Saturday, February 19, 2011

An acronym in cheminformatics: MDAM for molecular detail annotation marker

MDAM stands for molecular detail annotation marker. An MDAM is used in CurlySMILES notations to encode atomic, substructural and molecular details. An MDAM is a pair of two characters. The first character is an exclamation mark indicating that attention is drawn to some special molecular feature. The MDAM !r, for example, indicates an annotation with detailed information for a particular ring in the molecular graph, as illustrated with the CurlySMILES notation for the fluorotropylium ion ([C7H6F]+):


The MDAM annotation is anchored at the right-most atomic ring node of the SMILES notation. The annotation dictionary entry e=+ specifies the formal ring charge for this heptagonally planar, aromatic cation with a delocalized charge. Notice that the rules of the SMILES language require a formal charge to be localized at an atomic node. In this case, four different notations—distinctive by formal charge placement at C-atom 1, 2, 3, or 4—are possible, which even remain distinguishable after applying the CANGEN algorithm, typically used to derive a unique notation when a single chemical species is considered. The MDAM !r annotation of the CurlySMILES language provides a way to represent the one species in mind (here, the one with the delocalized ring charge); unless the goal is to intentionally represent distinguishable resonance structures individually.

In addition to the MDAM !r, the current version of CurlySMILES includes the markers !a, !p, !m, !H, and !I to encode details of an atom, pair of atoms, multiplet of atoms, hydrogen-bonding atom and an otherwise (for example, van der Waals) interacting atom, respectively.

[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 [].

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