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Searching for Organometallic Substances: Cambridge Structural Database

Accessing Cambridge Structural Database

Cambridge Structural Database

Cambridge Structural Database

The Cambridge Structural Database is produced by the Cambridge Crystallographic Data Center (http://www.ccdc.cam.ac.uk/products/csd/).  It is a database of x-ray diffraction and neutron diffraction crystal structures of organic and organometallic substances.  The crystal structures contained were all deposited in the database by individual scientists, usually at the time of journal publication, and records include the crystal structure coordinates, as well as information about the unit cell, experimental details and parameters, and the reference to the article in which each structure is introduced.  Because the coordinates are part of the record, users can both download them into a viewer software package of choice or use statistical software to analyze trends in a set of structures.  CSD is not useful for locating physical properties and reactions of organometallic substances.

Structure Searching in the Cambridge Structural Database

The default structure search in CSD is substructure.  The structure editor functions in a manner similar to other tools; commonly used atoms and rings have buttons on the main screen, and lesser-used options appear in the menus at the top of the window.

Selecting a Metal

There are several ways in which you can specify the metal or type of metal that you would like to have in your complex.

  • If you have a specific metal in mind, you can select it from the periodic table by clicking the  button and selecting “Other Elements.”  Then click “OK,” and draw it into your structure as you would any other atom.
  • If you would like to select two or more specific metals, click on the  button, and select “Other Elements.”  Click on the “multi-pick” radial button, and choose the elements that you would like.  If you wish to select an entire row or column of the periodic table, click on its orange header.  Then click “OK,” and draw it into your structure as you would any other atom.

 

 

 

 

 

 

 

 

 

 

 

 

  • If you would like any transition metal, click on the  button and select “Any Transition Metal.”  Draw it into your structure as you would any other atom.
  • If any metal will do, click on the  button and select “Any Metal.” .”  Draw it into your structure as you would any other atom.
  • If you do not want to specify how the ligand will coordinate to the metal but you care which metal you use, draw the ligand and the metal separately.  When you run your search, the system will, by default, search for the two fragments in the same molecule.
  • If you do not care either which metal you use or how it coordinates to the ligand, simply draw the ligand.  Then, when you go to run your search, specify that you wish to search only organometallics.

 

 

Bonds, Coordination, and Bond Types

CSD is very particular about the types of bonds used in its structures.  Unless you choose the correct type of bond, you will not locate any matches to your query.  Unfortunately, it is also very inconsistent about the types of bond used in its structures.  The best way to get a good idea of which bonds to use at which points in your structure is by reading “Bond Type Conventions,” located in Appendix A of the CSD help documentation.  Here are some general principles, derived from that document.

  1. For many ligand-metal coordination, you want to use a pi-bond, found in your list of bonds at the bottom.
  2. Aromatic systems should use all aromatic bonds, rather than alternating single or double bonds.  If you use the ring builder, it will do this automatically.
  3. Metal-metal bonds are tricky because they may or may not be represented in the database.  You can either leave them out entirely or use a variable bond to represent them.

There are a few special systems that CSD treats in a fairly standard manner.

  • Carbonyl groups or ligands are represented -CºO, and cyano groups and ligands are represented -CºN.
  • Nitro groups are represented O=N=O.
  • Carboxylates coordinated to a metal use two delocalized bonds between the C and the O’s.
  • In polymers, CSD uses a special “polymer bond” to connect two monomers.

 

If, at any time, you are uncertain of which bond order to use, a variable bond will do the trick.