From chemistry-request@server.ccl.net Mon Jan 14 04:03:05 2002 Received: from titanium.mater.unimib.it (root@[149.132.101.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0E934I09462 for ; Mon, 14 Jan 2002 04:03:04 -0500 Received: from rutenio.mater.unimib.it (rutenio.mater.unimib.it [149.132.99.56]) by titanium.mater.unimib.it (8.9.3 (PHNE_22672)/8.9.3) with ESMTP id KAA09833 for ; Mon, 14 Jan 2002 10:03:13 +0100 (MET) Message-Id: <5.1.0.14.0.20020114100147.00aaebb0@titanium.mater.unimib.it> X-Sender: narducci@titanium.mater.unimib.it X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Mon, 14 Jan 2002 10:02:27 +0100 To: chemistry@ccl.net From: Dario Narducci Subject: External fields in Gaussian98 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hello. I'm about to use Gaussian98 to make simulations on the electronic structure of molecules in an external electrical field. I'm slightly confused about the way Gaussian98 applies the field. The Field keyword allows the application of external multipoles, but the only parameter the user is allowed to set is the electric dipole field value. Now, as far as I know, the field generated by a dipole (or by any multipole) is not uniform, its actual value being a function of the charges of each pole and of its mutual distance. How charges and distances are set up by Gaussian (or, equivalently, what field are we talking about? Thanks to all ================================= oOo ============================== Prof. Dario Narducci, Univ. of Milano Bicocca Dept. of Materials Science, v. R. Cozzi 53, I-20125 Milano ph. +39-02-6448-5137, fax -5400, mailto:dario.narducci@unimib.it http://www.mater.unimib.it/narducci/ ================================= oOo ============================== From chemistry-request@server.ccl.net Mon Jan 14 06:26:37 2002 Received: from wb486.ch.pwr.wroc.pl ([156.17.2.50]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g0EBQaI11606 for ; Mon, 14 Jan 2002 06:26:37 -0500 Received: by wb486.ch.pwr.wroc.pl via smail with stdio id for chemistry@ccl.net; Mon, 14 Jan 2002 11:36:09 +0100 (MET) (Smail-3.2 1996-Jul-4 #16 built 1998-Dec-01) Message-Id: Date: Mon, 14 Jan 2002 11:36:09 +0100 (MET) From: zalesny@wb486.ch.pwr.wroc.pl (Robert Zalesny) To: chemistry@ccl.net, dario.narducci@unimib.it Subject: Re: CCL:External fields in Gaussian98 Hi, Actually I am not very familiar with calculations of the influence of external electric field on molecules by the use of Gaussian, but here it is what I can advise you: * maybe instead of introducing external field as a dipole Gaussian put into Hamiltonian term -dipole*Electric field? In this way one obtains uniform electric field... * As a matter of fact the electric field applied as a "sparkles" or dipoles (put at the ends of molecule) is not uniform To obtain quasi-uniform electric field with the value let us say 0.001 you should separate your + and - sparkles by the distance about 50 Angstroms. In between you will obtain almost uniform electric field. In between means the distance about 15 A. * Try to use GAMESS instead of Gaussian - there is also possiblity of optimizing the geometry in the field. * In MOPAC there is possibility of simulating electric field by sparkles. I hope that my remarks will help you somehow. Best regards Zalesny Robert Undergraduate student Quantum Chemistry Group Wroclaw University of Technology Poland From chemistry-request@server.ccl.net Mon Jan 14 07:26:30 2002 Received: from imo-m04.mx.aol.com ([64.12.136.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0ECQUI12412 for ; Mon, 14 Jan 2002 07:26:30 -0500 Received: from femtohertz@netscape.net by imo-m04.mx.aol.com (mail_out_v31_r1.9.) id g.ef.2c44a70 (22686) for ; Mon, 14 Jan 2002 07:26:18 -0500 (EST) Received: from netscape.com (mow-m03.webmail.aol.com [64.12.184.131]) by air-in04.mx.aol.com (v82.22) with ESMTP id MAILININ47-0114072618; Mon, 14 Jan 2002 07:26:18 -0500 Date: Mon, 14 Jan 2002 07:26:18 -0500 From: femtohertz@netscape.net (abcdefg hijklm) To: CHEMISTRY@ccl.net Subject: Propylene glycol Message-ID: <07AC40FF.0198307D.0EDDF854@netscape.net> X-Mailer: Atlas Mailer 1.0 Content-Type: text/plain; charset=iso-8859-1 Dear all, I would like to get the value of the free energy of aq. solvation for the following compound : *********************************** Propylene glycol (1,2-propane diol) *********************************** I tried searching some experimental journals, but couldn't locate the numerical value (in kJ/mol) anywhere. Thanks in advance, The TCG. -- __________________________________________________________________ Your favorite stores, helpful shopping tools and great gift ideas. Experience the convenience of buying online with Shop@Netscape! http://shopnow.netscape.com/ Get your own FREE, personal Netscape Mail account today at http://webmail.netscape.com/ From chemistry-request@server.ccl.net Mon Jan 14 06:21:41 2002 Received: from mh1-cam.cam.accelrys.com ([192.190.183.253]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0EBLeI11511 for ; Mon, 14 Jan 2002 06:21:41 -0500 Received: from dhcp81.scipark.cam.accelrys.com ([192.168.122.81] helo=water) by mh1-cam.cam.accelrys.com with smtp (Exim 3.12 #1 (Debian)) id 16Q5B8-0003A6-00 for ; Mon, 14 Jan 2002 11:21:26 +0000 Message-ID: <011f01c19ced$98235880$517aa8c0@water> From: "Tien Luu" To: Subject: Accelrys Life Science Training in Cambridge, UK Date: Mon, 14 Jan 2002 11:13:57 -0000 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Accelrys Inc. will be holding a pair of 2-day workshops at our office in Cambridge, UK, in March 2002. On March 5-6, the workshop "Introduction to Life Science Modelling with InsightII" will be offered. This course provides an overview of molecular modelling techniques for life sciences applications in the InsightII graphical user environment. Prior modelling experience is not assumed making this course a great place to start molecular modelling. On March 7-8, the "Homology-Based Protein Design" training will be offered. This workshop is relevant to any of our customers who are interested in predicting protein structure and who would like to make more effective use of modelling in their work. During the two-day workshop, the process of producing a three-dimensional model from an amino acid sequence will be covered step-by-step. Both manual and automatic methodologies will be discussed. Prerequisites for this course are the "Introduction to Life Science Modelling with InsightII" workshop or extensive experience with InsightII. Fees for each 2-day course are GBP 700 commercial, GBP 350 government, and GBP 280 academic. However, register for both courses and receive a 25% discount for the second course. Registration is on-line at URL http://www.accelrys.com/training/lifesci/registration.php. Further detailed information about this and other Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/lifesci/schedule.html). Please do not hesitate to contact us should you have any questions. Please note that on 1 June 2001, MSI, Synopsys, Oxford Molecular, and GCG became Accelrys. Thank you very much. Tien Luu +44 1223 402 895 Chris Arzt +1 858-799-5340 From chemistry-request@server.ccl.net Sun Jan 13 13:47:20 2002 Received: from web12908.mail.yahoo.com ([216.136.174.75]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g0DIlKI21458 for ; Sun, 13 Jan 2002 13:47:20 -0500 Message-ID: <20020113184712.59180.qmail@web12908.mail.yahoo.com> Received: from [144.32.180.37] by web12908.mail.yahoo.com via HTTP; Sun, 13 Jan 2002 18:47:12 GMT Date: Sun, 13 Jan 2002 18:47:12 +0000 (GMT) From: =?iso-8859-1?q?Meike=20Reinhold?= Subject: G98 - internal input file deleted? To: ccl MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCl'ers lately I am having great troubles with G98 in the sense that all my calculation abort with the following message: Internal input file was deleted! Error termination via Lnk1e. A restart using the checkpoint file is not possible. Could anybody advise me what to do? Many thanks in advance, Meike __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page > from News and Sport to Email and Music Charts http://uk.my.yahoo.com From chemistry-request@server.ccl.net Mon Jan 14 10:09:59 2002 Received: from iris.chimfarm.unipg.it ([141.250.13.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0EF9wI15807 for ; Mon, 14 Jan 2002 10:09:58 -0500 Received: from apollo.chimfarm.unipg.it ([141.250.13.72] ident=mirco) by iris.chimfarm.unipg.it with esmtp (Exim 2.04 #2) id 16QESA-0007kc-00 for chemistry@ccl.net; Mon, 14 Jan 2002 13:15:38 -0800 Date: Mon, 14 Jan 2002 17:21:44 +0100 (CET) From: Mirco Meniconi X-Sender: mirco@localhost.localdomain To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id g0EF9xI15808 Dear CCL users: I'm working on variables selection in QSAR models via GA.  I've just written a computational routine capable of carrying out such calculations.  Now I need to test my routine on very well-known datasets.   I'm looking for very classical datasets, like steroids and/or benzodiazepine datasets, however I need not only molecular structures and biological activity, but all matrixes from which one can perform chemometric analysis (as for example the complete steroids data matrix obtained from COMFA).   Does anybody know where I can find this? -- Dr. Mirco Meniconi dip. chimica e tecnologia del farmaco via del liceo 1 06100 Perugia university of Perugia (ITALY) phone: +39 075 585 5114 e-mail: mirco.me@inwind.it e-mail: mirco@unipg.it From chemistry-request@server.ccl.net Mon Jan 14 14:27:31 2002 Received: from mailout02.sul.t-online.com ([194.25.134.17]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0EJRVI20746 for ; Mon, 14 Jan 2002 14:27:31 -0500 Received: from fwd07.sul.t-online.de by mailout02.sul.t-online.com with smtp id 16QClN-0004IG-04; Mon, 14 Jan 2002 20:27:21 +0100 Received: from (0241709933-0001@[62.224.22.186]) by fwd07.sul.t-online.com with smtp id 16QClE-04HMC8C; Mon, 14 Jan 2002 20:27:12 +0100 From: mhbdh@t-online.de (M. Hoelscher) To: chemistry@ccl.net Subject: SCRF=PCM X-Mailer: T-Online eMail 2.33 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8BIT Date: Mon, 14 Jan 2002 20:27:12 +0100 Message-ID: <16QClE-04HMC8C@fwd07.sul.t-online.com> X-Sender: 0241709933-0001@t-dialin.net Hi folks, I have run some geometry optimisations using B3LYP/Gen SCRF=(PCM,Solvent=8) OPT with no problem (at least not that I am aware of). On some other molecules (which are chemically absolutely identic, just different conformers) the calculation aborts with a statement like: Maximum number of bonds =12 on atom 1 exceeded. Does anyone have an idea of how to get around this problem? Thanx in advance for your help, Markus Dr. Markus Hölscher Institute for Technical Chemistry and Makromolekular Chemistry University of Technology, Aachen Germany Please reply to either: mhbdh@t-online.de or to markus.hoelscher@texmc.rwth-aachen.de From chemistry-request@server.ccl.net Mon Jan 14 19:52:18 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0F0qII28870 for ; Mon, 14 Jan 2002 19:52:18 -0500 Received: from TheWorld.com (pcls2.std.com [199.172.62.104]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id TAA08045 for ; Mon, 14 Jan 2002 19:52:16 -0500 (EST) Received: from vaio.world.std.com (ppp0c154.std.com [208.192.102.154]) by TheWorld.com (8.9.3/8.9.3) with ESMTP id TAA12942 for ; Mon, 14 Jan 2002 19:52:07 -0500 Message-Id: <5.1.0.14.1.20020114195338.009f1e40@pop.theworld.com> X-Sender: jle@pop.theworld.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Mon, 14 Jan 2002 19:57:34 -0500 To: chemistry@ccl.net From: Joe Leonard Subject: Gasteiger charges questions Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Folks, 1) When people refer to Gasteiger (or Gasteiger-Marsili) charges, do they refer to the sigma charges from the original paper or the sigma/pi charges > from the second paper? J. Gasteiger, M. Marsili, Tetrahedron, 36, 1980, 3219; M. Marsili, J. Gasteiger, Croat. Chem. Acta, 53, 1980, 601 2) Have these parameters been updated or extended over the last, what, 20+ years? If so, are they accessible/published? OELib has what looks like extensions, but they aren't documented and only seem to refer to the sigma charges... 3) Is there any kind of validation suite for this work? If so, where? 4) Does anybody have a copy of the Croat. Chem. Acta paper mentioned above that they could email me? I've found many of the others listed, but this one's a little too obscure... Comments/suggestions welcome, and if I get some replies, I'll summarize for the net! Thanks in advance! Joe Leonard jle@world.std.com