A square-bracket atomic code (SQC) is a special type of an atomic node code (ANC). In a SMILES and CurlySMILES notation an SQC encodes a node of the hydrogen-supressed molecular graph. SQC is mandatory for any non-hydrogen atom that does not belong to the organic subset and that has a hydrogen count which differs from the implicit hydrogen attachment assuming that hydrogen atoms make up the remainder of an atom's lowest normal valence, consistent with explicit bond specification [1]: 3, 4, 3, 2, 1 for B, C, N, O, and the halogen atoms, respectively, 3 or 5 for phosphorus and 2, 4, or 6 for aliphatic sulfur atoms. In the following examples the germanium atom, not belonging to the organic subset, and the aromatic nitrogen atom with a special H-count require SQC encoding:

CC[GeH2]CC Ge node in diethylgermane
[nH]1cccc1 N node in aromatic 1H-pyrrole

Isotopically labelled atoms and nodes with formal charge specification are always SQC-endoded:

C=[N+]=[N-] formally charged N atoms in diazomethane
CCOC(=[17O])[17O]C O-ethyl-17O-methyl[17O2]carbonate

In CurlySMILES, atomic-wildcard nodes and atoms with an incident quadruple or unspecified bond have to be SQC-encoded [2]:

CC[*H2]CC C, Si, and Ge will match, for example
[Cl-][Re](Cl)(Cl)(Cl)$[Re](Cl)(Cl)(Cl)[Cl-] [Re2Cl8]2- anion with Re-Re quadruple bond
[NH3]~[B](F)(F)F adduct of ammonia and boron trifluoride

Note that [Re+3]{+Lc=[Cl-]{4}}$[Re+3]{+Lc=[Cl-]{4}} is an alternate encoding of [Re2Cl8]2-, which correctly represents the topological equivalence of the eight Cl atoms using the CurlySMILES' OPAM annotation to encode the Cl anions as ligands of a —in this case— dinuclear cluster.

References

[1] D. Weininger: SMILES, a Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules . J. Chem. Inf. Comput. Sci. 1988, 28, 31-36; doi: 10.1021/ci00057a005 .
[2] A. Drefahl: CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures . J. Cheminf. 2011, 3:1; doi: 10.1186/1758-2946-3-1 .
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