From: Eugen Leitl (eugen$##$leitl.org)
Date: Mon Dec 06 2004 - 07:23:52 EST
----- Forwarded message from James Lumley <JLumley$##$arrowt.co.uk> -----
From: "James Lumley" <JLumley$##$arrowt.co.uk>
Date: Mon, 6 Dec 2004 11:40:49 -0000
To: "Eugen Leitl" <eugen$##$leitl.org>
Subject: RE: [chemweb] ORGLIST: SMILES List of Cheap Starting Materials? (fwdfrom yadavm$##$scripps.edu)
Look for the ACD (Available chemicals directory). You can also request
SDF files from all suppliers, some with cost info in e.g.: email
lancaster then build your own database. I can email you the suppliers
we use but most are those you get in ACD - just takes time to collate.
All suppliers give SDF files if you email, you can then convert to
smiles using e.g.: daylight / corina / bable etc. Look at the daylight
web site for the reaction version of smiles.
Dr. James A. Lumley
> -----Original Message-----
> From: chemweb-bounces$##$imperial.ac.uk
> [mailto:chemweb-bounces$##$imperial.ac.uk] On Behalf Of Eugen Leitl
> Sent: 06 December 2004 11:13
> To: chemweb$##$imperial.ac.uk
> Subject: [chemweb] ORGLIST: SMILES List of Cheap Starting
> Materials? (fwdfrom yadavm$##$scripps.edu)
> ----- Forwarded message from Maneesh Yadav <yadavm$##$scripps.edu> -----
> From: "Maneesh Yadav" <yadavm$##$scripps.edu>
> Date: Sat, 4 Dec 2004 20:48:39 -0800
> To: <everybody$##$orglist.net>
> 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 list.
> 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 strings.
> 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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> Eugen* Leitl leitl
> ICBM: 48.07078, 11.61144 http://www.leitl.org
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> http://moleculardevices.org http://nanomachines.net
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