SMIRKS reactant

The use of Simplified Molecular Input Line Entry System (SMILES) as a string representation of chemical structure makes possible much of what has been discussed in earlier chapters of this book. A chemical reaction could be represented as a collection of SMILES, some identified as reactants and some as products. It is possible to define a table to do this, or perhaps use some arrays of character data types, but a syntax extension of standard SMILES allows reaction to be expressed easily. SMIRKS is an extension of SMILES and SMiles ARbitrary Target Specification (SMARTS). It is used to represent chemical transformations. SMIRKS can also be used in a transformation function to combine SMILES reactants to produce SMILES products. 

Reaction SMILES represents a specific reaction between specific reactants yielding specific products. As such, it can be very useful to store a library of reactions of interest. These might be a record of reactions that have been carried out at a company, a set of reaction plans in an academic research group, or even a set of hypothetical reactions that might never succeed in the laboratory. There is another extension of SMILES called SMIRKS that is more general and can represent a class of reactions. 

The word reaction is typically used to represent a specific reaction as well as a general transformation. In this chapter, the word reaction is used to mean a specific reaction represented using reaction SMILES. The word transformation is used to indicate a change in a set of reactants to products. SMIRKS is the language used to specify precisely how this transformation is to be carried out. 

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. 

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