The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules
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)
The term Canonical SMILES refers to the version of the SMILES specification that includes rules for ensuring that each distinct chemical molecule has a single unique SMILES representation The term Canonical SMILES refers to the version of the SMILES specification that includes rules for ensuring that each distinct chemical molecule has a single unique SMILES representation - A common application of Canonical SMILES is for indexing and ensuring uniqueness of molecules in a database
The term Isomeric SMILES refers to the version of the SMILES specification that includes extensions to support the specification of isotopes, chirality, and configuration about double bonds - A notable feature of these rules is that they allow rigorous partial specification of chirality.
In terms of a graph-based computational procedure, SMILES is a string obtained by printing the symbol nodes encountered in a depth-first tree traversal of a chemical graph In terms of a graph-based computational procedure, SMILES is a string obtained by printing the symbol nodes encountered in a depth-first tree traversal of a chemical graph The chemical graph is first trimmed to remove hydrogen atoms and cycles are broken to turn it into a spanning tree Where cycles have been broken, numeric suffix labels are included to indicate the connected nodes Parentheses are used to indicate points of branching on the tree
SMILES Bonds SINGLE* DOUBLE TRIPLE AROMATIC*
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
SMILES Bonds Ethene Chloroethene 1,1-Dichloroethene cis-1,2-Dichloroethene Trichloroethene Perchloroethene
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
Other SMILES Atoms Aliphatic or nonaromatic carbon: C Designate ring closure with pairs of matching digits, e.g. - c1ccccc1 is Benzene, whereas
- C1CCCCC1 is Cyclohexane
SMILES Charges Specify attached hydrogens and charges in square brackets Number of attached hydrogens is the symbol H followed by optional digit
SMILES Charges [H+] [OH-] [OH3+] [Fe++] [NH4+]
SMILES Cyclic Structures Number in any order - Designate ring-breaking atoms by the same digit following the atomic symbol
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
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
Further Restrictions 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
SMILES Fragments Nitro Nitrate Nitrite Sulfonic acid Cyanide/Nitrile Azide Azido
Disconnected Structures Tetramethyl ammonium bromide C[N+]C(C)C.[Br-]
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
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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