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Understanding SMILES: A Primer on Simplified Molecular Input Line Entry System

Explore the basics of the SMILES system, a widely used and computationally efficient way to represent molecular structures. Learn about SMILES bonds, atoms, charges, cyclic structures, conventions, and more. Discover how to use SMILES for isomeric and chiral molecules, as well as its applications in various software tools.

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Understanding SMILES: A Primer on Simplified Molecular Input Line Entry System

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  1. SMILES • Simplified Molecular Input Line Entry System (SMILES) • Widely used AND computationally efficient • Uses atomic symbols and a set of intuitive rules • Uses hydrogen-suppressed molecular graphs (HSMG)

  2. SINGLE* DOUBLE TRIPLE AROMATIC* * can be omitted - = # : SMILES Bonds

  3. Butanols 2-Butanol iso-Butanol tert-Butanol

  4. SMILES Branches • Represented by enclosure in parentheses • Can be nested or stacked • Examples: CC(O)CC is 2-Butanol OCC(C)C is iso-Butanol OC(C)(C)C is tert-Butanol

  5. Ethene Chloroethene 1,1-Dichloroethene cis-1,2-Dichloroethene Trichloroethene Perchloroethene C=C ClC=C ClC(Cl)=C ClC=CCl ClC(Cl)=CCl ClC(Cl)=C(Cl)Cl SMILES Bonds

  6. SMILES Atoms • Use normal chemical symbols • Add punctuation symbols if necessary • No super- or subscripts

  7. SMILES Symbols • String of alphanumeric characters and certain punctuation symbols • Terminates at the first space encountered when read left to right • The ORGANIC SUBSET: B, C, N, O, P, S, F, Cl, Br, I

  8. Other SMILES Atoms • Aliphatic or nonaromatic carbon: C • Atom in aromatic ring: lowercase letter • Designate ring closure with pairs of matching digits, e.g. c1ccccc1 (or C1=CC=CC=C1) is Benzene, whereas C1CCCCC1 is Cyclohexane

  9. SMILES Charges • Specify attached hydrogens and charges in square brackets • Number of attached hydrogens is the symbol H followed by optional digit

  10. [H+] [OH-] [OH3+] [Fe++] [NH4+] proton hydroxyl anion hydronium cation iron(II) cation ammonium cation SMILES Charges

  11. SMILES Cyclic Structures • Break one single or one aromatic bond in each ring • Number in any order • Designate ring-breaking atoms by the same digit following the atomic symbol

  12. 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

  13. c12ccccc1cccc2 Naphthalene

  14. 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

  15. 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

  16. 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

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

  18. Disconnected Structures • Indicated by a dot • Tetramethyl ammonium bromide C[N+]C(C)C.[Br-]

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

  20. Some Applications • JMDraw/SMILESViewer (Christoph Steinbeck) • 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/

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

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