Monday, February 21, 2011

An acronym in cheminformatics: OPAM for operational annotation marker

OPAM stands for operational annotation marker. An OPAM is used in CurlySMILES notations to encode coordination compounds and molecules with structural repeat units. Further, compound classes and diverse sets of molecules are encodable by applying the OPAM format. The adjective operational means formally constructable or generic. For instance, a macromolecule (polymer) is encoded by a single repeating monomer unit, annotated in such a way that a human reader or a machine is informed of how to connect monomer units together to build the macromolecular chain. The following example shows a CurlySMILES notation for poly(dimethylsiloxane) (PDMS), [-Si(CH3)2O-]n:


The OPAM +n instructs to repeat the monomer unit n times by connecting the O-atom of one unit to the open bond at the Si atom of the next unit. Another illustration has been given with poly(3-hexylthiophene). Ring molecules that are based on a structural repeat unit, can be encoded with OPAM +r. Metal-ligand systems such as complexes with ambidentate ligands can be encoded with OPAM +L. Sets of molecules can be encoded with OPAM +R, +X and +Y, for example, classes of alkyl-substituted compounds with +R.

[1] Axel Drefahl: CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures. Journal of Cheminformatics 2011, 3:1.
DOI: 10.1186/1758-2946-3-1.
[2] Axel Drefahl: CurlySMILES: molecular detail annotation [].

No comments:

Post a Comment