Michel -- Organic chemistry was known to be the most difficult course in
Columbia University.  But I got interested in it, worked very hard
constantly, and I achieved an  'A'.  But what you say here indicates several
orders of magnitude more difficulty than what I played with in university.
 For me this raises a question about the 'realms of nature', as in the
subsumptive hierarchy: {physical realm {chemical realm {biological realm}}.
 Do you think one should place an 'organic realm' between chemical and
biological?  Or, otherwise, do you think it possible that there might be
organic realms out in the universe not entrained into biology?


On Sat, Sep 17, 2011 at 1:53 PM, Michel Petitjean <
petitjean.chi...@gmail.com> wrote:

> Dear Joe, dear FISErs,
> An organic chemist is able to predict a number of properties from the
> structural formula, including much about reactivity of the compound.
> But as you know, doing that properly is extremely difficult in a
> number of cases, because the rules governing reactivity are much more
> complicated that the ones which are taught at Universities, and the
> number of rules expands rapidly each year. In fact, an experienced
> Organic Chemist has in his head a so extraordinary rich collection of
> rules and a so enormous knowledge that even many chemists which are
> not Organicians cannot imagine the extent of this knowledge.
> It is clear that the "doing chemistry" process derives from these
> rules (these rules are chemical information), not only from the
> formulas.
> Since the 70's, some cheminformaticians tried to store that in
> databases: reactions databases plus databases of reactivity rules for
> computer sssisted synthesis or retrosynthesis, etc., then built
> programmes intended to output proposals supposed to help the chemist.
> As far as I know, the brain of the Organician is still by far much
> more efficient than the best softwares which were produced.
> So, I may tell that the information available in the brain of the
> Organician is extremely difficult to store on computer, and it is even
> very difficult to teach it, apart the very beginning.
> There are examples other than reactivity. A huge of QSAR studies were
> done in order to predict various physico-chemical properties of simple
> chemical compounds, e.g., predicting from the structural formulas the
> boiling temperatures of monofunctional compounds such as alcohols,
> cetones, etc. at 20 C under 1 atm. But even in these apparently simple
> cases, the chemical information we need to do that with an acceptable
> accuracy is difficult to extract: the conclusions of such QSAR studies
> cannot be applied to any alcohol or cetone (still assumed to be
> monofunctional compounds), and it is even difficult to know the extent
> of validity of the published empirical rules, concretely often
> summarized by some regression coefficients.
> The example of spectroscopic databases is also of interest. How
> simulate spectras (infrared, NMR, mass spectras, etc.) of chemical
> compounds ? Starting from the structural formula, it is really hard to
> simulate, e.g. a low resolution mass spectra. Most time, it was
> attempted to extract rules from spectroscopic databases, then try to
> predict the spectra of a compound absent from the database, or
> conversely, retrieving the structural formula of a compound from its
> spectra(s). Many such softwares were developped since the 70's (one of
> the oldest ones is STIRS), but really the chemical information needed
> to do that properly is very difficult to extract.
> To conclude, I retain your example of crystallization: for sure when
> we will able to retrieve from the structural formula H-O-H that water
> under 1 atm should crystallize at 0 C, then for sure we will be ready
> to predict more about crystallization of chemicals.
> Best regards,
> Michel.
> 2011/9/17 joe.bren...@bluewin.ch <joe.bren...@bluewin.ch>:
> > Dear Michel and FIS Colleagues,
> >
> > This will be an interesting discussion, since the core nature and role of
> > information will be involved. Here is just one first point: to me, as a
> > chemist, chemical information is only secondarily an "object" capable of
> > being formalized, archived, etc. A formula has meaning for me in terms
> > of the potential reactions the molecule to which it refers can undergo,
> what
> > it looked like when crystallized for the first time and so on.
> >
> > Cheminformatics seems not to deal with such aspects of chemical
> information
> > as part of a process of "doing chemistry". Can this be captured by
> another system?
> >
> > Best wishes,
> >
> > Joseph
> >
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