Monday, February 7, 2011

An acronym in cheminformatics: SFN for stoichiometric formula notation

SFN stands for stoichiometric formula notation [1-3]. An SFN describes a chemical compound in terms of its composition based on atoms and characteristic groups of atoms (structural subunits). For example, the mineral genthelvite, Zn4(Be3Si3O12)S, can be encoded as Zn4(Be3Si3O12)S. This SFN matches the displayed formula, only excluding its markup. An SFN is a document-neutral linear notation.

The versatility of SFN strings is appreciated when used with the CurlySMILES language, providing a format to specify materials due to phase, nanostructure, doping and other characteristics; for example: {*TiO2}{tfphn=rutile} encodes a titanium dioxide thin film with TiO2 in the rutile phase, {*Fe3O4}{np}{dp} encodes dispersed magnetite nanoparticles, and {*ZnO}{IMa=F} encodes fluorine-doped zinc oxide.

SFNs also occur in composite and nanocomposite notations such as {/{*WS2}/{*WO3}}{np}, encoding tungsten-based WS2/WO3 nanoparticles.

SFNs are further used in combination with SMILES notations to encode functionalized material surfaces, particles and clusters, such as a thiophenolate capped cadmium sulfide nanoparticle: c1ccccc1S{-|c={*CdS}{np}}.

Keywords: chemical materials encoding, empirical formula, molecular formula, structural formula, brutto formula, summary chemical formula, nanostructures, functionalized material surfaces

[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: The CurlySMILES Project: Stoichiometric Formula Notation (SFN) [].

[3] Examples E5, E16, E17, E18 and E20 in additional file of [1] entitle CurlySMILES encoding examples [].

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