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Article ID: 416 - Last Modified:

How should I prepare reactant, product, and transition state guess structures for a transition state search?

We recommend that you start with one structure, duplicate it in the Project Table and then change the duplicates into the other structures by making and breaking the appropriate bonds. Building the reactant from the product (or vice versa) ensures that the atom numbers and labels remain the same, which is critical for the transition state search. It is highly recommended to build a guess at the transition state and use the QST method. The reactant and product structures should be pre-positioned for the reaction, not necessarily at the minimum. Doing this will make the search quicker and more likely to succeed.

You can use the following procedure to prepare the structures from scratch:

  1. In the Preferences panel (CTRL+, to open) check that the preference "Adjust number of hydrogens following build operations" in the Builder tab is turned off.
  2. Build one of the structures in the Workspace.
  3. Add the structure to the project as a project entry (CTRL+SHIFT+N).
  4. Duplicate the structure in the Project Table (select it, press CTRL+D).
  5. Do the necessary bond breaking and making and structural adjustments to create one of the other structures.
  6. Duplicate the structure again and edit it to produce the third structure (for QST, which is recommended).

If you already have one of the structures, import it into the project instead of building it and adding it (steps 2 and 3).

Keywords: atom numbers, renumber, Maestro, Jaguar

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