Computer Representations of Molecular Structures - Design and Use of Relational Databases in Chemistry - page 80

7.5.4 Valence
The valence of an atom in an organic molecular structure is almost always
typical. Most all carbon atoms have valence 4, oxygen atoms 2, and nitro-
gen atoms 3. However, some nitrogen atoms might be represented as
having valence 5. For example, nitromethane is written as CN(=O)=O
showing a valence of 5 for the nitrogen atom. However, it is possible to
represent nitromethane as C[N+](=O)[O-] in which nitrogen retains it
“normal” valence of 3. The rules of SMILES impose no valence require-
ments and either representation is acceptable and correct. The rules for
canonical SMILES also do not modify the valence, only the order in which
the atoms appear in a SMILES.
If canonical SMILES are used in a table to facilitate direct lookup of
molecular structure, it is necessary that only one unique name be used for
any one structure. Similarly, if one is searching for structure-containing
nitro groups, it is necessary that all nitro groups be represented using the
same valence conventions. For these reason, it is essential to make a deci-
sion about the use of SMILES in certain cases, such as nitro groups. Sulfur
and phosphorous atoms also must be considered carefully since they are
commonly found with “unusual” valence.
It is possible to use SMIRKS transformations to modify SMILES
to conform to a standard valence model. For example, if a SMILES for
nitromethane is entered in the charge separated form C[N+](=O)[O-], it
can be transformed to the other form CN(=O)=O. Chapter 9 discusses
transformations and gives examples that will help resolve issues with
structures that can be represented equally well using two distinct valence
forms.
7.5.5 Chirality
It is possible to represent chirality in SMILES. This is essential to correctly
define the appropriate enantiomer or stereoisomer. Many databases will
contain isomers. It is possible to relate the various isomers of a structure
by using their common canonical SMILES. This might be done by relaxing
the uniqueness constraint on the cansmi column in a structure table,
or by adding another table of stereoisomers that is related to the master
table. Chirality may be used in SMARTS as well.
The cansmiles function will not preserve any stereochemical infor-
mation in the input SMILES. This is done so that the canonical SMILES
for all stereoisomers is the same. It may be preferable to keep each isomer
as a unique entry in a database. The isosmiles function preserves the
stereochemical information while also reordering the atoms in the same
way as the canonical SMILES.