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Searching for Organometallic Substances: SciFinder

Accessing Scifinder

Scifinder

SciFinder performs structure searches in the REGISTRY database and the CASREACT database.  At the time of this writing, REGISTRY contains over 100 million small molecules, many of which are organometallic substances, and CASREACT contains over 72 million graphical reactions, many of which include or are catalyzed by organometallic species.  However, there are certain challenges to searching for organometallic substances using SciFinder.

Searching by Substructure in the SciFinder Substance Context

When you Explore Substance in SciFinder, you are searching through the CAS REGISTRY.  This database offers you the ability to restrict your search to a certain class of substance, and coordination compounds are one of the many classes available for direct searching under advanced search.

 

 

There are three options you can use to retrieve information about organometallics in SciFinder:

  • An exact structure search, a name or Registry Number search, a formula search
  • Coordination compounds that contain one or more ligands that you specify
  • A substructure search for a general or specific organometallic core. 

The first options are self-explanatory, so, we will devote more attention to the two structure search options. 

Coordination compounds that contain one or more ligands that you specify

In general, metal-ligand coordinations in SciFinder are represented by single bonds from every coordinating atom in the ligand to the metal center, with the exception of certain metal-oxygen bonds, which can be double.  If you are unsure which type of bond to use when drawing your complex, use an unspecified bond.  It is important to bear in mind that, when there is more than one coordination drawn between a single metal and a ligand, the database interprets the resulting topology as ring; therefore, use the topological restriction tool with caution.

Any time you select the Coordination compounds class of substance in the SciFinder structure search mode, your search results will be metal-containing substances. As long as this limit is specified, it is not necessary to draw the metal itself.  For best results, you will want to perform a substructure search for the ligand, rather than an exact search, so, it is important to draw in hydrogen atoms where you do not want any non-hydrogen substitutents.  Do not use the lock atoms tool  or you may inadvertently restrict coordination. 

The search above will yield all coordination compounds that have at least one salen-type ligand.  If you want your complex to include another type of ligand, you can refine this search by structure and draw the structure of the new ligand, once again being careful not to lock ring fusion or atom attachments at sites that could coordinate to the metal.

  • Searching for Coordination Compounds in Which Both Ligand and Metal Are Specified

 Draw your complex in as much detail as you wish to specify.

  • If you have a single metal that you wish to coordinate to your ligands, draw it into the complex, and be sure to draw a bond to each coordinating atom in the ligands.  Draw the ligands in as great detail as you want.  If you wish to allow additional ligands, be sure not to lock out ring fusion or formation.
  • If you have a group of metals that would all be acceptable in your complex, define an R-group to represent the appropriate metals.
    • Click on the R-group button in the structure editor. 
    • Put your cursor in the R1 section, and click the Atoms button. 
    • Select all appropriate metals, and then click on the Close buttons in both the periodic table menu and the R-group menu.  R1 will be your active atom, and you can draw it into the structure.
  • If you don’t care which metal coordinates to your ligands, but you care where the coordination happens, use the variable M (any metal) from the variables menu, and draw a bond to each coordinating atom in the ligands.

If you do not want your metal to coordinate to undrawn ligands, you will need to lock the metal atom using the Lock atoms tool .  If you choose to limit the number of coordination in this way, it is essential that you use the Precision analysis option located to the right of the structure thumbnail. 

Note: a precision analysis will not work if you have stereo or geometric bonds in your structure.