From chemistry-request@www.ccl.net Mon Sep 7 02:39:16 1998 Received: from frontier.tno.nl (frontier.tno.nl [134.221.1.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id CAA21373 Mon, 7 Sep 1998 02:37:33 -0400 (EDT) Received: from stevin.pml.tno.nl (stevin.pml.tno.nl [134.221.122.11]) by frontier.tno.nl (8.8.8/8.8.8) with SMTP id IAA12805 for ; Mon, 7 Sep 1998 08:36:58 +0200 (MET DST) Received: from mailrouter.pml.tno.nl (wnt-950140) by stevin.pml.tno.nl (4.1/1.53) id AA15176; Mon, 7 Sep 98 08:31:33 +0200 Received: from exchange.pml.tno.nl (EXCHANGE [134.203.134.74]) by mailrouter.pml.tno.nl with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.1960.3) id 3D6QGLRS; Mon, 7 Sep 1998 08:33:16 +0200 Received: by postoffice.pml.tno.nl with Internet Mail Service (5.5.1960.3) id ; Mon, 7 Sep 1998 08:37:03 +0200 Message-Id: <97C27A97BB05D211B37100805FE2A63814A2AB@postoffice.pml.tno.nl> From: "Gurp, Ron van" To: "'chemistry@www.ccl.net'" Cc: "Linders, Marco" Subject: Summary: Molecular area of adsorbates Date: Mon, 7 Sep 1998 08:36:58 +0200 Mime-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Content-Type: text/plain Dear Netters, Thanks for all responses to our question. Here is our summary as promised Ron van Gurp and Marco Linders Our question was: >Dear Netters, >We are looking for a program that calculates the area of a molecule, >which is projected on a surface. The practical background is the >following: consider molecules that are adsorbed on a surface. What is >the average area they occupy on that surface ? This depends of course >on how a particular molecule adsorbs on a surface, i.e. its orientation >relative to the surface. As a first estimate one may take the average of >a certain number of projections (or cross sectional areas). Does anyone >know of a program that calculates such projected surfaces from a MOL, >XYZ, PDB or QUANTA MSF file input, or, even better, a program which >also takes into account the preferred orientations of a molecule on a >surface? Jack A. Smith wrote: Look at Craig Taverner's steric program (ftp://hobbes.gh.wits.ac.za/pub/steric/) based on solid angles. The solid angle corresponds to a projection onto an enclosing sphere, but if you set the origin far enough away from the molecule (effectively increasing the radius of the enclosing sphere), the solid angle projection will approach an orthogonal projection. The projected area would be R*R*(Solid Angle), where R is the radius of the sphere (the distance between the origin and the furthest atom). The program will read PDB format, and it will generate a GnuPlot plot of the angular profile. The program should be easily modified to give the othogonal projection directly without resetting the origin Donald B. Boyd wrote: Hello Ronald, Check out the software products of Oxford Molecular. I think they have a program (for sale) that projects molecules onto a surface. Oxford Molecular, QCPE, etc. have programs that calculate molecular surface areas. See the appendix of Vol. 7 of Reviews in Computational Chemistry for more details. Dayong He wrote Hi, Gurp: go to the page : http://www.polymer.uakron.edu/~hoon I know he has done this. Good luck. Yong Cory Bystrom wrote: Two software packages you might be most interested in: Surfnet: http://bsmcha1.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html MSRoll http://www.biohedron.com/msp.html Hope this helps, Fuad Abdallah wrote: Dear Ronald, you could try surfnet http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html that comes free for academic users (as far as i remember) or, icm, http://www.molsoft.com a (very good) commercial solution for your problem. Once again, many thanks. We feel our problem has been solved!! Ron and Marco From chemistry-request@www.ccl.net Mon Sep 7 05:20:46 1998 Received: from dirac.cnrs-orleans.fr (dirac.cnrs-orleans.fr [163.9.6.67]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA22310 Mon, 7 Sep 1998 05:20:46 -0400 (EDT) Received: (from hinsen@localhost) by dirac.cnrs-orleans.fr (AIX4.3/UCB 8.8.8/8.7) id LAA16030; Mon, 7 Sep 1998 11:19:33 +0200 Date: Mon, 7 Sep 1998 11:19:33 +0200 Message-Id: <199809070919.LAA16030@dirac.cnrs-orleans.fr> From: Konrad Hinsen To: chemistry@www.ccl.net Subject: New free program: DomainFinder finds dynamical domains in proteins DomainFinder is an interactive program for the determination and characterization of dynamical domains in proteins. Its key features are: - computational efficiency: even large proteins can be analyzed using a desktop computer in a few minutes - ease of use: a state-of-the-art graphical user interface - export of results for visualization and further analysis (VRML, PDB, and MMTK object format) DomainFinder is free to use for anyone, and should work on any Unix system. For more information and for downloading, see http://dirac.cnrs-orleans.fr/DomainFinder/ -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@www.ccl.net Mon Sep 7 05:24:38 1998 Received: from anne.chemie.unibas.ch (anne.chemie.unibas.ch [131.152.112.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id FAA22330 Mon, 7 Sep 1998 05:24:36 -0400 (EDT) From: barbosa@anne.chemie.unibas.ch Received: by anne.chemie.unibas.ch (AIX 3.2/UCB 5.64/4.03) id AA15322; Mon, 7 Sep 1998 11:23:40 +0200 Message-Id: <9809070923.AA15322@anne.chemie.unibas.ch> Subject: summary: uhf and biradicals 3 To: chemistry@www.ccl.net Date: Mon, 7 Sep 1998 11:23:40 +0200 (DFT) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCl, Apparently an error occured for the submission of my last email therefore I post again the complete email. ______________________________________________________________________ After sending a first summary on my question about uhf and biradicals, I received new answers. Therefore I post a second summary of this answers. Frederique ______________________________________________________________________ My question: Dear CCL, I am looking for some references on calculations with unrestricted hartree fock method on singlet biradicals in the ground state. Thanks in advance Frederique ______________________________________________________________________ >From assfeld@host23.lctn.u-nancy.fr Salut Frederique, je suppose que tu utilises G94? Dans ce cas, utilise le mot clef : GUESS=MIX ca brise la symetrie spatiale des spinorbitales. Le mot clef NOSYM peux aussi aider. Il y a des papiers de Pople et d'autres de Tim Clark datant des annees 80 a propos des dipoles 1-3, qui utilisent cette methode. Xavier Assfeld assfeld@lctn.u-nancy.fr and in a second email: Re, il y a eu recemment des articles de C. Cramer sur les biradicaux : "Density Functional Theory: Excited States and Spin Annihilation" C. J. Cramer, F. J. Dulles, D. J. Giesen and J. Almlof, Chem. Phys. Lett. je ne me rappelle plus le numero mais c'est paru en 1995 ou debut 1996. "Density Funcitonal Calculations of Radicals and Diradicals" M. H. Lim, S. E. Worthington, F. J. Dulles and C. J. Cramer in Density Functional Methods in Chemistry. ACS Symposium Series, B. B. Laird, T. Ziegler, R. Ross Eds. American Chemical Society: Washington, DC, 1996. ______________________________________________________________________ >From boyd@chem.iupui.edu Hello Frederique, I saw your posting on CCL. We will have a beautiful tutorial on diradicals and UHF in Vol. 13 of Reviews in Computational Chemistry. This volume will not appear till next March unfortunately. It is presently in press. The wait will be long, but I assure you that it will be worthwhile. Don Donald B. Boyd, Ph.D. Research Professor of Chemistry Editor, Reviews in Computational Chemistry Editor, Journal of Molecular Graphics and Modelling Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Telephone 317-274-6891, FAX 317-274-4701 E-mail boyd@chem.iupui.edu Web http://chem.iupui.edu/rcc/rcc.html ______________________________________________________________________ >From segalemb@usp.br Dear Frederique, Recently it is published a very interestig paper of E. Davidson (Int. J. Quantum Chem., 69, 241-245) that analyse the pitfails of calculations of diradicals using DFT methods. Hope this help you, Sergio ______________________________________________________________________ ======================================================================= Frederique BARBOSA Institute for Organic Chemistry University of Basel E-mail: barbosa@anne.chemie.unibas.ch St. Johanns-Ring 19 phone : 061/267 11 57 4056 Basel fax : 061/267 11 05 Switzerland ======================================================================= From chemistry-request@www.ccl.net Mon Sep 7 06:18:28 1998 Received: from ntu-kpi.kiev.ua (root@ntu-kpi.kiev.ua [195.178.136.20]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA22568 Mon, 7 Sep 1998 06:18:17 -0400 (EDT) Received: from [10.0.2.42] ([10.0.2.42]) by ntu-kpi.kiev.ua (8.8.8/8.7.3) with SMTP id NAA07131 for ; Mon, 7 Sep 1998 13:17:41 +0300 (EEST) X-Authentication-Warning: ntu-kpi.kiev.ua: [10.0.2.42] didn't use HELO protocol Message-ID: <35F43F6E.4E19@ntu-kpi.kiev.ua> Date: Mon, 07 Sep 1998 13:17:50 -0700 From: "M. Sychev" Reply-To: sytsh@ntu-kpi.kiev.ua Organization: Chem X-Mailer: Mozilla 3.01 (Win16; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Problem with C6H5CN Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLs, During optimization of C6H5CN (in G92) I have problem: the bond lenght C - H was extended till 1.25 A, and the convergence was not met for maximum number of a cycles. In what the reason? Any references is welcome. All responses will be summarized. Thanks in advance. best regards, Tatyana Shubina Department of Organic chemistry KPI -"NTUU" Kiev Ukraine From chemistry-request@www.ccl.net Mon Sep 7 13:39:59 1998 Received: from wiley.csusb.edu (wiley.csusb.edu [139.182.2.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA23575 Mon, 7 Sep 1998 13:39:59 -0400 (EDT) Received: from localhost (kcousins@localhost) by wiley.csusb.edu (8.9.1a/8.9.1) with SMTP id KAA19654; Mon, 7 Sep 1998 10:38:25 -0700 (PDT) Date: Mon, 7 Sep 1998 10:38:25 -0700 (PDT) From: Kimberley Cousins To: "Rzepa, Henry" cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:Re: Surge in Sales for the Macintosh. In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Just thought I'd mention the source of the Mac sales jump is Oxford Molecular. It may be a coincidence, but they have been pushing hard recently in academic sales, an area where Macintosh still has a strong hold. They also appear to be serving the Mac community well, another reason for their status. Kimberley Cousins Associate Professor of Chemistry California State University, San Bernardino 5500 University Parkway San Bernardino, CA 92407 (909)880-5391 kcousins@wiley.csusb.edu http://chem.csusb.edu/~kcousins