Section 2.4.6. Bonding conventions

Chemical information systems use a variety of conventions to specify attributes such as aromaticity, bond-order alternation, tautomerism etc. These system-dependent conventions decide the values that are permitted for quantities such as bond order, electronic charge and hydrogen-atom count. Most systems also provide for redundancy between chemical attributes. For example, the valency, the number of connected non-hydrogen atoms, the number of terminal hydrogen atoms and the bond types associated with a given atom are clearly related. Operational systems make use of these relationships to perform internal checks and to provide flexibility in substructure search processes.

The MIF data definitions provide for three bonding conventions. These are the data items _bond_type_mif, _bond_type_casreg3 and _bond_type_ccdc. The `mif' convention defines only single, double, triple and other bonds, while the `casreg3' convention (Mockus & Stobaugh, 1980) extends these to include aromaticity in terms of `ring alternating normalized bonds' and tautomerism via a `tautomer normalized bond'. The `ccdc' convention is that employed in the Cambridge Structural Database System (Allen et al., 1991; Allen, 2002) to categorize bond types encountered in both organic and metal-organic molecules.

An important advantage of the MIF approach is that a molecule can be represented using all three bonding conventions within the same data block. An example of alternative bonding conventions encoded for toluene is shown in Fig. 2.4.6.1.

Figure 2.4.6.1 | top | pdf | Three alternative bonding conventions for toluene stored in the same MIF data block.