Molecules and Packing Diagrams
Molecules can easily be built from the atoms of the parameter list. Symmetry
operations are invoked automatically, if the atoms in the parameter list do
not describe an entire molecule. To generate a packing diagram, you may start
creating all or a portion of atoms within a given cell range, e.g. the unit cell,
then call the Complete Fragments function to get entire molecules.
Packing diagram
The picture shows a special packing diagram of a metal-organic structure
(Oxo-diperoxo-hexamethylphosphoramide-aqua-molybdate(vi)) containing four cells with two
molecules of the phosphoramide each and the Mo8O26 polyhedra in the
corners [1].
[1] CSD Reference Code DEXTOP:
Name: Oxo-diperoxo-hexamethylphosphoramide-aqua-molybdate(vi)
Formula: 2(C22 H22 O2 P1 1+),2(C4 H12 N1 1+),Mo8 O26 4-
Author(s): H.Arzoumanian,A.Baldy,R.Lai,A.Odreman,J.Metzger,M.Pierrot
Journal: JORCAI 295 (1985), pp. 343 - 343
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Molecule cage for polymeric structures
The molecule cage, if activated, stops generation of atoms during the search for
neighbouring atoms behind selected "walls". The most useful application is not
for (organic) molecules but for inorganic polymeric networks, e.g. for the Si-O-network in
analcime (Sodium tecto-hexaoxoalumodisilicate hydrate, NaAlSi2O6 x H2O)
[2]. With a cage of the unit cell's size, the Si and O atoms outside the unit cell will be
generated but not serve as starting point for other O and Si neighbours. These neighbours
are rather intimated by so-called broken-off bonds.
[2] ICSD Collection Code 2930:
Name: Sodium tecto-hexaoxoalumodisilicate hydrate
Formula: Na (Al Si2 O6) (H2 O)
Author(s): Ferraris G, Jones D W, Yerkess J
Title: A neutron-diffraction study of the crystal structure of analcime, Na Al Si2 O6 H2 O
Journal: ZEKGA 135 (1972), pp. 240 - 252
Mineral name: Analcime
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