The Complex Formation Only AutoTS Workflow

The workflow selected with jobtype = complex_formation_only forms entrance and exit complexes from the individual molecules passed in as “reactant” and “product”.

Input file example:

reactant = [A.mae, B.mae]
product = [C.mae, D.mae]
jobtype = complex_formation_only
charge = 0
multiplicity = 1

Output:

jobname_reactant_complex.mae and jobname_product_complex.mae contain the reactant (entrance) and product (exit) complexes.

Known limitations:

• High topological symmetry and situations where there is a choice to break one of two locally identical bonds. An example of the latter limitation is lactonization. These instances may require intervention.

• Numbering-induced chirality which changes over the course of a reaction. One example is the chirality change of numbered hydrogens in the reaction CH3Cl + Br- -> Cl + CH3Br. Corrections for this reaction (invoked by -sn2) and syn addition reactions exist but may not cover all possible cases.

• Structures that contain many rings inside rings, such as graphene sheets, nanotubes and macrocycles.

• Structures that contain saturated rings.

• Reactions that involve spectator molecules are not supported and those jobs will exit fatally.