From chemistry-request@server.ccl.net Fri Dec 15 10:17:30 2000 Received: from mailrelay2.lrz-muenchen.de (mailrelay2.lrz-muenchen.de [129.187.254.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA32432 for ; Fri, 15 Dec 2000 10:17:30 -0500 Received: from olymp.cup.uni-muenchen.de by mailrelay2.lrz-muenchen.de; Fri, 15 Dec 2000 16:17:08 +0100 Received: by olymp.cup.uni-muenchen.de (AIX 3.2/UCB 5.64/4.03) id AA37966; Fri, 15 Dec 2000 16:17:06 +0100 Date: Fri, 15 Dec 2000 16:17:05 +0100 (MET) From: Stefan Seidler To: CHEMISTRY@ccl.net Cc: mth@dmu.dk Subject: hcmolfix (how to call multiple times from ms-dos) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > It is possible to run the program from dosshell just writing "hcmolfix > unfixedfilname.mol > fixedfilename.mol" for one mol-file at a time. > I have tried the MS-DOS command "FOR in (c\:FILES\*.mol) DO hcmolfix" to run > the programme on a set of files, but it is not working. As far as i remember the correct syntax is for %i in (*.mol) do hcmolfix < %i > fixed\%i Don't forget to double the % if used in a batch program. Regards, Stefan mailto:stefan.seidler@cup.uni-muenchen.de From chemistry-request@server.ccl.net Fri Dec 15 03:59:29 2000 Received: from mail2.netcologne.de (mail2.netcologne.de [194.8.194.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA30077 for ; Fri, 15 Dec 2000 03:59:28 -0500 Received: from cosmologic.de (dial-213-168-89-93.netcologne.de [213.168.89.93] (may be forged)) by mail2.netcologne.de (8.9.3/8.9.3) with ESMTP id JAA26268 for ; Fri, 15 Dec 2000 09:59:18 +0100 (MET) Message-ID: <3A39DD61.1114EE7@cosmologic.de> Date: Fri, 15 Dec 2000 09:59:13 +0100 From: "Dr. Andreas Klamt" Organization: COSMOlogic GmbH&CoKG X-Mailer: Mozilla 4.7 [de] (Win98; I) X-Accept-Language: en,pdf MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Visualization of COSMO polarization charge densities and logP Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleagues, I like to inform you about novel way of visualizing COSMO polarization charge densities and of thermodynamic properties like logP on the molecular surface. As I pointed out in my COSMO-RS papers (for references see http://www.cosmologic.de) the polarization charge density sigma of a molecule embedded in a conductor is a very good, local descriptor for molecular interactions in solution. Indeed it is an even better descriptor than electrostatic potential (ESP), because ESP is rather longe-ranging while interactions are more local. As an example consider a surfactant with a positively charged head group. ESP shows a positive sign on the entire alkane chain of the surfactant, although this alkane chain behaves like a normal alkane chain. In contrast, the polarization charge density sigma shows high polarity on the head group, but describes the alkane chain just as a normal alkane chain. As demonstrated in my COSMO-RS work, even hydrogen bonding and "hydrophobicity" can be described by sigma. Hence sigma is the most important interaction descriptor which should be studied on the surface of molecules to analyse their physicochemical behaviour. Our next release of COSMOtherm will be able to generate high quality VRML visualizations of sigma on the molecular surface. Find a bunch of example WRL-files on our homepage: http://www.cosmologic.de/visual.html As COSMO-RS/COSMOtherm calculates physicochemical properties like logP as a surface integral of a function of sigma, it is trivial for us to visualize any such property on the molecular surface. Thus you can study such properties as a function of chemical structure and of conformation, without any restriction by missing fragments. Examples for logP are given on the homepage as well. Have fun with the colorful pictures. Best regards Andreas Klamt -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: 49-2171-73168-1 Fax: ...-9 e-mail: andreas.klamt@cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Dec 15 13:38:22 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA00481 for ; Fri, 15 Dec 2000 13:38:22 -0500 Received: from uscmail.usc.es (uscmail.usc.es [193.144.75.8]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id NAA21625 for ; Fri, 15 Dec 2000 13:37:57 -0500 (EST) Received: from qfsaulo.usc.es (qfsaulo.usc.es [193.144.74.185]) by uscmail.usc.es (8.9.1/8.9.1) with ESMTP id TAA10967 for ; Fri, 15 Dec 2000 19:37:57 +0100 (MET) Message-Id: <5.0.0.25.0.20001215193649.009f77e0@correo.usc.es> X-Sender: qfsaulo@correo.usc.es X-Mailer: QUALCOMM Windows Eudora Version 5.0 Date: Fri, 15 Dec 2000 19:40:39 +0100 To: chemistry@ccl.net From: Saulo =?iso-8859-1?Q?V=E1zquez?= Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear subscribers, We would like to know what could be considered the spin-orbit coupling of the CH3O (methoxy) radical to estimate the electronic degeneracy for its ground state. The literature only reports spin-orbit splitting values for individual vibrational modes (for instance, Lee et al. J. Chem. Phys. 99, 9465 (1993). The question is: How do we estimate the spin orbit coupling of the methoxy radical in its ground state (doublet E) which we need for the electronic degeneracy? Would it be an average of the splitting of each mode? Any hints on how to approach this problem would be deeply appreciated. A summary of the responses will be sent to the list. Many thanks in advance. Saulo A. Vazquez Departamento de Quimica Fisica Universidad de Santiago de Compostela Santiago de Compostela Spain