From zoran@robig.pmf.ukim.edu.mk Tue Jul 15 01:07:13 1997 Received: from robig.pmf.ukim.edu.mk for zoran@robig.pmf.ukim.edu.mk by www.ccl.net (8.8.3/950822.1) id AAA27287; Tue, 15 Jul 1997 00:43:50 -0400 (EDT) Message-Id: <199707150443.AAA27287@www.ccl.net> Received: (qmail 3101 invoked from network); 15 Jul 1997 04:44:26 -0000 Received: from remote.pmf.ukim.edu.mk (HELO zoran.pmf.ukim.edu.mk) (194.149.146.139) by robig.pmf.ukim.edu.mk with SMTP; 15 Jul 1997 04:44:26 -0000 From: "Zoran Zdravkovski" To: Subject: unsubscribe Date: Tue, 15 Jul 1997 06:44:33 +0200 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_01BC90EA.8DE0D3C0" Content-Transfer-Encoding: 7bit This is a multi-part message in MIME format. ------=_NextPart_000_01BC90EA.8DE0D3C0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Please unsubscribe me from the list. Sincerely yours, Zoran Zdravkovski Institute of Chemistry Skopje, Macedonia ------=_NextPart_000_01BC90EA.8DE0D3C0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable


Please unsubscribe me from = the list.

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Skopje, = Macedonia

------=_NextPart_000_01BC90EA.8DE0D3C0-- From cdac.ernet.in!gadre@parcom.ernet.in Tue Jul 15 09:07:17 1997 Received: from sangam.ncst.ernet.in for cdac.ernet.in!gadre@parcom.ernet.in by www.ccl.net (8.8.3/950822.1) id IAA29114; Tue, 15 Jul 1997 08:20:59 -0400 (EDT) Received: from iucaa (iucaa.ernet.in [144.16.31.4]) by sangam.ncst.ernet.in (8.7.5) with SMTP id RAA11256 for ; Tue, 15 Jul 1997 17:59:12 +0530 (GMT+05:30) Received: from iucaa.iucaa.ernet.in by iucaa (5.65v3.2/SMI-4.1) id AA17545; Tue, 15 Jul 1997 17:47:51 +0500 Received: by parcom.cdac.ernet.in (4.1/SMI-4.1) id AA27142; Tue Jul 15 17:14:58 1997 (GMT + 0530) Date: Tue Jul 15 17:14:58 1997 (GMT + 0530) From: gadre@cdac.ernet.in Message-Id: <9707151144.AA27142@parcom.cdac.ernet.in> To: CHEMISTRY@www.ccl.net Subject: ICCCRE Deadline : Registration Fees for ICCCRE Dear Sirs and Madams : The last date of payment of Registration Fees for the conference (US$150 for students and $300 for others) is July 31, 1997. The payment may be made by a Banker's draft drawn on the State Bank of India (DG, Pune) payable to "The Registrar, University of Pune(ICCCRE)". The draft should be mailed to Professor S. R. Gadre Department of Chemistry University of Pune Pune-411007. INDIA. Thanks and looking forward to meet you in Pune in January 1998! Shridhar Gadre, Convenor, XII ICCCRE. From MAILER-DAEMON@www.ccl.net Tue Jul 15 09:07:23 1997 Received: from schiele for MAILER-DAEMON@www.ccl.net by www.ccl.net (8.8.3/950822.1) id IAA29090; Tue, 15 Jul 1997 08:18:03 -0400 (EDT) Received: by schiele (950911.SGI.8.6.12.PATCH825/940406.SGI.AUTO) id OAA09612; Tue, 15 Jul 1997 14:18:28 +0200 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9707151418.ZM9610@eros.ccc.uni-erlangen.de> Date: Tue, 15 Jul 1997 14:18:25 -0600 In-Reply-To: Ascanio DiPippo "CCL:Reaction Pathway Program" (Jul 14, 20:15) References: Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: Ascanio DiPippo Subject: Re: CCL:Reaction Pathway Program Cc: CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit , Joe Golab wrote: > > > Dear CCL Member: > > > > Do you know of any (engineering, chemistry, biological, etc) program that > > given a compound would suggest any and all reaction pathways toward that > > compound (no matter how outlandish from a thermodyanmic standpoint)? > > > > For example, given tolune, the program would suggest: > > > > 1) benzene + methane -> toluene > > 2) methylcyclohexane -> toluene + H2 > > 3) methane + heat/pressure -> toluene + H2 > > 4) ETC. > > > > Perhaps this is really a database that is part of a program. Any leads > > would be gratefully appreciated! Thanks. Programs which perform exhaustive bond reordering for reaction prediction or synthesis planning, or assemble reaction networks between speicified endpoints, can do this. Typically, these programs employ additional constraints to prevent entering the outlandish domains, but these checks can be disabled :-), and thus all reaction pathways generated. Be warned: You quickly generate truly enourmous numbers of pathways. Example programs which could work in this mode are EROS5 (Gasteiger) and IGOR/RAIN (Ugi). For literature references and an overview, see Angewandte Chemie, Int. Ed. 1995, 34, 2613-2633. -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From jtgolab@amoco.com Tue Jul 15 18:07:21 1997 Received: from interlock.amoco.com for jtgolab@amoco.com by www.ccl.net (8.8.3/950822.1) id RAA02300; Tue, 15 Jul 1997 17:52:32 -0400 (EDT) Received: by interlock.amoco.com id AA20799 (InterLock SMTP Gateway 3.0 for CHEMISTRY@www.ccl.net); Tue, 15 Jul 1997 16:52:31 -0500 Message-Id: <199707152152.AA20799@interlock.amoco.com> Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-4); Tue, 15 Jul 1997 16:52:31 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-3); Tue, 15 Jul 1997 16:52:31 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-2); Tue, 15 Jul 1997 16:52:31 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-1); Tue, 15 Jul 1997 16:52:31 -0500 From: jtgolab@amoco.com (Joe Golab) Date: Tue, 15 Jul 1997 16:51:21 -0500 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: SUMMARY - Reaction Pathway Programs Cc: jtgolab@amoco.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi CCL: Below is the summary of responses to the "retro-synthesis" question I recently asked. Thanks to all who have responded. I have edited some of the answers and so I take full responsibility for any errors. If I get any more answers, I will re-post summary. << Tue Jul 15 16:50:53 CDT 1997 >> Execute Summary of Answers 1) SYNGEN, Jim Hendrickson, Brandeis University 2) CAMEO, Bill Jorgensen, Yale 3) SYNTREE, Commerical Software, Vendor? 4) SYNLIB, Dan Chodosh, may not exist anymore 5) REACCS, MDL 6) CAS's reaction data base 7) Chiron, Steve Hannisan (spl?) of U. of Montreal. 8) LAHSA, E.J. Corey, Harvard U. 9) Unknow, Michael Mavrovouniotis, Northwestern 10) Crossfile, Beilstein :Joe jtgolab@amoco.com (630) 961-7878 ______________________________ Original Note __________________________________ Subject: CCL:Reaction Pathway Program Author: chemistry-request (chemistry-request@www.ccl.net) at unix,sh Date: 7/14/97 4:43 PM Dear CCL Member: Do you know of any (engineering, chemistry, biological, etc) program that given a compound would suggest any and all reaction pathways toward that compound (no matter how outlandish from a thermodyanmic standpoint)? For example, given tolune, the program would suggest: 1) benzene + methane -> toluene 2) methylcyclohexane -> toluene + H2 3) methane + heat/pressure -> toluene + H2 4) ETC. Perhaps this is really a database that is part of a program. Any leads would be gratefully appreciated! Thanks. _____________________________Reply Separator_________________________________ Subject: Re: CCL:Reaction Pathway Program Author: lchen (lchen@mdli.com) at unix,mime Date: 7/14/97 5:16 PM Dear Joe: Please check the following SYNGEN site: http://syngen2.chem.brandeis.edu/syngen.html you may find something interesting you. -Lingran ********************************************************** Lingran Chen, Ph.D. Senior Scientific Programmer MDL Information Systems, Inc. 14600 Catalina Street San Leandro CA 94577 Phone: (510) 895-1313, Ext. 1305 FAX: (510) 614-3616 Email: LCHEN@MDLI.COM URL: http://www.mdli.com http://syngen2.chem.brandeis.edu/~chen/lingran.html ********************************************************** _____________________________Reply Separator_________________________________ Subject: Re: CCL:Reaction Pathway Program Author: eslone (eslone@patriot.net) at unix,mime Date: 7/14/97 6:32 PM Talk to Jim Hendrickson at Brandeis University. He has a program called SynGen. ___________________________________________________________________ J. Eric Slone Scientific Consulting Services 5500 Holmes Run Parkway, Suite 501 Alexandria, Virginia 22304-2851 Phone: (703) 461-7078 mailto:eslone@patriot.net Fax: (703) 751-6639 http://www.patriot.net/users/eslone ___________________________________________________________________ _____________________________Reply Separator_________________________________ Subject: Re: CCL:Reaction Pathway Program Author: dsmith (dsmith@CTCnet.Net) at unix,mime Date: 7/14/97 9:12 PM Joe: I am not familiar with any program that will suggest ALL reaction pathways... there are just way too many possibilities, which is why we still have synthetic organic chemists. You are probably familiar with Bill Jorgensen's CAMEO program (I hope I have the name correct), which can suggest 'reasonable' synthetic routes to various types of compounds and functionality. There is also a commercial program (not that Bill doesn't sell his programs, ;)) called SYNTREE (I believe). There were some papers about this at either the last ACS National meeting in San Francisco or at the Midland, MI, ACS Regional meeting in May. I can look for more information if you wish, but I am at home and just finishing up a vacation while I write this. Regardless, both of these programs use a combination (I believe) of data bases and "expert" algorithms to select likely reactions. I don't know of anything that will give you all possible routes, except perhaps an aggressive undergraduate who has just finished his/her organic final exam. There was also SYNLIB that came from the late Dan Chodosh... I don't know if anyone picked up that program so I can't tell you if it still exists. This was purely data base based and matched based on user-defined descriptors, if I remember correctly from my postdoc days. MDL REACCS and CAS's reaction data base are two others that come to mind. I would also love to hear from anyone else about similar programs. Please post to CCL rather than just to Joe. Doug Smith -- Dr. Douglas A. Smith, President and CEO | voice: (814) 255-7859 The DASGroup, Inc. | fax: (814) 255-3517 1732 Lyter Drive, 2nd Floor | email: dsmith@dasgroup.com Johnstown, PA 15905 | WWW: http://www.dasgroup.com Contract R&D specialists in modeling, simulation, synthesis and risk assessment for chemistry, materials science, and biotechnology. _____________________________Reply Separator_________________________________ Subject: Re: CCL:Reaction Pathway Program Author: Willie (Willie@microsimulations.com) at unix,mime Date: 7/15/97 1:12 AM Joe, Two programs that can do retrosynthetic analysis, 1. Chiron, from Prof. Steve Hannisan (wrong spelling?) of U. of Montreal. 2. LAHSA, from prof. E.J. Corey of Harvard U. -- Willie Cui, Ph.D. voice 201-512-0486 MicroSimulations fax: 201-512-0489 478 Green Mountain Rd. email: willie@microsimulations.com Mahwah, NJ 07430 URL: http://www.microsimulations.com _____________________________Reply Separator_________________________________ Subject: RE: Reaction Pathway Program Author: RICHEYFA (RICHEYFA@ucarb.com) at unix,mime Date: 7/15/97 6:12 AM Hi, Joe, I had a similar question when looking for new routes to commodity chemicals. I found references to techniques for making expensive [usually pharmaceutical] chemicals which would take a target structure and elaborate[!] multistep pathways from known precursors. I think one was E.J. Corey's group's product. At least one of these gave synthetically viable guesses for transformations so probably weeded out a lot of the thermodynamically infeasible routes. I haven't pursued this very far but was left with the feeling that there was a lot of work in the 80's and the only thing that has survived outside academe has been the pharmaceutical part. I may be wrong in this. I never did summarize my work but if you are interested I can send you references with brief comments. I wanted this approach to automate the cataloging of possible synthetic routes including finding the ones that I'd overlook because of my particular chemical background. Forrest Richey Union Carbide Corporation Technical Center Bldg 740 Room 4107 S. Charleston, WV 25303 (304)747-4964 Two things happen when you reach fifty, and if I could remember one, I wouldn't worry about the other two. _____________________________Reply Separator_________________________________ Subject: Reaction Pathways Author: burkhart (burkhart@goodyear.com) at unix,mime Date: 7/15/97 9:00 AM Hi Joe, If I'm not mistaken, Prof. Bill Jorgensen's group @Yale worked on a program called CAMEO. As I remember it, they were trying to use it as a reaction chemistry "assistant"--but I'm not sure how far they got. ----------------------------------+------------------------------------ Papernet: Craig W. Burkhart | Baseball & summer--What could be Goodyear Research | better? The birds are singing and 142 Goodyear Blvd. | the BATS are out! Akron, OH 44305 | Indians update: 48-37 (.564) Mouthnet: 330.796.3163 | 'Best little .500 club' $60 mil Faxnet: .3304 | can buy... (swampland, anyone?) Internet: cburkhart@goodyear.com | Pitching REALLY Stinks!!! UGH! ----------------------------------+------------------------------------ _____________________________Reply Separator_________________________________ Subject: Re: CCL-Reaction Pathway Pro Author: mnliebman (mnliebman@vysis.com) at unix,sh Date: 7/15/97 9:59 AM RE>CCL:Reaction Pathway Program 7/15/97 Joe try contactine Michael Mavrovouniotis at Northwestern- mlmavro@nwu.edu I think Michael 271 7190 _____________________________Reply Separator_________________________________ Subject: Your e-mail to CCL Author: pierre (pierre@mdli.com) at unix,mime Date: 7/15/97 10:14 AM Dear Joe, I received a copy of your e-mail attached at the end of my reply. You may remember that we talked on the phone a few month ago. Although my answer is obviously biased by the fact that I work for MDL, my experience after 9 years working with the large pharma and chemical industries in Europe and in the US is that there seems to be no good way to have a prediction program. A lot of companies have tried, and they have ended up licensing our databases or other (like Beilstein Crossfire). The advantage they have found in our system, compared to other database systems, (especially since we introduced ISIS, the client server system we provide now) is the flexibility of our querying interface. You can search not only on exact reactions, but also on things like " find an example of a reaction where this fragment is formed". Or "find an example of a reaction using these conditions where a fragment is unaltered". As an example, to address your query below, we would draw the toluene, and define it as a product, and then we would perform a search known as "structure as product not as reactant, or "sub-structure as product, not as reactant". Which basically defines that the toluene has to be formed during the reaction. You could also refine the query by specifying certain classes of reactions you do not want (list catalysts that are expensive etc). Running the query you use as an example on our databases leaded to 113 reactions out of 107 publications. The query was exclusively dealing with the toluene as product, no substituted toluene was allowed. In some of these reactions the benzene is a by product, and probably a lot of them are dealing with cleavage from a larger structure, but these reactions could still be of interest, you would have to judge. >> [Parts of Original Message Edited/Deleted] << Sincerely Pierre Allemand Ph.D. Senior Account Manager >-- END -- :Joe jtgolab@amoco.com (630) 961-7878 +---------------------------------------------------------+ | You can pick your friends but you can't pick your nose. | +---------------------------------------------------------+ From MAILER-DAEMON@www.ccl.net Tue Jul 15 19:07:21 1997 Received: from schiele for MAILER-DAEMON@www.ccl.net by www.ccl.net (8.8.3/950822.1) id SAA03163; Tue, 15 Jul 1997 18:59:58 -0400 (EDT) Received: by schiele (950911.SGI.8.6.12.PATCH825/940406.SGI.AUTO) id BAA19483; Wed, 16 Jul 1997 01:00:15 +0200 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9707160100.ZM19481@eros.ccc.uni-erlangen.de> Date: Wed, 16 Jul 1997 01:00:11 -0600 In-Reply-To: Richard Bone "CCL:SMILES Database?" (Jul 11, 14:39) References: <199707111412.OAA28712@petersgate.proteus.co.uk> Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: Richard Bone Subject: Re: CCL:SMILES Database? Cc: CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit On Jul 11, 14:39, Richard Bone wrote: > Subject: CCL:SMILES Database? > > Does anyone know of a public-domain database of SMILES strings for commonly- > occurring small organic molecules and functional groups? I'm looking for > something containing several hundred or more species. > > It would need to be something in ASCII format, for general utility, i.e., not > in a format specific to some commercial package. > > Richard Bone > Well, I made you one in a few minutes. You find it at ftp://schiele.organik.uni-erlangen.de/pub/nci/nci4000.smi.gz It is small, just 45K. These are the first 4000 entries from the NCI database which do not contain a metal atom (just to keep the structures simple). Because the original file does not contain stereochemical information, the SMILES strings do not have any either. Behind the SMILES string, separated by a tab, the corresponding CAS number is appended. Most SMILES readers will understand that only the first word is the string and ignore the second part or even assign it to a name property. At the same site you will find the full original NCI database as SD file, and the same structures in another file with added 3D coordinates. The full database contains about 126.705 structures and is public domain. Since we just has on the CCL a discussion about using scripting languages to control modular programs, here is the short CACTVS Tcl script used to produce this file: set outhandle [molfile open "|gzip >nci4000.smi.gz" w \ format smiles \ hydrogens add \ writeflags {writearo writename}] set cnt 0 molfile loop ftp://schiele/pub/nci/nciopen.mol.gz enshandle { if {![lempty [ens atoms $enshandle metal]]} continue ens assign $enshandle E_*CAS_RN* E_NAME molfile write $outhandle $enshandle if {[incr cnt]>=4000} break } BTW, beware if you want to repeat this with the popular Babel conversion program (V1.6). First, the program will not be able to read the original datafile because it contains neither display coordinates nor 3D coordinates, only connectivity. Babel will report a cryptic message 'No atoms found in this structure', although the file is syntactically correct. You must use the 3D-enhanced file. Second, from the first 1000 records the CACTVS results and Babel results are structurally different for 69 records (7%). As far as I have checked, this is all because the MDL read routines of Babel do not read the atomic charge field in the SD file. This is of course deadly when reading back the SMILES string without charge information, since the SMILES standard contains hydrogen addition rules. So a nitro group which was coded with a positively charged N and a negatively charged O will suddenly contain an N-O-H group because the SMILES string N(=O)O without charge information demands the addition of a hydrogen atom to the single-bonded oxygen. The N will also receive an extra hydrogen, or end up as a radical, depending on your reader software. -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu