JChem supports the search of reactions with substructure or reaction queries. (In addition to the reaction search features described in this section, all query features of non-reaction search can be used.)
Structures to the left of the reaction arrow are reactants (starting materials), structures to the right of the reaction arrow are products, and those molecules drawn just above or below the arrow are agents (ingredients). Corresponding atoms containing changing bonds (created, destroyed or modified) are marked with map numbers both in the reactants and in the products (Table 1.).
Searching for a substructure in a reaction equation does not differ from the classical substructure search process described above. Any matching in any reaction components (reactants, agents, products) is a hit. This is not the case when the query itself is a reaction.
Table 1. Searching for simple query structure in reaction
Reaction queries are not necessarily complete reactions. Reaction queries sometimes contain reactants only. In this case, the search engine retrieves reactions containing reactants matching to the given structure. When just a product is specified in the query, those reactions will be returned which contain matching products (Table 2).
Table 2. Searching for query structure in reaction components
See also SMARTS component level grouping.
When a reaction query has mapped atoms, the reaction center of a matching reaction is mapped correspondingly. Although, the actual value of the map numbers might be different in the query and the target, the hit atoms have to be paired exactly as they are in the query (Table 3).
Table 3. Searching by mapped reaction queries
Note : If you plan to execute database searches with mapped reaction queries then the target reactions must be mapped before database import. We offer Standardizer application, built in JChem, for mapping reactions.
You can restrict your reaction search by applying reacting center query features on bonds to express the bond's role in the reaction mechanism. Table 4. describes these query features.
Symbol on bond
The bond takes part in the reaction. (Its bond type changes or the bond is created or disappears in the reaction.)
Make or break
The bond is created or disappears in the reaction. (Depending if it is present on the reactant or product side.)
The bond remains in the reaction, but its bond type changes, for example from single to double.
Make and change
Currently it works exactly as "Center" above
The bond must not change in the reaction.
Table 5. shows some examples.
Note : Reacting center bond features of reactions in database are not considered.
In case of mapped reactions, reacting center stereo query features - inversion and retention - can be applied on the chiral atom in the reacting center. In case of unmapped reactions, these query features are not applicable.
Table 6. Effect of reacting center stereo query features during reaction search
A query structure occasionally consists of some disjunct fragments. Since these fragments belong to a single reaction component in the query, their corresponding hits must belong to a single component as well. Two components of a reaction query are matching to two components of a target reaction (Table 7).
Table 7. Component identification during reaction search