From chemistry-request@ccl.net Tue Apr 19 05:16:03 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3J9G2w1001567 for ; Tue, 19 Apr 2005 05:16:02 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j3J9G2hu001566 for chemistry(at)ccl.net; Tue, 19 Apr 2005 05:16:02 -0400 Date: Tue, 19 Apr 2005 05:16:02 -0400 Message-Id: <200504190916.j3J9G2hu001566(at)server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request(at)ccl.net using -f From: "Chenk, , Huncu" To: chemistry(at)ccl.net X-Web-Message-Number: 050419051428-1452 Subject: W:Double bond problem on transition metals X-Spam-Status: No, score=-0.6 required=5.0 tests=ALL_TRUSTED, FORGED_YAHOO_RCVD autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Hello All, I do SP+FREQ calculations of some transition metals on B3lYP/LANL2DZ level with Gaussian03. For some of the compounds i.e. Cu2M=O, CuHM=O or Cu=M=O (M=Ti,Zr,Si...) I cannot produce double bond between M and O or Cu and M. What should I do to fix this problem? Many Thanks, Chenk Huncu che_hun(at)yahoo.com Osmangazi University Chemical Engineering Department Eskisehir From chemistry-request@ccl.net Tue Apr 19 07:18:12 2005 Received: from web53709.mail.yahoo.com (web53709.mail.yahoo.com [206.190.37.30]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j3JBI5Fx008857 for ; Tue, 19 Apr 2005 07:18:05 -0400 Received: (qmail 47486 invoked by uid 60001); 19 Apr 2005 11:18:04 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=6CDYuVnDIk1I4cIpmTwu2dxVAwweOMbgihD2+S20s4i7UwWJrnFv6GvQ1ihDUzLtZMrfW016mNPOMKAjzNwx5aISTWMVdtvJAEJ2VoAq4zuG+j4A7znSPk/77R788vEZ46nP3OO75mIlboOoWLF2tojVJi6Pjl4Sv8AZK4MYrFE= ; Message-ID: <20050419111804.47484.qmail*at*web53709.mail.yahoo.com> Received: from [68.192.170.107] by web53709.mail.yahoo.com via HTTP; Tue, 19 Apr 2005 04:18:04 PDT Date: Tue, 19 Apr 2005 04:18:04 -0700 (PDT) From: Wendy Cornell Subject: CCL: COMP - Abstract submission deadline for D.C. meeting is Apr 25 To: CHEMISTRY*at*ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1574480613-1113909484=:44010" X-Spam-Status: No, score=0.9 required=5.0 tests=DNS_FROM_RFC_ABUSE,HTML_20_30, HTML_MESSAGE autolearn=no version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net --0-1574480613-1113909484=:44010 Content-Type: text/plain; charset=us-ascii Reminder -- April 25 is the ACS COMP division deadline for submitting abstracts for the Fall 2005 meeting in Washington D.C. http://oasys.acs.org Best regards, -Wendy Cornell Program Chair, COMP Division Director, Molecular Systems Merck & Co, Inc. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com --0-1574480613-1113909484=:44010 Content-Type: text/html; charset=us-ascii
Reminder -- April 25 is the ACS COMP division deadline for submitting abstracts for the Fall 2005 meeting in Washington D.C.
 
http://oasys.acs.org
 
Best regards,
-Wendy Cornell
Program Chair, COMP Division
Director, Molecular Systems
Merck & Co, Inc.

__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com --0-1574480613-1113909484=:44010-- From chemistry-request@ccl.net Tue Apr 19 00:20:54 2005 Received: from sandmail01.sd.accelrys.com (rrcs-67-52-158-62.west.biz.rr.com [67.52.158.62]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3J4Kn55012650 for ; Tue, 19 Apr 2005 00:20:50 -0400 To: chminf-l[at]listserv.indiana.edu, chemistry[at]server.ccl.net, qsar_society[at]accelrys.com Subject: QSAR Society elections for 2006-2010 MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.5.1 January 21, 2004 Message-ID: From: Osman F Guner Date: Mon, 18 Apr 2005 21:20:31 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.5.2|June 01, 2004) at 04/18/2005 09:20:31 PM, Serialize complete at 04/18/2005 09:20:31 PM Content-Type: multipart/alternative; boundary="=_alternative 0017E0A088256FE8_=" X-Spam-Status: No, score=0.5 required=5.0 tests=DNS_FROM_RFC_ABUSE, FORGED_RCVD_HELO,HTML_40_50,HTML_MESSAGE autolearn=no version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net This is a multipart message in MIME format. --=_alternative 0017E0A088256FE8_= Content-Type: text/plain; charset="US-ASCII" Hello all: I apologize for multiple posting. The QSAR Society elections for the 2006-2010 officers and board members have started and will run until May 15, 2005 at 5 PM (U.S. Pacific time). Each member of the QSAR and Modelling Society with a functional e-mail address that is registered at the Society listserver should have received an e-mail ballot with the subject "International QSAR and Modelling Society - 2006-2010 Election of the Chair and Board" from Election.Ballot[at]Campus-Vote.com. If you are a QSARMS member and have not received the e-mail ballot, the most likely reason may be that your Email address is incorrect or obsolete. Please check the QSAR Society Web site to the membership list at (http://www.qsar.org/members.htm). If your name is listed and have not received the ballot, please contact me and I will send you a ballot this weekend with your personal access code. Candidates for the Chair 2006-2010 position are: Klaus Gundertofte David Livingstone Tudor I. Oprea Alexander Tropsha Candidates for the Board membership are: Dimitris Agrafiotis, Antonia Tavares do Amaral, Stefan Balaz, Curt Breneman, Marvin Charton, Henryk Chojnacki, Jacques Chretien, Gabrielle Cruciani, Toshio Fujita, Klaus Gundertofte, Osman Guner, Lemont Kier, Hugo Kubinyi, David Livingstone, Yvonne Martin, Cherif Matta, Carlos Alberto Montanari, Tudor Oprea, Oleg Raevsky, Kunal Roy, Esin Aki Sener, Veer Shanmugasundaram, Alex Tropsha, Han van de Waterbeemd, Herschel Weintraub, and Dave Winkler. Cheers...Osman Executive Director Cheminformatics and Rational Drug Design Accelrys Inc., 858-799-5341 osman[at]accelrys.com, http://www.accelrys.com --=_alternative 0017E0A088256FE8_= Content-Type: text/html; charset="US-ASCII"
Hello all:

I apologize for multiple posting.

The QSAR Society elections for the 2006-2010 officers and board members have started and will run until May 15, 2005 at 5 PM (U.S. Pacific time).

Each member of the QSAR and Modelling Society with a functional e-mail address that is registered at the Society listserver should have
received an e-mail ballot with the subject "International QSAR and Modelling Society - 2006-2010 Election of the Chair and Board" from
Election.Ballot[at]Campus-Vote.com.  If you are a QSARMS member and have not received the e-mail ballot, the most likely reason may be that your Email address is incorrect or obsolete.  Please check the QSAR Society Web site to the membership list at (http://www.qsar.org/members.htm).  If your name is listed and have not received the ballot, please contact me and I will send you a ballot this weekend with your personal access code.

Candidates for the Chair 2006-2010 position are:

Klaus Gundertofte  
David Livingstone  
Tudor I. Oprea  
Alexander Tropsha  

Candidates for the Board membership are:

Dimitris Agrafiotis,
Antonia Tavares do Amaral,
Stefan Balaz,
Curt Breneman,
Marvin Charton,
Henryk Chojnacki,
Jacques Chretien,
Gabrielle Cruciani,
Toshio Fujita,
Klaus Gundertofte,
Osman Guner,
Lemont Kier,
Hugo Kubinyi,
David Livingstone,
Yvonne Martin,
Cherif Matta,
Carlos Alberto Montanari,
Tudor Oprea,
Oleg Raevsky,
Kunal Roy,
Esin Aki Sener,
Veer Shanmugasundaram,
Alex Tropsha,
Han van de Waterbeemd,
Herschel Weintraub, and
Dave Winkler.
Cheers...Osman

Executive Director
Cheminformatics and Rational Drug Design
Accelrys Inc.,  858-799-5341
osman[at]accelrys.com, http://www.accelrys.com --=_alternative 0017E0A088256FE8_=-- From chemistry-request@ccl.net Tue Apr 19 10:21:09 2005 Received: from leitl.org (leitl.org [217.172.178.65]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3JEL3fM021196 for ; Tue, 19 Apr 2005 10:21:04 -0400 Received: by leitl.org (Postfix, from userid 500) id 9D1DC3A84DB; Tue, 19 Apr 2005 16:21:28 +0200 (CEST) Date: Tue, 19 Apr 2005 16:21:28 +0200 From: Eugen Leitl To: lhhu [] yangtze.hku.hk, chemistry [] ccl.net Subject: Re: CCL:Partition Coefficient Calculation Message-ID: <20050419142128.GY21209 [] leitl.org> References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: User-Agent: Mutt/1.4i X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net On Mon, Apr 18, 2005 at 04:21:57PM +0800, lhhu [] yangtze.hku.hk wrote: > > Dear All, > > I want to calculate LogP for a series of drug molecules. Any one could > recommend a program or method? A number of methods are compared in http://pubwww.srce.hr/acphee/9104.pdf (unfortunately, the statistical significance of above paper is about zero). (I've made a relatively thorough websearch on *logP and docking in context of drug discovery, and saved the results in http://leitl.org/docs/drug/ -- it might be of some use). HTH, -- Eugen* Leitl leitl ______________________________________________________________ ICBM: 48.07078, 11.61144 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE http://moleculardevices.org http://nanomachines.net From chemistry-request@ccl.net Tue Apr 19 13:38:57 2005 Received: from arwen.arqule.com (smtp.arqule.com [64.119.137.200] (may be forged)) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3JHcr6q006129 for ; Tue, 19 Apr 2005 13:38:53 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.0.6487.1 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: Final call for papers for Visualization of Models at the Washington ACS Fall 2005 Date: Tue, 19 Apr 2005 12:38:26 -0400 Message-ID: <59527B219115AA4CBBE9DEF5D729F22201C84459{at}ACE.arqule.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Final call for papers for Visualization of Models at the Washington ACS Fall 2005 Thread-Index: AcVE/jXRdgMg/IR8SXSyYW/nVzLH1A== From: "Smellie, Andrew" To: X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j3JHcv6q006135 230th ACS National Meeting, Washington DC,August 28 - September 1, 2005 COMP division Final Call for papers Deadline for abstract submission is April 25th, 2005 The Visualization and Interpretation of Computational Models ============================================================ There are many different approaches available for modeling chemical data. Biological activities can be estimated using a number of approaches such as numerical modeling, pharmacophore construction or structural comparisons. The interaction of small molecules to binding sites can be described using docking models, shape comparisons or pharmacophores. Physico-chemical properties can be estimated using a variety of techniques. All these problems share one common and often unresolved issue. Whatever the model is teaching us about the system in question must be communicated to the clients of the model. This symposium will focus on methods that have been developed to aid in the interpretation of models of all types common in Computational Chemistry. The symposium will not discuss new modeling techniques, but will focus on methods that have been devised to extract the maximum information from the models and communicate that information to clients. Papers are invited that cover issues on * Visualization of Modeling Data * Interpretation of Modeling Data * Communication of knowledge from the model to clients (e.g. chemists, biologists etc) The organizers are Andrew Smellie, Anton Filikov and Rocio Palma of Arqule Inc. Please submit your abstracts to via the ACS OASYS system at http://oasys.acs.org/acs/230nm/oasys.htm Further information about the symposium can be found at www.arqule.com/acs230 We look forward to your contribution is this vital area of research and development. Dr. Andrew Smellie Senior Scientist Arqule Inc. 19 Presidential Way, Woburn MA 01801 USA asmellie{at}arqule.com 781-994-0559 (direct) 781-994-0679 (fax) From chemistry-request@ccl.net Tue Apr 19 10:26:55 2005 Received: from hawk.dcu.ie (mail.dcu.ie [136.206.1.5]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3JEQpAm021787 for ; Tue, 19 Apr 2005 10:26:51 -0400 Received: from drugs.ucd.ie (137.43.140.40) by hawk.dcu.ie (7.0.016) id 41108D190104D086 for chemistry{at}ccl.net; Tue, 19 Apr 2005 15:26:50 +0100 Subject: Effect of oxidation on electron density From: "Noel O'Boyle" To: chemistry{at}ccl.net Content-Type: text/plain Message-Id: <1113920796.31132.16.camel{at}drugs.ucd.ie> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.4.5 (1.4.5-9) Date: Tue, 19 Apr 2005 15:26:50 +0100 Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Dear CCLers, I have a question related to visualising the instantaneous change in electron density accompanying oxidation (of a metal complex). I am using Gaussian03 and have calculated the electron density of the molecule in its oxidised state (at the geometry of the native state) and subtracted this from the electron density of the molecule in its native state. However, I have just noticed that the total spin density of the oxidised molecule gives an almost identical picture. Is this true in general? (I don't have a good understanding of what the total spin density shows.) Regards, Noel O'Boyle, University College Dublin. From chemistry-request@ccl.net Tue Apr 19 19:28:52 2005 Received: from newultra.chem.ucsb.edu (ultra.chem.ucsb.edu [128.111.114.119]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3JNSo9R029577 for ; Tue, 19 Apr 2005 19:28:50 -0400 Received: from localhost (localhost [127.0.0.1]) by newultra.chem.ucsb.edu (Postfix) with ESMTP id 5617A74FB8D; Tue, 19 Apr 2005 15:18:43 -0700 (PDT) Received: from newultra.chem.ucsb.edu ([127.0.0.1]) by localhost (ultra [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 10089-03; Tue, 19 Apr 2005 15:18:42 -0700 (PDT) Received: by newultra.chem.ucsb.edu (Postfix, from userid 3016) id 6113B74FB89; Tue, 19 Apr 2005 15:18:42 -0700 (PDT) Received: from localhost (localhost [127.0.0.1]) by newultra.chem.ucsb.edu (Postfix) with ESMTP id 5F64376B908; Tue, 19 Apr 2005 15:18:42 -0700 (PDT) Date: Tue, 19 Apr 2005 15:18:42 -0700 (PDT) From: John Bushnell To: "Chenk, , Huncu" Cc: chemistry = ccl.net Subject: Re: CCL:W:Double bond problem on transition metals In-Reply-To: <200504190916.j3J9G2hu001566 = server.ccl.net> Message-ID: References: <200504190916.j3J9G2hu001566 = server.ccl.net> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed X-Virus-Scanned: amavisd-new at chem.ucsb.edu X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net This is a bit confusing: "SP+FREQ": Single point followed by a frequency calculation? Frequencies are calculated at local minima, so I assume that you really did an optimization followed by a frequency calculation? "cannot produce double bond": How do you define a double bond looking at results from a B3LYP calculation? If you don't see a "double bond" in some kind of visualization software, it just means that the bond distance cutoffs used in that program don't indicate a typical double bond. Perhaps from NBO or AIM analysis? This isn't clear. Without having any more information, it is quite possible that you aren't finding the electronic configuration that you expected. But it isn't very clear what you did, or what it is you're not finding. - John Bushnell On Tue, 19 Apr 2005, Chenk, , Huncu wrote: > Hello All, > > I do SP+FREQ calculations of some transition metals on B3lYP/LANL2DZ > level with Gaussian03. > > For some of the compounds i.e. Cu2M=O, CuHM=O or Cu=M=O (M=Ti,Zr,Si...) > I cannot produce double bond between M and O or Cu and M. What should I > do to fix this problem? > > Many Thanks, > Chenk Huncu > > che_hun = yahoo.com > Osmangazi University > Chemical Engineering Department > Eskisehir From chemistry-request@ccl.net Mon Apr 18 12:06:55 2005 Received: from mailer.gwdg.de (mailer.gwdg.de [134.76.10.26]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3IG6mg1025215 for ; Mon, 18 Apr 2005 12:06:48 -0400 Received: from pcboehme.gwdg.de ([134.76.5.4]) by mailer.gwdg.de with esmtpsa (TLSv1:RC4-MD5:128) (Exim 4.42) id 1DNXbJ-0000Rw-Eh; Mon, 18 Apr 2005 16:51:49 +0200 Message-ID: <4263C980.9020303 = gwdg.de> Date: Mon, 18 Apr 2005 16:51:44 +0200 From: Christian Boehme User-Agent: Mozilla Thunderbird 1.0 (X11/20041206) To: help = gaussian.com, chemistry = ccl.net Subject: Compiling g03 rev c02 on Opteron with pgf 5.2-4 Hello! I have tried to compile Gaussian03 on our Opteron machines running under SuSE SLES 9 using pgf version 5.2-4. While PGI 5.2-x is the supported compiler suite according to gaussian.com webpages the build scripts of our g03 version still contain 5.1 pathnames. I fixed this and Gaussian seemed to compile without errors. However, the resulting binaries segfault after just a few lines of output: Entering Gaussian System, Link 0=g03 Initial command: /usr/product/gaussian64/g03/l1.exe /home/gwdg/GWDG/cboehme1/test/g03tests/Gau-28741.inp -scrdir=/ho me/gwdg/GWDG/cboehme1/test/g03tests/ I looked at the strace and seemingly l1.exe segfaults for no obvious reasons. What can I do? Best wishes Christian Boehme -- Dr. Christian Boehme GWDG Private: Am Fassberg Wilhelm-Raabe-Str. 15 37077 Gvttingen 37083 Gvttingen email: Christian.Boehme = gwdg.de ChristianBoehme = web.de phone: +49 (0)551 201-1839 +49 (0)551 3077000 fax: +49 (0)551 201-2150 +49 (0)551 3077077