Modifying Molecules

Once a Molecule is created, it is often necessary to modify the resulting structure. MoleculeModify can perform a wide assortment of modifications, from changing atomic properties like charge and mass number to adding and removing entire substructures.

Add a ring-closing bond to -hexane to form cyclohexane.

Add a double-bonded oxygen atom to make cyclohexanone.

Convert phenol to phenolate by adding a negative charge to the oxygen atom.

When the charge on the oxygen atom was changed, the number of attached hydrogen atoms was changed accordingly. This can be disabled using the ValenceErrorHandling option.

Replace a carbon atom with nitrogen.