Electron density dictionary (rhoCIF) version 1.0.1
This category allows the definition of local axes around each atom in terms of vectors between neighbouring atoms. High-resolution X-ray diffraction methods enable the determination of the electron density distribution in crystal lattices and molecules, which in turn allows for a characterization of chemical interactions (Coppens, 1997; Koritsanszky & Coppens, 2001). This is accomplished by the construction of a mathematical model of the charge density in a crystal and then by fitting the parameters of such a model to the experimental pattern of diffracted X-rays. The model on which this dictionary is based is the so-called multipole formalism proposed by Hansen & Coppens (1978). In this model, the electron density in a crystal is described by a sum of aspherical "pseudoatoms" where the pseudoatom density has the form defined in the _atom_rho_multipole_* items. Each pseudoatom density consists of terms representing the core density, the spherical part of the valence density and the deviation of the valence density from sphericity. The continuous electron density in the crystal is then modelled as a sum of atom-centred charge distributions. Once the experimental electron density has been established, the "atoms in molecules" theory of Bader (1990) provides tools for the interpretation of the density distribution in terms of its topological properties. Ref: Bader, R. F. W. (1990). Atoms in molecules: a quantum theory. Oxford University Press. Coppens, P. (1997). X-ray charge densities and chemical bonding. Oxford University Press. Hansen, N. K. & Coppens, P. (1978). Acta Cryst. A34, 909-921. Koritsanszky, T. S. & Coppens, P. (2001). Chem. Rev. 101, 1583-1621.Example:
Example 1 - This example shows how the local axes can be defined
around each atom in terms of vectors between neighbouring
atoms. If necessary, dummy atoms can be introduced into
the atom_site list for this purpose.
loop_ _atom_local_axes_atom_label _atom_local_axes_atom0 _atom_local_axes_ax1 _atom_local_axes_atom1 _atom_local_axes_atom2 _atom_local_axes_ax2 Ni2+(1) DUM0 Z Ni2+(1) N(1) X loop_ _atom_site_label _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_occupancy DUM0 0.80000 0.80000 0.80000 0.0