Introduction to Chemistry Resources: Structural Databases

Structural Databases

Cambridge Structural Database

CSD is the world’s leading repository of small organic and metal-organic crystal structures with over 500,000 x-ray and neutron diffraction analyses. Each structure within the CSD undergoes extensive validation and cross-checking via automated workflows and through manual curation by expert chemists and crystallographers. This means you can trust that all the data within the CSD is accurate, consistent and high-quality.

In addition, all the data is enriched with bibliographic, chemical and physical property information, adding further value to the original structural data, enabling you to interpret structures in a chemically significant way.

You can search and browse crystal strcutures and associated information in CSD through WebCSD.

Search Functionality of WebCSD

  • Text and numeric
  • Reduced cell
  • 2D structure
  • 2D structure similarity (desktop application cannot do)
  • View specific refcode or browser the CSD

What can you not do through WebCSD?

  • The 3D structure search function is not available in the WebCSD.
  • You cannot validate molecular geometries of your crystal structure in WebCSD, you will need to use Mogul in the CSDS suite to do so.
  • You cannot investigate interactions between molecules in WebCSD.

Learn more about WebCSD through their online tutorial videos here. 

USC subscribes both to the online web version and desktop version for Windows, Mac OS, and Linux. The majority of users will be best served by using the web version of CSD, but if your research requires an offline, desktop version of CSD, please contact the Chemistry Librarian, aquezada@usc.edu, for more information. 

Protein Databank

PDB provides access to 3D structure data for large biological molecules (proteins, DNA, and RNA). These are the molecules of life, found in all organisms on the planet.  Knowing the 3D structure of a biological macromolecule is essential for understanding its role in human and animal health and disease, its function in plants and food and energy production, and its importance to other topics related to global prosperity and sustainability.

Highlights:

  • Large biological molecules (proteins, DNA, and RNA).
  • Access to over 150,00 structures.
  • Structures obtained by X-ray crystallography, NMR spectroscopy, or cryo-electron microscopy. 
  • Freely accessible.

Inorganic Crystal Structure Database

The Inorganic Crystal Structure Database (ICSD) is a database of the crystal structures of inorganic substances, including pure elements, metals, minerals, and other purely inorganic substances.  No organic or organometallic substances appear. 

How Do I Search?

  1. Enter ICSD by visiting  Inorganic Crystal Structure Database. You will be prompted for your USC login information.  The username is everything before the '@' symbol from your USC email username and the password is the same password you use for your USC email account.  Please note you need to log in with your USC username and password for this resource even if you are on campus.
  2. In the Navigation menu on the left side of the screen, click on the Chemistry option under Advanced Search and Retrieve.
  3. Under Composition, enter the formula of the inorganic oxide or other substance that you wish to retrieve.  Be sure to put a space between the elements in your formula.  Under Number of Elements, indicate the number of elements that you will permit in your substance.
  4. Click on the Run Query button to the right to run your search.

ICSD Query Screen

 

How Do I Interpret My Results

The results will be presented as a list of substances that have published crystal structures.  The default presentation for this list is the Brief View, which includes the substance's ICSD accession number, the HMS, the structural formula and type of crystal, and information about the document in which the structure was published.  You will see a blue star beside every entry that is deemed to be high-quality data, and each entry ends in a little computer disk icon that you can click to download the .cif file.

Check the boxes beside any of the results that particularly interest you.  In the left-most column, an option will open in the Navigation section to allow you to get a Detailed View of all the substances that you've checked.  This gives you much more detailed information, including the ability to examine the individal bond lengths and angles in the unit cell.