be sp2-hybridized. (a) From the CCD, the bond orders on both relevant rings are single, with no charge. Most programs interpreting this molecule with these bond orders will assume that all C atoms are sp3-hybridized, with two H atoms attached. Moreover, the metal atom (Ru) will be assumed to be neutral. (b) The bond orders and nominal charges on the cyclopentadienyl rings have been corrected. Now the rings are aromatic with a nominal charge of −1, and both rings are planar. According to MetalCoord, the coordination class is sandwich_5_5. Note that the structure, for example, in PDB entry 4xxr appears to be structurally sound (Lewandowski et al., 2015). These figures were produced using ChemDraw version 23.01. |