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Introduction to the Chemical Database Service

Introduction to the Chemical Database Service

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Introduction to the Chemical Database Service

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  1. Introduction to the Chemical Database Service

  2. Introduction • Present Service started 1993 • Originally Grant funded by EPSRC but is now a 3 Year contract with EPSRC • 2 Staff covered by contract • Provide networked access to up-to-date, high quality, comprehensive chemistry databases along with support and training • Currently over 5,000 users from over 100 sites • Service free of charge to users (UK Academics) free

  3. Need to be registered user

  4. Registration

  5. Access Data

  6. Database coverage • Structural Data • Physical Chemistry • Spectroscopy • Synthetic Organic Chemistry • Procuring Chemical Compounds • Links to primary electronic literature ISIS Databases removed May 2007 Databases removed May 2007 What they contain and how you access them.

  7. Crystallography Databases Cambridge Structural Database (CSD) Crystal structure data for 512,881 organic and organo-metallic compounds. Inorganic Crystal Structure Database (ICSD) Over132,526 Inorganic structures – also includes minerals and (recently) metals & alloys entries. CrystMet Crystal structure data for over126,000 metals, alloys, intermetallics, etc. Crystal Data Identification File (CDIF) Crystal class and unit cell data for 237,671 crystal structures.

  8. Crystallography Access ICSD – Web access through own interface WWW-ICSD • CSD - X-Windows based graphical Interface via • ConQuest • All Crystallogrpahy Data - Web accessvia • CrystalWeb • (click the chevron symbols to view a related Flash Movie clip)

  9. Crystallography Access ConQuest Query Building

  10. Crystallography Access ConQuest Viewing Results

  11. Crystallography Access WebCSD Coming soon

  12. Crystallography Access WWW-ICSD Query Screen

  13. Crystallography Access WWW-ICSD Results Use the buttons for further information or to view a structure

  14. Crystallography Access WWW-ICSD Results

  15. Crystallography Access CrystalWeb Search Form

  16. Crystallography Access CrystalWeb Results Use the buttons for further information or to view a structure

  17. Crystallography Access JMOL Display

  18. Crystallography Access Search for Spectra Button

  19. Crystallography Access

  20. Crystallography Access ChemSpider Button

  21. Crystallography Access ChemSpider Button

  22. Crystallography Utilities Crystallographic file format converters • Bedlamis a generalised format converter very similar to the widely used converter program, Babel, but handles crystallographic data better. • Babelremains 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.

  23. Crystallography Utilities Mercury

  24. Crystallography Utilities VISTA

  25. CSD Knowledge Bases ISOSTARnon-bonded interactions

  26. CSD Knowledge Bases MogulMolecular Geometries Results and Analysis for target fragment (angle) View Structure selected from Histogram

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

  28. Physical Chemistry DETHERM • One of the world's largest thermophysical property databases of pure compounds and compound mixtures • Contains ~6 Million data sets for around 127,000 systems (about 26,500 pure substances and 103,000 mixtures) • covering more than 500 property fields.

  29. Physical Chemistry Detherm - Data / Property Coverage

  30. Physical Chemistry - Access Substance/Mixture DETHERM • Client Version 2007

  31. Physical Chemistry - Access DETHERM • Client Version 2007 Property Search

  32. Physical Chemistry - Access Literature Search DETHERM • Client

  33. Physical Chemistry - Access • DETHERM • Web Search Options

  34. Physical Chemistry - Access • DETHERM • Web Results It supports data export in IKC-PPDX (Physical Property Data Exchange format).

  35. Physical Chemistry ACD/Labs • I-Lab allows you to search the database for:- • pKa (about 16,000 structures) • LogP (over 18,000 structures) • Solubility (over 5,000 compounds) • A number of physical property predictions are also available:- • LogP • Aqueous solubility • Enthalpy of vaporization • Molar Refractivity • Parachor • Surface Tension • Dielectric Constant calculation • Monoisotopic Mass • Nominal Mass • Average Mass pKa LogD Boiling point/Vapour pressure Adsorption coefficient/ Bioconcentration factor Molar Volume Refractive Index Density Dielectric Constant calculation Polarizability

  36. ACD/Labs Physical Chemistry • In addition, ACD/Labs I-Lab has compound name generation . . . • Generate a Name according to IUPAC rules • Generate an Index name according to CAS rules • Generate a Structure from a chemical name

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

  38. SpecInfofrom Chemical Concepts, Searches can be conducted by inputting then matching a query spectrum (or fragment), a (sub-) structure or bibliographic information such as name, formula or CAS number. Spectroscopy The Spectroscopy databases are designed to aid the chemist in structure elucidation and spectral interpretation problems. • ACD/Labs • ACD/Labs set of databases allows you to draw a (sub)structure and either • Search the available NMR databases • Predict a spectrum • Or search Bibliographic information plus Name, Formula or Molecular Weight

  39. ACD/Labs Spectroscopy SpecInfo

  40. Access - SpecInfo SpecSurf - Web interface

  41. Access - SpecInfo SpecSurf - Web interface - Editors

  42. Access – ACD/Labs ChemSketch pc client Structure Editor Can also be used to search other molecule databases.

  43. Access – ACD/Labs ChemSketch Links to other databases

  44. Access – ACD/Labs ChemSketch Allows you to log in to the main databases… … or calculate some properties… … or generate a name, SMILES or InChI

  45. Access – ACD/Labs ChemSketch 3D Viewer

  46. Access – ACD/Labs ChemSketch 2D - 3D

  47. Access – ACD/Labs ChemSketch NMR Spectrum Viewer

  48. Access – ACD/Labs I-Lab - Web interface

  49. Access – ACD/Labs I-Lab - Web interface – Drawing Applet

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