From chemistry-request@server.ccl.net Mon Oct 2 03:16:48 2000 Received: from tci001.uibk.ac.at (tci001.uibk.ac.at [138.232.32.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA30856 for ; Mon, 2 Oct 2000 03:16:47 -0400 Received: from tci005.uibk.ac.at (tci005.uibk.ac.at [138.232.32.5]) by tci001.uibk.ac.at (Postfix) with SMTP id 3C0FB4EB2 for ; Mon, 2 Oct 2000 09:16:24 +0200 (MET DST) Sender: hal@tci005.uibk.ac.at To: chemistry@ccl.net Subject: ion-water three-body potential From: Hannes Loeffler Date: 02 Oct 2000 09:16:38 +0200 Message-ID: Lines: 26 User-Agent: Gnus/5.0807 (Gnus v5.8.7) XEmacs/21.1 (Channel Islands) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers, we would like to improve our MD simulations of ions in aqueous solution with a three-body potential between the ion and water. Currently we use the flexible CF2 water model including a special intra-molecular potential. The ion-water interactions are calculated ab initio at an appropriate level. Now we would like to know if we can get away with a simple three-body potential by sampling at various O-ion-O distances and angles (the water geometry remains rigid). However, the question is how the forces of the atoms of the water molecule should be calculated. Some rigid water models from the literature compute forces for just the ion and the oxygens. Is it possible to adopt such a simple model also to a flexible water molecule? Is it valid to assume that the hydrogens will adjust properly under the influence of the two-body and intra-molecular forces only? We would be grateful for pointers to the literature or any other hint. Hannes Loeffler. -- Hannes Loeffler, Tel. +43-512-507-5166 Institute for General, Inorganic and Theoretical Chemistry University of Innsbruck/Austria From chemistry-request@server.ccl.net Mon Oct 2 05:30:57 2000 Received: from mel.ruc.dk (mel.ruc.dk [130.225.220.27]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA31574 for ; Mon, 2 Oct 2000 05:30:56 -0400 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by mel.ruc.dk (8.9.3/8.9.1) with ESMTP id LAA22444; Mon, 2 Oct 2000 11:30:36 +0200 (MET DST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3+Sun/8.9.3) with ESMTP id LAA26559; Mon, 2 Oct 2000 11:20:05 +0200 (MEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.44); 2 Oct 00 11:30:36 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.44); 2 Oct 00 11:30:16 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "Kiniu WONG Kin-Yiu" Date: Mon, 2 Oct 2000 11:29:59 +0100 Subject: CCL:How to calculate excitation energy in high accuracy by CC: chemistry@ccl.net Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <101DC80A2ACA@virgil.ruc.dk> Kiniu WONG Kin-Yiu: > I couldn't get an accurate excitation energy by Gaussian, even a simple > atom such as Hydrogen and Beryllium. The excitation energy of H is 10.2eV, but > by UCIS(50-50)/6-31+G(d), it gives the excitation energy = 26.1eV: > > CIS wavefunction symmetry could not be determined. > Excited State 1: ?Spin -?Sym 26.1001 eV 47.50 nm f=0.0000 Dear Kiniu, calculation of excitation energies of the H atom with the 6-31+G(d) basis set is meaningless. The electronic transitions of atomic hydrogen are of Rydberg-type, corresponding to a change in the main quantum number n: 1s->2s, 1s->2p, and so forth. But the basis set 6-31+G(d) does not include any "diffuse functions" on hydrogen, and is unsuitable for description of excited states. Inclusion of a 2s-type diffuse function leads to a drastic decrease in the computed transition energy: 6-31++G(d): 1s->2s = 10.4 eV However, this basis set does not predict the three optically allowed 1s->2p transitions, that are energetically degenerate with the optically forbidden 1s->2s transition. Computation of 1s->2p transitions requires basis sets with an accurate representation of 2p functions. But degeneracy with 1s->2s is not easily predicted with standard sets, for example: AUG-cc-pVTZ: 1s->2s = 10.2 eV, 1s->2p = 11.2 eV AUG-cc-pVQZ: 1s->2s = 10.2 eV, 1s->2p = 10.9 eV AUG-cc-pV5Z: 1s->2s = 10.2 eV, 1s->2p = 10.7 eV Evidently, different angular momenta are treated at different levels of accuracy. Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://www.rub.ruc.dk/dis/chem/psos/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Mon Oct 2 06:01:41 2000 Received: from mel.ruc.dk (mel.ruc.dk [130.225.220.27]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA31696 for ; Mon, 2 Oct 2000 06:01:40 -0400 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by mel.ruc.dk (8.9.3/8.9.1) with ESMTP id MAA15716; Mon, 2 Oct 2000 12:01:21 +0200 (MET DST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3+Sun/8.9.3) with ESMTP id LAA26763; Mon, 2 Oct 2000 11:50:51 +0200 (MEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.44); 2 Oct 00 12:01:21 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.44); 2 Oct 00 12:01:03 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "Kiniu WONG Kin-Yiu" Date: Mon, 2 Oct 2000 12:00:59 +0100 Subject: CCL:How to compute LUMO eighen energy value by Gaussian or CC: chemistry@ccl.net Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <101E4B5565A2@virgil.ruc.dk> Kiniu WONG Kin-Yiu: > By Gaussian, we could get HOMO energy and LUMO energy by just looking at > the computed occupied eighen value and virtual unoccupied eighen value > respectively. In order to get values in higher accuracy, we could equate HOMO > to be E(cation) - E(neutral). Since HOMO energy means the minimum input energy > to the system in order to remove an electron from the system. So during this > process, the final state is just the cation of initial state. With this > approach, I could get a much better HOMO when compared with the experimental > value of the molecule (Alq3) in my project. .......... Dear Kiniu, I am somewhat confused by your question. You wish to compute accurate HOMO and LUMO energies. Molecular orbitals (MOs) are matematical functions defined within the so-called independent-particle model, and in order to compute them with "high accuracy" you would need to solve this model accurately. But apparently, this is not really what you want to do? What you want is probably accurate computation of ionization energies and similar quantities, but this is not the same as accurate computation of model quantities like MO energies. You state that "HOMO energy means the minimum input energy to the system in order to remove an electron from the system". But this is only an approximation (usually called Koopmans' approximation) and does not in general lead to an accurate prediction of the ionization energy. Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://www.rub.ruc.dk/dis/chem/psos/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Mon Oct 2 07:33:50 2000 Received: from facepe.dqf.ufpe.br (root@facepe.dqf.ufpe.br [150.161.5.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA00177 for ; Mon, 2 Oct 2000 07:33:47 -0400 Received: from npd.ufpe.br (arnobio2.dqf.ufpe.br [150.161.5.23]) by facepe.dqf.ufpe.br (8.9.3/8.8.7) with ESMTP id IAA08555 for ; Mon, 2 Oct 2000 08:37:04 -0300 Message-ID: <39D87494.65678A14@npd.ufpe.br> Date: Mon, 02 Oct 2000 08:42:13 -0300 From: silmar X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Carbon bromine bonds Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, Does anyone knows inexpensive basis sets for Bromine in order to get a good description of Carbon-bromine bonds in organic molecules(with G98)? Thanks in advance, Silmar. UFPE-DQF-Brazil. From chemistry-request@server.ccl.net Mon Oct 2 10:48:56 2000 Received: from rjaeger (slip-32-100-146-170.az.us.prserv.net [32.100.146.170]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA01012 for ; Mon, 2 Oct 2000 10:48:35 -0400 From: genie42@accessmicromail.com Message-Id: Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: 7BIT Subject: Find Out the Truth About AnyOne ! X-Mailer: ÐÏࡱá To: chemistry@ccl.net Date: Mon, 02 Oct 2000 07:46:12 -0800 Find Out the Truth About Anyone!

From chemistry-request@server.ccl.net Mon Oct 2 11:13:13 2000 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA01252 for ; Mon, 2 Oct 2000 11:13:13 -0400 Received: from verdun.ks.uiuc.edu (verdun.ks.uiuc.edu [130.126.120.129]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id KAA00591 for ; Mon, 2 Oct 2000 10:13:01 -0500 (CDT) Received: from localhost (jim@localhost) by verdun.ks.uiuc.edu (8.9.1b+Sun/8.9.1) with ESMTP id KAA20209 for ; Mon, 2 Oct 2000 10:13:00 -0500 (CDT) X-Authentication-Warning: verdun.ks.uiuc.edu: jim owned process doing -bs Date: Mon, 2 Oct 2000 10:13:00 -0500 (CDT) From: Jim Phillips To: chemistry@server.ccl.net Subject: NAMD 2.2 Release Announcement Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII +--------------------------------------------------------------------+ | | | NAMD 2.2 Release Announcement | | | +--------------------------------------------------------------------+ September 29, 2000 The Theoretical Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD development is supported by the NIH National Center for Research Resources. NAMD 2.2 has several advantages over NAMD 2.1: - New ports to the IBM RS/6000 SP, Alpha Linux, and Windows. - Parallelized particle mesh Ewald FFT and reciprocal space sum with demonstrated scaling to 128 processors for large systems. - Release binaries contain FFTW (under special license) for better serial performance when using particle mesh Ewald. - Much faster minimizer based on conjugate gradient method, also more stable when dealing with very bad initial contacts. - Improved load balancer with demonstrated scaling to over 1024 processors for large cutoff systems. NAMD is available from http://www.ks.uiuc.edu/Research/namd/. The Theoretical Biophysics group encourages NAMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to namd@ks.uiuc.edu. We are eager to hear from you, and thank you for using our software! From chemistry-request@server.ccl.net Mon Oct 2 12:15:43 2000 Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA00611 for ; Mon, 2 Oct 2000 12:15:23 -0400 Received: from localhost (fgonzale@localhost) by lauca.usach.cl (8.10.0.Beta12/8.10.0.Beta10) with ESMTP id e92G82q17229 for ; Mon, 2 Oct 2000 12:08:02 -0400 (CST) Date: Mon, 2 Oct 2000 12:08:02 -0400 (CST) From: Fdo Danilo Gonzalez Nilo To: chemistry@ccl.net Subject: cross eyes glass Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all! I looking for any address for buy a glass (based in mirrors) to look stereo pictures using cross eyes. Thanks a lot! Danilo Gonzalez University of Santiago of Chile Faculty of Chemistry and Biology casilla 40, correo 33, Santiago CHILE Fax: 562 - 681 2108 From chemistry-request@server.ccl.net Mon Oct 2 13:43:24 2000 Received: from cid.csic.es (nunki.cid.csic.es [161.111.220.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA00986 for ; Mon, 2 Oct 2000 13:43:09 -0400 Received: from iiqab.csic.es (IDENT:ramon@picasoques.iiqab.csic.es [161.111.222.58]) by cid.csic.es (8.10.1/8.10.1) with ESMTP id e92Hc9k24956 for ; Mon, 2 Oct 2000 19:38:09 +0200 Sender: ramon@cid.csic.es Message-ID: <39D8C980.96DB292F@iiqab.csic.es> Date: Mon, 02 Oct 2000 19:44:35 +0200 From: Ramon Crehuet Organization: C.S.I.C. X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.12-20 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Need help to find a reference. Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CClers, I need help to find a reference I once saw and I can't find now. The info I can give you is very vague, that's why I can't find it in a database! If I am not wrong, professor Zewail studied the dimerisation of two ethylene molecules showing that there is no concerted pathway. I am not sure if it was ethylene or another molecule. But there was another article studying the same process by theoretical methods in which the authors calculated a theoretical PES and showed that the conclusions of Zewail were not entirely correct. I would be very grateful if anyone could tell me the reference of this article (or series of articles if it was really more than one). Thank you, Ramon Crehuet From chemistry-request@server.ccl.net Mon Oct 2 14:41:30 2000 Received: from chem.ufl.edu (server.chem.ufl.edu [128.227.16.141]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA01349 for ; Mon, 2 Oct 2000 14:41:29 -0400 Received: from chem.ufl.edu (chem.ufl.edu [128.227.16.141]) by chem.ufl.edu (8.9.1/8.9.1/map) with ESMTP id OAA22437 for ; Mon, 2 Oct 2000 14:40:58 -0400 (EDT) Date: Mon, 2 Oct 2000 14:40:58 -0400 (EDT) From: "Xiang(Simon) Wang" To: CHEMISTRY@ccl.net Subject: Warning Message in Charmm: STRING TOO SMALL Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers: I met the following warning message when reading thousands of TIP3 molecules in Charmm: ***** LEVEL -1 WARNING FROM ***** ***** STRING TOO SMALL Please help me if you know how to avoid such warning. Thanks. Simon WANG From chemistry-request@server.ccl.net Mon Oct 2 15:07:05 2000 Received: from red.cachesoftware.com (root@[12.17.172.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA01448 for ; Mon, 2 Oct 2000 15:07:04 -0400 Received: from daveg.cachesoftware.com (DAVEG-LIFEBOOK.cachesoftware.com [192.168.110.12]) by red.cachesoftware.com (8.9.3/8.9.3/3) with ESMTP id MAA23712 for ; Mon, 2 Oct 2000 12:05:36 -0700 Message-Id: <4.3.0.20000929140046.00d7a370@12.17.172.66> X-Sender: daveg@12.17.172.66 X-Mailer: QUALCOMM Windows Eudora Version 4.3 Date: Mon, 02 Oct 2000 12:08:32 -0700 To: chemistry@ccl.net From: David Gallagher Subject: CAChe Seminars: 23 & 24 October Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed "Prediction of Physical, Chemical, and Biological Properties with Computer Aided Chemistry" * Monday 23rd October 2000 in Wilmington, DE * Tuesday 24th October 2000 in Philadelphia, PA. ABSTRACT: The prediction of biological, chemical and physical properties such as reaction rates, UV-Visible & IR spectra, water solubility, vapor pressure, polymer properties, carcinogenicity, environmental fate, etc. will be illustrated with CAChe, an easy-to-use computer aided chemistry package for the experimental chemist that runs on a desktop PC. Prediction of reaction pathways, thermodynamics and kinetics will also be discussed as well as application to quantitative structure-property relationships (QSPR & QSAR). Chemists use CAChe to improve their success rate in the laboratory and speed up research by pre-screening candidates and testing their ideas, before investing valuable laboratory time. This presentation reviews the expanding scope of computer aided chemistry. After the 55 minute presentation, there will be a 10 minute review of the latest enhancements that MOPAC 2000 brings to CAChe, followed by a 15 minute software demonstration. Visit http://www.cachesoftware.com/news/seminars2000.shtml or to register, contact Heidi at hklein@cachesoftware.com or Ph: 503 746 3603. This seminar is sponsored by Fujitsu. ---------------------------------------------------- David Gallagher CAChe Group, Fujitsu Systems Business of America, Inc. 15244 NW Greenbrier Parkway, Beaverton, OR 97006-5733, USA Tel: 503 531 3600 Fax: 503 531 9966 www.cachesoftware.com From chemistry-request@server.ccl.net Mon Oct 2 19:14:05 2000 Received: from ivory.trentu.ca (trentu.ca [192.75.12.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA02835 for ; Mon, 2 Oct 2000 19:14:05 -0400 Received: from trentu.ca ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #29543) with ESMTP id <01JUVFBQC7Z2003SFC@trentu.ca> for chemistry@ccl.net; Mon, 2 Oct 2000 19:13:57 EDT Date: Mon, 02 Oct 2000 19:18:47 -0400 From: elewars Subject: MAX PLANCK, QUANTUM THEORY To: chemistry@ccl.net Message-id: <39D917D7.177F6EDB@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Monday, 2000 Oct 2 Hello, On October 19, 1900, Max Planck discovered the quantum discontinuity of blackbody radiation and sowed the basis for the calculations we all use. QUESTIONS: (1) When was the fundamental constant first denoted _h_? And why _h_? What word does h stand for? (I think in classical physics, too, energy x time is "action", but that starts with _a_.) (2) Have there been any announcements of the big celebrations that must surely be planned for the work that marked the transition from classical to modern physics, revolutionized much of science, and laid the foundations of new industries? thanks E. Lewars ====