From owner-chemistry@ccl.net Thu Sep 15 02:32:13 2005 From: "CCL" To: CCL Subject: CCL: W:Disclose your data, or not publish ! Message-Id: <-29168-050915023059-4777-ETc9kVj+VqHwexQEb/3djg###server.ccl.net> X-Original-From: "S.I.Gorelsky" Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 14 Sep 2005 23:30:54 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "S.I.Gorelsky" [gorelsky###stanford.edu] I wonder since when has CCL started to accept anonymous submissions ? (I am not mad enough to assume that there is an actual person, Chemical Bond) When someone is screaming about disclosing all the data and making accusations, he/she should, in the first place, have enough character to disclose his/her actual name instead of hiding under the made-up name from Yahoo. May I suggest that such e-mail should not be distributed by CCL. S.Gorelsky P.S. I am not in business of doing any protein-ligand docking & scoring studies. On Wed, 14 Sep 2005, CCL wrote: > > Sent to CCL by: "Chemical Bond" [chemicalbond001|"|yahoo.com] > Everyday, tons of new publications come out. > > Although there are some nice papers with novel ideas or new results, many times we see people are almost trying to repeat others' work, pouring the same water into the old bottle. The only goal for that seems to be just publishing, for tenure in academia or for promotion in industry, or for boasting some software! > > One obvious case is in the community of protein-ligand docking & scoring. Are not we tired of those studies? > > Yes, we are! We always see extremely excellent results published in papers or ACS talks by different kinds of people, especially those who made software and make money! > > The reality is that none of them really works! Not at all! Ask anyone in a big pharma doing docking & scoring business, see what you would get the performance for a scoring function applied in a real drug design case? > > That's all about business, to keep software company making money and keep computational chemists' in jobs. > > Fine, but in order to promote the advancement of science, we had better do something novel than that. I hope people in this list could make more suggestions, and here I like to propose a little to the community: > > To disclose your data, or not publish. > > (1)Disclose all numerical data files, input, output files & parameters in the publication (paper or talk), in the sense that at least it could be reproduced (statistically meaningful) if anyone else is trying to do it using the same software or method. So no one can be lying any more. > > (2)This could save much time for many other researchers on preparing testing data, so that new ideas could get tested & improved very quickly; > > (3)This could help build a very rich resource for research, things like docking decoys for many many protein targets and ligands; the data itself would be worth a million dollars ?! > > .. ... > > All in all, theose really good methods or software will survive without questions, and new technologies would evolve in the speed-of-light, we would see fewer but more meaningful new papers every day, what a relif from tons of new electronic papers... ... so that in the end science would get advanced by taking advantage of everyone's strength, and life could be improved in a different way...... > > Thanks for your attention! > -Bond> > > ---------------------------------------------------------------- Dr S.I. Gorelsky, Department of Chemistry, Stanford University Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA Phone: (650) 723-0041. Fax: (650) 723-0852. ---------------------------------------------------------------- From owner-chemistry@ccl.net Thu Sep 15 03:46:44 2005 From: "CCL" To: CCL Subject: CCL: W:Disclose your data, or not publish ! Message-Id: <-29169-050915015241-2973-ETc9kVj+VqHwexQEb/3djg*_*server.ccl.net> X-Original-From: Egon Willighagen Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="utf-8" Date: Thu, 15 Sep 2005 06:59:25 +0200 MIME-Version: 1.0 Sent to CCL by: Egon Willighagen [egonw*_*sci.kun.nl] On Thursday 15 September 2005 05:20, CCL wrote: > To disclose your data, or not publish. I think that it is more important to fully publish in detail what one has actually *done*. In wet chemistry terms, I don't need a sample of the starting material; I want a good description of the reaction conditions, solvents, etc. In terms of our bussines: I want access to the exact program details: the source code is most useful here. Hence the importance of open source! > (1)Disclose all numerical data files, input, output files & parameters in > the publication (paper or talk), in the sense that at least it could be > reproduced (statistically meaningful) if anyone else is trying to do it > using the same software or method. So no one can be lying any more. > > (2)This could save much time for many other researchers on preparing > testing data, so that new ideas could get tested & improved very quickly; > > (3)This could help build a very rich resource for research, things like > docking decoys for many many protein targets and ligands; the data itself > would be worth a million dollars ?! Thanx for this call. It's important we computer chemists (chemoinformatician, computation chemists, and whoever...) that we start work on reproducable science again. If we can reproduce experiments, we can't falsify it. When did we start disregard this important scientific step forward ?! Egon -- e.willighagen*_*science.ru.nl PhD student on Molecular Representation in Chemometrics Radboud University Nijmegen http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 From owner-chemistry@ccl.net Thu Sep 15 04:34:20 2005 From: "CCL" To: CCL Subject: CCL: W:Disclose your data, or not publish ! Message-Id: <-29170-050915043300-9700-ETc9kVj+VqHwexQEb/3djg]~[server.ccl.net> X-Original-From: Alessandro Contini Content-transfer-encoding: 8BIT Content-type: text/plain; charset=ISO-8859-15 Date: Thu, 15 Sep 2005 10:32:55 +0200 MIME-version: 1.0 Sent to CCL by: Alessandro Contini [alessandro.contini]~[unimi.it] I agree with Dr. Gorelsky! the points evidenced by "Dr. Bond" could be right, I guess he/she just got burned by some unreproducible results (and I think that not only the field of theoretical/medicinal chemistry lets you experience such emotion...) and aims to a return of morals in science. However, for honesty, when such charges are made they should be signed by a real person. regards Alessandro Contini Il giorno mer, 14/09/2005 alle 23.30 -0700, CCL ha scritto: > Sent to CCL by: "S.I.Gorelsky" [gorelsky###stanford.edu] > > > I wonder since when has CCL started to accept anonymous > submissions ? (I am not mad enough to assume that there is an actual > person, Chemical Bond) > > When someone is screaming about disclosing all the data and making > accusations, he/she should, in the first place, have enough character to > disclose his/her actual name instead of hiding > under the made-up name from Yahoo. > > May I suggest that such e-mail should not be distributed by CCL. > > S.Gorelsky > > P.S. I am not in business of doing any protein-ligand docking & scoring > studies. > > > > On Wed, 14 Sep 2005, CCL wrote: > > > > > Sent to CCL by: "Chemical Bond" [chemicalbond001|"|yahoo.com] > > Everyday, tons of new publications come out. > > > > Although there are some nice papers with novel ideas or new results, many times we see people are almost trying to repeat others' work, pouring the same water into the old bottle. The only goal for that seems to be just publishing, for tenure in academia or for promotion in industry, or for boasting some software! > > > > One obvious case is in the community of protein-ligand docking & scoring. Are not we tired of those studies? > > > > Yes, we are! We always see extremely excellent results published in papers or ACS talks by different kinds of people, especially those who made software and make money! > > > > The reality is that none of them really works! Not at all! Ask anyone in a big pharma doing docking & scoring business, see what you would get the performance for a scoring function applied in a real drug design case? > > > > That's all about business, to keep software company making money and keep computational chemists' in jobs. > > > > Fine, but in order to promote the advancement of science, we had better do something novel than that. I hope people in this list could make more suggestions, and here I like to propose a little to the community: > > > > To disclose your data, or not publish. > > > > (1)Disclose all numerical data files, input, output files & parameters in the publication (paper or talk), in the sense that at least it could be reproduced (statistically meaningful) if anyone else is trying to do it using the same software or method. So no one can be lying any more. > > > > (2)This could save much time for many other researchers on preparing testing data, so that new ideas could get tested & improved very quickly; > > > > (3)This could help build a very rich resource for research, things like docking decoys for many many protein targets and ligands; the data itself would be worth a million dollars ?! > > > > .. ... > > > > All in all, theose really good methods or software will survive without questions, and new technologies would evolve in the speed-of-light, we would see fewer but more meaningful new papers every day, what a relif from tons of new electronic papers... ... so that in the end science would get advanced by taking advantage of everyone's strength, and life could be improved in a different way...... > > > > Thanks for your attention! > > -Bond> > > > > > > ---------------------------------------------------------------- > Dr S.I. Gorelsky, Department of Chemistry, Stanford University > Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA > Phone: (650) 723-0041. Fax: (650) 723-0852. > ----------------------------------------------------------------> > > -- Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Universitą degli Studi di Milano, Facoltą di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini]~[unimi.it From owner-chemistry@ccl.net Thu Sep 15 05:02:37 2005 From: "CCL" To: CCL Subject: CCL: Basis set for B3LYP Message-Id: <-29171-050915045549-20304-ETc9kVj+VqHwexQEb/3djg^_^server.ccl.net> X-Original-From: "Igor Avilov" content-class: urn:content-classes:message Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="ISO-2022-JP" Date: Thu, 15 Sep 2005 10:08:10 +0200 MIME-Version: 1.0 Sent to CCL by: "Igor Avilov" [avilovi^_^averell.umh.ac.be] Dear Telkuni Tsuru, A couple of times I accidentally ran geometry optimizations of poly-atomic molecules with STO-3G basis (with B3LYP functional). The results were always meaningless. But already 6-31G did a good job, even for calculations of excited states. The choice of the basis set depends on molecular property in question and accuracy needed. Best regards, Igor Avilov. From owner-chemistry@ccl.net Thu Sep 15 05:27:51 2005 From: "CCL" To: CCL Subject: CCL: Basis set for B3LYP Message-Id: <-29172-050915052353-2638-ETc9kVj+VqHwexQEb/3djg*|*server.ccl.net> X-Original-From: "Jens Spanget-Larsen" Date: Thu, 15 Sep 2005 11:23:09 +0200 Sent to CCL by: "Jens Spanget-Larsen" [spanget*|*virgil.ruc.dk] Dear Tsuru, with respect to basis sets developed at the density functional level of theory, I draw your attention to the work of Frank Jensen: F. Jensen "Polarization Consistent Basis Sets. Principles." J. Chem. Phys. 115 (2001) 9113-9125 F. Jensen "Polarization Consistent Basis Sets. II. Estimating the Kohn-Sham Basis Set Limit." J. Chem. Phys. 116 (2002) 7372-7279 F. Jensen "Polarization Consistent Basis Sets III. The Importance of Diffuse Functions." J. Chem. Phys. 117 (2002) 9234-9240 Yours, Jens >--< >---------------------------------------------------------< JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget*|*ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget >---------------------------------------------------------< From owner-chemistry@ccl.net Thu Sep 15 06:07:29 2005 From: "CCL" To: CCL Subject: CCL: RE: W:Disclose your data, or not publish ! Message-Id: <-29173-050915054848-22311-ETc9kVj+VqHwexQEb/3djg__server.ccl.net> X-Original-From: Valentin Ananikov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Thu, 15 Sep 2005 13:06:42 +0400 MIME-Version: 1.0 Sent to CCL by: Valentin Ananikov [val__ioc.ac.ru] > Sent to CCL by: "Chemical Bond" [chemicalbond001|"|yahoo.com] > Everyday, tons of new publications come out. > Would it be possible to develop a numeric criterion to estimate the quality of publications? Without clear criteria for estimating quality, clarity, impact and significance of the publications such discussions tend to be rather philosophical and useless. I am really interesting if there was any research addressing this problem? Best regards, Valentin. Valentin Ananikov Zelinsky Institute of Organic Chemistry, Moscow Russian Academy of Sciences. From owner-chemistry@ccl.net Thu Sep 15 07:06:32 2005 From: "CCL" To: CCL Subject: CCL: transition metals Message-Id: <-29174-050915030419-15277-ETc9kVj+VqHwexQEb/3djg##server.ccl.net> X-Original-From: Goedele Roos Date: Thu, 15 Sep 2005 08:10:55 +0200 (MEST) Sent to CCL by: Goedele Roos [groos##vub.ac.be] Dear all, what is a good DFT functional touse with transitionmetals from the first d-block? Can I use B3LYP or rather BP86? Thank you for your advice, Goedele Drs. Goedele Roos Dienst Algemene Chemie (ALGC) Vrije Universiteit Brussel (VUB) Pleinlaan 2 B-1050 Brussels Tel: 0032-2-629 35 16 Fax: 0032-2-629 33 17 From owner-chemistry@ccl.net Thu Sep 15 08:54:03 2005 From: "CCL" To: CCL Subject: CCL: double vs. split valence basis sets Message-Id: <-29183-050915033717-23677-ETc9kVj+VqHwexQEb/3djg*o*server.ccl.net> X-Original-From: "Noko Phala" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 15 Sep 2005 09:01:10 +0200 MIME-Version: 1.0 Sent to CCL by: "Noko Phala" [nphala*o*angloresearch.com] I always thought that the notation is pretty straightforward, viz. describe each core orbital by a contraction of 6 Gaussians, and each valence orbital by two orbitals - one made out of a contraction of 3 Gaussians and another by a single Gaussian. So, it is indeed a split-valence basis, the DZ reference applies to the valence orbitals only. -----Original Message----- > From: owner-chemistry*o*ccl.net [mailto:owner-chemistry*o*ccl.net] Sent: Wednesday, September 14, 2005 6:49 PM To: Noko Phala Subject: CCL: double vs. split valence basis sets Sent to CCL by: Joslyn Y Kravitz [jyudenfr*|*umich.edu] Hello all, I have a question of semantics that I would appreciate opinions on. I have frequently seen the 6-31G* type basis sets referred to as double-zeta basis sets. Technically, they are not double zeta basis sets, but rather are split-valence basis sets because they don't use two basis functions for the core orbitals. Am I splitting hairs here or is it actually important that the distinction is made? Thanks, Joslyn Kravitz From owner-chemistry@ccl.net Thu Sep 15 08:54:01 2005 From: "CCL" To: CCL Subject: CCL: W:Disclose your data, or not publish ! Message-Id: <-29180-050915054301-21981-ETc9kVj+VqHwexQEb/3djg:-:server.ccl.net> X-Original-From: "Noko Phala" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 15 Sep 2005 11:42:45 +0200 MIME-Version: 1.0 Sent to CCL by: "Noko Phala" [nphala:-:angloresearch.com] Very fair point. On the other hand, is this not what the peer-reviewing/refereeing process is for? It is still puzzling that one finds, sometimes in reputable journals, work where it is not entirely clear what exactly was done to arrive at the results. Point taken, "Dr Bond". Noko Phala -----Original Message----- > From: owner-chemistry:-:ccl.net [mailto:owner-chemistry:-:ccl.net] Sent: Thursday, September 15, 2005 10:33 AM To: Noko Phala Subject: CCL: W:Disclose your data, or not publish ! Sent to CCL by: Alessandro Contini [alessandro.contini]~[unimi.it] I agree with Dr. Gorelsky! the points evidenced by "Dr. Bond" could be right, I guess he/she just got burned by some unreproducible results (and I think that not only the field of theoretical/medicinal chemistry lets you experience such emotion...) and aims to a return of morals in science. However, for honesty, when such charges are made they should be signed by a real person. regards Alessandro Contini Il giorno mer, 14/09/2005 alle 23.30 -0700, CCL ha scritto: > Sent to CCL by: "S.I.Gorelsky" [gorelsky###stanford.edu] > > > I wonder since when has CCL started to accept anonymous > submissions ? (I am not mad enough to assume that there is an actual > person, Chemical Bond) > > When someone is screaming about disclosing all the data and making > accusations, he/she should, in the first place, have enough character to > disclose his/her actual name instead of hiding > under the made-up name from Yahoo. > > May I suggest that such e-mail should not be distributed by CCL. > > S.Gorelsky > > P.S. I am not in business of doing any protein-ligand docking & scoring > studies. > > > > On Wed, 14 Sep 2005, CCL wrote: > > > > > Sent to CCL by: "Chemical Bond" [chemicalbond001|"|yahoo.com] > > Everyday, tons of new publications come out. > > > > Although there are some nice papers with novel ideas or new results, many times we see people are almost trying to repeat others' work, pouring the same water into the old bottle. The only goal for that seems to be just publishing, for tenure in academia or for promotion in industry, or for boasting some software! > > > > One obvious case is in the community of protein-ligand docking & scoring. Are not we tired of those studies? > > > > Yes, we are! We always see extremely excellent results published in papers or ACS talks by different kinds of people, especially those who made software and make money! > > > > The reality is that none of them really works! Not at all! Ask anyone in a big pharma doing docking & scoring business, see what you would get the performance for a scoring function applied in a real drug design case? > > > > That's all about business, to keep software company making money and keep computational chemists' in jobs. > > > > Fine, but in order to promote the advancement of science, we had better do something novel than that. I hope people in this list could make more suggestions, and here I like to propose a little to the community: > > > > To disclose your data, or not publish. > > > > (1)Disclose all numerical data files, input, output files & parameters in the publication (paper or talk), in the sense that at least it could be reproduced (statistically meaningful) if anyone else is trying to do it using the same software or method. So no one can be lying any more. > > > > (2)This could save much time for many other researchers on preparing testing data, so that new ideas could get tested & improved very quickly; > > > > (3)This could help build a very rich resource for research, things like docking decoys for many many protein targets and ligands; the data itself would be worth a million dollars ?! > > > > .. ... > > > > All in all, theose really good methods or software will survive without questions, and new technologies would evolve in the speed-of-light, we would see fewer but more meaningful new papers every day, what a relif from tons of new electronic papers... ... so that in the end science would get advanced by taking advantage of everyone's strength, and life could be improved in a different way...... > > > > Thanks for your attention! > > -Bond> > > > > > > ---------------------------------------------------------------- > Dr S.I. Gorelsky, Department of Chemistry, Stanford University > Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA > Phone: (650) 723-0041. Fax: (650) 723-0852. > ----------------------------------------------------------------> > > -- Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Universitą degli Studi di Milano, Facoltą di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini:-:unimi.it From owner-chemistry@ccl.net Thu Sep 15 08:54:02 2005 From: "CCL" To: CCL Subject: CCL: transition metals Message-Id: <-29178-050915082731-2890-ETc9kVj+VqHwexQEb/3djg()server.ccl.net> X-Original-From: "Shireen Al Falah" Content-Type: text/plain; format=flowed Date: Thu, 15 Sep 2005 13:40:23 +0200 Mime-Version: 1.0 Sent to CCL by: "Shireen Al Falah" [shireenfalah()hotmail.com] Hi, I have used BP86 for chrmoium and it was good. I think you can use it. Actually the DZ basis was compareble to the cc-pvdz. regards From owner-chemistry@ccl.net Thu Sep 15 08:54:01 2005 From: "CCL" To: CCL Subject: CCL: Computational drug design blues Message-Id: <-29176-050914230925-28822-ETc9kVj+VqHwexQEb/3djg(!)server.ccl.net> X-Original-From: Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 15 Sep 2005 11:36:16 +1000 MIME-Version: 1.0 Sent to CCL by: [Mitchell.Polley(!)csiro.au] I think they were referring to the Synthetic Feasibility score in the "LeapFrog" module of Sybyl by Tripos (www.tripos.com). I don't think it was ever published, as it was only ever a very rough guideline. You may be able to get more information from the Tripos website or technical support group (again through their website). Regards, Mitch > Sent to CCL by: Andrew Fant [fant{:}pobox.com] > By any chance, can you give a pointer into the literature on > that index? > I'm not able to get into chemical abstracts at the moment, but both > google and google scholar had no hits at all on "synthetic feasibility > index" > > Thanks, > Andy > > > CCL wrote: > > Sent to CCL by: "Srinivasan Parthiban" [parthiban-#-gvkbio.com] > > There must be few programs available on estimating the Synthetic > > feasibility Index. I have used it few years back using > Tripos software. It > > is purely an empirical method where the calculation is > based on the number > > of rings and the functional groups present in the molecule > and so on. > > - Parthi > > ----------------------------------- > > Srinivasan Parthiban > > Director-Informatics > > GVKBIO > > Vukan Towers > > #81 Tirumalai Pillai Road > > T. Nagar, Chennai 600 017 INDIA > > Ph: +91-44-5212 5522/3399 > > www.gvkbio.com > > > > -= This is automatically added to each message by the mailing > script =- > To send e-mail to subscribers of CCL put the string CCL: on > your Subject: line> > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST(!)ccl.net> > If your is mail bouncing from ccl.net domain due to spam > filters, please> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > From owner-chemistry@ccl.net Thu Sep 15 08:54:03 2005 From: "CCL" To: CCL Subject: CCL: W:Disclose your data, or not publish ! Message-Id: <-29182-050915082842-2957-ETc9kVj+VqHwexQEb/3djg(a)server.ccl.net> X-Original-From: "Stephen P. Molnar, Ph.D." Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Thu, 15 Sep 2005 07:27:58 -0400 Mime-Version: 1.0 Sent to CCL by: "Stephen P. Molnar, Ph.D." [s.molnar(a)sbcglobal.net] I concur. At 02:30 AM 9/15/2005, you wrote: >Sent to CCL by: "S.I.Gorelsky" [gorelsky###stanford.edu] > > >I wonder since when has CCL started to accept anonymous >submissions ? (I am not mad enough to assume that there is an actual >person, Chemical Bond) > >When someone is screaming about disclosing all the data and making >accusations, he/she should, in the first place, have enough character to >disclose his/her actual name instead of hiding >under the made-up name from Yahoo. > >May I suggest that such e-mail should not be distributed by CCL. > >S.Gorelsky > >P.S. I am not in business of doing any protein-ligand docking & scoring >studies. > > > >On Wed, 14 Sep 2005, CCL wrote: > > > > > Sent to CCL by: "Chemical Bond" [chemicalbond001|"|yahoo.com] > > Everyday, tons of new publications come out. > > > > Although there are some nice papers with novel ideas or new results, > many times we see people are almost trying to repeat others' work, > pouring the same water into the old bottle. The only goal for that seems > to be just publishing, for tenure in academia or for promotion in > industry, or for boasting some software! > > > > One obvious case is in the community of protein-ligand docking & > scoring. Are not we tired of those studies? > > > > Yes, we are! We always see extremely excellent results published in > papers or ACS talks by different kinds of people, especially those who > made software and make money! > > > > The reality is that none of them really works! Not at all! Ask anyone > in a big pharma doing docking & scoring business, see what you would get > the performance for a scoring function applied in a real drug design case? > > > > That's all about business, to keep software company making money and > keep computational chemists' in jobs. > > > > Fine, but in order to promote the advancement of science, we had better > do something novel than that. I hope people in this list could make more > suggestions, and here I like to propose a little to the community: > > > > To disclose your data, or not publish. > > > > (1)Disclose all numerical data files, input, output files & parameters > in the publication (paper or talk), in the sense that at least it could > be reproduced (statistically meaningful) if anyone else is trying to do > it using the same software or method. So no one can be lying any more. > > > > (2)This could save much time for many other researchers on preparing > testing data, so that new ideas could get tested & improved very quickly; > > > > (3)This could help build a very rich resource for research, things like > docking decoys for many many protein targets and ligands; the data itself > would be worth a million dollars ?! > > > > .. ... > > > > All in all, theose really good methods or software will survive without > questions, and new technologies would evolve in the speed-of-light, we > would see fewer but more meaningful new papers every day, what a relif > from tons of new electronic papers... ... so that in the end science > would get advanced by taking advantage of everyone's strength, and life > could be improved in a different way...... > > > > Thanks for your attention! > > -Bond> > > > > > >---------------------------------------------------------------- > Dr S.I. Gorelsky, Department of Chemistry, Stanford University > Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA > Phone: (650) 723-0041. Fax: (650) 723-0852. >----------------------------------------------------------------Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Multivariant and stochastic http://www.geocities.com/FoundationForChemistry From owner-chemistry@ccl.net Thu Sep 15 08:54:03 2005 From: "CCL" To: CCL Subject: CCL: W:Computational drug design blues Message-Id: <-29184-050915082911-3007-ETc9kVj+VqHwexQEb/3djg#%#server.ccl.net> X-Original-From: Gary Breton Content-transfer-encoding: 7bit Content-type: text/plain; charset="US-ASCII" Date: Thu, 15 Sep 2005 08:18:27 -0400 Mime-version: 1.0 Sent to CCL by: Gary Breton [gbreton#%#berry.edu] Christian, Thank you for your comments. I would be very interested in obtaining a reprint of your Mini-review from Medicinal Chemistry if you could send it to me. I had never really considered this subject before,but I find it very interesting. Thanks! Gary W. Breton Associate Professor Department of Chemistry Berry College PO Box 495016 Mount Berry, GA 30149 As other people have mentioned estimating synthetic accessibility is a > difficult problem particularly when considering compounds designed by people > or computers with little knowledge of synthetic chemistry. > > A number of groups working on de novo design programs have attempted to > include synthetic accessibility in their systems to various levels. These > include SPROUT (from Peter Johnson's group in Leeds) and SkelGen (from Denovo > Pharmaceuticals). There have also been a number of methods applied to > estimating synthetic accessibility including expert systems (CAESA, again from > Leeds) and neural networks (Takaoka et al, JCICS, 2003, 42, 1269-1275). We > recently wrote a review paper on the subject (Mini-Reviews in Medicinal > Chemistry, Volume 4, No. 6, 2004, 681-692) which covers a wide range of > techniques and uses. > > This is certainly an important area and anything that that could reliably stop > us suggesting synthetically infeasible compounds to medicinal chemists would > be very welcome. > > Best of luck, > > Christian > >> -----Original Message----- >> From: CCL [mailto:owner-chemistry#%#ccl.net] >> Sent: Wednesday, 14 September, 2005 7:10 AM >> To: Baber, Christian >> Subject: CCL: W:Computational drug design blues >> >> >> >> Sent to CCL by: "Sandeep Kumar" [kumarsan\a/jhu.edu] >> Dear CCLers: >> >> I need some advice about the drug discovery/design. Using >> structure based design, one could develope several potential >> small molecular inhibitors/drugs for a given protein target. >> Many of these compounds may appear very attractive as they >> satisfy all lipinski's rules and your requirements for >> selectivity/specificity and may even have desirable >> solubility/ADME profiles. These days its possible to >> incorporate all these features right at the computational >> design stage. However, the organic synthesis of the compound >> still remains a bottleneck as it turns out that many of the >> designed compounds are 'hard' to synthesize or may require >> many steps of synthesis. I was wondering if there are some >> simple guidelines in the form of literature or 'hands on' >> experience available which could tell the >> computational/medicinal chemist whether a designed compound >> would be easy or hard to synthesize before he/she talks to >> the organic chemist. >> >> All your responses are greatly appreciated. >> >> Yours sincerely >> Sandeep Kumar, Ph.D. >> Johns Hopkins University, >> Dept. of Biology, >> 106 Mudd Hall, >> 3400 N. Charles St. >> Baltimore, MD 21218. >> Phone: 410-516-8433 >> Email: kumarsan#%#jhu.edu >> >> >> >> -= This is automatically added to each message by the mailing >> script =- >> To send e-mail to subscribers of CCL put the string CCL: on >> your Subject: line> >> Send your subscription/unsubscription requests to: >> CHEMISTRY-REQUEST#%#ccl.net>> >> If your is mail bouncing from ccl.net domain due to spam >> filters, please>> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ >> -+-+-+-+-+ >> >> >> >> From owner-chemistry@ccl.net Thu Sep 15 08:54:02 2005 From: "CCL" To: CCL Subject: CCL: W:single crystal X-ray diffraction simulator Message-Id: <-29179-050915060624-23153-ETc9kVj+VqHwexQEb/3djg##server.ccl.net> X-Original-From: "Pablo Vitoria" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Thu, 15 Sep 2005 11:30:27 +0200 MIME-Version: 1.0 Sent to CCL by: "Pablo Vitoria" [pablo.vitoria##ehu.es] Hi Constantinos, You can obtain diffraction patterns with PLATON (http://www.cryst.chem.uu.nl/platon/) starting from a .cif file and other crystallographic formats. A Windows version is available at http://www.chem.gla.ac.uk/~louis/software/platon/index.html. Best regards Pablo ----- Original Message ----- > From: "CCL" To: "Vitoria, Pablo " Sent: Thursday, September 15, 2005 5:08 AM Subject: CCL: W:single crystal X-ray diffraction simulator > > Sent to CCL by: "Constantinos Zeinalipour-Yazdi" > [czeinali{}chem.ucsd.edu] > Greetings, everyone, > > I am looking for a free software that can simulate single crystal X-ray > diffraction patterns given the unit cell parameters and the cartesian or > fractional coordinates of the symmetry unique atoms in the unit cell. > Preferable in .CIF format but other formats are also welcome. > The program should be windows or linux compatible. > Any suggestions are welcome. > > best wishes, Constantinos> To send e-mail to subscribers of CCL put the string CCL: on your Subject: > line> > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST##ccl.net> > From owner-chemistry@ccl.net Thu Sep 15 08:54:03 2005 From: "CCL" To: CCL Subject: CCL: Computational drug design blues Message-Id: <-29181-050915003839-31425-ETc9kVj+VqHwexQEb/3djg%server.ccl.net> X-Original-From: "James T Metz" Content-Type: multipart/alternative; boundary="=_alternative 0005F6EB8625707D_=" Date: Wed, 14 Sep 2005 20:04:52 -0500 MIME-Version: 1.0 Sent to CCL by: "James T Metz" [james.metz%abbott.com] This is a multipart message in MIME format. --=_alternative 0005F6EB8625707D_= Content-Type: text/plain; charset="us-ascii" CCL Colleagues, Regarding prediction of synthetic difficulty, one approach to this problem might involve constructing a descriptor-based QSAR model of compound (catalogue) cost ($Cost/mg) or perhaps log ($Cost/mg). You might end up with an equation something like: Log($Cost/mg) = 0.5 * # chiral centers + 0.7 # large rings + # spiro-fused centers + ... This idea, of course, is based on an assumption that synthetic difficulty roughly equates to economics for thousands of compounds. Economics roughly equates to how difficult it is to make the molecule. There are of course problems with this approach. One obvious problematic group of compounds would be natural products. Some natural products have exquisitely complicated molecular skeletons, yet are obtained relatively inexpensively by extraction methods. So the cost for certain molecules will not reflect synthetic difficulty. You may (?) need to exclude those compounds > from your training set. But, it might be worth trying to build the model several different ways. Sources of data are plentiful. Pick up your Aldrich catalogue and you will find plenty of structure/cost information. Probably a good idea to use the costs from a single supplier so as not to add further noise (factors) to the analysis. As a check of your final model, you might want to make cost predictions for 100 molecules or so. Then have 10 synthetic chemist friends rate the difficulty of synthesis for each compound on a scale from 1 to 5. Don't be surprised if you get very different (inconsistent) answers. You will need to do some statistical averaging here. Not to get side-tracked, but regarding the (in)consistency of chemists in judging chemical structures, please see the interesting publication from Lajiness et al. "Assessment of Consistency of Medicinal Chemists in Reviewing Sets of Compounds" J. Med. Chem. 47 (2004) 4891. An interesting statement from the abstract of this paper is, "It was found that medicinal chemists were not very consistent in the compounds they rejected as being undesirable." Regards, Jim Metz James T. Metz, Ph.D. Abbott Laboratories james.metz%abbott.com --=_alternative 0005F6EB8625707D_= Content-Type: text/html; charset="us-ascii"
CCL Colleagues,

        Regarding prediction of synthetic difficulty, one approach to this problem might involve
constructing a descriptor-based QSAR  model of compound (catalogue) cost ($Cost/mg) or perhaps log ($Cost/mg).

        You might end up with an equation something like:

        Log($Cost/mg) = 0.5 * # chiral centers + 0.7 # large rings + # spiro-fused centers + ...

        This idea, of course, is based on an assumption that synthetic difficulty roughly equates
to economics for thousands of compounds.  Economics roughly equates to how difficult it is to make the molecule.

        There are of course problems with this approach.  One obvious problematic group of compounds
would be natural products.  Some natural products have exquisitely complicated molecular skeletons, yet
are obtained relatively inexpensively by extraction methods.  So the cost for certain molecules will not
reflect synthetic difficulty.  You may (?) need to exclude those compounds from your training set.  But, it
might be worth trying to build the model several different ways.

        Sources of data are plentiful.  Pick up your Aldrich catalogue and you will find plenty of structure/cost
information.  Probably a good idea to use the costs from a single supplier so as not to add further noise (factors)
to the analysis.

        As a check of your final model, you might want to make cost predictions for 100 molecules or so.  Then have 10
synthetic chemist friends rate the difficulty of synthesis for each compound on a scale from 1 to 5.  Don't be surprised
if you get very different (inconsistent) answers.  You will need to do some statistical averaging here.

        Not to get side-tracked, but regarding the (in)consistency of chemists in judging chemical structures, please
see the interesting publication from Lajiness et al. "Assessment of Consistency of Medicinal Chemists in Reviewing
Sets of Compounds" J. Med. Chem. 47 (2004) 4891.   An interesting statement from the abstract of this paper is,

        "It was found
that medicinal chemists were not very consistent in the compounds they rejected as being
undesirable."


        Regards,
        Jim Metz
       

James T. Metz, Ph.D.
Abbott Laboratories


james.metz%abbott.com
 --=_alternative 0005F6EB8625707D_=-- From owner-chemistry@ccl.net Thu Sep 15 08:54:02 2005 From: "CCL" To: CCL Subject: CCL: Re: Computational drug design blues Message-Id: <-29177-050915020221-3410-ETc9kVj+VqHwexQEb/3djg^^^server.ccl.net> X-Original-From: "Gunda Tamįs" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Thu, 15 Sep 2005 08:03:25 +0200 MIME-Version: 1.0 Sent to CCL by: "Gunda Tamįs" [tgunda2005^^^puma.unideb.hu] The presence of an organic/medicinal chemist with a good practical background is inevitable when synthesis is in question. The problem becomes more and more acute when molecules are planned by theoretical chemists with the aid of different softwares. This may lead to questions such as: "What reagents need I buy and use to introduce three additional methyl groups to an existing one in order to convert it to a tert-butyl group?" Several answers had to be written until he believed that it couldn't be done by the suggested method. Tamas E. Gunda Dept. of Pharmaceutical Chemistry University of Debrecen H-4010 Debrecen, POBox 36 Hungary tgunda2005 {at} puma.unideb.hu From owner-chemistry@ccl.net Thu Sep 15 08:54:04 2005 From: "CCL" To: CCL Subject: CCL: W:Disclose your data, or not publish ! Message-Id: <-29185-050915052626-4546-ETc9kVj+VqHwexQEb/3djg|a|server.ccl.net> X-Original-From: "Dr. Csaba Hetenyi" Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 15 Sep 2005 10:37:13 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: "Dr. Csaba Hetenyi" [csaba|a|ovrisc.mdche.u-szeged.hu] > One obvious case is in the community of protein-ligand docking & scoring. Are not we tired of those studies? > Yes, we are! No, we are not. Docking is not a good example. You can always validate your results with RMSD comparison to the X-ray structure position of the ligand, in the case of docking. Scoring can be validated with experimental delta G values too. If this validation is not done, of course, the manuscript should not be accepted. But this is the problem of the editor and the referees... --- Otherwise, anonymous contributions are not valuable, indeed. Best, Csaba Hetenyi From owner-chemistry@ccl.net Thu Sep 15 08:54:01 2005 From: "CCL" To: CCL Subject: CCL: W:gaussian Message-Id: <-29175-050915081516-2219-ETc9kVj+VqHwexQEb/3djg|-|server.ccl.net> X-Original-From: "Rafael Carlos Garcias" Sent to CCL by: "Rafael Carlos Garcias" [rafel.garcias|-|uib.es] Dear CCL members, I have a problem with my force calcultion. Once I have optimized an structure at B3LYP 6-31+g* level I start the force calculation by the keyword freq in the optimized structured obtained, but the problem is that the calculation finish because I have spent all the calculation time avaliable. I've tried to restart the freq calculation by the *.chk but it doesn't work. How can I restart the freq calculation or how can I reduce the computational time without changing the basis set? Thank you From owner-chemistry@ccl.net Thu Sep 15 10:59:21 2005 From: "CCL" To: CCL Subject: CCL: Computational drug design blues Message-Id: <-29187-050915092634-6913-Q0/ba8ktyANAsLcovOkC6g a server.ccl.net> X-Original-From: Eugen Leitl Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Thu, 15 Sep 2005 15:26:28 +0200 Mime-Version: 1.0 Sent to CCL by: Eugen Leitl [eugen a leitl.org] On Wed, Sep 14, 2005 at 05:23:25PM -0500, CCL wrote: > I note that the question of assessing the "ease of synthesis" has excited a > fair bit of comment. As I already pointed out, and as also stated by Gary > Breton, the organic chemistry community does not think it is actually > possible to meaningfully assess "ease of synthesis" by an algorithmic > approach. Algorithmic approach can mean many things. It could mean have the machine look up the structure in the supplier's catalogue, or a reaction database, which could result in a commercial product, or a literature citation. If the lead candidate is commercially available, or has been characterized in literature the problem is already (almost) solved. If this does not work, a substructure search would be in order. If this search provides no clear candidates, the system could try to reach close (in terms of synthetic steps) points in structure space, starting on the terra firma of the empirical island. If this still fails, it can propose a synthetic route from scratch (this is the last resort, and it will be likely not very good, or worse). We also have to look at the amount of chemical expertise of the user, from the worst case of naive user, to a reasonably competent chemist -- just not a synthetic chemist. Here many nonfertile branches can be pruned, before giving this into the hands of the (hopefully reasonably competent, and not just a bench monkey) synthetic chemist. The reasons for this might be a lack of good personnel, attempt to reduce costs, or just optimize the amount of compounds screened within a given cost envelope. Would it be effective, in the end? No idea. > Other issues that bear on the > practicality question are (not a comprehensive list): > > cost of raw materials > > cost of solvents > > cost of reagents, catalysts etc. This should be all on file, and preferrably directly accessible to the algorithm sorting the recommendations by the "practicality" rank. > > cost of disposal of waste materials Good point. Probably hard to obtain relevant data here. Ruthless cost-optimizers would just want to outsource the problem, preferrably to a place with less restrictive environmental regulations. > > health and lab safety hazards associated with reagents, solvents and > intermediate compounds Toxicity databases. There are even some de novo toxicity prediction tools, though probably not entirely reliable. > > level of selectivity actually attainable (stereoselectivity, > regioselectivity, chemoselectivity) If it's a literature reaction, the data is available. > > need for purification, particularly chromatography > > solubilities, boiling points and other physical parameters Physical properties database. Literature, too. > > expected thermodynamic and kinetic stability of intermediates > > scalability - can the proposed route be used only for milligram amounts or > can it be implemented on gram or kilo scales as needed? I do not think such practicality concerns arise already when one is just looking to obtain mg quantities for a bioassay, by the fastest and cheapest route available. It's just a candidate, after all, not even a lead. > The list could go on. The bottom line is that in order to determine whether > a proposed drug candidate is actually practical, you need to consider > numerous variables that cannot be reduced to a simple numerical scale. This > is where the experience and expertise of the bench chemist is essential. The bench chemist is ultimatively the person who's in charge of producing the compound, so the buck will eventually stop there. -- Eugen* Leitl leitl ______________________________________________________________ ICBM: 48.07100, 11.36820 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE From owner-chemistry@ccl.net Thu Sep 15 10:59:23 2005 From: "CCL" To: CCL Subject: CCL: W:Disclose your data, or not publish ! Message-Id: <-29189-050915105010-25269-yVAha9n2R3UB7nRoYuW1Mw^server.ccl.net> X-Original-From: Paul Hawkins Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Thu, 15 Sep 2005 07:54:10 -0600 MIME-Version: 1.0 Sent to CCL by: Paul Hawkins [phawkins^eyesopen.com] Dr. Hetenyi, Docking is an excellent example in this case, if the study in question uses docking as a virtual screening tool, and especially if the study was retrospective. A study that does not disclose the actives or decoys used in a retrospective virtual screen is close to useless, as the study cannot be reproduced and comments/conclusions on the efficacy of any docking tools used in the study are unsupportable. Consequently providing the compound sets used in such studies should be mandatory. As to judging the quality of a scoring function by correlation with binding affinity, no scoring function available in the popular docking tools in current use shows any meaningful correlation with binding affinity across diverse compound classes. Are you suggesting that any manuscript using these tools in any context should be denied publication? A consistent correlation between binding energy and score > from a given scoring function is not a pre-requisite for success in virtual screening. Paul Hawkins CCL wrote: >Sent to CCL by: "Dr. Csaba Hetenyi" [csaba|a|ovrisc.mdche.u-szeged.hu] > > >>One obvious case is in the community of protein-ligand docking & scoring. Are not we tired of those studies? >>Yes, we are! >> >> > >No, we are not. >Docking is not a good example. You can always validate your results with >RMSD comparison to the X-ray structure position of the ligand, in the case >of docking. >Scoring can be validated with experimental delta G values too. >If this validation is not done, of course, the manuscript should not be >accepted. But this is the problem of the editor and the referees... >--- >Otherwise, anonymous contributions are not valuable, indeed. >Best, >Csaba Hetenyi> > > > From owner-chemistry@ccl.net Thu Sep 15 10:59:22 2005 From: "CCL" To: CCL Subject: CCL: RES: W:gaussian Message-Id: <-29188-050915102046-3154-ywyS3C5lFBFDbtqcN2PB8w-*-server.ccl.net> X-Original-From: Ian Hovell Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 15 Sep 2005 11:20:35 -0300 MIME-Version: 1.0 Sent to CCL by: Ian Hovell [HOVELL-*-cetem.gov.br] Dear Rafael, An analytical frequency calculation can not be restarted. You can use the keyword option freq=numer which calls for a numerical frequency calculation which you can restart in the event of power cuts etc. It is how ever much slower and I believe not so accurate (somebody else might like to comment on this) Ian -----Mensagem original----- De: CCL [mailto:owner-chemistry-*-ccl.net] Enviada em: quinta-feira, 15 de setembro de 2005 09:58 Para: Hovell, Ian Assunto: CCL: W:gaussian Sent to CCL by: "Rafael Carlos Garcias" [rafel.garcias|-|uib.es] Dear CCL members, I have a problem with my force calcultion. Once I have optimized an structure at B3LYP 6-31+g* level I start the force calculation by the keyword freq in the optimized structured obtained, but the problem is that the calculation finish because I have spent all the calculation time avaliable. I've tried to restart the freq calculation by the *.chk but it doesn't work. How can I restart the freq calculation or how can I reduce the computational time without changing the basis set? Thank you From owner-chemistry@ccl.net Thu Sep 15 10:55:09 2005 From: "CCL" To: CCL Subject: CCL: transition metals Message-Id: <-29186-050915103142-11524-Zb1Nt/fsHXu9fNxirpy1Uw---server.ccl.net> X-Original-From: Victor Nemykin Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 15 Sep 2005 06:31:29 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Victor Nemykin [victor_nemykin---yahoo.com] Hello Goedele: You raised an interesting question, which actually has no straightforward answer. Which property (properties) you would like to calculate? I will choose B3P86 or B3LYP coupled with 6-31G(transition metal)/6-31G(d) (other atoms) or Wachters (transition metal, represented as 6-311+G in Gaussian)/ 6-31G(d) (other atoms) for geometry optimization because hybrid EC functionals usually gives a slightly better geometry as compared to the pure ones. Again, I am a Gaussian user and people who are using ADF can argue this point in favor of pure DFT EC functionals, for instance BP86. If you would like to calculate vertical excitation energies, it seems that both hybrid (B3P86, B3LYP) and pure (BP86) EC functiolans gives a reasonable results in many cases (test also PBE1PBE). For Mossbauer parameters calculations, I would recommend o use B3P86 or B3LYP, while EPR parameter calculations usually go better with pure EC functionals. Of course the choice of BS/EC functional is also depends on the size of the molecule you would like to calculate because in general pure EC functionals are faster as compared to hybrid ones. You can get some very general ideas from my web-site, but probably if you will provide me more information about the calculations you are interesting in, I can give you a better advise… Sincerely, Victor --- CCL wrote: > > Sent to CCL by: Goedele Roos [groos##vub.ac.be] > Dear all, > what is a good DFT functional touse with transitionmetals from the > first d-block? > Can I use B3LYP or rather BP86? > Thank you for your advice, > Goedele > > Drs. Goedele Roos > Dienst Algemene Chemie (ALGC) > Vrije Universiteit Brussel (VUB) > Pleinlaan 2 > B-1050 Brussels > Tel: 0032-2-629 35 16 > Fax: 0032-2-629 33 17 > > > > -= This is automatically added to each message by the mailing script > =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line> > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST---ccl.net> > If your is mail bouncing from ccl.net domain due to spam filters, > please> > > > ***** Dr. Victor N.Nemykin e-mail: victor_nemykin---yahoo.com ***** __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Thu Sep 15 11:37:55 2005 From: "CCL" To: CCL Subject: CCL: Computational drug design blues Message-Id: <-29190-050915111108-9301-WP29zbg7pUH/vTYl1lkD1g/./server.ccl.net> X-Original-From: Sivanesan Dakshanamurthy Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 15 Sep 2005 11:10:37 -0400 MIME-Version: 1.0 Sent to CCL by: Sivanesan Dakshanamurthy [sd233/./georgetown.edu] With hot topic of discussion started initially from my answer for the question of "Synthetic Feasibility", I would agree organic chemists important. At the same time one may want realize that synthetic feasibility incorporated in some programs with the consultation of expert organic chemists, not by computational chemists alone atleast. So one cannot throwout the computational prediction of synthetic feasibility to the bin. Prediction will give you raw guidance for the drug discovery people when doing virtual screening with large number datasets. -Siva D.Sivanesan, Ph.D. E401, New Research Building, Macromolecular Core (Molecular Modeling) & Dept. of Oncology, Lombardi Cancer Center (NCI Comprehensive Cancer Center), Georgetown University, Washington DC 20057 Phone: 202-687-2347 ----- Original Message ----- > From: CCL Date: Wednesday, September 14, 2005 9:36 pm Subject: CCL: Computational drug design blues > > Sent to CCL by: [Mitchell.Polley(!)csiro.au] > I think they were referring to the Synthetic Feasibility score in the > "LeapFrog" module of Sybyl by Tripos (www.tripos.com). I don't > think it > was ever published, as it was only ever a very rough guideline. > You may > be able to get more information from the Tripos website or technical > support group (again through their website). > > Regards, > > Mitch > > > > Sent to CCL by: Andrew Fant [fant{:}pobox.com] > > By any chance, can you give a pointer into the literature on > > that index? > > I'm not able to get into chemical abstracts at the moment, but both > > google and google scholar had no hits at all on "synthetic > feasibility> index" > > > > Thanks, > > Andy > > > > > > CCL wrote: > > > Sent to CCL by: "Srinivasan Parthiban" [parthiban-#-gvkbio.com] > > > There must be few programs available on estimating the Synthetic > > > feasibility Index. I have used it few years back using > > Tripos software. It > > > is purely an empirical method where the calculation is > > based on the number > > > of rings and the functional groups present in the molecule > > and so on. > > > - Parthi > > > ----------------------------------- > > > Srinivasan Parthiban > > > Director-Informatics > > > GVKBIO > > > Vukan Towers > > > #81 Tirumalai Pillai Road > > > T. Nagar, Chennai 600 017 INDIA > > > Ph: +91-44-5212 5522/3399 > > > www.gvkbio.com > > > > > > > > -= This is automatically added to each message by the mailing > > script =- > > To send e-mail to subscribers of CCL put the string CCL: on > > your Subject: line> > > Send your subscription/unsubscription requests to: > > CHEMISTRY-REQUEST/./ccl.net> > > If your is mail bouncing from ccl.net domain due to spam > > filters, please> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+-+-+-+-+-+ > > -+-+-+-+-+ > > > > > > > > > > -= This is automatically added to each message by the mailing > script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line> > Send your subscription/unsubscription requests to: CHEMISTRY- > REQUEST/./ccl.net > HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, > please> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > > From owner-chemistry@ccl.net Thu Sep 15 12:06:20 2005 From: "CCL" To: CCL Subject: CCL: Computational drug design blues Message-Id: <-29191-050915120459-14632-3fzysTmoW2O0YesKpHzDpQ-*-server.ccl.net> X-Original-From: Laurence Cuffe Content-disposition: inline Content-language: en Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Thu, 15 Sep 2005 17:04:54 +0100 MIME-version: 1.0 Sent to CCL by: Laurence Cuffe [Laurence.Cuffe-*-ucd.ie] ----- Original Message ----- > From: CCL Date: Thursday, September 15, 2005 2:04 am Subject: CCL: Computational drug design blues > CCL Colleagues, > > Regarding prediction of synthetic difficulty, one approach > to this > problem might involve > constructing a descriptor-based QSAR model of compound (catalogue) > cost > ($Cost/mg) or perhaps log ($Cost/mg). > > You might end up with an equation something like: > > Log($Cost/mg) = 0.5 * # chiral centers + 0.7 # large rings > + # > spiro-fused centers + ... > > There are of course problems with this approach. One > obvious > problematic group of compounds > would be natural products. Some natural products have exquisitely > complicated molecular skeletons, yet > are obtained relatively inexpensively by extraction methods. So > the cost > for certain molecules will not > reflect synthetic difficulty. Thats a nice elegant approach. One other class of compounds to look out for are those which are a byproduct of some other production proces, however this is unlikely to be a problem in the field of drug synthesis. You could also get a measure of the difficulty involved in purifying the synthons by looking at the relative cost of different grades of purity, although this figure is more likely to be a demand driven construct. All the best Dr Laurence Cuffe From owner-chemistry@ccl.net Thu Sep 15 12:33:51 2005 From: "CCL" To: CCL Subject: CCL: W:single crystal X-ray diffraction simulator Message-Id: <-29192-050915121241-24687-d6Sz0eQVVowKiCFOADxAdQ * server.ccl.net> X-Original-From: Vincent Xianlong Wang Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 15 Sep 2005 08:12:36 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Vincent Xianlong Wang [xloongw * yahoo.com] Mercury from the Cambridge Crystal Database can do it and it is free. http://www.ccdc.cam.ac.uk/products/csd_system/mercury/ Vincent --- CCL wrote: > > Sent to CCL by: "Constantinos Zeinalipour-Yazdi" > [czeinali{}chem.ucsd.edu] > Greetings, everyone, > > I am looking for a free software that can simulate > single crystal X-ray diffraction patterns given the > unit cell parameters and the cartesian or fractional > coordinates of the symmetry unique atoms in the unit > cell. Preferable in .CIF format but other formats > are also welcome. > The program should be windows or linux compatible. > Any suggestions are welcome. > > best wishes, Constantinos > > > > -= This is automatically added to each message by > the mailing script =- > To send e-mail to subscribers of CCL put the string > CCL: on your Subject: line> > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST * ccl.net > HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to > spam filters, please> > > > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Thu Sep 15 12:48:57 2005 From: "CCL" To: CCL Subject: CCL: W:Computational drug design blues Message-Id: <-29194-050915123333-1589-ZWRW2t5blh62dMU1PTqiKw]-[server.ccl.net> X-Original-From: Darryl Reid Content-Type: multipart/alternative; boundary="----=_Part_19326_12826581.1126798375774" Date: Thu, 15 Sep 2005 11:32:55 -0400 Mime-Version: 1.0 Sent to CCL by: Darryl Reid [darryl.reid]-[gmail.com] ------=_Part_19326_12826581.1126798375774 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Just to add a little to the discussion, the CAESA product is available for = a=20 free demo if you are interested in trying it out. You can find it at=20 www.simbiosys.ca . There is also a white paper for CAESA at the same site that may be of=20 interest to people: http://simbiosys.ca/solutions/white_papers/CAESA_v2_4_whitepaper.pdf Darryl On 9/14/05, CCL wrote: >=20 > As other people have mentioned estimating synthetic accessibility is a=20 > difficult problem particularly when considering compounds designed by peo= ple=20 > or computers with little knowledge of synthetic chemistry. >=20 > A number of groups working on de novo design programs have attempted to= =20 > include synthetic accessibility in their systems to various levels. These= =20 > include SPROUT (from Peter Johnson's group in Leeds) and SkelGen (from=20 > Denovo Pharmaceuticals). There have also been a number of methods applied= to=20 > estimating synthetic accessibility including expert systems (CAESA, again= =20 > from Leeds) and neural networks (Takaoka et al, JCICS, 2003, 42, 1269-127= 5).=20 > We recently wrote a review paper on the subject (Mini-Reviews in Medicina= l=20 > Chemistry, Volume 4, No. 6, 2004, 681-692) which covers a wide range of= =20 > techniques and uses. >=20 > This is certainly an important area and anything that that could reliably= =20 > stop us suggesting synthetically infeasible compounds to medicinal chemis= ts=20 > would be very welcome. >=20 > Best of luck, >=20 > Christian >=20 > > -----Original Message----- > > From: CCL [mailto:owner-chemistry]-[ccl.net] > > Sent: Wednesday, 14 September, 2005 7:10 AM > > To: Baber, Christian > > Subject: CCL: W:Computational drug design blues > > > > > > > > Sent to CCL by: "Sandeep Kumar" [kumarsan\a/jhu.edu] > > Dear CCLers: > > > > I need some advice about the drug discovery/design. Using > > structure based design, one could develope several potential > > small molecular inhibitors/drugs for a given protein target. > > Many of these compounds may appear very attractive as they > > satisfy all lipinski's rules and your requirements for > > selectivity/specificity and may even have desirable > > solubility/ADME profiles. These days its possible to > > incorporate all these features right at the computational > > design stage. However, the organic synthesis of the compound > > still remains a bottleneck as it turns out that many of the > > designed compounds are 'hard' to synthesize or may require > > many steps of synthesis. I was wondering if there are some > > simple guidelines in the form of literature or 'hands on' > > experience available which could tell the > > computational/medicinal chemist whether a designed compound > > would be easy or hard to synthesize before he/she talks to > > the organic chemist. > > > > All your responses are greatly appreciated. > > > > Yours sincerely > > Sandeep Kumar, Ph.D. > > Johns Hopkins University, > > Dept. of Biology, > > 106 Mudd Hall, > > 3400 N. Charles St. > > Baltimore, MD 21218. > > Phone: 410-516-8433 > > Email: kumarsan]-[jhu.edu > > > > > > > > -=3D This is automatically added to each message by the mailing > > script =3D- > > To send e-mail to subscribers of CCL put the string CCL: on > > your Subject: line> > > Send your subscription/unsubscription requests to: > > CHEMISTRY-REQUEST]-[ccl.net> > > > If your is mail bouncing from ccl.net domain due to=20 > spam > > filters, please> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > -+-+-+-+-+ > > > > > > > > >=20 >=20 > ------=_Part_19326_12826581.1126798375774 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Just to add a little to the discussion, the CAESA product is available for a free demo if you are interested in trying it out.  You can find it at www.simbiosys.ca.

There is also a white paper for CAESA at the same site that may be of inter= est to people:
http://simbiosys.ca/solutions/white_papers/CAESA_v2_4_whitepaper.pdf<= /a>

Darryl

On 9/14/05, CCL <owner-chemistry]-[= ccl.net> wrote:
As other people have mentioned estimating synthetic accessibility is a difficult problem particularly when considering compounds designed by people or computers with little knowledge of synthetic chemistry.

A number of groups working on de novo design programs have attempted to include synthetic accessibility in their systems to various levels. These include SPROUT (from Peter Johnson's group in Leeds) and SkelGen (from Denovo Pharmaceuticals). There have also been a number of methods applied to estimating synthetic accessibility including expert systems (CAESA, again from Leeds) and neural networks (Takaoka et al, JCICS, 2003, 42, 1269-1275). We recently wrote a review paper on the subject (Mini-Reviews in Medicinal Chemistry, Volume 4, No. 6, 2004, 681-692) which covers a wide range of techniques and uses.

This is certainly an important area and anything that that could reliably stop us suggesting synthetically infeasible compounds to medicinal chemists would be very welcome.

Best of luck,

Christian

> --= ---Original Message-----
> From: CCL [mailto:owner-chemistry]-[ccl.net]
> Sent: Wednesday, 14= September, 2005 7:10 AM
> To: Baber, Christian
> Subject: CCL: W:Computational drug de= sign blues
>
>
>
> Sent to CCL by: "Sandeep&nb= sp; Kumar" [kumarsan\a/jhu.edu]
> Dear CCLers:
>
&= gt; I need some advice about the drug discovery/design. Using
> structure based design, one could develope several potential
&g= t; small molecular inhibitors/drugs for a given protein target.
> Man= y of these compounds may appear very attractive as they
> satisfy all= lipinski's rules and your requirements for
> selectivity/specificity and may even have desirable
> solubi= lity/ADME profiles. These days its possible to
> incorporate all thes= e features right at the computational
> design stage. However, the or= ganic synthesis of the compound
> still remains a bottleneck as it turns out that many of the
>= ; designed compounds are 'hard' to synthesize or may require
> many s= teps of synthesis. I was wondering if there are some
> simple guideli= nes in the form of literature or 'hands on'
> experience available which could tell the
> computational/me= dicinal chemist whether a designed compound
> would be easy or hard t= o synthesize before he/she talks to
> the organic chemist.
>
> All your responses are greatly appreciated.
>
> Yours = sincerely
> Sandeep Kumar, Ph.D.
> Johns Hopkins University,> Dept. of Biology,
> 106 Mudd Hall,
> 3400 N. Charles St.
> Baltimore, MD 21218.
> Phone: 410-516-8433
> Email: kumarsan]-[jhu.edu
>
>
&= gt;
> -=3D This is automatically added to each message by the mailing
> script =3D-
> To send e-mail to subscribers of CCL put the s= tring CCL: on
> your Subject: line>
> Send your subscription= /unsubscription requests to:
> CHEMISTRY-REQUEST]-[ccl.net
> HOME Page: http://www.ccl.net   | Jobs Page: http://www.ccl.net/jobs
>
> If your is mail b= ouncing from=20 ccl.net domain due to spam
> filters, = please
> use the Web based form from CCL Home Page
> -+-+-+-+-+= -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
> -+-+-+-+-+
>
>
>
>



------=_Part_19326_12826581.1126798375774-- From owner-chemistry@ccl.net Thu Sep 15 12:48:57 2005 From: "CCL" To: CCL Subject: CCL: transition metals Message-Id: <-29195-050915124642-8977-eIMTeDLoMEiaNiKKd2vATw~!~server.ccl.net> X-Original-From: Konstantin Kudin Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 15 Sep 2005 08:46:35 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Konstantin Kudin [konstantin_kudin~!~yahoo.com] Check out this recent paper on bunch of dimers: N. E. Schultz, Y. Zhao, and D. G. Truhlar, J. Phys. Chem. A 109, 4388 (2005). It seems to suggest that hybrids are no good in this case ... Kostya --- CCL wrote: > > Sent to CCL by: Goedele Roos [groos##vub.ac.be] > Dear all, > what is a good DFT functional touse with transitionmetals from the > first d-block? > Can I use B3LYP or rather BP86? > Thank you for your advice, > Goedele > > Drs. Goedele Roos > Dienst Algemene Chemie (ALGC) > Vrije Universiteit Brussel (VUB) > Pleinlaan 2 > B-1050 Brussels > Tel: 0032-2-629 35 16 > Fax: 0032-2-629 33 17 > > > > -= This is automatically added to each message by the mailing script > =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line> > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST~!~ccl.net> > If your is mail bouncing from ccl.net domain due to spam filters, > please> > > > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Thu Sep 15 12:48:57 2005 From: "CCL" To: CCL Subject: CCL: Computational drug design blues Message-Id: <-29193-050915124143-6069-OmDtpM9EfmaI4CmBOasg1Q{=}server.ccl.net> X-Original-From: "Phil Hultin" Content-Type: multipart/alternative; boundary="----=_NextPart_000_001A_01C5B9EA.6DEFB900" Date: Thu, 15 Sep 2005 11:41:28 -0500 MIME-Version: 1.0 Sent to CCL by: "Phil Hultin" [hultin{=}cc.umanitoba.ca] This is a multi-part message in MIME format. ------=_NextPart_000_001A_01C5B9EA.6DEFB900 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit Regarding Dr. Metz's very interesting comments: The issue is not whether medicinal chemists are consistent in how they assess feasibility, but 1) whether the process is amenable to a purely algorithmic solution, and 2) if it is, can such a solution be implemented in a practical way on current computers or on machines reasonably expected to arrive in the near future? The problem is teaching a computer what is "easy" and what is "hard". Teaching a computer how to devise a possible pathway for synthesis has been addressed many times - an excellent historical review has recently appeared at http://pubs.rsc.org/ej/CS/2005/b104620a.pdf and it makes a very strong case for the ultimate success of computers at synthesis design. What it does not really address is the difference between assessing the quality of an overall strategy (necessary for synthesis design and a problem that has to some extent been solved) and assessing the practicality of implementing that strategy. My argument is that the practicality issue has so many variables that it is very difficult to implement in an algorithmic fashion. I also am quite confident in saying that no existing program has made any realistic attempt to model practicality at the level of the bench chemist. So, without this kind of input, I do not believe that any existing program can make a meaningful assessment of synthetic feasibility (as distinct from strategic efficiency, which has been addressed to a fair degree). Dr. Philip G. Hultin Associate Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin{=}cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin _____ > From: owner-chemistry{=}ccl.net [mailto:owner-chemistry{=}ccl.net] Sent: September 14, 2005 8:05 PM To: Hultin, Philip G. Subject: CCL: Computational drug design blues CCL Colleagues, Regarding prediction of synthetic difficulty, one approach to this problem might involve constructing a descriptor-based QSAR model of compound (catalogue) cost ($Cost/mg) or perhaps log ($Cost/mg). You might end up with an equation something like: Log($Cost/mg) = 0.5 * # chiral centers + 0.7 # large rings + # spiro-fused centers + ... This idea, of course, is based on an assumption that synthetic difficulty roughly equates to economics for thousands of compounds. Economics roughly equates to how difficult it is to make the molecule. There are of course problems with this approach. One obvious problematic group of compounds would be natural products. Some natural products have exquisitely complicated molecular skeletons, yet are obtained relatively inexpensively by extraction methods. So the cost for certain molecules will not reflect synthetic difficulty. You may (?) need to exclude those compounds > from your training set. But, it might be worth trying to build the model several different ways. Sources of data are plentiful. Pick up your Aldrich catalogue and you will find plenty of structure/cost information. Probably a good idea to use the costs from a single supplier so as not to add further noise (factors) to the analysis. As a check of your final model, you might want to make cost predictions for 100 molecules or so. Then have 10 synthetic chemist friends rate the difficulty of synthesis for each compound on a scale from 1 to 5. Don't be surprised if you get very different (inconsistent) answers. You will need to do some statistical averaging here. Not to get side-tracked, but regarding the (in)consistency of chemists in judging chemical structures, please see the interesting publication from Lajiness et al. "Assessment of Consistency of Medicinal Chemists in Reviewing Sets of Compounds" J. Med. Chem. 47 (2004) 4891. An interesting statement > from the abstract of this paper is, "It was found that medicinal chemists were not very consistent in the compounds they rejected as being undesirable." Regards, Jim Metz James T. Metz, Ph.D. Abbott Laboratories james.metz{=}abbott.com ------=_NextPart_000_001A_01C5B9EA.6DEFB900 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable Normal Document Template

Regarding Dr. Metz’s very interesting comments:

 

The issue is not whether medicinal chemists are consistent in how they assess feasibility, but 1) whether = the process is amenable to a purely algorithmic solution, and 2) if it is, = can such a solution be implemented in a practical way on current computers or on machines reasonably expected to arrive in the near = future?

 

The problem is teaching a computer = what is “easy” and what is “hard”.  Teaching a = computer how to devise a possible pathway for synthesis has been addressed many = times – an excellent historical review has recently appeared at http://pubs.rsc.org/= ej/CS/2005/b104620a.pdf and it makes a very strong case for the ultimate success of computers at synthesis design.  What it does not really address is the = difference between assessing the quality of an overall strategy (necessary for = synthesis design and a problem that has to some extent been solved) and assessing = the practicality of implementing that strategy.

 

My argument is that the = practicality issue has so many variables that it is very difficult to implement in an = algorithmic fashion.  I also am quite confident in saying that no existing = program has made any realistic attempt to model practicality at the level of the = bench chemist.  So, without this kind of input, I do not believe that any existing program can make a meaningful assessment of synthetic = feasibility (as distinct from strategic efficiency, which has been addressed to a fair = degree).

 

Dr. Philip G. = Hultin

Associate Professor of = Chemistry,

University= of Manitoba

Winnipeg, MB

R3T = 2N2

hultin{=}cc.umanitoba.ca

http://umanitoba.ca/= chemistry/people/hultin

 

From: owner-chemistry{=}ccl.net [mailto:owner-chemistry{=}ccl.net]
Sent: September 14, 2005 = 8:05 PM
To: Hultin, Philip G. =
Subject: CCL: = Computational drug design blues

 


CCL Colleagues,

        Regarding prediction of synthetic difficulty, one = approach to this problem might involve
constructing a descriptor-based QSAR  model of compound (catalogue) cost = ($Cost/mg) or perhaps log ($Cost/mg).

        You might end up with an equation something = like:

        Log($Cost/mg) =3D 0.5 * # chiral centers + 0.7 # = large rings + # spiro-fused centers + ...

        This idea, of course, is based on an assumption = that synthetic difficulty roughly equates
to economics for thousands of compounds.  Economics roughly equates to = how difficult it is to make the molecule.

        There are of course problems with this approach. =  One obvious problematic group of compounds
would be natural products.  Some natural products have exquisitely = complicated molecular skeletons, yet
are obtained relatively inexpensively by extraction methods.  So the = cost for certain molecules will not
reflect synthetic difficulty.  You may (?) need to exclude those compounds = > from your training set.  But, it
might be worth trying to build the model several different ways. =

        Sources of data are plentiful.  Pick up your = Aldrich catalogue and you will find plenty of structure/cost
information.  Probably a good idea to use the costs from a single supplier so as = not to add further noise (factors)
to the analysis.

        As a check of your final model, you might want to = make cost predictions for 100 molecules or so.  Then have 10 =
synthetic chemist friends rate the difficulty of synthesis for each compound on a = scale > from 1 to 5.  Don't be surprised
if you get very different (inconsistent) answers.  You will need to do = some statistical averaging here.

        Not to get side-tracked, but regarding the = (in)consistency of chemists in judging chemical structures, please
see the interesting publication from Lajiness et al. "Assessment of Consistency of Medicinal Chemists in Reviewing
Sets of Compounds" J. Med. Chem. 47 (2004) 4891.   An interesting statement from the abstract of this paper is,

        "It was found
that medicinal chemists were not very consistent in the compounds they = rejected as being
undesirable."


        Regards,
        Jim Metz
       

James T. Metz, Ph.D.
Abbott Laboratories


james.metz{=}abbott.com

------=_NextPart_000_001A_01C5B9EA.6DEFB900-- From owner-chemistry@ccl.net Thu Sep 15 13:04:16 2005 From: "CCL" To: CCL Subject: CCL: PSC WORKSHOP: COMPUTATIONAL BIOPHYSICS WORKSHOP Message-Id: <-29196-050915125556-14843-R0KHU4pzMwOlgk/OYlGfDA(~)server.ccl.net> X-Original-From: Troy Wymore Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 15 Sep 2005 12:12:56 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Troy Wymore [wymore(~)psc.edu] ************************************************** PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE WORKSHOP This workshop is funded by a grant to the PSC from the NIH National Center for Research Resources. The grant provides tuition, hotel, supercomputing time, and workshop materials for US academic participants. COMPUTATIONAL BIOPHYSICS WORKSHOP Nov. 28 - Dec. 1 Application Deadline: October 17 Primary Instructor: Prof. Klaus Schulten (UIUC) www.psc.edu/biomed/training/workshops/2005/NAMD/index.html The workshop will explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level. The course will be based on case studies including the properties of membranes and membrane proteins, mechanisms of molecular motors, trafficking in the living cell through water and ion channels, and signaling pathways. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers and steered molecular dynamics simulations. The workshop is designed for graduate students and postdoctoral researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which students will be able to set up and run simulations. For specific details, including an electronic application form, see: www.psc.edu/biomed/training/workshops/2005/NAMD/index.html Please direct any questions about the workshop to Dr. Troy Wymore (wymore(~)psc.edu). From owner-chemistry@ccl.net Thu Sep 15 14:13:50 2005 From: "CCL" To: CCL Subject: CCL: W:Any open-source molecular descriptor software for short peptides? Message-Id: <-29197-050915135210-27872-R0KHU4pzMwOlgk/OYlGfDA!^!server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="Windows-1252" Date: Thu, 15 Sep 2005 11:41:22 -0500 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci!^!utmb.edu] > Could anyone recommend a nice open-source molecular descriptor > calculation software for short peptides with 8-15 amino acid long? The AAindex database (http://www.genome.ad.jp/dbget/aaindex.html) has 516 amino acids indices that can be used in QSAR. Peptide QSAR uses also special descriptors, based on PLS or PCA, such as the z1-z5 scale proposed by S. Wold (see PubMed: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9651153&query_hl=1) or the E1-E5 scale (J. Mol. Model. 7, 445-453; send me an EMail if you need a reprint). Here you have the E1-E5 decriptors: 0.008, 0.134, -0.475, -0.039, 0.181, /* 1 A */ 0.171, -0.361, 0.107, -0.258, -0.364, /* 2 R */ 0.255, 0.038, 0.117, 0.118, -0.055, /* 3 N */ 0.303, -0.057, -0.014, 0.225, 0.156, /* 4 D */ -0.132, 0.174, 0.070, 0.565, -0.374, /* 5 C */ 0.149, -0.184, -0.030, 0.035, -0.112, /* 6 Q */ 0.221, -0.280, -0.315, 0.157, 0.303, /* 7 E */ 0.218, 0.562, -0.024, 0.018, 0.106, /* 8 G */ 0.023, -0.177, 0.041, 0.280, -0.021, /* 9 H */ -0.353, 0.071, -0.088, -0.195, -0.107, /* 10 I */ -0.267, 0.018, -0.265, -0.274, 0.206, /* 11 L */ 0.243, -0.339, -0.044, -0.325, -0.027, /* 12 K */ -0.239, -0.141, -0.155, 0.321, 0.077, /* 13 M */ -0.329, -0.023, 0.072, -0.002, 0.208, /* 14 F */ 0.173, 0.286, 0.407, -0.215, 0.384, /* 15 P */ 0.199, 0.238, -0.015, -0.068, -0.196, /* 16 S */ 0.068, 0.147, -0.015, -0.132, -0.274, /* 17 T */ -0.296, -0.186, 0.389, 0.083, 0.297, /* 18 W */ -0.141, -0.057, 0.425, -0.096, -0.091, /* 19 Y */ -0.274, 0.136, -0.187, -0.196, -0.299}; /* 20 V */ You can also use the weighted E1-E5 decriptors, where WEi = sqrt(Li)*Ei, with Li=eigenvalue i: 0.354, 3.762, -11.036, -0.649, 2.828, /* 1 A */ 7.573, -10.135, 2.486, -4.291, -5.687, /* 2 R */ 11.294, 1.067, 2.718, 1.963, -0.859, /* 3 N */ 13.420, -1.600, -0.325, 3.742, 2.437, /* 4 D */ -5.846, 4.885, 1.626, 9.397, -5.843, /* 5 C */ 6.599, -5.166, -0.697, 0.582, -1.750, /* 6 Q */ 9.788, -7.861, -7.318, 2.611, 4.734, /* 7 E */ 9.655, 15.778, -0.558, 0.299, 1.656, /* 8 G */ 1.019, -4.969, 0.953, 4.657, -0.328, /* 9 H */ -15.634, 1.993, -2.045, -3.243, -1.672, /* 10 I */ -11.825, 0.505, -6.157, -4.557, 3.219, /* 11 L */ 10.762, -9.517, -1.022, -5.405, -0.422, /* 12 K */ -10.585, -3.959, -3.601, 5.339, 1.203, /* 13 M */ -14.571, -0.646, 1.673, -0.033, 3.250, /* 14 F */ 7.662, 8.029, 9.456, -3.576, 6.000, /* 15 P */ 8.813, 6.682, -0.348, -1.131, -3.062, /* 16 S */ 3.012, 4.127, -0.348, -2.195, -4.281, /* 17 T */ -13.110, -5.222, 9.038, 1.380, 4.640, /* 18 W */ -6.245, -1.600, 9.874, -1.597, -1.422, /* 19 Y */ -12.135, 3.818, -4.345, -3.260, -4.672}; /* 20 V */ Regards, Ovidiu ********************************* Ovidiu Ivanciuc Sealy Center for Structural Biology, Department of Human Biological Chemistry & Genetics, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0857 USA From owner-chemistry@ccl.net Thu Sep 15 15:14:53 2005 From: "CCL" To: CCL Subject: CCL: RE: W:Disclose your data, or not publish ! Message-Id: <-29198-050915150914-1509-V1O9Y1PfYFcjeju1tb3eSw(-)server.ccl.net> X-Original-From: Andrew Fant Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 15 Sep 2005 15:08:40 -0400 MIME-Version: 1.0 Sent to CCL by: Andrew Fant [fant(-)pobox.com] CCL wrote: > > Sent to CCL by: Valentin Ananikov [val__ioc.ac.ru] > >> Sent to CCL by: "Chemical Bond" [chemicalbond001|"|yahoo.com] >> Everyday, tons of new publications come out. > > > Would it be possible to develop a numeric criterion to estimate the > quality of publications? > > Without clear criteria for estimating quality, clarity, impact and > significance of the publications such discussions tend to be rather > philosophical and useless. > > I am really interesting if there was any research addressing this problem? > > Best regards, > Valentin. Valentin, You might want to check into ISI's impact ratings. They are based (no surprise here) on their scientific citation index databases, and attempt to judge which journals publish papers that tend to be cited more and for a longer period of time after the initial publication. They have both a generic set of "high impact" journals, and ratings in specific fields. Hope this helps, Andy From owner-chemistry@ccl.net Thu Sep 15 16:24:59 2005 From: "CCL" To: CCL Subject: CCL: W:Disclose your data, or not publish ! Message-Id: <-29199-050915161542-306-SlGYGGzN40/oWCtOOtG77g+*+server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="Windows-1252" Date: Thu, 15 Sep 2005 15:15:38 -0500 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci+*+utmb.edu] Re: Disclose your data, or not publish ! The X-ray community is a good example for open acces to data: all structures must be deposited in a public database prior to publication. Similar databases exist for nucleic acids and protein sequences (GenBank, SwissProt, PIR). While computational models of proteins can be deposited in PDB, there is no public database for computational models of organic compounds (including MD simulations and docking results). A simple solution for publishers would be to ask for mandatory deposition of such data as supplementary materials. Regards, Ovidiu ********************************* Ovidiu Ivanciuc Sealy Center for Structural Biology, Department of Human Biological Chemistry & Genetics, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0857 USA From owner-chemistry@ccl.net Thu Sep 15 18:16:03 2005 From: "CCL" To: CCL Subject: CCL: transition metals Message-Id: <-29202-050915134720-27506-qcQqvXOXLkucMGqhMnWLkw-#-server.ccl.net> X-Original-From: "Gardner, Elizabeth A." Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 15 Sep 2005 11:00:07 -0600 MIME-Version: 1.0 Sent to CCL by: "Gardner, Elizabeth A." [eagardner-#-utep.edu] Where is your website? Elizabeth Gardner Assistant Professor Department of Chemistry University of Texas at El Paso El Paso, TX 79968 Phone: (915) 747-7551 Fax: (915) 747-5748 Office: 121D Physical Sciences Bldg. -----Original Message----- > From: owner-chemistry-#-ccl.net [mailto:owner-chemistry-#-ccl.net] Sent: Thursday, September 15, 2005 7:31 AM To: Gardner, Elizabeth A. Subject: CCL: transition metals Sent to CCL by: Victor Nemykin [victor_nemykin---yahoo.com] Hello Goedele: You raised an interesting question, which actually has no straightforward answer. Which property (properties) you would like to calculate? I will choose B3P86 or B3LYP coupled with 6-31G(transition metal)/6-31G(d) (other atoms) or Wachters (transition metal, represented as 6-311+G in Gaussian)/ 6-31G(d) (other atoms) for geometry optimization because hybrid EC functionals usually gives a slightly better geometry as compared to the pure ones. Again, I am a Gaussian user and people who are using ADF can argue this point in favor of pure DFT EC functionals, for instance BP86. If you would like to calculate vertical excitation energies, it seems that both hybrid (B3P86, B3LYP) and pure (BP86) EC functiolans gives a reasonable results in many cases (test also PBE1PBE). For Mossbauer parameters calculations, I would recommend o use B3P86 or B3LYP, while EPR parameter calculations usually go better with pure EC functionals. Of course the choice of BS/EC functional is also depends on the size of the molecule you would like to calculate because in general pure EC functionals are faster as compared to hybrid ones. You can get some very general ideas from my web-site, but probably if you will provide me more information about the calculations you are interesting in, I can give you a better advise... Sincerely, Victor From owner-chemistry@ccl.net Thu Sep 15 18:16:02 2005 From: "CCL" To: CCL Subject: CCL: W:Y zeolite coordinates needed Message-Id: <-29201-050915135721-28315-7ads/R9DgFJd6FFcwo+X+Q===server.ccl.net> X-Original-From: Charles McCallum Content-Type: multipart/alternative; boundary=Apple-Mail-2-321271536 Date: Thu, 15 Sep 2005 10:20:43 -0700 Mime-Version: 1.0 (Apple Message framework v734) Sent to CCL by: Charles McCallum [mmccallum===pacific.edu] --Apple-Mail-2-321271536 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed This link may be of use: http://www.ch.ic.ac.uk/vchemlib/course/zeolite/atlas.html There is a bit of an issue getting for example PDB files from the link, but if you examine the page source, you can find the direct URL for each PDB. Hope this helps, Mike On Sep 14, 2005, at 11:56, CCL wrote: > I have coordinates for Faujasite, in CIF, ENT and MOPAC data set > forms. > > But what address do you want them sent to? The address "walk!A! > vm.uff.br" is not recognized by my E-mail. > > Best wishes, > > Jimmy > > At 11:52 AM 9/14/2005, you wrote: > >> Sent to CCL by: "Jos Walkimar Carneiro" [walk!A!vm.uff.br] >> Does anybody has the cartesian coordinates of the T20 model of >> faujasite (Y) zeolite? >> Thank you >> Walkimar Carneiro >> >> >> >> -= This is automatically added to each message by the mailing >> script =->> >> ( === === ) >> .-----------------oOOo----(_)---- >> oOOo-------------------------------------. >> | James J. P. Stewart >> | | >> | Stewart Computational Chemistry LLC | E-mail: >> jstewart===us.fujitsu.com | >> | 15210 Paddington Circle | 39/03/15 N, 104/49/29 >> W | >> | Colorado Springs CO 80921-2512 >> | | >> | USA .ooo0 | Phone: USA +(719) >> 488-9416 | >> | ( ) Oooo. >> | | >> .------------------------\ (---- >> ( )-------------------------------------. >> \_) ) / >> (_/ -- C. Michael McCallum http://chemistry.cop.uop.edu/ cmccallum.html Associate Professor Department of Chemistry, UOP mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209) 946-2607 fax --Apple-Mail-2-321271536 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 This link may be of use:


There is a bit of an issue = getting for example PDB files from the link, but if you examine the page = source, you can find the direct URL for each PDB.

Hope this = helps,

Mike

= On Sep 14, 2005, at 11:56, CCL wrote:

I have coordinates for Faujasite, in CIF, ENT and MOPAC data = set forms.

But what address do you want them sent to?=A0 The = address "walk!A!vm.uff.br" is not recognized by my E-mail.

Best = wishes,

Jimmy

At 11:52 AM 9/14/2005, you wrote:

=
Sent to CCL by: "Jos = Walkimar Carneiro" [walk!A!vm.uff.br]
Does anybody has the cartesian = coordinates of the T20 model of faujasite (Y) zeolite?
Thank you
= Walkimar Carneiro



-=3D This is automatically added to = each message by the mailing script =3D- and send your message to:=A0 CHEMISTRY===ccl.net
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= =A0.-----------------oOOo----(_)----oOOo----------------------------------= ---.
=A0| James J. P. Stewart=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0 |=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 |
=A0| Stewart Computational = Chemistry LLC | E-mail:=A0 jstewart===us.fujitsu.com=A0 = |
=A0| 15210 Paddington Circle=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 = |=A0 39/03/15 N, 104/49/29 W=A0=A0=A0=A0=A0=A0=A0=A0=A0 |
=A0| = Colorado Springs CO 80921-2512=A0=A0=A0=A0=A0 = |=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0 |
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=A0|=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 (=A0=A0 )=A0=A0 Oooo. = |=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0 |
=A0.------------------------\ (----(=A0=A0= )-------------------------------------.
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 \_)=A0=A0=A0 ) /
= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0 (_/ =


--

C. Michael McCallum =A0 =A0 =A0 =A0 =A0 http://chemistry.cop.= uop.edu/cmccallum.html

Associate Professor =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0

Department of Chemistry, UOP = =A0 =A0

mmccallum .at. pacific .dot. = edu=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = (209) 946-2636 v=A0 = / (209) 946-2607 fax


= --Apple-Mail-2-321271536-- From owner-chemistry@ccl.net Thu Sep 15 18:16:02 2005 From: "CCL" To: CCL Subject: CCL: W:Y zeolite coordinates needed Message-Id: <-29200-050915153822-14972-y5b7V/ULBD9myz8aGrzN/g|-|server.ccl.net> X-Original-From: Xiaobo Zheng Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" Date: Thu, 15 Sep 2005 11:57:06 -0700 MIME-Version: 1.0 Sent to CCL by: Xiaobo Zheng [Xiaobo|-|email.arizona.edu] I really need the same cluster model. Could you please kindly send a copy to me too? Also, is there anybody has large (>5) cluster models for H-ZSM5? Besh wishes Xiaobo Quoting CCL : > I have coordinates for Faujasite, in CIF, ENT and MOPAC data set forms. > > But what address do you want them sent to? The address > "walk!A!vm.uff.br" is not recognized by my E-mail. > > Best wishes, > > Jimmy > > At 11:52 AM 9/14/2005, you wrote: > >> Sent to CCL by: "Jos Walkimar Carneiro" [walk!A!vm.uff.br] >> Does anybody has the cartesian coordinates of the T20 model of >> faujasite (Y) zeolite? >> Thank you >> Walkimar Carneiro( |-| |-| ) > .-----------------oOOo----(_)----oOOo-------------------------------------. > | James J. P. Stewart | | > | Stewart Computational Chemistry LLC | E-mail: jstewart|-|us.fujitsu.com | > | 15210 Paddington Circle | 39/03/15 N, 104/49/29 W | > | Colorado Springs CO 80921-2512 | | > | USA .ooo0 | Phone: USA +(719) 488-9416 | > | ( ) Oooo. | | > .------------------------\ (----( )-------------------------------------. > \_) ) / > (_/ <><><><><><><><><><><><><><><><><><><> Xiaobo Zheng Research Assistant Department of Chemical and Environmental Engineering the University of Arizona P.O. Box 210011 Tucson, Arizona 85721-0011 (520) 245-6854 phone (520) 621-6048 fax xiaobo|-|u.arizona.edu From owner-chemistry@ccl.net Thu Sep 15 18:38:42 2005 From: "CCL" To: CCL Subject: CCL: RE: W:Disclose your data, or not publish ! Message-Id: <-29203-050915183747-6048-mDvFBOEXVmT5zj6uaZrJJg]_[server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="Windows-1252" Date: Thu, 15 Sep 2005 17:37:40 -0500 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci]_[utmb.edu] Replace ]_[ with ]_[ to recover original email address. > Would it be possible to develop a numeric criterion to estimate the > quality of publications? > I am really interesting if there was any research addressing this problem? Several journals are dedicated to scientometrics: Cybermetrics, http://www.cindoc.csic.es/cybermetrics/ Scientometrics, http://springerlink.metapress.com/link.asp?id=101080 Regards, Ovidiu ********************************* Ovidiu Ivanciuc Sealy Center for Structural Biology, Department of Human Biological Chemistry & Genetics, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0857 USA From owner-chemistry@ccl.net Thu Sep 15 18:56:07 2005 From: "CCL" To: CCL Subject: CCL: W:Disclose your data, or not publish ! Message-Id: <-29204-050915183836-6109-UDco7DVutMfiE/Iav+VehA---server.ccl.net> X-Original-From: jle Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Thu, 15 Sep 2005 18:43:46 -0400 Mime-Version: 1.0 (Apple Message framework v622) Sent to CCL by: jle [jle---theworld.com] Replace --- with --- to recover original email address. On Sep 15, 2005, at 4:15 PM, CCL wrote: > > Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci+*+utmb.edu] > > Re: Disclose your data, or not publish ! > > While computational models of proteins can be deposited in PDB, > there is no public database for computational models of > organic compounds (including MD simulations and docking > results). > A simple solution for publishers would be to ask for > mandatory deposition of such data as supplementary materials. Perhaps interesting in the abstract, but a number of problems come to mind: 1. If publishers hold the data, would we not have to check with each publisher in turn to get the information? And if so, how much would it cost? 2. We are, err, blessed with a wide range of file formats, many of which aren't described, or even readable. Whose formats would be supported, and would the vendors and other authors provide the necessary conversion routines? 3. I would think the modeling community produces WAY more data than the Xtal community. I am unaware of modeling packages which sit atop databases so as to organize a single user's or site's data. How can those holding the data organize the sheer mass of data provided by the manuscript's authors. If we're going to even start proposing "modeling databases", lets first settle the data/file format and other mundane yet necessary things first. Joe Leonard jle---theworld.com > > Regards, > Ovidiu > ********************************* > Ovidiu Ivanciuc > Sealy Center for Structural Biology, > Department of Human Biological Chemistry & Genetics, > University of Texas Medical Branch, > 301 University Boulevard, > Galveston, Texas 77555-0857 > USA> To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line> > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST---ccl.net> > If your is mail bouncing from ccl.net domain due to spam filters, > please> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > From owner-chemistry@ccl.net Thu Sep 15 19:05:24 2005 From: "CCL" To: CCL Subject: CCL: Basis set for B3LYP Message-Id: <-29205-050915190113-29317-td4/YbMf2/5NDjTMCsIafg%a%server.ccl.net> X-Original-From: Antonio Hernandez Content-Type: multipart/alternative; boundary="----=_Part_7119_12181237.1126825269269" Date: Thu, 15 Sep 2005 16:01:09 -0700 Mime-Version: 1.0 Sent to CCL by: Antonio Hernandez [pescaomayor%a%gmail.com] Replace %a% with %a% to recover original email address. ------=_Part_7119_12181237.1126825269269 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline "[CCL]"=20 On 9/14/05, Antonio Hernandez wrote:=20 >=20 > Dear Tsuru: > In theory, you can use any contracted or uncontracted Gaussian basis set= =20 > with B3LYP functional calculations. Nevertheless, mostly all these basis= =20 > sets were optimized at the HF level of theory (or HF+correlation level).= =20 > For consistency, I would prefer to use basis sets optimized at the=20 > Density Functional Theory level of theory, as those described by Salahub = in: > N. Godbout, D. R. Salahub, J. Andzelm and E. Wimmer, Can. J. Chem. 70=20 > (1992) 560.=20 > You can get these at the website=20 > http://www.emsl.pnl.gov/forms/basisform.html > under DZVP(DFT Orbital) , DZVP2(DFT orbital) and TZVP(DFT Orbital) or=20 > DGauss Polarized DFT Orbitals Basis Sets. > I have personally obtained excellent results with this DFT + Salahub=20 > basis sets combination=20 > (see for instance: Theor. Chem. Acc. 106 (2001) 218).=20 > Best Whishes: Antonio Hernandez. > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D > On 9/13/05, CCL wrote:=20 > >=20 > >=20 > > Sent to CCL by: errol lewars [elewars-$-trentu.ca ] > > 2005 Sept 14 > >=20 > > Hello, > >=20 > > The B3LYP functional is normally used with the 6-31G* basis set or > > higher (e.g. 6-31G**, 6-311G*--of course there are other basis sets > > besides these Pople sets; the Dunning correlation-consistent sets are= =20 > > also popular). It is generally thought that the use of a smaller basis > > with a correlated method (DFT or correlated ab initio) is pointless, bu= t > > I know of no definitive study of this. > >=20 > > A rare case of B3LYP/3-21G is the calc. of IEs of carbenes by=20 > > optimization at this level followed by B3LYP/6-31+G* single point > > energies: H M Muchall et al., Can J Chem, 1998, 76, 221. The 3-21G basi= s > > was better than the 6-31G* with CASSCF (not a DFT method) in a study of > > the Cope rearrangement: D A Hrovat et al., J Am Chem Soc, 1999, 121,=20 > > 169. > >=20 > > E. Lewars > > =3D=3D=3D > >=20 > >=20 > >=20 > > CCL wrote: > >=20 > > >Sent to CCL by: "Telkuni Tsuru" [telkuni : venus.dti.ne.jp > > ] > > >Hello, CCLers. > > > > > >I like to know suitable basis set level for B3LYP on G98W. > > > > > >For example, MP2 calculation should not be carried out with > > >low level basis set(e.g . STO-3G). So I like to know lowest basis > > >set for B3LYP. Is "B3LYP/STO-3G" possible ? > > > > > > All responses, I will appreciate. > > > I will summarize them and send to CCL. > > > > > > > > > Thanks in advance > > >--------------------------------------------------- > > > Telkuni Tsuru telkuni%a%venus.dti.ne.jp> > > > > > > > > > > > > > >=20 > >=20 > >=20 > > -=3D This is automatically added to each message by the mailing script = =3D- > > To send e-mail to subscribers of CCL put the string CCL: on your=20 > > Subject: line> >=20 > > Send your subscription/unsubscription requests to:=20 > > CHEMISTRY-REQUEST%a%ccl.net> >=20 > > If your is mail bouncing from ccl.net domain due to= =20 > > spam filters, please> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-= +=20 > >=20 > >=20 > >=20 > >=20 > >=20 > ------=_Part_7119_12181237.1126825269269 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline "[CCL]"

On 9/14/05, = Antonio Hernandez <pescaoma= yor%a%gmail.com> wrote:
Dear Tsuru:
 
In theory, you can use any contracted or uncontracted Gaussian basis s= et with B3LYP functional calculations.  Nevertheless, mostly all = these basis sets were optimized at the HF level of theory (or HF+correlatio= n level).=20
 
For consistency, I would prefer to use basis sets optimized at the Den= sity Functional Theory level of theory, as those described by Salahub in:
 
N. Godbout, D. R. Salahub, J. Andzelm and E. Wimmer, Can. J. Chem. 70 = (1992)  560.  
   
   You can get these at the website 
    under DZVP(DFT Orbital) , DZVP2(DFT orbital) and TZ= VP(DFT Orbital) or DGauss Polarized     DFT Orbitals Ba= sis Sets.
 
I have personally obtained  excellent results with this DFT + Sal= ahub basis sets combination
(see for instance:  Theor. Chem. Acc. 106 (2001) 218).  = ;            &n= bsp;            = ;     
 
Best Whishes: Antonio Hernandez.
 
 
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D
On 9/13/05, = CCL <owner-chemistry%a%ccl.= net > wrote:=20

Sent to CCL by: errol lewars= [elewars-$- trentu.ca]
2005 Sept 14

Hello,

The B3LYP functional is= normally used with the 6-31G* basis set or
higher (e.g. 6-31G**, 6-311G= *--of course there are other basis sets
besides these Pople sets; the Du= nning correlation-consistent sets are=20
also popular). It is generally thought that the use of a smaller basis<= br>with a correlated method (DFT or correlated ab initio) is pointless, but=
I know of no definitive study of this.

A rare case of B3LYP/3-21= G is the calc. of IEs of carbenes by=20
optimization at this level followed by B3LYP/6-31+G* single point
en= ergies: H M Muchall et al., Can J Chem, 1998, 76, 221. The 3-21G basis
w= as better than the 6-31G* with CASSCF (not a DFT method) in a study of
the Cope rearrangement: D A Hrovat et al., J Am Chem Soc, 1999, 121, 169.
E. Lewars
=3D=3D=3D



CCL wrote:

>Sent to C= CL by: "Telkuni Tsuru" [telkuni : venus.dti.ne.jp]
>Hello, CCLers.
>
>I like to know su= itable basis set level for B3LYP on G98W.
>
>For example, MP2 c= alculation should not be carried out with
>low level basis set(e.g . STO-3G). So I like to know lowest basis
>set for B3LYP. Is "B= 3LYP/STO-3G" possible ?
>
>  All responses, I wi= ll appreciate.
>  I will summarize them and send to CCL.>
>
>  Thanks in advance
>----------------------------------= -----------------
>       Telkuni Tsuru=      telkuni%a%venus.dti.ne.jp>
>
>
>
>


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