Curly SMILES is a chemical language for the communication of
structures based on molecular graphs as well as structures
that lack characterization by discrete molecules. In the
latter case, an empirical formula is
often used in the chemical literature to describe the
composition via atomic symbols.
The stoichiometric formula notation
(SFN) applies the empirical formula
syntax, but does not require alphabetical ordering of the atomic
symbols. Symbols are allowed to occur in any order and
repeatedly at any location. Further, symbols may be grouped by
enclosing them with round braces. An appropriate integer subscript
(different from 1) follows the closing round brace to account
for the stoichiometry of the group within the denoted compound.
The following examples illustrate SFN encoding:
| Cu5Zn8 |
Cu5Zn8, pentacopper octazincide |
| MnO(OH) |
MnO(OH), manganite (mineral) |
| Cu2Pb5(SO4)3(CO3)(OH)6 |
Cu2Pb5(SO4)3(CO3)(OH)6, caledonite (mineral) |
An SFN of an ionic species includes a charge notation
(n+) or
(n-), where
n ≥ 1. The charge notation is
placed at the end of the SFN string:
| O2Cl2(1+) |
O2Cl2+,
dioxygen dichloride)(1+) cation |
| HMo6O19(1-) |
HMo6O19-,
hydrogen(nonadecaoxidohexamolybdate)(1-) anion |
An isotopical label precedes the atomic symbol and is
indicating with a beginning ^
character. Example notations for isotopically labelled
molecules are :
| ^16O2(2-) |
[16O]22-,
labelled dioxidanediide anion |
| ^32P2^16O5 |
[32P]2[16O]5,
labelled phosphorus pentoxide |
SFN integration with a CurlySMILES notation.
To be a component of a CurlySMILES notation, an SFN is placed
between {* and
}. An appended annotation may
further specify the shape and phase of the targeted material.
For example, a thin film of titanium dioxide in the rutile
modification is encodes as
| {*TiO2}{tfphn=rutile} |
rutile thin film |
CurlySMILES allows the combination of SMILES- and
SFN-components:
| [K+].[K+].{*Sn5(2-)} |
dipotassium pentastannide(2-) |
An SFN notation can also appear inside an annotation as the value
of key sfn. The following notation
encodes a pheny group, which is covalently linked to the surface
of cadmium selenide (CdSe) material:
| c1ccccc1{-|sfn=CdSe} |
phenyl group grafted to CdSe surface |
|
Please, email comments and suggestions to
axeleratio@yahoo.com
|
|
© 2010, 2011 Axel Drefahl. All rights reserved.
|
|
|
