ORGLIST: What can we get from a chemical structure?

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From: Dmitry Korkin (z17b3$##$
Date: Wed Apr 11 2001 - 22:14:00 EDT

Dear colleagues,

I`m working on the problem of structural representation and classification of
organic compounds (from the point of view of a formal model). The thing is,
there is no formal notion of a chemical structure. Instead, scientists use
intuitive understanding of this notion. But when you are dealing with the
automation of the representation and classification process using computers,
it is necessary to define the notion of chemical structure formally.

So, suppose you have a structural representation of molecules which includes
the following features:
- molecular connectivity
- structural individuality of each atom and each bonding type (including
hydrogen bonding)
- basic 2D and 3D isomerism
- the "evolutionary" molecular class structure (how should one go about
building the molecule).

Suppose all the molecules are represented only using this structural
information. What can you say about physical, chemical properties, and
biological activity of these compounds? In other words, which information is
"extractable" and which one is not?

Another question, if it is not enough, what would you add in terms of
structural (not numerical) information to "complete the picture"? (Probably,
one of the first "candidate" to be added are the basic geometries of the
molecular fragments)

I would appreciate greatly any information related to this questions.

Thank you and best regards,

Dmitry Korkin,
                               PhD student
                               Faculty of Computer Science
                               University of New Brunswick

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