cse computational science & engineering department chemical database service 1 introduction to...

1 CSE Computational Science & Engineering Department

CHEMICAL DATABASE SERVICECHEMICAL DATABASE SERVICE

Introduction to the Chemical Database Service



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 CSDX-Windows based graphical CSD Interface -

ConQuest(click the chevron symbols to view a

related Flash Movie clip)

All DataWeb access CrystalWeb



Crystallography Access• ICSD

WWW-ICSD - Web based system for ICSD

CrystalWeb - Web access to all crystal data

• CrystMetCrystalWeb



Crystallography UtilitiesCrystallographic 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 BasesIsoStar



CSD Knowledge BasesMogul

Results and Analysis for target fragment (angle)

View Structure selected 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.



Synthetic Organic Chemistry 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)






• Spectroscopy





Searching Chemical CataloguesACD (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 SuppliersSCD (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





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 BrowserACD Finder

ChemscapeWeb based system

ReactionWebACD on web

The National Cancer Institute databases are also available via ISIS/Base and the web






• Spectroscopy





Spectroscopy

SpecInfo• From Chemical Concepts, contains spectral data sets

with their associated structure connection tables.

• A variety of features are available within the program tohelp with spectrum prediction and searching.

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

13C NMR Heteroatom NMR

1H NMR Infra-red Mass spectra

102,369 43,851 117,379 20,898 138,727



SpecInfo - Access SpecSurf - Web interface






Spectroscopy





Physical ChemistryDETHERM

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 ChemistryDetherm - Data / Property CoverageDetherm - 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).






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






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 [email protected] 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….

cse computational science & engineering department chemical database service 1 introduction to...

Documents

d models nci database

crystallographic data

histogram slide

epsrc service free of

d molecular structure

compounds databa

lvista csd package

icsd web based system