1 / 9

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

latham
Télécharger la présentation

Cyclic Structures

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related