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Searching for a Specific Ligand or Ligand Type Coordinated to a Metal
Use a user-defined atom group.
Click the Periodic Table button on the structure editor .
Click the Atom List button.
Select the atoms that you wish to include in your atom list.
Click the Close button. You will see that the atom attached to the cursor has turned to a list of atoms.
Insert the list “atom” at the position in your structure in which you would like the atom list to appear. Use a single bond to represent the coordination between ligand and metal.
If you want to coordinate your metal to particular sites but you don’t care which metal you use, use the M generic. You can find this in the variable menu
Using Query builder
If you don’t care where the metal coordinates, but you do care which metal appears in the structure
In the gray Fields section at the right of the screen, expand the Identification section to find Element Symbols. Click and drag this field to the central search area.
Click on the magnifier to enter the field index. Type the symbol of the element that you desire in the search area at the top left (marked with another magnifier), and it will scroll you to the appropriate place in the index. Check the box beside any element you wish to include. Then, click the button.
Your search will now locate substances that have the substructure you drew, as well as at least one of the metals you specified (Boolean OR).
Enter the Formula into the database
Enter the Formula into the database.
In the Search Fields section of the Query Builder screen, navigate to Multi-Center Ligands. Click and drag the field to the central search area. Click on the down arrow beside the Exist link to expand the option and show all searchable fields.
To search for a complete ligand formula (all metals and ligands included, and no additional ligands permitted), use the Base Formula option. Click on the magnifier link beside Base Formula to open the index
Type your formula into the search section beside the magnifier at the top right corner of the window, and press Enter. When you have found the formula that you want, click it to highlight it, and then click search
To search for a complete ligand formula (all metals and ligands included, and no additional ligands permitted), use the Base Formula option. Click on the magnifier link beside Base Formula to open the index.
Type your formula into the search section beside the magnifier at the top right corner of the window, and press Enter. When you have found the formula that you want, click it to highlight it, and then click.
As you can see, ligand formula searching says nothing about the ways in which ligands are coordinated to the metals in the complex. You can combine a ligand formula search for the entire complex with a ligand formula search for ligands around one particular metal center in the complex (One-Center Ligands) or even include some substructure features in order to make portions of the search more specific.
Search by Ligand Formula
Determining ligand formula - the critical pieces are the number of atoms of each metal, the number of ligands, and the number and type of atoms in each ligand that coordinate to the metal.
First list the metals in alphabetical order
If there is more than one atom of each metal, the number of atoms of that type will follow the atom symbol
Next establish the kinds of ligands, each type of atom is given a code, according to the following chart
The codes are ordered alphabetically
“special ligands,” such as carbonyls and cyano ligands have their own codes
Each formula is enclosed in curly brackets when it is added to the full ligand formula of the complex.
Ligands are ordered in alphabetical order
If the complex contains more than one of a particular type of ligand, the number follows the closing brace for that ligand