From: Eugen Leitl (eugen$##$leitl.org)
Date: Mon Dec 06 2004 - 09:39:13 EST
----- Forwarded message from Darren Rhodes <darren.rhodes$##$GMAIL.COM> -----
From: Darren Rhodes <darren.rhodes$##$GMAIL.COM>
Date: Mon, 6 Dec 2004 14:13:19 +0000
Subject: Re: FW: [chemweb] ORGLIST: SMILES List of Cheap Starting Materials? (fwdfrom yadavm$##$scripps.edu)
Reply-To: Darren Rhodes <darren.rhodes$##$gmail.com>
snip - header
MDPI <http://www.mdpi.org/> "Molecular Diversity Preservation
International (MDPI) is a nonprofit organization for deposit and
exchange of molecular and biomolecular samples" is doing what you
Publish your synthesis here ...
<http://www.mdpi.org/molecules/index.htm> there just isn't any point
in publishing in a closed access journal anymore. (Publishing in a
closed access journal is like giving people some outdated cure for a
terminal disease when a new effective cure is available). Also, I
think that for this journal the author keeps the copyright. That
means that if you were funded by a government agency (ie taxpayer);
you aren't in the dubious position of giving away someone else's
Apparently, it is possible for a spider to crawl the web; get
molecular structures and convert them to smiles. (The chaps at
Daylight will correct me if I'm wrong). If my understanding is
correct this would open up a lot of the chemical catalogues on the web
because the ones that didn't display structure and price would be
overlooked and hence would loose revenue. There may be a programme
ongoing by google to provide this service - I don't know - but it
would certainly be useful.
I'd be interested in seeing your wiki ... what would be of use would
be a list of chemicals wanted. At the moment everyone has to try and
second guess what to make in order to try and sell it. This is
inefficient from the point of customer and supplier (the customers is
offered something that they don't want and end up taking time to make
what they need; the supplier has to try and sell something that
doesn't have a strong market).
Hope my comments are useful ... Darren.
> Subject: ORGLIST: SMILES List of Cheap Starting Materials?
> Dear ORGLIST/CHEMINF readers,
> I recently found myself synthesizing a simple molecule which can be used
> as a photoacid, namely, 4-formyl-6-methoxy-3-nitrophenoxyacetic acid,
> accessible in two simple steps from vanillin*1.
> I am always surprised when I can make such interesting and useful
> molecules so darn easily and cheaply, I am interested in a method where
> I could produce an exhaustive list of all such molecules, i.e. every
> small molecule that is synthetically accessible in under five steps from
> the pool of cheap starting materials, using only "easy" reactions.
> I have a few questions, and wanted to subject myself to some
> critisism/comment, I try to detail my idea below.
> What Are Cheap Starting Materials?
> Naturally the definition of "cheap" depends on supply and demand (which
> also drives discovery of new chemical knowledge); but I think a good
> criteria would be anything I could buy on the gram scale for under $100.
> This list would include things like vanillin, citronellal, carvone,
> industrial dyes, natural amino acids, common acids/bases (sulphuric
> acid, sodium hydroxide), cyclopentadiene, benzene, acetone, ethanol,
> methanol etc. I think you get the idea.
> It is surprisingly difficult to construct such a list of starting
> materials (in the form of a list of SMILES strings). Aldrich does not
> seem to have the ability to query by price in their internal database
> system (that is what they tell me at least). If anyone can think of a
> better way to do this than burning me eyes out in front of Chemdraw and
> an Aldrich catalog for a few weekends, please let me know. I think 1000
> compounds would be a good place to start. I'd put up a wiki/database
> system linked to suppliers if anyone else would find value in such a
> What Are Easy Reactions?
> Sharpless et. al define the notion of "Click Chemistry"*2 as a set of
> reactions which been demonstrated to posses very favorable
> exergonicities in multiple contexts (among a few other qualifiers). The
> basic idea is that the these reactions tend to "just work" and include
> reactions like Diels-Alder, acetylene-azide dipolar cycloaddition and
> epoxide formation/opening. While I wouldn't necessarily limit myself
> strictly to "click" reactions, the idea is to limit the number of
> reactions that will be applied to good easy ones.
> I haven't run across an elegant way to specify chemical reactions in
> detail. I am collaborating with Gabriel Valiente, who has implemented a
> basic reaction facility to PerlMol. He has also wondered if there is
> some sort of algebra by which we can make smaller descriptions, specify
> branched outcomes etc. that take advantage of the fact the most
> reactions have very "natural" atom mappings, as opposed to the
> completely explicit mappings we are using right now. I know that
> Sertanty Inc. has something neat in the works, but given it is
> commercial, I don't have too much of an idea.
> What Good Would It Be?
> The final result would be to iteratively apply our easy reactions to our
> cheap starting materials (filtering conformationally implausible beasts,
> at each step) to generate a list of compounds and plausible synthetic
> routes to them. It'd be interesting to ask about the comparative
> molecular diversity of the final list, and statistical information about
> the synthetic routes.
> Again please let me know about any ideas about:
> a)How to get a large list of cheap compounds in the form of SMILES
> b)A better way of specifying chemical reactions, rather than explicit
> atom mapping (software etc.).
> Biochim Biophys Acta. 1987 Dec 11;905(2):409-16.
> Proton concentration jumps and generation of transmembrane pH-gradients
> by photolysis of 4-formyl-6-methoxy-3-nitrophenoxyacetic acid.
> Janko K, Reichert J.
> Angew. Chem. Int. Ed. 2001, 40,2004--2021
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