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The problem of molecular structure elucidation is that of identifying a molecule
from a given set of (mostly spectroscopical) data. Thus, in order to make that
a little bit more precise, we have to make up our mind according to what we
do mean by molecule. This means we first of all have to tell which
mathematical models of a molecule we would like to use.
So lets agree upon that we usually use approximative models for molecules, and
that the first three approximations are the following ones:
There are further refinements, using energy models, quantum chemistry etc.
But in many cases, the molecular structure elucidation primarily aims at
the generation of the complete set of constitutional formulae that match with
the given input data.
MOLGEN is designed for that problem, i.e. it provides the constitutional
formulae corresponding to a given compound and subject to restrictions
on substructures etc. (see below).
- The first approximation is that of the chemical formula, for
example, CH for benzene.
- The second step of approximating reality is the introduction of
constitutional formulae, for example, there are exactly 217
constitutional isomers that correspond to the same chemical formula as
benzene, and so this is a
considerable refinement compared with the first step of approximation,
where there was exactly one model of benzene only.
- The third step of approximation takes the spatial arrangement into
account. To a constitutional formula there may correspond several
configurational isomers, which contain besides the constitution
also geometrical descriptors. For example, in the case of benzene, there are
958 such isomers for the chemical formula; again this step provides a
considerable refinement of the second approximation.
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