X-Ray Crystallography : CSD (Cambridge)
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)
- single crystal studies
- powder diffraction studies
- Determined using:
- X-ray diffraction
- neutron diffraction
Searching Web Cambridge Structural Database (WebCSD)
Licensed for use by UW-Madison faculty, staff, students
WebCSD Teaching Examples
NOTE: CCSD recommends using Safari for Macs and any Windows browsers.
See technical requirements for WebCSD access.
Available search types include:
- 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.
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.
WebCSD Chemical Sketcher drawing program supports .xml, .mol, and .sdf file types.
- Click desired atom.
- (Optional) Click OTHER to select generic atom groups or create a custom group.
- (Optional) Click CHOOSE in TEMPLATE box to view available template fragments.
- Click PENCIL to draw structure.
- Click START SEARCH.
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.
- Use standard parentheses characters
- 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.
- Select AUTHOR NAME in the QUERY TYPE drop-down menu.
- Enter last name in the QUERIC QUERY box.
- (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)
- Select type of match in the MATCH drop-down menu.
- Click SUBMIT SEARCH.
Results can be viewed online in two different 3-D viewers:
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.
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