Swap Fragments Panel

Replace a selected fragment in each of a set of reference structures with a selected fragment from another structure. The structures are aligned by superposition before replacement is done.

To open this panel: click the Tasks button and browse to Materials → Quantum Mechanics → Reaction Network → Swap Fragments.

The following licenses are required to use this panel: MS Maestro

  • Using
  • Features
  • Additional Resources

Using the Swap Fragments Panel

This panel was designed around the substitution of fragments in organometallic catalysts. Given a reaction scheme in which the reactants, products, transition states, and intermediates are defined, the panel allows you to make substitutions on the substrate or the catalyst in the stages of this scheme. The structures for each step of the input reaction scheme are treated as a set of reference structures, and the new catalyst or substrate is treated as the novel structure. For the novel structure and each reference structure, you designate atoms to keep (or remove) in the new structure, then specify how the structures are to be aligned so that the correct bonds are formed and the fragments have the desired relative orientation.

This workflow is not just applicable to catalysts: it is perfectly general, and could be applied to any pair of structures or structure sets, where the goal is to make a particular substitution at a particular location with a particular orientation.

Swap Fragments Panel Features

Color collections of atom indices to be kept and replaced color chooser buttons and Color button

Specify the color to be used in the Workspace for the atoms to be kept and replaced, by clicking the color to open a color chooser. The atoms are colored in the Workspace when you click the Color button.

Common features

These features are common to both the Novel Structure section and the Reference Structures section.

Import from Workspace button

Import the structure from the Workspace. It must be the only entry included in the Workspace. You can replace the structure in the Workspace for each structure you want to import.

Name text box

Name to be used as part of the title of each new structure. The name is initially taken from the entry title. You can edit the text to specify whatever name you want.

Show in Workspace button

Replace the Workspace with the structure. This allows you to view the structure, with its coloring, whenever you need to inspect it.

Specify a collection of atom indices to be replaced/kept text box

Specify the atom numbers of the atoms you want to replace in the structure, or the atoms you want to keep in the structure. Whether the atoms are replaced or kept depends on the choice from the Collections of atom indices should be option menu (see below). You can enter the indices directly into the text box, or click Define to pick the atoms.

Specify novel atom indices for superposition text box

Specify the atoms in the novel structure for superposition of the novel structure on the reference structure. The superposition is done by creating atom pairs from this list and the one given in the Specify reference atom indices for superposition text box, in the order given in the text boxes. These atoms should be chosen to properly align the two structures for swapping the fragments.

If you specify the novel atom indices in the Novel Structure section, they are propagated to the corresponding text box for each reference structure.

Define button

Define the atoms to be replaced/kept, in terms of an ASL expression (see Atom Specification Language for more information). Opens the Define ASL text box, in which you can use the standard picking tools to pick the desired atoms.

Novel Structure section

Specify the novel structure and the fragment to be transferred to the reference structures. The tools in this section are defined above, under Common features. The Name text is used as the first part of the title of the new structures.

If you specify atom indices in the Specify novel atom indices for superposition text box, these are propagated to the corresponding text box for all reference structures that you include. This is a quick way of ensuring the same atoms are superimposed on all reference structures. You can specify these atom indices by selecting Pick atoms and picking the atoms in the Workspace. If you specified reference atom indices in the Indices of superposable atoms text box of the Create Reaction Network Profiler Input Structures Panel, you must make sure that you pick the atoms in the order corresponding to these indices. It might help to display a reference structure and label it by element and atom number (see Labeling Atoms and Bonds for more information), so you know which atoms in the reference structure have these indices, and then display the novel structure to pick the atoms you want to superimpose on the reference atoms.

Reference Structures section

Define the reference structures and the fragments to be replaced by the fragment from the novel structure. Each reference structure is defined with a common set of tools that can be duplicated for each structure.

Import button

Import the reference structures from the selected entries in the Project Table. A set of tools to define the structure is added for each entry and populated with the entry title.

Collections of atom indices should be option menu

Choose whether to keep the atoms that are chosen in each reference structure, or replace them. The label of the text box is updated for the Specify a collection of atom indices to be action text boxes in both the Novel Structure section and the Reference Structures section. The choice made from this option menu (kept or replaced) is used in the Reference Structures section, and the other one (replaced or kept) in the Novel Structure section.

This option menu allows you to make a choice of how the atoms are treated so that you can minimize the number of atoms you need to specify. For example, you would choose keep if the number of atoms to keep in the reference structure was smaller (or easier to specify) than the number of atoms to replace.

Reference structure controls

The controls for each reference structure are the same for each reference structure. The Common features described above are used here; the Name text is used for the second part or the title of the new structures. If you specified atom indices in the Specify novel atom indices for superposition text box, these are propagated to the corresponding text box for all reference structures.

reference management buttons

These buttons perform display and ordering operations on the reference. They allow for easy duplication and rearrangement of references.

    Show or hide the contents of the reference. When hidden, only the reference number, label (if any) and these buttons are displayed. This is useful when you have a number of references and want to compare two separate references, for example.
    Move the reference up or down one place in the list.
Duplicate the reference. This is useful for creating similar references with variations on the settings.
Delete the reference.

Specify reference atom indices for superposition text box

Specify the atoms in this reference structure for superposition of the novel structure on this reference structure. The superposition is done by creating atom pairs from this list and the one given in the Specify novel atom indices for superposition text box, in the order given in the text boxes. These atoms should be chosen to properly align the two structures for swapping the fragments.

If you specified reference atom indices in the Indices of superposable atoms text box of the Create Reaction Network Profiler Input Structures Panel, these indices are loaded automatically into this text box. If you did not do this, and novel atom indices were specified in the Novel Structure section, you will have to type the corresponding indices for the reference structure into this text box. Atom indices are displayed in the status bar in the Workspace when you pause the pointer ("hover") over an atom.

Pick (novel, reference) superposition atom pairs in Workspace option

Select this option to pick pairs of atoms in the Workspace for superposition (as in the Superposition panel). The novel structure and the reference structure are placed in the Workspace and the Workspace is tiled so you can see both structures clearly. You must pick at least three atom pairs. The atom pair indices are appended to the lists in the Specify novel atom indices for superposition text box and Specify reference atom indices for superposition text box.

You should not use this option if the novel atom indices were specified in the Novel Structure section and you want to use these indices.

Show Superposition in Workspace button

Show the superposition of the current reference structure on the novel structure in the Workspace.

Add Reference Structure button

Add a set of controls for a new reference structure.

Require identical bonds option

Require the bonds that are broken when the fragments are swapped to have the same bond order in the reference structure and the novel structure. If you deselect this option, you can change the types of bonds between the two fragments: for example, a ligand atom with a single bond to a metal might be replaced with an eta-coordinated ring.

Run button

Run the workflow to swap the fragments and create the new structures. The structures are created as ungrouped entries in the Project Table.

Status bar

Use the Reset button to reset the panel to its default settings and clear any data from the panel. If the panel has a Job toolbar, you can also reset the panel from the Settings button menu.

If you can submit a job from the panel, the status bar displays information about the current job settings and status for the panel. The settings include the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

The status bar also contains the Help button , which opens an option menu with choices to open the help topic for the panel (Documentation), launch Maestro Assistant, or if available, choose from an option menu of Tutorials. If the panel is used by one or more tutorials, hover over the Tutorials option to display a list of tutorials. Choosing a tutorial opens the tutorial topic.

Tutorials

Related Topics