Independent Atom Model (IAM) is a good estimate for the atoms for which the valence electron density is a minor part of the total. When the quality of structure is reasonably good, you can see areas of bond-related residual positive density located on C-C, C-N and C=O bonds. With resolution better than 0.6-0.5 Å, these peaks can be higher than 0.4 e/Å<sup>3</sup>; R-factor and goodness of fit are abnormally large. Controversially, this discourages high resolution measurements!<br/>The quality of routine datasets is not sufficient for applying charge density formalism; Hirshfeld atom refinement currently cannot treat transition metals. As a simple alternative, we employ an empirical approach using traditional IAM software (SHELXL-201X, Jana2006). Scattering centers are placed at fixed calculated positions between C, N, and O atoms, with ‘occupancies’ being different for single, double, aromatic and triple bonds. Scattering is approximated by a single Gaussian which can be possibly justified by a small value of correction. The number of introduced parameters can be as low as one (for overall occupancy of pseudo-atom part of the structure). Introduction of virtual atoms makes the effect similar to one hydrogen atom per 4-5 C-C bonds, which is significant enough to justify the effort. Alternatively, each bond can be treated separately (number of additional parameters is roughly equal to the number of bonds) which leads to further improvement.<br/>This enable us to remove most of residual bond density from the Fourier difference map allowing then to address other sources of error such as disorder and, of course, experimental and data processing limitations. Uncertainties of bond distances are also lower by 20-30%. The procedure is illustrated by a number of macrocyclic complexes of 3d transition metal ions.

Bond electron densities in macrocyclic complexes: what is visible in a routine X-ray diffraction experiment

2019 Spring National Meeting

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