International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

International Tables for Crystallography (2006). Vol. G, ch. 2.4, pp. 47-48

Section 2.4.5. Atoms, bonds and molecular representations

F. H. Allen,a* J. M. Barnard,b A. P. F. Cookb and S. R. Hallc

aCambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, England,bBCI Ltd, 46 Uppergate Road, Stannington, Sheffield S6 6BX, England, and cSchool of Biomedical and Chemical Sciences, University of Western Australia, Crawley, Perth, WA 6009, Australia
Correspondence e-mail:  allen@ccdc.cam.ac.uk

2.4.5. Atoms, bonds and molecular representations

| top | pdf |

The MIF dictionary (see Chapter 4.8[link] ) contains definitions of the principal data items needed to specify molecular connectivity and spatial representations. These definitions are grouped according to purpose or, as referred to in the DDL dictionary language (Hall & Cook, 1995[link]), by category. Categories are formally specified in the MIF dictionary using the data attribute _category but they may also be identified from the data-name construction `_<category>_<subcategory>_<descriptor>'. Note that data items appearing in the same looped list must belong to the same category.

The values of some data items are restricted, by definition in the MIF dictionary, to standard codes or states. For example, the item _bond_type_mif can only have values S, D, T or O as in its dictionary definitions:

  • S: single (two-electron) bond;

  • D: double (four-electron) bond;

  • T: triple (six-electron) bond;

  • O: other (e.g. coordination) bond.

The MIF dictionary plays the important additional role of validating and standardizing data values. This is illustrated with the data item _display_colour, which identifies the colours of `atom' and `bond' graphical objects. The colour codes or states for this item are specified in its dictionary definitions as a set of permitted red/green/blue (RGB) ratios, and no other colours may be used in a MIF. This has the technical advantage of making colour states searchable for chemical applications.

Fig. 2.4.4.2[link] shows MIF data for the molecule (+)-3-bromocamphor. The `atom' list contains the items _atom_id, _atom_type and _atom_attach_h, which identify the chemical properties of the atoms, plus the items _atom_coord_x, *_y and *_z, which specify the 3D molecular structure in Cartesian coordinates [these are taken from diffraction results (Allen & Rogers, 1970[link])]. The item _atom_label is also used with any graphical depiction of the 3D model. The `bond' loop in this example uses the simple _bond_type_mif conventions described above. The data names needed to depict stereochemistry are discussed with examples (Figs. 2.4.8.1[link], 2.4.8.2[link] and 2.4.8.3[link]) in Section 2.4.8[link].

The MIF approach to representing 2D chemical structure separates the specification of chemical atom and bond properties. This provides additional flexibility in the description of the graphical objects, such as atomic nodes and bonded connections. The MIF data required to generate a 2D chemical diagram are shown in Fig. 2.4.4.2[link]. The diagram generated from this data will be in a display area of 500 × 500 coordinate units at a scale of 50 units per cm (the 2D chemical diagram shown in Fig. 2.4.4.2[link] is not to this scale). The default origin (the bottom left corner of the display area) can be specified with the item _display_define_origin. The data used to depict a 2D structure form a two-level loop with the `atomic' graphical objects at level 1 and the `bond' graphical objects at level 2. The item _display_object has the values `.' (null or no object), `text' (an element or number string) or `icon'. The size and colour of the atom site are specified with _display_size and _display_colour. The bonds connected to each atom site are specified as a sequence of _display_conn_id numbers (in loop level 2). These numbers must match one of the _display_id numbers at level 1. The connection object is specified with a _display_conn_symbol code, which must be a standard value in the dictionary definition, as is the colour of the icon if specified by _display_conn_colour.

References

Allen, F. H. & Rogers, D. (1970). X-ray studies of terpenoid derivatives, Part III. A re-determination of the crystal structure of (+)-3-bromocamphor: the absolute configuration of (+)-camphor. J. Chem. Soc. B, pp. 632–636.
Hall, S. R. & Cook, A. P. F. (1995). STAR Dictionary Definition Language: initial specification. J. Chem. Inf. Comput. Sci. 35, 819–825.








































to end of page
to top of page