Introduction to the Chemical Database Service

1
Introduction to the Chemical Database Service
2
CDS Overview

• Grant funded by EPSRC
• Service free of charge to users
• Based at Daresbury Lab (STFC)
• Present Service started 1993
• 3 Staff (April -gt 2 staff)
• Provide access to data, support and training
• Currently 3,400 users from 100 sites

3
Database coverage

• Structural Data
• Synthetic Organic Chemistry
• Procuring Chemical Compounds
• Spectroscopy
• Physical Chemistry
• Links to primary electronic literature

Databases removed May 2007
Databases removed May 2007
4
Crystallography Databases

• Cambridge Structural Database (CSD)
• Crystal structure data for 436,000 organic and
  organo-metallic compounds
• Inorganic Crystal Structure Database (ICSD)
• Over 100,000 inorganic structures also includes
  minerals and (recently) metals alloys entries.
• CrystMet
• Crystal structure data for over 115,000 metals,
  alloys, intermetallics, etc.

5
Crystallography Access

• CSD
• X-Windows
• based graphical
• CSD Interface -
• ConQuest
• (click the chevron symbols to
• view a related Flash Movie clip)
• All Data
• Web access
• CrystalWeb

6
Crystallography Access

• ICSD
• WWW-ICSD - Web based system for ICSD
• CrystalWeb - Web access to all crystal data
• CrystMet
• CrystalWeb

7
Crystallography Utilities

• Crystallographic file format converters
• Bedlam is a generalised format converter very
  similar to the widely used converter program,
  Babel, but handles crystallographic data better.
• Babel remains the package of choice to handle
  formats for a whole range of molecular modelling
  packages.
• Babel and Bedlem are both used by CrystalWeb
  to provide a wide range of output formats.
• Display and Analysis packages
• Mercury - The 3D molecular structure viewer
  designed for use with the Cambridge structural
  database (CSD).
• VISTA CSD package for statistical analysis of
  geometrical feature.
• Crad - A crystal radial distribution calculation
  program.

8
Crystallography Utilities

• Mercury

9
Crystallography Utilities

• VISTA

10
CSD Knowledge Bases

• ISOSTAR

11
CSD Knowledge Bases

• Mogul

Results and Analysis for target fragment (angle)
View Structure selected from Histogram
12
Database coverage

• Structural Data
• Spectroscopy
• Physical Chemistry
• Links to primary electronic literature

13
Spectroscopy
The Spectroscopy databases are designed to aid
the chemist in structure elucidation and
spectral interpretation problems.

• SpecInfo
• From Chemical Concepts, contains spectral data
  sets
• with their associated structure connection
  tables.
• A variety of features are available within the
  program to
• help with spectrum prediction and searching.

14
SpecInfo - Access

• SpecSurf - Web interface

15
SpecInfo - Access

• SpecSurf - Web interface - Editors

16
Database coverage

• Structural Data
• Spectroscopy
• Physical Chemistry
• Links to primary electronic literature

17
Physical Chemistry

• DETHERM
• One of the world's largest thermophysical
  property databases of pure compounds and
  compound mixtures
• Contains 5 Million data sets for around 118,000
  systems
• (about 24,500 pure substances and 94,000
  mixtures)
• covering more than 500 property fields.

18
Physical Chemistry
Detherm - Data / Property Coverage
19
Physical Chemistry - Access

• DETHERM
• Client/Server

Version 2.1
20
Physical Chemistry Client

• Version 2.1 of the DETHERM Client was made
  available to CDS users in March 2006 and is now
  the only supported version.
• Version 2.x (first introduced in November 2004)
  has a better look and feel than previous versions
  and a number of new features including improved
  integration with AspenPlus.
• It support data export in IK-CAPE PPDX (Physical
  Property Data Exchange format).

21
Database coverage

• Structural Data
• Spectroscopy
• Physical Chemistry
• Links to primary electronic literature

22
Supporting utilities

• Literature Linking
• Single click access to primary literature.
• Used with CrystalWeb, ICSD-WWW, and ConQuest
• Link to electronic sources of the article.

23
Supporting utilities
DOI lookup
e.g.
Requires ID/password
Click logos for more information.
24
Supporting utilities
25
Supporting utilities
26
Supporting utilities
Drop-down menus show list of hits and display
options
The Journal of Organic Chemistry, 69 (2004) p4500
The link appears here
clickable
27
Supporting utilities
28
Supporting utilities
29
Database coverage

• Structural Data
• Spectroscopy
• Physical Chemistry
• Links to primary electronic literature

30
Help/support

• Website http//cds.dl.ac.uk
• About the Service http//cds.dl.ac.uk/cds/service
  _info/about.html
• User Training and Online Information
• Manuals, Tutorials (e.g. ConQuest, Detherm and
  SpecSurf) and arranging Courses
• Flash movies
• CDS Newsletters
• Helpdesk available
• E-mail cdsbb_at_dl.ac.uk or Phone [phone]

31
Registration

• Individual usernames required
• You can register online
• But registrations must to be verified by your
  local User Representative or Head of Department
• Current Reps List

32
Further Information

• This PowerPoint demonstration is available online
• It will be augmented and kept up to date
• You can access it online via the URL
  http//cds.dl.ac.uk/overview
• Feel free to download this and related material
  and make it available to colleagues

33
Chemical Database Service

• Thank you for your attention.