SMIRKS bonds

In order to carry out a transformation, it is necessary to know precisely which bonds are to be broken and which are to be made. While this information is implicit in the SMIRKS above and can be understood by any chemist, a more specific set of instructions is necessary in order to make the transformation possible using a computer. Numbering the atoms of the reactants and the corresponding atoms in the products accomplishes this. This produces an atom mapping. Many sketching programs can do this automatically or with some additional input from the user. Using the example shown previously, an atom-mapped SMIRKS would... 

Before considering how SMIRKS can be used to carry out transformations with multiple reactants, first consider simpler unimolecular transformations. These are discussed separately because of the important use of unimolecular transformations to enforce the consistent use of SMILES throughout the database. This improves the integrity of the data in a chemical sense, rather than a relational database sense as discussed previously. The root of the issue is this There are multiple ways to represent the same molecular structure due to the limitations of valence bond theory. In valence bond theory, upon which SMILES is based, atoms have formal charges, most often zero. The bonds between atoms are shared pairs of electrons and may consist of multiple shared pairs giving rise to double, triple, or possibly even higher-order bonds between atoms. This simple theory, while quite powerful and applicable to a majority of chemical structures, leads to certain ambiguities. 

Figure 6.3 A SMIRKS notation specifying the conversion of a charge-separated nitro group to a representation with two double bonds and a 5-valent nitrogen atom. Corresponding atoms on each side have the same number (shown after the colon in the SMIRKS), and the atom attached to the nitro group is shown in the SMIRKS as indicating any atom .

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