From chemistry-request@www.ccl.net Wed Aug 12 06:03:22 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 GAA29548 Wed, 12 Aug 1998 06:03:21 -0400 (EDT) From: barbosa@anne.chemie.unibas.ch Received: by anne.chemie.unibas.ch (AIX 3.2/UCB 5.64/4.03) id AA23661; Wed, 12 Aug 1998 12:03:22 +0200 Message-Id: <9808121003.AA23661@anne.chemie.unibas.ch> Subject: uhf and biradicals To: chemistry@www.ccl.net Date: Wed, 12 Aug 1998 12:03:21 +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, I am looking for some references on calculations with unrestricted hartree fock method on singlet biradicals in the ground state. Thanks in advance Frederique ======================================================================= 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 Wed Aug 12 06:05:21 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 GAA29565 Wed, 12 Aug 1998 06:05:20 -0400 (EDT) Received: (from hinsen@localhost) by dirac.cnrs-orleans.fr (AIX4.3/UCB 8.7/8.7) id MAA29684; Wed, 12 Aug 1998 12:04:37 +0200 (DFT) Date: Wed, 12 Aug 1998 12:04:37 +0200 (DFT) Message-Id: <199808121004.MAA29684@dirac.cnrs-orleans.fr> From: Konrad Hinsen To: ihtrap@hotmail.com CC: chemistry@www.ccl.net In-reply-to: <19980807215711.29564.qmail@hotmail.com> (ihtrap@hotmail.com) Subject: Re: CCL:permittivity References: <19980807215711.29564.qmail@hotmail.com> > In the expression for Coulombic potential > > e^2 > V(r) = - ----------- > 4 pi Eo r > > where Eo the permittivity of free space; e charge; r distance between > electron and proton. Could someone enlighten me the significance > of permittivity, what actually it means and why does the coulombic > potential decreases with the increase in permittivity. The "permittivity of free space" is a universal physical constant, like the speed of light or the gravitational constant. In fact, you can make it disappear by choosing different units of measurement for the electrostatic quantities. The concept of permittivity comes from the theory of electrostatics in matter. This theory was developed at a time when the structure of matter was not yet understood, and so "free space" was considered a material just like any other. It was found empirically that the influence of simple materials on electrostatic fields could be described by a single parameter, called "permittivity". If you put charges into some material (meaning a macroscopic sample, not just a few atoms), the field generated by the charges will cause polarization in the material, and this polarization will weaken the effective electrostatic field. The permittivity indicates how strong this induced polarization is in a given material. This explains why a higher permittivity leads to a smaller effective potential. In vacuum there is no polarization, and the permittivity of vacuum is simply a universal constant whose name says more about the history of electrostatics than about the quantity itself. -- ------------------------------------------------------------------------------- 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 Wed Aug 12 07:49:36 1998 Received: from news.uni-kl.de (mmdf@news.uni-kl.de [131.246.137.51]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id HAA29752 Wed, 12 Aug 1998 07:49:35 -0400 (EDT) Received: from iris1.chemie.uni-kl.de ( iris1.chemie.uni-kl.de [131.246.9.107] ) by news.uni-kl.de id aa07571 for ; 12 Aug 98 13:50 MESZ Received: from oktarin by iris1.chemie.uni-kl.de via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for id NAA04364; Wed, 12 Aug 1998 13:49:12 +0200 Received: from localhost by oktarin with smtp (Smail3.1.28.1 #7) id m0z6ZOz-0000AOC; Wed, 12 Aug 98 13:49 CETDST Date: Wed, 12 Aug 1998 13:49:13 +0200 (CETDST) From: Stefan Konietzny To: "Comp. Chem. List" Subject: Question about statistics? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi there! I am german and not familiar with the meaning of SDMean in the context of statistics. Can anybody tell me the german word for it, so that i can find out the formula, or even better, does anybody know the formula? Am i right that SDSample is the "usual" standard deviation? Thanks in advance, Stefan. !!!!! reply to: konietz@chemie.uni-kl.de !!!!! finger or talk request: konietz@oktarin.chemie.uni-kl.de **************************************************************** * Stefan Konietzny * *--------------------------------------------------------------* *Fachbereich Chemie, AK Frank | Dept. of Chemistry * *Universitaet Kaiserslautern | University of Kaiserslautern * *Erwin-Schroedingerstr. | Erwin-Schroedingerstr. * *67663 Kaiserslautern | D-67663 Kaiserslautern * *0631/205-2964 (62) | +49-631/205-2964 (62) * **************************************************************** From chemistry-request@www.ccl.net Wed Aug 12 09:36:40 1998 Received: from s-cwis.unomaha.edu (s-cwis.unomaha.edu [137.48.1.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA00806 Wed, 12 Aug 1998 09:36:39 -0400 (EDT) Received: from cas.unomaha.edu (cas.unomaha.edu [137.48.34.40]) by s-cwis.unomaha.edu (8.8.5/8.8.5) with ESMTP id IAA01843 for ; Wed, 12 Aug 1998 08:32:15 -0500 (CDT) Received: from CAS/MAILQUEUE by cas.unomaha.edu (Mercury 1.21); 12 Aug 98 08:36:41 -600 Received: from MAILQUEUE by CAS (Mercury 1.21); 12 Aug 98 08:36:31 -600 Received: from zinc.unomaha.edu by cas.unomaha.edu (Mercury 1.21); 12 Aug 98 08:36:21 -600 Received: by zinc.unomaha.edu with Microsoft Mail id <01BDC5CC.E3D095A0@zinc.unomaha.edu>; Wed, 12 Aug 1998 08:40:42 -0500 Message-ID: <01BDC5CC.E3D095A0@zinc.unomaha.edu> From: "Douglas E. Stack" To: "'CCL'" Subject: Mulliken Bond Orders Date: Wed, 12 Aug 1998 08:40:41 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id JAA00807 Is it safe to say, that since Mulliken atomic charges do not converge with increasing basis set size, then Mulliken bond orders also don't converge with increasing size? Is it the nature of the partitioning scheme that causes this lack of convergence? Douglas E. Stack Assistant Professor Department of Chemistry University of Nebraska at Omaha Omaha, NE 68182-0109 (402) 554-3647 (402) 544-3888 (fax) destack@unomaha.edu From chemistry-request@www.ccl.net Wed Aug 12 10:47:16 1998 Received: from email.nist.gov (email.nist.gov [129.6.2.7]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA01492 Wed, 12 Aug 1998 10:47:15 -0400 (EDT) From: chem@feldmann.nist.gov Received: from feldmann.nist.gov (feldmann.nist.gov [129.6.178.78]) by email.nist.gov (8.8.8/8.8.8) with SMTP id KAA04352; Wed, 12 Aug 1998 10:45:36 -0400 (EDT) Received: from localhost by feldmann.nist.gov (SMI-8.6/SMI-SVR4) id KAA09689; Wed, 12 Aug 1998 10:42:00 -0400 Date: Wed, 12 Aug 1998 10:41:59 -0400 (EDT) To: CHEMCHAT@UAFSYSB.UARK.EDU, CHEMIG@LIST.NIH.GOV, CHEMISTRY@www.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, ICS-L@UMDD.UMD.EDU, isisforum-l@mdli.com, listproc@msi.com, listserver@ic.ac.uk, mailbase@mailbase.ac.uk, molecular-dynamics-news@mailbase.ac.uk, pdb-l@pdb.pdb.bnl.gov Subject: ChemInt 98 - Poster Session Added Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A poster session has been added to the Chemistry and the Internet Conference (ChemInt98). Posters will be presented both Sunday and Monday after lunch. There will be just one poster session - all posters will be available at both times. Contributors who wish to show a poster at the meeting should email the title, the authors names, their affiliation and an abstract to Steven Bachrach, smb@smb.chem.niu.edu, prior to August 31, 1998. Authors should also indicate what medium they will be using for their poster, i.e. paper, computer, etc. The conference will be held from Sep. 12-15, 1998 in Irvine CA. For complete information, see http://www.ijc.com/ci1/ You can register for the conference using the conference secure server. From chemistry-request@www.ccl.net Wed Aug 12 13:18:11 1998 Received: from pnl.gov (relay.pnl.gov [130.20.128.34]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA05794 Wed, 12 Aug 1998 13:18:11 -0400 (EDT) From: d3e102@emsl.pnl.gov Received: from odyssey.emsl.pnl.gov by pnl.gov (PMDF V5.1-10 #21283) with ESMTP id <01J0IGPV36RK922UVA@pnl.gov> for chemistry@www.ccl.net; Wed, 12 Aug 1998 10:17:47 PDT Received: from ames.emsl.pnl.gov (ames.emsl.pnl.gov [198.128.80.135]) by odyssey.emsl.pnl.gov (8.8.5/8.8.5) with ESMTP id KAA18269 for ; Wed, 12 Aug 1998 10:17:41 -0700 (PDT) Received: (from d3e102@localhost) by ames.emsl.pnl.gov (8.8.5/8.8.5) id KAA05184 for chemistry@www.ccl.net; Wed, 12 Aug 1998 10:17:42 -0700 (PDT) Date: Wed, 12 Aug 1998 10:17:42 -0700 Subject: A Calculated Structures Database To: chemistry@www.ccl.net Message-id: <9808121017.ZM5182@ames.emsl.pnl.gov> MIME-version: 1.0 X-Mailer: Z-Mail (3.2.0 06sep94) Content-type: text/plain; charset=us-ascii A Computational Results Database Earlier today (August 12), Gijs Schaftenaar from the Dutch CAOS/CAMM Center asked whether there was any support for a "Calculated Structures Database" among the subscribers to the CCL. Here at the Environmental Molecular Sciences Laboratory we have had an on-going database project focused currently on ab initio electronic structure results. We are actively working on making a first crude web-based interface available that would allow scientists to access optimized geometries, total energies, vibrational frequencies and relative energetics (e.g. dissociation energies or electron affinities) for 208 molecules and the first 4 periods of the periodic table. A literature citation is associated with every result and the overwhelming majority of results have at least one experimental value available for comparision. Most of the popular Pople-style basis sets, plus the Huzinaga MINI and MIDI and correlation consistent basis sets are represented. In terms of levels of theory, we have Hartree-Fock, MP2, MP3, MP4(SDTQ), CCSD, CCSD(T) and various kinds of CI. We have also developed a form that people could fill-in if they wish to submit the results of thier own calculations. But a "gatekeeper" would have final say over whether externally contributed data made it into the database. I've spoken about and written about this project several timess and feel that I probably owe an explanation for the delay in getting it out. It basically boils down to a matter of resources. We are in the proccess of loading total energies and it is imperative that the numbers be correct. That involves a lot of manual checking, which translates into human time. Simply stated, we won't make it available until we're convinced that the data is as correct as it's humanly possible to make it. After the release of the first version, which will have a limited number of ways that a user can interrogate the database, we plan to make available a second release with greatly enhanced flexibility and more types of information. This isn't meant to preclude any initiatives by the Dutch CAOS/CAMM Center. The task of building a database of computational results is a very daunting one. There's lots for various groups to do. When the EMSL Computational Results Database becomes available, I will post a message to the CCL. -- David Feller | Mail Stop K1-96 Environmental Molecular Sciences Laboratory | 906 Battelle Blvd Battelle Pacific Northwest National Lab | Richland, WA 99352 | e-mail:d3e102@emsl.pnl.gov | Fax: (509)-375-6631 From chemistry-request@www.ccl.net Wed Aug 12 15:07:37 1998 Received: from post-ofc06.srv.cis.pitt.edu (root@post-ofc06.srv.cis.pitt.edu [136.142.185.43]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA11721 Wed, 12 Aug 1998 15:07:36 -0400 (EDT) Received: from hathi.chem.pitt.edu (hathi.chem.pitt.edu [136.142.109.10]) by post-ofc06.srv.cis.pitt.edu with SMTP (8.8.8/8.8.8/cispo-7.2.2.2) ID for <@smtp.pitt.edu:chemistry@www.ccl.net>; Wed, 12 Aug 1998 15:07:35 -0400 (EDT) Received: by hathi.chem.pitt.edu (940816.SGI.8.6.9/920502.SGI.AUTO) for chemistry@www.ccl.net id PAA24566; Wed, 12 Aug 1998 15:07:45 -0400 From: "Gustavo Moura" Message-Id: <9808121507.ZM24564@hathi.chem.pitt.edu> Date: Wed, 12 Aug 1998 15:07:42 -0400 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Summary: Off-diagonal elements of the CI matrix Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL readers, last week I sent a message to the CCL list asking how to calculate the number of permutations necessary to obtain maximum coincidence between two determinants. To my surprise I have received ONE answer. Probably my question was not simple after all. Below you can find my original questions followed by the anser that I have received. My thanks to Michael E. Beck for answering my question. Gustavo Moura gustavo@hathi.chem.pitt.edu My original question: Dear CCL readers, I am writing a program to do CI calculations on some conjugated molecules using semiempirical (PPP) parameters. Unfortunately, I am having problems to calculate the off-diagonal elements of the CI matrix. In their book Szabo e Ostlund show (tables 2.3 and 2.4) how to calculate these elements when the determinants are in maximum coincidence. I am looking for references where I can find the answer to the following simple(?) question: HOW TO CALCULATE THE NUMBER OF PERMUTATIONS NECESSARY TO OBTAIN MAXIMUM COINCIDENCE BETWEEN THE DETERMINANTS? In other words: WHEN SHOULD I MULTIPLY THE EQUATIONS SHOWN IN THE BOOK BY -1? Thank you very much in advance. I will sumarize. Sincerely yours, Gustavo L.C. Moura gustavo@hathi.chem.pitt.edu The answer: On Wed, 5 Aug 1998, Gustavo Moura wrote: > Dear CCL readers, > I am writing a program to do CI calculations on some conjugated > molecules using semiempirical (PPP) parameters. Unfortunately, I am having > problems to calculate the off-diagonal elements of the CI matrix. In their book > Szabo e Ostlund show (tables 2.3 and 2.4) how to calculate these elements when > the determinants are in maximum coincidence. I am looking for references where > I Dear Sir, maybe this not quite the answer you are expecting, but from your letter i suspect that your program is in a very early stage of development. A very elegant way to set up the Hamiltonian in a basis of spin adapted configurations (CCFs) is to use the graphical approach pioneered by Paldus and Shavitt, GUGA. This approach also gives a very smooth way to construct the configuration space. GUGA seems to be applied mainly in ab initio theory, but personally i think it's very well suited for semiempirics, too. Once you have got used to the graphs, you'll love them, promise. Coming back to your question: In GUGA problems like "maximal coincidence" just do not arise. sincerly Michael E. Beck ___________________________________________________________________ Dr. Michael E. Beck | privat: Organisch--Chemisches Institut | Zschokkestr. 12a Theoretische Gruppe, Prof. W. Thiel | CH--8037 Zuerich Universitaet Zuerich | +41-1-271 54 39 Winterthurerstr. 190 |___________________________ CH--8057 Zuerich Tel.: +41-1-635-6117 web : www.unizh.ch/~mbeck Fax.: 6836 mail: mbeck@unizh.ch ___________________________________________________________________ From chemistry-request@www.ccl.net Wed Aug 12 15:55:59 1998 Received: from interlock.amoco.com (texgate.amoco.com [204.149.20.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id PAA12000 Wed, 12 Aug 1998 15:55:58 -0400 (EDT) Received: by interlock.amoco.com id OAA06720 (InterLock SMTP Gateway 3.0 for CHEMISTRY@www.ccl.net); Wed, 12 Aug 1998 14:55:26 -0500 Message-Id: <199808121955.OAA06720@interlock.amoco.com> Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-3); Wed, 12 Aug 1998 14:55:26 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-2); Wed, 12 Aug 1998 14:55:26 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-1); Wed, 12 Aug 1998 14:55:26 -0500 From: jtgolab@amoco.com (Joe Golab) Date: Wed, 12 Aug 1998 15:04:45 -0500 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Software question Cc: jtgolab@amoco.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi All: Do you know of any software which can help in designing molecules with a set of prescribed properties? For example, if I set the conditions that the MW be a certain value, and that the structure must contain certain functional groups, and that it must be limited to certain atoms, for example C, H, and O, is there any software which can show me all reasonable combinations? -- :Joe jtgolab@amoco.com (630) 961-7878 +---------------------------------------------------------------+ | The Journal of Industrial Engineers reports that nine out of | | ten engineers agree that one out of ten engineers are idiots. | +---------------------------------------------------------------+ From chemistry-request@www.ccl.net Wed Aug 12 17:47:37 1998 Received: from s-cwis.unomaha.edu (s-cwis.unomaha.edu [137.48.1.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA13046 Wed, 12 Aug 1998 17:47:36 -0400 (EDT) Received: from cas.unomaha.edu (cas.unomaha.edu [137.48.34.40]) by s-cwis.unomaha.edu (8.8.5/8.8.5) with ESMTP id QAA29771 for ; Wed, 12 Aug 1998 16:43:12 -0500 (CDT) Received: from CAS/MAILQUEUE by cas.unomaha.edu (Mercury 1.21); 12 Aug 98 16:47:38 -600 Received: from MAILQUEUE by CAS (Mercury 1.21); 12 Aug 98 16:47:22 -600 Received: from zinc.unomaha.edu by cas.unomaha.edu (Mercury 1.21); 12 Aug 98 16:47:15 -600 Received: by zinc.unomaha.edu with Microsoft Mail id <01BDC611.75C880A0@zinc.unomaha.edu>; Wed, 12 Aug 1998 16:51:32 -0500 Message-ID: <01BDC611.75C880A0@zinc.unomaha.edu> From: "Douglas E. Stack" To: "'CCL'" Subject: Xwindows terminal emulator Date: Wed, 12 Aug 1998 16:51:31 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id RAA13047 Our department will be adding some new Win98 PC. I'd like to install a Xwindows terminal emulator on each. My only experience with such products has been with Exdous by White Pine. Does anyone have a preference for a good, inexpensive Xwindows emulator for running modeling programs from SGI workstations? Thanks in advance for any suggestions. Douglas E. Stack Assistant Professor Department of Chemistry University of Nebraska at Omaha Omaha, NE 68182-0109 (402) 554-3647 (402) 544-3888 (fax) destack@unomaha.edu From chemistry-request@www.ccl.net Wed Aug 12 21:33:50 1998 Received: from csb0.IPC.PKU.EDU.CN (csb0.ipc.pku.edu.cn [162.105.177.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id VAA14266 Wed, 12 Aug 1998 21:33:47 -0400 (EDT) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA03271; Thu, 13 Aug 98 09:32:17 -0700 Date: Thu, 13 Aug 1998 09:32:16 -0700 (PDT) From: Fenglou Mao To: "CHEMISTRY@www.ccl.net" Subject: rasmol problem Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, When I run rasmol in my linux box, it always tells me: "No suitable DISPLAY!" Had someone meet this problem? And how to solve it? Thank you for youe help! Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Peking University BeiJing P.R.China Tel:86-10-62751490 Fax:86-10-62751725