An allene stereoisomer should keep its identity when its SMILES is rewritten for a compound list. chematic v1.1.3 adds support for reading allene axial stereochemistry, writing canonical SMILES, and reading the result back. Structures with opposite configurations retain distinct strings.

In the RDKit 2026.09.1 comparison, both example inputs become CC=C=CCC. RDKit issue #9678 reports this loss of allene stereo notation during a SMILES round trip. Here, the published chematic v1.1.3 npm package retains the stereochemical distinction for the same inputs.

Distinguish two configurations with the same connectivity

Allenes contain consecutive double bonds, C=C=C. When each terminal carbon has two different substituents, their arrangement around the axis distinguishes stereoisomers. SMILES can specify these arrangements with @AL1 and @AL2. Section 3.3.4 of the Daylight specification describes the allene class.

The comparison uses these two inputs:

CC=[C@AL1]=CCC
CC=[C@AL2]=CCC

RDKit 2026.09.1 produces the following canonical SMILES even with isomericSmiles=True. The setting that permits non-tetrahedral stereochemistry is also enabled.

CC=[C@AL1]=CCC -> CC=C=CCC
CC=[C@AL2]=CCC -> CC=C=CCC

Keep distinct canonical SMILES with chematic

With Node.js installed, save v113-allene.mjs in an empty working directory and run:

npm init -y
npm install --save-exact @kent-tokyo/chematic@1.1.3
node v113-allene.mjs
CC=[C@AL1]=CCC -> C(=[C@AL2]=CC)CC
CC=[C@AL2]=CCC -> C(=[C@AL1]=CC)CC
distinct: 2

The APIs are parse_smiles and mol.canonical_smiles(). The script also reparses each output and confirms that it returns the same canonical string.

The @AL1 and @AL2 labels swap in the output because the atom order has changed. SMILES stereo notation is relative to the order of atoms in the string. chematic adjusts the stereo label during canonical writing to retain the same configuration.

Carry the axial configuration through structure I/O

The v1.1.3 implementation follows the double-bond arms from the allene center and represents the ordering of substituents at the terminal atoms. The writer uses that ordering to retain axial stereochemistry as it rearranges atoms for SMILES output. The allene implementation and WASM regression test show the operation and examples.

For this pair, opposite configurations produce separate canonical strings. A compound-list key or a structure passed to the next processing step can therefore retain the distinction between these allene stereoisomers. We also checked the equivalent @ and @@ shorthand inputs, which canonicalize to the corresponding @AL forms.

The comparison ran on macOS arm64 on October 13, 2026. The comparison data records all four inputs and reparsing results; the RDKit script shows the reference calls, and the execution record identifies the packages and file hashes.