As a result, a ring compound may be represented by many different but equally valid SMILES strings. For example, a six-membered ring has six bonds, each of which can be a ring-closure point. As a result, different aromaticity detection algorithms often disagree with each other on whether a given molecule is aromatic or not, making it difficult to interchange information between databases that use different aromaticity detection algorithms for SMILES generation.Īlso note that a ring structure can have multiple potential ring-closure points. Note that aromaticity is not a measurable physical quantity, but a concept without a unanimous mathematical definition. For example, the following is a valid SMILES string for benzene. One can also represent an aromatic compound as a non-aromatic, KeKulé structure. Therefore, cyclohexane and benzene can be represented by the following SMILES.Īlthough the carbon-carbon bonds in these two SMILES are omitted, it is possible to deduce that the omitted bonds are single bonds (for cyclohexane) and aromatic bonds (for benzene). Atoms in aromatic rings are specified by lower cases letters. Rings are represented by breaking one single or aromatic bond in each ring, and designating this ring-closure point with a digit immediately following the atoms connected through the broken bond. CC(CCC(=O)N)CN 5-amino-4-methylpentanamide.CC(C)CO Isobutyl alcohol (CH3-CH(CH3)-CH2-OH).Here are some examples of SMILES strings.īranches are specified by enclosures in parentheses and can be nested or stacked, as shown in these examples. Single and aromatic bonds may be, and usually are, omitted. Single, double, triple, and aromatic bonds are represented by the symbols, -, =, #, and :, respectively. A formal charge is represented by one of the symbols + or. “Explicitly” attached hydrogens and formal charges are always specified inside brackets. Square brackets may be omitted for elements in the “organic subset” (B, C, N, O, P, S, F, Cl, Br, and I) if the proper number of “implicit” hydrogen atoms is assumed. Each non-hydrogen atom is specified independently by its atomic symbol enclosed in square brackets, (for example, or ). The second letter of two-character atomic symbols must be entered in lower case. In SMILES, atoms are represented by their atomic symbols. INTERNATIONAL CHEMICAL IDENTIFIER (InChI) AND InChI KEY.

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