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X-Ray Crystallography : CSD (Cambridge)

About CSD

CSD is the world repository for small molecule crystal structures. The database contains:

  • Bibliographic, chemical and crystallographic information
    • organic molecules
    • metal-organic compounds
    • >501,000 structures
  • 1923 - present; quarterly updates (Site Code & Confirmation Code required)
  • Results:
    • single crystal studies
    • powder diffraction studies
  • Determined using:
    • X-ray diffraction
    • neutron diffraction

Searching Web Cambridge Structural Database (WebCSD)

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Licensed for use by UW-Madison faculty, staff, students
WebCSD Teaching Examples

NOTE: CCSD recommends using Safari for Macs and any Windows browsers.

Basics

See technical requirements for WebCSD access.

Available search types include:

  • Substructure
  • Similarity
  • Text/Numeric
  • Reduced Cell
  • Browse collection

Database entries are displayed in three columns:

  • Left column: Lists results of search query or browse by CSD code. Shaded codes denote records for which 3D coordinates are not available.
  • Center column: Displays selected CSD code entry in 3D JMOL viewer. Viewer contains display options.
  • Right column: Details of CSD code entry, including line diagram, record details, and export function.

Truncating Terms

Text/Numeric Search: Select type of truncation in the MATCH drop-down menu. 

Combining Search Types

Combine searches of the same type in the query window, such as a TEXT/NUMERIC query containing an author's last name and a compound name. 

Substructure Searching

WebCSD Chemical Sketcher drawing program supports .xml, .mol, and .sdf file types.

  1. Click desired atom.
  2. (Optional) Click OTHER to select generic atom groups or create a custom group.
  3. (Optional) Click CHOOSE in TEMPLATE box to view available template fragments.
  4. Click PENCIL to draw structure.
  5. Click START SEARCH.

Similarity Searching

Similarity calculations are based on molecular fingerprints using either of the Tanimoto or Dice coefficients.

Search tip: Draw a full molecule rather than a substructure. It is not necessary to draw the hydrogens on your molecule because hydrogens are not included explicitly in the similarity calculation.

Text/Numeric Searching

Search tips:

  • Use standard parentheses characters
    Example: bicyclo[3.3.1]nonane
  • Use '+' and '-' characters to define stereochemistry
  • Use Latin alphabet descriptions for lower case Greek characters
    Example: alpha (for α)
  • Use the prefix c and spell out upper case Greek characters
    Example: cdelta (for Δ)
  • Enclose superscripts or subscripts within the characters $ (up) and ! (down)
    Example: eta$5!-cyclopentadienyl (Retrieves 'η5-cyclopentadienyl')
  • MATCH options are specific to QUERY TYPE.  

Author Searching

  1. Select AUTHOR NAME in the QUERY TYPE drop-down menu.
  2. Enter last name in the QUERIC QUERY box.
  3. (Optional) Enter authors' first and middle initials. Initials must be followed by a period with no spaces between initials or last name.
    Example: F.H.Allen (Retrieves F.H.Allen but not F.Allen)
  4. Select type of match in the MATCH drop-down menu.
  5. Click SUBMIT SEARCH.

Data Visualization

Results can be viewed online in two different 3-D viewers:

  1. Jmol
  2. OpenAstexViewer

Crystal structures can be exported for vewing in Mercury (http://www.ccdc.cam.ac.uk/products/mercury/). Basic Mercury is free; UW-Madison users may download Licensed Mercury. UW-Madison users should email librarian Ariel Andrea for the license.

CSD Desktop

CSD System is available for download and installation on your office computer. Please contact askchem@library.wisc.edu or Ariel Andrea for more information.

Check for the latest CSD Updates and subscribe to the CSD email list to receive notification when a new database update is available.

CSDS Software includes:

  • ConQuest, WebCSD - search and information retrieval
  • Mercury CSD - structure visualization
  • Vista - statistical analysis of retrieved data
  • PreQuest - database creation software
  • Mogul - validates molecular geometries
  • IsoStar - assess intermolecular interactions