Electron density dictionary (rhoCIF) version 1.0.1

Category ATOM_LOCAL_AXES

Name:
'_atom_local_axes_[rho]'

Definition:

   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

Type: null

Category: category_overview