Ligand Creator Panel

Create and edit ligands for metal complexes and manage ligand libraries.

To open this panel: click the Tasks button and browse to Materials → Enumeration → Ligand Creator.

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

  • Features
  • Additional Resources

Ligand Creator Panel Features

Create Ligands Tab

Create new ligands by sketching them, defining them from an existing set of structures, or analyzing a set of complexes to extract ligands.

Choose method for creating new ligands options

Select a method for creating new ligands, from the following:

  • Sketch ligands—Sketch ligands in 2D using the 2D sketcher.
  • Analyze ligands from complexes—Analyze a set of congeneric complexes to locate a common core and extract ligands that are attached to the common core from each complex.
Sketcher tool

Sketch a ligand using the standard 2D sketching tools (see 2D Sketcher Panel for more information). You should add terminal atoms to designate as the coordination sites, which you can do by right-clicking on this atom, choosing Set R Group and selecting a label. For bidentate ligands, you must specify two coordination sites, R1 and R2. For ligands with a single haptic coordination site, connect each eta-bonded atom in the pi system to a single coordination site, designated R1. If the ligand has two haptic coordination sites, or one haptic and one kappa site, you should specify two sites, R1 and R2, and make the appropriate connections.

When you have finished sketching, use the Add ligand to library tools to add the new ligand to the desired libraries. To clear the sketcher for another (unrelated) ligand, click Reset Sketcher. You can also continue on with the current structure to create another, related ligand.

Ligand analysis tools

Analyze a set of structures in terms of a common core and attachments to the core. Once the core is identified, the attachments are listed and can be used as ligands. The core can be identified either by a search for the maximum common substructure or by matching a SMARTS pattern.

Analyze structures from option menu

Choose the structure source for analysis into a core and ligands.

  • Project Table (selected entries)—Use the entries that are currently selected in the Project Table.
  • Workspace (included entries)—Use the entries that are currently included in the Workspace, treated as separate structures.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.
File name text box and Browse button

Enter the file names in this text box, or click Browse and navigate to the files. The names of the files you selected is displayed in the text box. The allowed file types are: Maestro.The structures are imported into the project and the first one is displayed in the Workspace.

Core definition option menu

Choose the method for defining the common core. The MCS and SMARTS methods don't require a metal atom to be part of the structure, so in principle you can create ligands from structures that aren't metal complexes. However, the MCS and SMARTS methods can only find monodentate ligands. If you use either of these methods, you should be sure that the structures you provide have a common core whose removal leaves useful ligands.

  • Metal atom—Use the metal atoms in the complex as the core. Any non-metal atoms are taken to be part of a ligand.
  • Maximum common substructure—Determine the maximum common substructure using Canvas MCS. This method searches for the largest substructure that is common to all structures, using a scheme that defines which atoms are considered to be equivalent for matching purposes. This scheme could be useful for complexes that consist of ligands bound to a small inorganic cluster, such as Fe4S4.
  • SMARTS—Determine the core from a single SMARTS pattern. In this method, a structure is skipped if a match to the SMARTS pattern is not found.
Settings button

Open a dialog box in which you can make settings for the treatment of rings and atom equivalences for the maximum common substructure method. It is recommended that you select Do not allow partial rings in the core. The atom equivalences are described in Table 1 in canvasFPGen

SMARTS text box and Get from Workspace Selection button

Enter the SMARTS pattern for the core in the text box, or select the atoms in the Workspace for the SMARTS pattern and click Get from Workspace Selection. When you click the button, a SMARTS pattern is generated for the Workspace selection and replaces the contents of the SMARTS text box. You can modify the SMARTS pattern after it is obtained from the Workspace. Only available if you choose SMARTS for the core definition.

Analyze button

Analyze the structures to locate the core by the chosen method, and populate the table with the attachments to the core (ligands) that are found for each structure.

View Core button

Opens a panel that displays the 2D structure of the core, with labels at the coordination points.

Ligand table

Displays the ligands found for the analyzed structures. You can select all the ligands in a column by clicking on the column heading. To select ligands in the table, you can drag over cells, use control-click (command-click) to add or remove single cells from the selection, or use shift-click to add multiple cells to the collection.

For MCS and SMARTS methods, each column shows the unique ligands found at a particular attachment point (including hydrogen). Click View Core to show the locations on the core of each attachment point.

Select All button

Select all the ligands in the table.

Ligand base title text box

Enter a base title for the ligands generated by the structure analysis. Each ligand found in the analysis is given a title consisting of the base title and a unique numerical suffix.

Add ligand to library option menu and Add button
Add ligands to library option menu and Add button
Add selected ligands to library option menu and Add button

Add the current ligand or ligands, or the selected ligands, to the library chosen from the option menu. Click Add to add the ligand to the library; you are prompted to provide a title for the ligand. You can choose an existing library or create a new library, and you can add the ligand to the libraries that are selected in the Manage Ligands tab.

Manage Ligands tab

In this tab you can create, view, delete, and edit ligand libraries. Libraries are stored in your User resources directory, under matsci_templates/ligands.

Ligand Libraries section

This section provides tools for managing the libraries themselves and selection of libraries for other actions. The total number of libraries and selected libraries is reported next to the heading.

List of ligand libraries

The available libraries are listed in this area. Each library has a check box, which you can use to select libraries for actions. When you select a library, its members are displayed in the ligand display area below. You can select multiple libraries. The All check box allows you to select or deselect all libraries. To clear the selection, use the All button twice.

You can rename a library by right-clicking on the name and choosing Rename.

New button

Create a new empty library. Opens a dialog box in which you can name the library. The new library is automatically selected, and the ligand display area provides links for creating or adding ligands to the library, that take you to the Create Ligands tab or open a file selector to add ligands from file.

Import button

Import ligand libraries from file. These must be pre-existing libraries. The libraries are added to your library set and are shown in the list.

Export button

Export the selected ligand library to a file, in Maestro format. Only one library must be selected. A file selector opens so you can navigate to a location and name the file.

Delete button

Delete the selected libraries from your library set, after confirmation.

Ligands section

This section displays the ligands in the selected libraries and allows you to add or remove ligands.

Display area

The 2D structures of the ligands are displayed in a grid in this area, with the ligand title in the top left. You can select ligands with click, shift-click, and control-click, or by dragging. Shift-click selects all ligands in the rectangle between the previous click and the shift-click: it does not fill entire rows. To clear the selection entirely, click in a cell, then control-click the same cell.

Number of columns box

Set the number of columns to show in the grid of ligands.

Select All button

Select all ligands shown in the display area.

Add button

Add ligands to the selected libraries. Opens a file selector so you can locate and read ligands from file. All the ligands are added to each selected library.

Duplicate button

Duplicate the selected ligand. Only one ligand must be selected. Opens a 2D sketcher so you can make modifications before saving the ligand. When you save the ligand, it is added to all selected libraries, and you are prompted to name the ligand.

Delete button

Delete the selected ligands from their libraries.

More Actions option menu

This option menu offers other actions that you can perform on the selected ligands.

  • Export—Export the selected ligands in Maestro format. Opens a file selector so you can navigate to a location and name the file.
  • Copy—Copy the selected ligands to the clipboard.
  • Paste—Paste the ligands from the clipboard into the selected libraries.
  • Edit—Edit a ligand. Opens a 2D sketcher panel so you can edit the ligand. The ligand is replaced with the modified version when you click Update Ligand, and you are prompted to supply or edit the ligand name.
  • Edit Name—Edit the name (title) of the ligand. Opens a dialog box where you can enter or change the name.

Related Topics