CSE
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Introduction to the Chemical Database Service 1 CSE Computational Science & Engineering Department Introduction • Present Service started 1993 • Originally Grant funded by EPSRC but is now a Tender contract with EPSRC • 2.4 Staff covered by contract • Provide networked access to up-to-date, high quality, comprehensive chemistry databases along with support and training • Currently over 6,200 users from over 100 sites • Service free of charge to users (UK Academics) 2 CSE Computational Science & Engineering Department Need to be registered user 3 CSE Computational Science & Engineering Department Registration 4 CSE Computational Science & Engineering Department Access Data 5 CSE Computational Science & Engineering Department NAME (ACDLabs) 7-chloro-1-methyl-5-phenyl-1,3,4,5-tetrahydro-2H-1,4-benzodiazepin-2-one Diazepam SUPPLIERS Query Compound SPRESI Reaction & Molecule Database 6 CSE Computational Science & Engineering Department Other Properties – Physical Data Thermophysical Data DETHERM NMR Data ChemSketch (ACDLabs) Structural Data ConQuest Calculated Phys.Chem. Data ChemSketch (ACDLabs) ConQuest Predicted 3D Data ChemSketch (ACDLabs) 7 CSE Computational Science & Engineering Department Database coverage • Structural Data • Physical Chemistry • Spectroscopy • Synthetic Organic Chemistry • Procuring Chemical Compounds • Links to primary electronic literature What they contain and how you access them. 8 CSE Computational Science & Engineering Department Crystallography Databases Cambridge Structural Database (CSD) Crystal structure data for over 603,297 organic and organo-metallic compounds. Inorganic Crystal Structure Database (ICSD) 142,179 Inorganic structures – also includes minerals and (recently) metals & alloys entries. CrystMet Crystal structure data for over 139,000 metals, alloys, intermetallics, etc. Crystal Data Identification File (CDIF) Crystal class and unit cell data for 237,671 crystal structures. 9 CSE Computational Science & Engineering Department Crystallography Access CSD - X-Windows based graphical Interface via ConQuest [Hope to make a web version available very soon] ICSD – Web access through own interface WWW-ICSD All Crystallogrpahy Data - Web access via CrystalWeb (click the chevron symbols to view a related Flash Movie clip) 10 CSE Computational Science & Engineering Department Crystallography Access ConQuest Query Building 11 CSE Computational Science & Engineering Department Crystallography Access ConQuest Viewing Results 12 CSE Computational Science & Engineering Department Crystallography Access WebCSD Coming soon 13 CSE Computational Science & Engineering Department Crystallography Access WWW-ICSD Query Screen 14 CSE Computational Science & Engineering Department Crystallography Access WWW-ICSD Results Use the buttons for further information or to view a structure 15 CSE Computational Science & Engineering Department Crystallography Access WWW-ICSD Results 16 CSE Computational Science & Engineering Department Crystallography Access CrystalWeb Search Form 17 CSE Computational Science & Engineering Department Crystallography Access CrystalWeb Results Use the buttons for further information or to view a structure 18 CSE Computational Science & Engineering Department Crystallography Access CrystalWorks - Top Level Menu 19 CSE Computational Science & Engineering Department Crystallography Access CrystalWorks - Structure Display 20 CSE Computational Science & Engineering Department Crystallography Access JMOL Display 21 CSE Computational Science & Engineering Department Crystallography Access Search for Spectra Button 22 CSE Computational Science & Engineering Department Crystallography Access 23 CSE Computational Science & Engineering Department Crystallography Access ChemSpider Button From CrystalWeb CrystalWorks Links & Data Aggregators Screen 24 CSE Computational Science & Engineering Department Crystallography Access 25 CSE Computational Science & Engineering Department 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 Bedlam 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). This will now take over from VISTA for VIsual STatistical Analysis of geometrical feature. Crad - A crystal radial distribution calculation program. 26 CSE Computational Science & Engineering Department Crystallography Utilities Mercury 27 CSE Computational Science & Engineering Department Crystallography Utilities VISTA 28 CSE Computational Science & Engineering Department CSD Knowledge Bases ISOSTAR non-bonded interactions 29 CSE Computational Science & Engineering Department CSD Knowledge Bases Mogul Molecular Geometries Results and Analysis for target fragment (angle) 30 CSE Computational Science & Engineering Department View Structure selected from Histogram Database coverage Structural Data • Physical Chemistry • Spectroscopy • Synthetic Organic Chemistry • Procuring Chemical Compounds • Links to primary electronic literature 31 CSE Computational Science & Engineering Department Physical Chemistry DETHERM One of the world's largest thermophysical property databases of pure compounds and compound mixtures Contains 7.53 Million data sets for around 160,500 systems (about 36,500 pure substances and 124,000 mixtures) covering more than 500 property fields. 32 CSE Computational Science & Engineering Department Physical Chemistry Detherm - Data / Property Coverage 33 CSE Computational Science & Engineering Department Physical Chemistry - Access DETHERM Client Version 2010-2 34 CSE Computational Science & Engineering Department Substance/Mixture Physical Chemistry - Access DETHERM Client Version 2010-2 Property Search 35 CSE Computational Science & Engineering Department Physical Chemistry - Access DETHERM Literature Search Client 36 CSE Computational Science & Engineering Department Physical Chemistry - Access DETHERM Web Search Options 37 CSE Computational Science & Engineering Department Physical Chemistry - Access DETHERM Web Results It supports data export in IKC-PPDX (Physical Property Data Exchange format). 38 CSE Computational Science & Engineering Department 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:• • • • • • • • • CSE pKa LogD Boiling point/Vapour pressure Adsorption coefficient/ Bioconcentration factor Molar Volume Refractive Index Density Dielectric Constant calculation Polarizability Computational Science & Engineering Department • • • • • • • • • • LogP Aqueous solubility Enthalpy of vaporization Molar Refractivity Parachor Surface Tension Dielectric Constant calculation Monoisotopic Mass Nominal Mass Average Mass Physical Chemistry ACD/Labs 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 40 CSE Computational Science & Engineering Department Database coverage Structural Data Physical Chemistry • Spectroscopy • Synthetic Organic Chemistry • Procuring Chemical Compounds • Links to primary electronic literature 41 CSE Computational Science & Engineering Department 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 SpecInfo from 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. 42 CSE Computational Science & Engineering Department Spectroscopy SpecInfo 1H NMR 11B NMR 13C NMR 15N NMR 17O NMR 19F NMR 31P NMR IR SPECTRA MASS SPECTRA 130,000 10,238 359,000 7.661 5,184 32,780 25,656 20,898 138,727 ACD/Labs 43 1H NMR 13C NMR 15N NMR 19F NMR 31P NMR 210,700 200,100 9.287 17,000 27,000 CSE Computational Science & Engineering Department Access - SpecInfo SpecSurf 44 CSE - Web interface Computational Science & Engineering Department Access - SpecInfo SpecSurf 45 CSE - Web interface - Editors Computational Science & Engineering Department Access – ACD/Labs ChemSketch pc client Structure Editor 46 CSE Computational Science & Engineering Department Can also be used to search other molecule databases. Access – ACD/Labs ChemSketch Links to other databases 47 CSE Computational Science & Engineering Department Access – ACD/Labs ChemSketch Allows you to log in to the main databases… … or calculate some properties… … or generate a name, SMILES or InChI 48 CSE Computational Science & Engineering Department Access – ACD/Labs ChemSketch 3D Viewer 49 CSE Computational Science & Engineering Department Access – ACD/Labs ChemSketch 2D - 3D 50 CSE Computational Science & Engineering Department Access – ACD/Labs ChemSketch NMR Spectrum Viewer 51 CSE Computational Science & Engineering Department Access – ACD/Labs I-Lab 52 CSE - Web interface Computational Science & Engineering Department Access – ACD/Labs I-Lab 2.0 Start Screen Structure Drawing Applet 53 CSE Computational Science & Engineering Department Access – ACD/Labs I-Lab 2.0 Results Screen 54 CSE Computational Science & Engineering Department Database coverage Structural Data Physical Chemistry Spectroscopy • Synthetic Organic Chemistry • Procuring Chemical Compounds • Links to primary electronic literature 55 CSE Computational Science & Engineering Department Synthetic Organic Chemistry SPRESI (Storage and Retrieval of Chemical Structure Information) • 8.7 million structures • 4.1 million reactions • 32 million factual data entries extracted from:- 658,000 references; 164,000 Patents covering the years 1974 - 2009 Contains:• Own drawing package (ICEDIT) • Synthesis planning tool. • Links with other web sites of interest such as Chemicals Suppliers. 56 CSE Computational Science & Engineering Department Synthetic Organic Chemistry SPRESI Searches can be conducted for: • Molecules (Exact, Substructure, Parent, Tautomer, Isomer, Flex Match, Similarity or All-In-One) • Reactions (Exact, Substructure, Similar Reaction, All-In-One or Contains Exact Reaction, Reactants or Products) • References (e.g. Author, Year, Journal Name, Coden, ISSN, Patent Number). Quick Search - Enter keywords to search through the basic index of structures, reactions and references. 57 CSE Computational Science & Engineering Department Synthetic Organic Chemistry SPRESI 58 CSE Accessed over the Web via SPRESIweb Computational Science & Engineering Department Synthetic Organic Chemistry SPRESI 59 CSE Synthesis Tree Search (STS) Computational Science & Engineering Department Synthetic Organic Chemistry SPRESI Results Select a supplier from the dropdown list to go to their web site. 60 CSE Computational Science & Engineering Department Accelrys Databases • BioCatalysis Synthesis using enzymes and micro-organisms, which can offer advantages of excellent chemo-, regio- and entantio-selectivity, coupled with important environmental benefits. • Protecting Groups Selected protection, deprotection and transprotection reactions demonstrating the range of conditions under which the reactions can be performed and the conditions under which the protecting groups are stable or labile. • Solid Phase Synthesis Information for combinatorial synthesis including information on the Polymer, Substrate and Resin and attachment and detachment conditions. Accessed using the Accord Database Explorer (Windows only) 61 CSE Computational Science & Engineering Department Accelrys Databases Query By Form 62 CSE Computational Science & Engineering Department Accelrys Databases Query Builder 63 CSE Computational Science & Engineering Department Accelrys Databases Default Forms - Protecting Groups 64 CSE Computational Science & Engineering Department Database coverage Structural Data Physical Chemistry Spectroscopy Synthetic Organic Chemistry • Procuring Chemical Compounds • Links to primary electronic literature 65 CSE Computational Science & Engineering Department Procuring Chemical Compounds Available Chemicals over 323,000 entries Searchable catalogue data from several off-the-shelf suppliers: • Sigma-Aldrich (Aldrich; Fluka, Riedel, Sigma and Supelco) • Acros/Maybridge/Fisher • Key Organics • FluoroChem • Tractus • Apollo • Zelinsky • JRD FluoroChemicals • Toronto Research • BioBlocks Building Blocks over 927,000 entries • Maybridge • Life Chemicals • UORSY • Enamine • Key Organics • ChemDiv • Zelinsky Screening Compounds over 3.5 Million searchable compounds 66 CSE Computational Science & Engineering Department Procuring Chemical Compounds Available Chemicals Access via the Web using ChemAxon’s JChem software 67 CSE Computational Science & Engineering Department Procuring Chemical Compounds Atom Lists and NOT lists are available There is a tab for Markush structures but are currently not searchable 68 CSE Computational Science & Engineering Department Procuring Chemical Compounds Chemical Terms Filter Lipinski's rule of five says that, in general, an orally active drug has no more than one violation of the following criteria: • Not more than 5 hydrogen bond donors (nitrogen or oxygen atoms with one or more hydrogen atoms) • Not more than 10 hydrogen bond acceptors (nitrogen or oxygen atoms) • A molecular weight under 500 • An octanol-water partition coefficient logP of less than 5 (Note that all numbers are multiples of five, which is the origin of the rule's name) 69 CSE Computational Science & Engineering Department Procuring Chemical Compounds Chemical Terms Filter Veber filter (The original “rule of 2”) The rule predicts a high probability of good oral bioavailability in the rat if a compound has 10 or fewer rotatable bonds and a polar surface area (PSA) equal to or less than 140 Å i.e. (rotatableBondCount() <= 10) && J. Chem. Inf. Comput. Sci., (PSA() <= 140); 2004, 44 (2), pp 643–651 70 Lead-likeness: Bioavailability: mass <= 450) logD("7.4") between -4 and 4 ringCount <= 4 rotatableBondCount <= 10 donorCount <= 5 acceptorCount <= 8 mass <= 500 logP <= 5 donorCount <= 5 acceptorCount <= 10 rotatableBondCount <= 10 PSA <= 200 fusedAromaticRingCount <= 5 >= 6 CSE Computational Science & Engineering Department Procuring Chemical Compounds Chemical Terms Filter – Drug Likeness Ghose Filter mass between 160 and 480 atomCount between 20 and 70 logP between -0.4 and 5.6 refractivity between 40 and 130 More than 80% of the compounds of the Comprehensive Medicinal Chemistry database Ver. 97.1 were found with the filter developed by Ghose. Muegge filter mass between 200 and 600 ringCount <= 7 atomCount"6" >= 5 and atomCount - atomCount"6" - atomCount"1" >= 2 rotatableBondCount <= 15 donorCount <= 5 acceptorCount <= 10 logP >= -2 && logP <= 5 PSA <= 150 71 CSE Computational Science & Engineering Department Procuring Chemical Compounds Available Chemicals 72 CSE Computational Science & Engineering Department Procuring Chemical Compounds Screening Compounds 73 CSE Computational Science & Engineering Department Database coverage Structural Data Physical Chemistry Spectroscopy Synthetic Organic Chemistry Procuring Chemical Compounds • Links to primary electronic literature 74 CSE Computational Science & Engineering Department Supporting utilities Literature Linking * Single click access to primary literature. * Used with CrystalWeb, ICSD-WWW, and ConQuest * Link to electronic sources of the article. [There is also a link to Suppliers Web page in Sourcing Databases and to the actual compound for SigmaAldrich hits] 75 CSE Computational Science & Engineering Department Supporting utilities DOI lookup e.g. Requires ID/password Click logos for more information. 76 CSE Computational Science & Engineering Department Supporting utilities 77 CSE Computational Science & Engineering Department Supporting utilities 78 CSE Computational Science & Engineering Department 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 79 CSE Computational Science & Engineering Department Database coverage Structural Data Spectroscopy Physical Chemistry Synthetic Organic Chemistry Procuring Chemical Compounds Links to primary electronic literature 80 CSE Computational Science & Engineering Department 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: o Manuals, Tutorials (e.g. ConQuest, Detherm and SpecSurf) and arranging Courses o Flash movies o CDS Newsletters • Helpdesk available: o E-mail cdsbb@dl.ac.uk or Phone 01925 603162 81 CSE Computational Science & Engineering Department 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 82 CSE Computational Science & Engineering Department Chemical Database Service Thank you for your attention…. 83 CSE Computational Science & Engineering Department
