Introduction To The Chemical Database Service

CHEMICAL DATABASE SERVICE
Introduction to the
Chemical Database Service
1 CSE Computational Science & Engineering Department

CDS Overview
• Grant funded by EPSRC
• Service free of charge to users
• Based at Daresbury Lab (CCLRC)
• Present Service started 1993
• 4 staff
• Provide access to data, support and training
• Currently 4100+ users from 100+ sites

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

Crystallography Databases
Cambridge Structural Database (CSD)
Crystal structure data for ~355,000 organic and organo-metallic
compounds
Inorganic Crystal Structure Database (ICSD)

Around 83,000 inorganic structures – also includes minerals and
(recently) metals & alloys entries.
CrystMet
Crystal structure data for over 81,000 metals, alloys,
intermetallics, etc.

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

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

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.
Display and Analysis packages

 Rasmol - A 3D molecular structure viewer.
 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.

CSD Knowledge Bases

IsoStar

CSD Knowledge Bases

Mogul
Results and Analysis for View Structure selected

target fragment (angle) from Histogram

Structural Data from 3D models
In addition structural information data is being added from

modelling and simulation studies
Development work is in progress based on the use the
IUPAC/NIST Unique Chemical Identifier (INChI) with a pilot
study based on the NCI and ACD databases.
ACD(Available Chemicals Directory)

MDL database with almost 500,000 compounds from commercial catalogues
NCI (National Cancer Institute)
213,628 compounds + 3D models
 NCI Database (126,705 compounds)
 Plated Compounds Database (139,735 compounds)
 Cancer Screened Database (37,330 compounds)
 AIDS Screened Database (42,687 compounds)

Database coverage
 Structural Data
• Synthetic Organic Chemistry
• Spectroscopy

Synthetic Organic Chemistry

The Service gives easy access to a variety of
selected chemical databases that cover over 50
years of published literature.
Providing established and current awareness in

synthetic organic chemistry, and now contains
almost 1,400,000 searchable reactions.
Increasing at rate of nearly 100,000 per year.


Core Reaction Databases
• REFLIB (Reference Library Of Synthetic Methodology)

Consisting of CHC, THEILHEIMER, METALYSIS, CHIRAS ,
CLF and ORAC/CORE. (nearly 210,000 reactions from 1946 -
1991)
• CIRX (ChemInform RX - 1992 - present, over 987,000 reactions)
• DJSM (Derwent Journal of Synthetic Methods 1980 - present
83,905 reactions)
• ORGSYN (Organic Synthesis 1921-present 5,857 reactions)

Specialist reaction and related databases
• SPG (Synopsys Protecting Groups - 42,132 reactions)

• SPS (Solid Phase Synthesis - over 23,000 reactions)
• ChirBase (Chiral separations of enantiomers by
chromatography - over 60,000 entries)
• BioCatalysis (Biomolecules as Catalysts - over 41,000

reactions)

Database coverage
 Structural Data
 Synthetic Organic Chemistry
• Spectroscopy

Searching Chemical Catalogues

ACD (Available Chemicals Directory)
a database of suppliers of chemicals worldwide.
• This is updated every 3 months

• currently contains nearly ½ million unique compounds from 683 suppliers.

Screening Compounds Suppliers

SCD (Screening Compounds Database)
over 4.6 Million compounds
SALOR BIONET MAYBRIDGE TIMTEC
ASINEX CHEMBRIDGE CHEMDIV CHEMSTAR
SPECS INTERBIOSCREEN I.F. LABS ENAMINE
MICROSOURCE PHARMEKS VITAS-M BIOTECH
AURORA OTAVA SPSAU AMBINTER
ACB BLOCKS WORLDMOLECULE TOSLAB ARKIVE
Searchable by:-
Structure, Formula, Molecular Weight, LogP, Number of Donors,
Acceptors and Rotational Bonds

Database coverage
 Structural Data
 Procuring Chemical Compounds
• Spectroscopy

Database Access using ISIS

ISIS (ISIS is used for both Reaction & Chemicals database
searching)
Client/server system (ISIS/Base + ISIS/Draw)

Reaction Browser
ACD Finder
Chemscape
Web based system
ReactionWeb
ACD on web
The National Cancer Institute databases are also available via

ISIS/Base and the web
Database coverage
 Structural Data
• Spectroscopy

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.
13
C NMR Heteroatom 1
H NMR Infra-red Mass
NMR spectra
102,369 43,851 117,379 20,898 138,727

SpecInfo - Access
SpecSurf - Web interface

Database coverage
 Structural Data
 Spectroscopy

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.

Physical Chemistry
Detherm - Data / Property Coverage

Physical Chemistry - Access

DETHERM
 Client/Server
Version 2

Physical Chemistry – Client

• Version 2.0 of the DETHERM Client was made
available to CDS users late 2004.
• It 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).

Database coverage
 Structural Data
 Spectroscopy
 Physical Chemistry

Supporting utilities
LitLink
* Single click access to primary literature.
* Used with CrystalWeb, ICSD-WWW,
ConQuest, ReactionWeb or ISIS
* Link to electronic sources of the article.

Supporting utilities

Database coverage
 Structural Data
 Spectroscopy
 Physical Chemistry
 Links to primary electronic literature

Help/support
• Website:
• http://cds.dl.ac.uk
• User Training and Online Information:

• Manuals, Tutorials, and arranging Courses
• Flash movies
• CDS Newsletters
• Helpdesk available:
• E-mail cdsbb@dl.ac.uk or Phone 01925 603162

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

Further Information
• This Powerpoint demonstration is
available online
• It will be 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

Chemical Database Service
Thank you for your attention….

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CHEMICAL DATABASE SERVICE

1 CSE Computational Science & Engineering Department

2 CSE Computational Science & Engineering Department

• Synthetic Organic Chemistry

• Procuring Chemical Compounds

• Links to primary electronic literature

3 CSE Computational Science & Engineering Department

Inorganic Crystal Structure Database (ICSD)

4 CSE Computational Science & Engineering Department

related Flash Movie clip)

5 CSE Computational Science & Engineering Department

CrystalWeb - Web access to all crystal data

6 CSE Computational Science & Engineering Department

Display and Analysis packages

7 CSE Computational Science & Engineering Department

CSD Knowledge Bases

8 CSE Computational Science & Engineering Department

CSD Knowledge Bases

Results and Analysis for View Structure selected

9 CSE Computational Science & Engineering Department

Structural Data from 3D models

In addition structural information data is being added from

ACD(Available Chemicals Directory)

10 CSE Computational Science & Engineering Department

• Synthetic Organic Chemistry

• Procuring Chemical Compounds

• Links to primary electronic literature

11 CSE Computational Science & Engineering Department

Synthetic Organic Chemistry

Providing established and current awareness in

Increasing at rate of nearly 100,000 per year.

12 CSE Computational Science & Engineering Department

Synthetic Organic Chemistry

• REFLIB (Reference Library Of Synthetic Methodology)

13 CSE Computational Science & Engineering Department

Synthetic Organic Chemistry

Specialist reaction and related databases

• SPG (Synopsys Protecting Groups - 42,132 reactions)

• BioCatalysis (Biomolecules as Catalysts - over 41,000

14 CSE Computational Science & Engineering Department

 Synthetic Organic Chemistry

• Procuring Chemical Compounds

• Links to primary electronic literature

15 CSE Computational Science & Engineering Department

Searching Chemical Catalogues

• This is updated every 3 months

16 CSE Computational Science & Engineering Department

Screening Compounds Suppliers

17 CSE Computational Science & Engineering Department

 Synthetic Organic Chemistry

 Procuring Chemical Compounds

• Links to primary electronic literature

18 CSE Computational Science & Engineering Department

Database Access using ISIS

Client/server system (ISIS/Base + ISIS/Draw)

The National Cancer Institute databases are also available via

 Synthetic Organic Chemistry