You can impose or forbid a substructure during a retrosynthesis search, either forcing the results to contain the substructure or forbidding the substructure from appearing among your results. To access this Advanced Search feature, click on the “Intermediates” tab in the Advanced Search window.
In the “Intermediates” tab, you’ll see fields where you can directly enter structure SMILES or substructure SMARTS or where you can click on the pen icon to open the sketcher tool from which you can draw your desired structures.
To impose substructures, enter or draw the structure in the “Impose one or several substructures” field. Spaya will use OR logic when there are multiple imposed substructures added to this field.
To forbid substructures, enter or draw the structure in the “Forbid one or several substructures” field. Spaya will use AND logic when there are multiple forbidden substructures added to this field.
If you want to impose or forbid several substructures in one molecule, they should be drawn in one sketcher window. If the substructures to be imposed or forbidden appear in separate molecules, they should be drawn separately.
Spaya will impose or forbid your substructure everywhere in the retrosynthesis tree except the target molecule.
If you draw your molecule in the sketcher, Spaya will consider implicit hydrogens in your molecule as per default during the retrosynthesis search. If you want to use explicit Hydrogens, please type SMARTS according to Daylight Systems logic (for more details, please, click here https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html )