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Material notations |
By Axel Drefahl |
Introduction |
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Annotation-free SFNZrO2 to be consistent with the ZrO2 formula,
in which the symbol fore the oxygen atoms occurs at the end as it does in
metal oxide formulae. Atomic symbols can be grouped by enclosing them with round brackets. A stoichiometric integer follows the closing round bracket, when required; for example:
When an SFN represents an ionic species, a charge notation (n+) or (n-) with n ≥ 1 is placed at the end of the notation; for example:
An isotopical label is encoded as a caret followed by the label integer placed directly in front of an atomic symbols:
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Annotated SFN
An SFN enclosed by
cr followed by appropriate
annotation dictionary entries such as a phase name
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Plain and Annoted SQC nodeThe SQC is a special type of the atomic node code (ANC), a SMILES and CurlySMILES format to encode atomic nodes of the hydrogen-suppressed molecular graphs. Since MM! allows the entry of bare SFNs, ANC entry is not possible without ambiguity. MM! requires atomic nodes to be entered as SQC. SQC are used to represent chemical elements, isotopically labeled atoms and chemical species, including cations and anions, which contain not more than one non-hydrogen atom.
An SQC notation represents either a single atom or molecule or a material composed thereof, depending on context. CurlySMILES provides a rich annotation grammar to specify contextual details. For example, the carbon SQC can be annotated to specify a structural modification (allotrope) in which carbon compounds are known to exist:
Annotations can assign a role to atoms and ions, for example as impurities or dissolved species in a medium:
CurlySMILES provides a format to encode a mononuclear complex by presenting the metal center as SQC and the ligands as a list of SMILES notations within an annotation. For example, cis-dichlorobis(dibenzyl sulfido-κS)platinum(II) can be encodes as
[Pt+2]
as a query. The sniplinks will then be listed in the domain of coordination compounds.
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