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Diamond 2.1: Molecules and packing diagrams

Diamond 2.1 Features Overview...
Previous: Adjusting bond spheres...
Next: Investigation of coordination spheres...

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. 

Oxo-diperoxo-hexamethylphosphoramide-aqua-molybdate(vi) with Mo8O26 polyhedra

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

Sodium tecto-hexaoxoalumodisilicate hydrate with broken-off bonds

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


Diamond 2.1 Features Overview...
Previous: Adjusting bond spheres...
Next: Investigation of coordination spheres...