|
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:
|
|
[Na+]{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:
|
|
[Na+]{VAc=[Na+].[Cl-]{sc}}
|
|
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:
|
|
[Na+]{VAe=-}
|
|
sodium vacancy with singular negative charge, V′Na+
|
|
|
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.
|
_
__
__
__
__
Share on Tumblr
___
|
