A vacancy in a crystal is a lattice site where an atom is missing—a special type of a point defect. Notations for such sites are straightforward: take the symbol of the atom or ion that is supposed to occupy the site and indicate vacancy. In the literature, the letter V is typically used to indicate a vacant site and the atomic symbol is given as a subscript; for example VNa+ for a site missing a sodium ion. In CurlySMILES, the corresponding notation consists of the SMILES notation for the ion followed by the MIAM annotation with marker VA:
sodium ion vacancy, VNa+
Such a notation encodes a vacancy in generic terms with respect to its environment. A vacant site in a particular material, such as sodium chloride (rock salt), is encoded as follows:
sodium ion vacancy in a sodium chloride single crystal
If one likes to indicate a negative charge due to the missing, positively charged ion (excess charge relative to the neutral site), one can do so:
sodium vacancy with singular negative charge, VNa+
Notice that the Kröger-Vink notation is typically used in the scientific literature to formulate point defect species in crystal structures, using superscript dot, prime and superscript cross as symbols to encode an effective positive charge, an effective negative charge and no effective (neutral) charge (see page 240 in [2]). The respective values to be associated with key e in a CurlySMILES notation are +, - and 0.
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[1] 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.
[2] N. G. Connelly, T. Damhus, R. M. Hartshorn and A. T. Hutton (publication preparators): Nomenclature of Inorganic Chemistry. IUPAC Recommendation 2005. RSC Publishing, Cambridge, 2005. pdf: Red Book.

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