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Cyclic Structures

Cyclic Structures. Numbers indicate start and stop of ring Same number indicates start and end of the ring, entered immediately following the start/end atoms Only numbers 1 – 9 are used A number should appear only twice

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Cyclic Structures

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  1. Cyclic Structures • Numbers indicate start and stop of ring • Same number indicates start and end of the ring, entered immediately following the start/end atoms • Only numbers 1 – 9 are used • A number should appear only twice • Atom can be associated w. 2 consecutive numbers, e.g., Napthalene: c12ccccc1cccc2

  2. SMILES Conventions • Avoid two consecutive left parentheses if possible • Strive for the fewest number of possible branches • Tautomeric bonds are not designated; enter the appropriate form

  3. Further Restrictions • A branch cannot begin a SMILES notation • A branch cannot immediately follow a double- or triple-bond symbol • Example: C=(CC)C is invalid, but • C(=CC)C or C(CC)=C are valid SMILES

  4. Nitro Nitrate Nitrite Sulfonic acid Cyanide/Nitrile Azide Azido N(=O)(=O) ON(=O)(=O) ON(=O) S(=O)(=O)O C#N N=N#N N+=N- SMILES Fragments

  5. SMILES Metals [Al] [As] [Au] [Be] [Bi] [Cd] [Ca] [Fe] [Hg] [K] [Li] [Mg] [Na] [Ni] [Pt] [Sb] [Sn] [Zn] [Zr]

  6. Disconnected Structures • Tetramethyl ammonium bromide C[N+]C(C)C.[Br-]

  7. Isomeric and Chiral SMILES • Isomeric configuration indicated by forward and backward slashes: / \ • Examples: • trans-1,2-dibromoethene: Br/C=C/Br • cis-1,2-dibromoethene: Br/C=C\Br • Chirality indicated by the “@” symbol

  8. Some Applications • JMDraw/SMILESViewer (Christoph Steinbeck) http://jmdraw.sourceforge.net • JME Molecular Editor (Peter Ertl) • STN Express (SMILES as output) • Tripos (dbtranslate: SMILES to MOL) • Marvin (Ferenc Csizmadia) http://chemaxon.com/marvin/ • CACTVS http://www2.ccc.uni-erlangen.de/cactvs/

  9. Another Application • SMILESCAS Database http://esc.syrres.com/interkow/smilecas.htm • Over 103,000 SMILES notations • Input CAS Registry Number • Leads to SMILES and thence to a structure search

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