Chirality Representations in SMILES

Cheminformatics Tutorials - Herong's Tutorial Examples

∟SMILES (Simplified Molecular-Input Line-Entry System)

∟Chirality Representations in SMILES

This section provides a quick introduction on chirality representations in SMILES. Different types of chirality are represented in as different chiral class codes in an format of [x@ccn].

How Chirality Representations Are Represented in SMILES? - Different types of chirality are represented in as different chiral class codes in an format of [x@ccn] according to the following rules:

1. Tetrahedral chiral class code: TH - A tetrahedral center with 4 different neighboring atoms has 2 configurations:

"a[x@TH1](b)(c)d" - "b", "c" and "d" are in anticlockwise order, if looking from atom "a".
"a[x@TH2](b)(c)d" - "b", "c" and "d" are in clockwise order, if looking from atom "a".

2. Allene-like chiral class code: AL - A sequence of an even number of double bonds with 4 different neighboring atoms has 2 configurations:

"aC(b)=[C@AL1]=C(c)d" - "b", "c" and "d" are in anticlockwise order, if looking from atom "a" with C=C=C "collapsed" to a tetrahedral center.
"aC(b)=[C@AL2]=C(c)d" - "b", "c" and "d" are in clockwise order, if looking from atom "a" with C=C=C "collapsed" to a tetrahedral center.

3. Square-planar chiral class code: SP - A square-planar chiral has 4 configurations:

"a[x@SP1](b)(c)d" - "a", "b", "c" and "d" forms a U shape square-planar.
"a[x@SP2](b)(c)d" - "a", "b", "c" and "d" forms a 4-shape square-planar.
"a[x@SP3](b)(c)d" - "a", "b", "c" and "d" forms a Z shape square-planar.

4. Trigonal-bipyramidal chiral class code: TB - A trigonal-bipyramidal chiral has 20 configurations:

"a[x@TB1](b)(c)(d)e" - "b", "c" and "d" are in anticlockwise order, if looking at the direction from atom "a" to "e".
"a[x@TB2](b)(c)(d)e" - "b", "c" and "d" are in clockwise order, if looking at the direction from atom "a" to "e".
...

5. Octahedral chiral class code: OH - A Octahedral chiral has 30 configurations:

"a[x@OH1](b)(c)(d)(e)f" - "b", "c", "d" and "e" are in anticlockwise order, if looking at the direction from atom "a" to "f".
"a[x@OH2](b)(c)(d)(e)f" - "b", "c", "d" and "e" are in clockwise order, if looking at the direction from atom "a" to "f".
...

6. There is a default chiral class defined to a chiral center based on the number of connected atoms:

Chiral center with 4 connected atoms - The default chiral class is "TH" for "Tetrahedral". [x@TH1] and [[x@TH2] can be simplified as [x@] and [x@@].
Chiral center with 2 connected atoms at each end of the double-bond chain. The default chiral class is "AL" for "Allene-like". [x@AL1] and [[x@AL2] can be simplified as [x@] and [x@@].
Chiral center with 5 connected atoms - The default chiral class is "TB" for "Trigonal-bipyramidal". [x@TB1] and [[x@TB2] can be simplified as [x@] and [x@@].
Chiral center with 6 connected atoms - The default chiral class is "OH" for "Octahedral". [x@OH1] and [[x@OH2] can be simplified as [x@] and [x@@].