From chemistry-request@www.ccl.net Fri Mar 12 00:57:05 1999 Received: from pegasus.arc.nasa.gov (pegasus.arc.nasa.gov [128.102.199.140]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id AAA17647 Fri, 12 Mar 1999 00:57:05 -0500 (EST) Received: from localhost by pegasus.arc.nasa.gov (8.9.1/8.9.1) with SMTP id VAA08098 for ; Thu, 11 Mar 1999 21:57:06 -0800 (PST) Date: Thu, 11 Mar 1999 21:57:05 -0800 (PST) From: "S. Parthiban" To: chemistry@www.ccl.net Subject: Avogadro's Number Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Amedeo Avogadro (1776-1856) in 1811 proposed the hypothesis that equal volumes of gases at the same temperature and pressure contained the same number of molecules, the latter being stable, multi-atomed particles. In point of fact Avogadro's hypothesis was without any impact or influence on the calculation of atomic weights at this time. Not until the explanatory power of electrochemical theory had temporarily waned in the 1850s under the weight of difficulties in organic chemistry, and chemists and physicists found it convenient to accept (without explanation) that dimers such as H2 and O2 could exist, was a complete reconciliation of gravimetric and volumetric data possible. Until then the dimerization of like-charged atoms remained impossible. -parthi From chemistry-request@www.ccl.net Fri Mar 12 02:03:18 1999 Received: from techunix.technion.ac.il (root@techunix.technion.ac.il [132.68.1.28]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id CAA18977 Fri, 12 Mar 1999 02:03:17 -0500 (EST) Received: from tx.technion.ac.il (cedl09.technion.ac.il [132.68.80.95]) by techunix.technion.ac.il (8.9.1/8.8.5) with ESMTP id JAA15399; Fri, 12 Mar 1999 09:03:17 +0200 (IST) Message-ID: <36E8C6CD.EE78A475@tx.technion.ac.il> Date: Fri, 12 Mar 1999 09:48:29 +0200 From: Irena Efremenko Organization: Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa 32000 X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: CCL Computational Chemistry List , cermsge@techunix.technion.ac.il Subject: ZINDO program Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Dear CCLers, I would like to calculate reliable adsorption energies and optimized geometries for small molecules on/in relatively large transition metal clusters (50-100 atoms). My main interest is in adsorbent-induced changes in metal skeleton. To my best knowledge the ZINDO program is the best choice for such calculations. May somebody here point me out how can I get it? Any suggestions on other semiempirical programs with parametrization for transition metals will be appreciated, as well. Thanks in advance, Irena Efremenko From chemistry-request@www.ccl.net Fri Mar 12 06:20:20 1999 Received: from si.unizar.es (si.unizar.es [155.210.9.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA23990 Fri, 12 Mar 1999 06:20:14 -0500 (EST) Received: from posta.unizar.es (root@posta.unizar.es [155.210.11.16]) by si.unizar.es (8.8.5/8.8.5) with ESMTP id MAA25421 for ; Fri, 12 Mar 1999 12:18:30 +0100 (MET) Received: from posta.unizar.es ([155.210.15.138]) by posta.unizar.es (8.8.5/8.7.3) with ESMTP id MAA16331 for ; Fri, 12 Mar 1999 12:19:45 +0100 (MET) Message-ID: <36E8F62B.E14C433B@posta.unizar.es> Date: Fri, 12 Mar 1999 12:10:35 +0100 From: Luis Salvatella =?iso-8859-1?Q?Ib=E1=F1ez?= X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Re: Avogadro's number Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, The Avogadro's number was firstly determined by Loschmidt in 1865, 9 years after the death of Avogadro. This calculation was based on the application of the kinetic theory of gases. In 1913, Jean Perrin published his book "Les atomes", where the Avogadro's number was calculated by means of 13 different ways, this fact being usually considered as the final victory of the atomic theory. For a very brief explanation of the Loschmidt's calculation, see: KOHN, MORITZ, Josef Loschmidt. Journal of Chemical Education 1945, 22, 381-384. Best wishes, LUIS SALVATELLA From chemistry-request@www.ccl.net Fri Mar 12 10:01:29 1999 Received: from neriserv.chim.unisi.it (neriserv.chim.unisi.it [192.167.124.14]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA29379 Fri, 12 Mar 1999 10:01:28 -0500 (EST) Received: from neriserv.chim.unisi.it (andrea@localhost [127.0.0.1]) by neriserv.chim.unisi.it (8.8.7/8.8.7) with ESMTP id PAA01218; Fri, 12 Mar 1999 15:54:40 +0100 Sender: andrea@neriserv.chim.unisi.it Message-ID: <36E92AAE.4D8ECD60@neriserv.chim.unisi.it> Date: Fri, 12 Mar 1999 15:54:38 +0100 From: Andrea Bernini X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.35 i586) X-Accept-Language: en, it MIME-Version: 1.0 To: molecular-dynamics-news , Computational Chemistry list Subject: Seraching for Nickel parameters Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I'm working on small peptides which complex nickel II ion via histidines, and want to model such structures with amber molecular dynamics, but the force field lack of nickel parameters. Does anyone got information or can give references to nickel II parameters such as armonic force constants, torsional barriers, 6-12 potentials? Or are there other force-fields/softwares which got yet these nickel parameters? Thanks in advance, Andrea Bernini. ______________________________________________ Dr. Andrea Bernini BioTechnology Ph.D. at Molecular Biology Dept. University of Siena Via Fiorentina 1, 53100 Siena, Italy Phone +39 577 227911 Fax +39 577 227903 From chemistry-request@www.ccl.net Fri Mar 12 11:49:52 1999 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA06144 Fri, 12 Mar 1999 11:49:49 -0500 (EST) Received: from localhost by dedalus.lcc.ufmg.br (AIX 3.2/UCB 5.64/4.03) id AA83712; Fri, 12 Mar 1999 13:46:01 -0300 Organization: Universidade Federal de Minas Gerais - LCC - Brasil Date: Fri, 12 Mar 1999 13:46:01 -0300 (BSC) From: andre mauricio de oliveira To: John Marelius Cc: chemistry@www.ccl.net, Karin Kolmodin , Isabella Feierberg Subject: Re: CCL:Molecular modelling software in education: recommendations? In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Prof. Marelius, In your case I think that programs MacroModel (mmod@still3.chem.columbia.edu) or Sybyl (http://www.tripos.com) are more factible for your purpose. Greetings. On Wed, 10 Mar 1999, John Marelius wrote: > Dear CCL members, > > I teach a course in molecular and statistical mechanics for third-year > biotechnology students. Until now the students have used Insight II from > MSI for the computer exercises, but now I am looking into what other > software packages could be used. I would appreciate if you would share > any experience you have with other packages, particularly in an > undergraduate course context. > > The exercises contain > * visualisation of proteins > * building small molecules and peptides > * energy minimisation > * conformational search > * molecular dynamics of small molecules and proteins with explicit solvent > * free energy perturbation simulations > * receptor-ligand docking and scoring > > I would prefer a package which runs on one or more of MS Windows NT, > Linux or Sun Solaris. > > I will be happy to summarise the responses to the list. > > regards, > > John Marelius > > +-----------------------------------------------------------------+ > | John Marelius | > | Dept. of Molecular Biology, Uppsala University | > | E-mail: John.Marelius@molbio.uu.se | > | phone: +46 18 4714988, fax: +46 18 536971 | > | address: Box 590, S-751 24 Uppsala, Sweden | > +-----------------------------------------------------------------+ > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: chemistry-request@www.ccl.net > -- Original Sender From: Address: John.Marelius@molbio.uu.se > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > Andre Mauricio de Oliveira VOICE +55-031-374-1325 +55-031-499-5765 FAX +55-031-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal (NEQUIM) NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim Departamento de Quimica ICEx Federal University of Minas Gerais Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 Belo Horizonte MG Brazil From chemistry-request@www.ccl.net Fri Mar 12 13:28:55 1999 Received: from chrs1.chem.lsu.edu (chrs1.chem.lsu.edu [130.39.132.111]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id NAA10730 Fri, 12 Mar 1999 13:28:54 -0500 (EST) Received: from localhost by chrs1.chem.lsu.edu (AIX 4.1/UCB 5.64/4.03) id AA23906; Fri, 12 Mar 1999 12:28:14 -0600 Date: Fri, 12 Mar 1999 12:28:14 -0600 (CST) From: Chris Harwell To: Irena Efremenko Cc: CCL Computational Chemistry List , cermsge@techunix.technion.ac.il Subject: Re: CCL:ZINDO program In-Reply-To: <36E8C6CD.EE78A475@tx.technion.ac.il> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 12 Mar 1999, Irena Efremenko wrote: > Dear CCLers, > > I would like to calculate reliable adsorption energies and optimized > geometries for small molecules on/in relatively large transition metal > clusters (50-100 atoms). My main interest is in adsorbent-induced > changes in metal skeleton. To my best knowledge the ZINDO program is the > best choice for such calculations. May somebody here point me out how > can I get it? Zerner's Group at University of Florida: http://www.qtp.ufl.edu/zindo.html charwel@chrs1.chem.lsu.edu From chemistry-request@www.ccl.net Fri Mar 12 13:29:32 1999 Received: from schrodinger.com (root@thermidore.schrodinger.com [192.156.98.99]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA10784 Fri, 12 Mar 1999 13:29:26 -0500 (EST) Received: from sally.schrodinger.com (sally.schrodinger.com [206.231.140.227]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id KAA03293 for ; Fri, 12 Mar 1999 10:29:40 -0800 Received: from localhost (shenkin@localhost) by sally.schrodinger.com (8.8.5/8.8.5) with ESMTP id NAA30851 for ; Fri, 12 Mar 1999 13:23:09 -0500 X-Authentication-Warning: sally.schrodinger.com: shenkin owned process doing -bs Date: Fri, 12 Mar 1999 13:23:09 -0500 (EST) From: Peter Shenkin To: chemistry@www.ccl.net Subject: Re: CCL:Avogadro's number In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 11 Mar 1999, Chris Harwell wrote: > On Thu, 11 Mar 1999, Anatoli Korkin wrote: > > Last time I was visiting my dentist, he asked me how Avogadro > > could come with his number at that time. > i think he only came up with the idea of a mole and relatvie proportions. > > someone else actually came up with the number after boltzmann & maxwell > came up with the necessary stat. mech. Sigh. What do they teach in freshman chemistry these days? Based on the observation that gasses combine chemically in the ratio of small whole numbers, Avogadro *hypothesized* that equal volumes of gasses (at the same T & P) have the same number of molecules. I believe this was around 1811. Dalton opposed this view, because an observation like 1(volume of H) + 1(volume of Cl) -> 2(volumes of HCl) would then imply that H and Cl are diatomic, which seemed preposterous to him. Of course, we now know that Dalton was wrong in this. But measurements weren't so good then, and there was room for disagreement. It wasn't until Canizzaro did better experiments in the 1840's that Avogadro's hypothesis was accepted. Still, nobody knew what the number was. In the late 19th century, people referred to Loschmidt's number, which was something like the number of molecules in a gram of hydrogen gas. (I forget the exact definition -- it was something like this.) It could be approximated from the kinetic theory of gasses by comparing several measurements; this gave the right order of magnitude. This is what Chris is referring to, I think (though I wouldn't call it stat mech). Getting a precise value of Avogadro's number was a hot topic in experimental physics around the turn of the century. Einstein's work on Brownian motion (1905) provided the most precise values to date, AFAIK. I'm not sure when the quantity we refer to started to be called Avogadro's number, but it was probably during the late 19th century, after Avogadro's death. (He died in 1856.) If I recall correctly, Mahan's freshman chemistry text goes into a lot of the above history (especially the Avogadro/Dalton/Canizzaro part). -P. P.S. Here's a homework problem. What does a gram of any ordinary matter contain Avogadro's number of? -- *********** Peter S. Shenkin; Schrodinger, Inc.; (201)433-2014 ************ *********** shenkin@schrodinger.com; http://www.schrodinger.com *********** From chemistry-request@www.ccl.net Fri Mar 12 19:23:39 1999 Received: from mentecolectiva.com (collecti@mentecolectiva.com [192.41.26.99]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA25257 Fri, 12 Mar 1999 19:23:38 -0500 (EST) Received: from mentecolectiva.com ([168.176.51.17]) by mentecolectiva.com (8.8.5) id RAA28779; Fri, 12 Mar 1999 17:05:45 -0700 (MST) X-Authentication-Warning: mentecolectiva.com: Host [168.176.51.17] claimed to be mentecolectiva.com Message-ID: <36E9ACB3.38AC5601@mentecolectiva.com> Date: Fri, 12 Mar 1999 19:09:23 -0500 From: Mauricio Esguerra Organization: Grupo de Quimica Teorica X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: "chemistry@www.ccl.net" Subject: h2-oh Content-Type: text/plain; charset=big5 Content-Transfer-Encoding: 7bit Dear CCLers, I am trying to do some calculations on a reaction that I am sure that some of you might have worked with: H2 + OH = = = H2---OH = = =H2O + H my problem is that I have not found in a very brief search, any references to the geometry of the TS. I would be most grateful to anyone who could point me to any reference on this. Thank You, Mauricio Esguerra Grupo de Quimica Teorica Facultad de Ciencias Universidad Nacional de Colombia esguerra@mentecolectiva.com From chemistry-request@www.ccl.net Fri Mar 12 19:25:10 1999 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA25272 Fri, 12 Mar 1999 19:25:09 -0500 (EST) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.9.3/8.9.3) id SAA10484 for chemistry@www.ccl.net; Fri, 12 Mar 1999 18:04:42 -0500 (EST) Date: Fri, 12 Mar 1999 18:04:42 -0500 (EST) From: "E. Lewars" Message-Id: <199903122304.SAA10484@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: IR INTENSITIES__SUMMARY;THANKS 1999 March 12 SUMMARY OF REPLIES TO Q ABOUT HOW TO CALC INTENSITY RATIO OF IR BANDS IN A SIMPLE WAY Hello, Thanks very much to all who replied to my question (below). Here is the summary of answers. ------------- QUESTION: >From E. Lewars: Subject: Re: CCL:G:IR INTENSITIES Date: Mon, 1 Mar 1999 15:21:12 +0300 >1999 Feb 26 > >I have a question about calculating the relative intensities of IR vibrations. >Let me say at the outset that my interest here is to *illustrate* in a simple >way how intensities can be calc from the change in dipole moment >accompanying the normal-mode vibration; I know there are sophisticated >algorithms for calculating the intensity of IR bands. I just want to show >how, in principle, one might get relative intensities in a conceptually >simple way. > >The intensity of a normal-mode vibration is approximately > > I = k(dm/dq)**2 > >where > k is a proportionality constant (we are interested in _relative_ > intensities) > m = dipole moment > q = a geometric parameter like bond length > >Approximating the derivative as the ratio of finite increments enables us >to readily calculate relative intensities for the single mode of diatomic >molecules: > > I = k(delta m/delta q)**2 > >Thus for H-F and HCl, using HF/6-31G* calcs: > H-F r(0.9109=r-equil), m = 1.9719 D; r(0.9209), m = 1.9897 > I = k(0.0178/0.01)**2 = 3.17k > > H-Cl r(1.2662=r-equil), m = 1.5017 D; r(1.2762), m = 1.5081 > I = k(0.0064/0.01)**2 = 0.41k > > Intensity ratio, I(HF)/I(HCl) = 3.17/0.41 = 7.7 > > A calc using Gaussian 98 gives an intensity ratio of 141.5/24.3 = 5.8 > Fine. >------------- >QUESTION: >Suppose we have, say H2O, and want to calc the relative intensities of >the asym and the sym stretching modes. In principle we can distort the geom >a little (as for H-F and H-Cl, above) and calc the change in dipole moment, >delta m. But what do we take as delta q when there is not just *one* simple >geometric parameter like r=(H--X)? I suppose either q is composite, or the >expression for I has several terms. > > > O > / \ > H H > > Thanks > E. Lewars =========================== ANSWERS #1 In your expression I = k(dm/dq)**2 , the quantity q is not just a geometrical parameter but it is a normal coordinate. So that, in your finite difference approximation, you should use a normal coordinate vector as delta q. For example, in order to calculate the intensity of full-symmetric mode, you should take a positive increments for both OH bond lengths. For asymmetric mode, you should take +delta for one bond lengths, and simultaneously -delta for another one. More exactly, you should use a realistic normal coordinate vector received e.g. from hessian calculation. Yours, -S. ******************************************************************* Dr. Stanislav K. Ignatov Department of Chemistry, University of Nizhny Novgorod 23 Gagarin Avenue, Nizhny Novgorod 603600 Russia Phone: +7-(831)-265-8035 Email: tcg@ichem.unn.runnet.ru http://quark.unn.runnet.ru ******************************************************************* =========== #2 To: "E. Lewars" Subject: RE: G:IR INTENSITIES Date: Sun, 28 Feb 1999 02:27:10 +0100 Dear Prof. Lewars, I would suggest to use linear combinations of bond distances. For the water example: asym. mode : +delta_r(O-H1)-delta_r(O-H2) sym. mode : +delta_r(O-H1)+delta_r(O-H2) with abs(delta_r(O-H1)) = abs(delta_r(O-H1)). There will be a problem with bigger molecules since modes of equal symmetry tend to interact and spread over the whole molecule. Stefan ______________________________________________________________________ Dr. Stefan Fau Fachbereich Chemie, AK Frenking Philipps-Universit\344t Marburg 35032 Marburg, Germany fau@chemie.uni-marburg.de ========= #3 Date: Sun, 28 Feb 1999 11:26:38 -0800 (PST) Subject: Re: CCL:G:IR INTENSITIES To: elewars@alchemy.chem.utoronto.ca You need to refer to the classic, Wilson, Decius, and Cross, Molecular Vibrations. In the expression, d(mu)/dq, q is not a single internal coordinate but a normal coordinate. Cotton's book on group theory gives a short discussion of how to obtain the normal coordinates. I thought that Gaussian calculated them as well. ====== #4 1-MAR-1999 12:32:21.97 >From: IN%"mathieu@ripault.cea.fr" "Didier MATHIEU" To: IN%"elewars@alchemy.chem.utoronto.ca" "E. Lewars" CC: IN%"chemistry@www.ccl.net" Subj: CCL:IR INTENSITIES per.syst.& Berry phase reply to E. Lewars + additional question E. Lewars wrote: > ------------- > QUESTION: > Suppose we have, say H2O, and want to calc the relative intensities of > the asym and the sym stretching modes. In principle we can distort the geom > a little (as for H-F and H-Cl, above) and calc the change in dipole moment, > delta m. But what do we take as delta q when there is not just *one* simple > geometric parameter like r=(H--X)? I suppose either q is composite, or the > expression for I has several terms. As the distortion of a given mode q is given by the associated eigenvector U, then I think "delta q" should be taken as the magnitude (e.g. in Angstrom) of the distortion vector (delta q).U after conversion from the mass-weighted cartesian coordinates Q to the standard cartesian coordinates X. In other words, (delta q).U is given e.g. in amu^(1/2).Anqstroms. Each coordinate of this mass-weighted cartesian vector (delta q).U should be divided by the square root of the mass of the associated atom. This gives a new vector (delta x).X in angstroms, whose magnitude is (delta x). Then, delta m is the difference between the dipole calculated on the distorted geometry and the one calculated on the equilibrium geometry. To be consistent with to diatomic case, it seems to me, although I didn't studied to question in depth, that one should divide the magnitude of delta m (in Angstroms) by the magnitude of the vector (delta q).U in amu^(1/2).Angstroms, and then take the square of this quantity to obtain the intensity in Debye^2.Angstrom^-2.amu^-1. If this works, then such a scheme might be of practical value (instead of chain-rule differentiation of (delta m)/(elta q)) in the following context: * normal modes are available * IR intensities are to be obtained from a higher theoretical level as normal modes * one is only interested only in intensities in a restricted region of the spectrum Indeed, the IR intensities sought should be obtainable from a few dipole moment calculations for geometries distorted according to the few associated eigenvectors. BTW, I have another question related to IR intensities, more specially for periodic systems. It seems to me that some papers reported IR intensities for periodic systems in a purely classic approach, using a parameterized model for charge distribution (e.g. electro-optic parameters). On the other hand, I have been told that calculation of IR intensities of periodic systems should take into account the quantum "Berry Phase" (I don't know what it is) to make up for the lack of a proper definition of the "dipole moment" of such a system. How can one reconcile this requirement for the Berry phase with classical simulations for which no quantum concept is used ?? Thanks -- Didier MATHIEU CEA - Le Ripault, BP 16 37260 Monts (France) Tel. 33(0)2.47.34.41.85 ================= From chemistry-request@www.ccl.net Fri Mar 12 19:25:41 1999 Received: from broadway.gc.cuny.edu (broadway.gc.cuny.edu [146.96.128.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id TAA25282 Fri, 12 Mar 1999 19:25:40 -0500 (EST) Received: by broadway.gc.cuny.edu id AA00927; Fri, 12 Mar 1999 16:33:00 -0500 Date: Fri, 12 Mar 1999 16:33:00 -0500 (EST) From: Artem Masunov X-Sender: amasunov@broadway.gc.cuny.edu To: CCL Computational Chemistry List Cc: Irena Efremenko , cermsge@techunix.technion.ac.il Subject: Re: CCL:ZINDO program In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The web page > http://www.qtp.ufl.edu/zindo.html sends you to MSI. There are rumors ZINDO from MSI does not reproduce original Zerner's results in some cases. ZINDO/S was also implemented in Gaussian98. However, you need ZINDO/1 to get energies and geometries.. Hope this helps, Artem > > I would like to calculate reliable adsorption energies and optimized > > geometries for small molecules on/in relatively large transition metal > > clusters (50-100 atoms). My main interest is in adsorbent-induced > > changes in metal skeleton. To my best knowledge the ZINDO program is the > > best choice for such calculations. May somebody here point me out how > > can I get it? > > Zerner's Group at University of Florida: > http://www.qtp.ufl.edu/zindo.html > > charwel@chrs1.chem.lsu.edu > From chemistry-request@www.ccl.net Fri Mar 12 19:47:51 1999 Received: from finch-post-10.mail.demon.net (finch-post-10.mail.demon.net [194.217.242.38]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA25378 Fri, 12 Mar 1999 19:47:50 -0500 (EST) Received: from [158.152.18.238] (helo=wartnaby.demon.co.uk) by finch-post-10.mail.demon.net with smtp (Exim 2.12 #1) id 10LaY9-0001uR-0A for chemistry@www.ccl.net; Fri, 12 Mar 1999 22:37:02 +0000 Message-ID: <3gKndeAU5Y62EwUq@wartnaby.demon.co.uk> Date: Fri, 12 Mar 1999 21:59:48 +0000 To: chemistry@www.ccl.net From: Charlie Wartnaby Subject: Advert: molecular dynamics educational package for Windows MIME-Version: 1.0 X-Mailer: Turnpike (32) Version 4.01 Dear CCL members, The first full version of SimChemistry for Windows is now available for download from http://www.wartnaby.demon.co.uk It uses on-screen molecular dynamics in two dimensions, involving hard disk or Lennard-Jones molecules, together with walls, pistons, graphs and text, as an educational tool to explore the microscopic behaviour behind macroscopic phenomena in physical chemistry. While members of this group would not find it useful in day-to-day work, you might find it of interest or use in teaching theoretical or physical chemistry courses, in lecture presentations or practical session demonstrations. Please see the website above for further details. -- Charlie Wartnaby, Cambridge, England O OO O OO oO OOo Oo oOO Oo OooOo Oo oOoo OooOo OoOOo o oo OOo SimChemistry for Windows -- Live molecular dynamics for chemical education -- download free from http://www.wartnaby.demon.co.uk E-mail chem@wartnaby.demon.co.uk to join mailing list for updates From chemistry-request@www.ccl.net Fri Mar 12 20:01:33 1999 Received: from swan2.uspnet.usp.br (swan2.uspnet.usp.br [143.107.253.69]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id UAA25495 Fri, 12 Mar 1999 20:01:30 -0500 (EST) Received: from ligquim ([143.107.194.89]) by swan2.uspnet.usp.br (8.9.1a/8.9.1) with SMTP id VAA10581 for ; Fri, 12 Mar 1999 21:58:15 -0300 (EST) Message-ID: <000301be6cec$e9675ea0$0100005a@ligquim.ffclrp.usp.br> From: "Sergio Emanuel Galembeck" To: "CCL mail list" Subject: NBO: $CHOOSE and $DEL Date: Fri, 12 Mar 1999 22:00:33 -0300 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 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Content-Transfer-Encoding: 7bit Dear netters, In NBO 3..0 I generate a particular Lewis structure of an conjugated molecule, using $CHOOSE command, but I am not able to calculate the energy of deletion of some excited orbitals of this structure with $DEL. Is it possible? Thank you in advance, Sergio ============================================== Sergio Emanuel Galembeck Assistant Professor in Physical Chemistry Laboratorio de Modelagem Molecular Departamento de Quimica Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto Universidade de Sao Paulo fax: +55-16-633-81-51 e-mail: segalemb@usp.br =============================================== From chemistry-request@www.ccl.net Fri Mar 12 20:31:51 1999 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id UAA25772 Fri, 12 Mar 1999 20:31:35 -0500 (EST) Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id WAA10425; Fri, 12 Mar 1999 22:16:05 +0100 From: Jochen Kuepper Organization: Heinrich-Heine-Universitaet To: Peter Shenkin , chemistry@www.ccl.net Subject: Re: CCL:Avogadro's number Date: Tue, 19 Apr 2135 04:42:47 +0100 X-Mailer: KMail [version 1.0.17] Content-Type: text/plain References: MIME-Version: 1.0 Message-Id: <99031222160400.08446@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id UAA25773 >P.S. Here's a homework problem. What does a gram of any ordinary >matter contain Avogadro's number of? amus, not to say amusement :-) Cheers