From chemistry-request@server.ccl.net Wed Jul 19 11:49:43 2000 Received: from dalton.quimica.unlp.edu.ar ([163.10.18.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA32009 for ; Wed, 19 Jul 2000 11:49:41 -0400 Received: from bilbo (jubert4.quimica.unlp.edu.ar [163.10.18.18]) by dalton.quimica.unlp.edu.ar (8.10.2/8.10.2) with SMTP id e6JGqWv26173 for ; Wed, 19 Jul 2000 12:52:32 -0400 Message-Id: <3.0.6.32.20000720004842.007bb5e0@dalton.quimica.unlp.edu.ar> X-Sender: pis_diez@dalton.quimica.unlp.edu.ar X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Thu, 20 Jul 2000 00:48:42 -0300 To: chemistry@ccl.net From: Dr Reinaldo Pis Diez Subject: G98: Oniom energies --> Summary Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear ccl'ers, A few days ago I posted the following to the list > I'm doing some calculations using the oniom method as implemented in g98. > My system is a 30-atoms organic molecule surrounded by almost hundred > solvent molecules. I'm using dft/mm (svwn:uff) for higher and lower layers, > respectively. > The first calculation seems to be a mm one giving an energy which I call > E_3. > Then, the program jumps into the dft job achieving self consistency with > an energy E_scf. > As a third step, it enters into another job having less electrons than > the higher layer, organic molecule, giving an energy E_1. > Finally, the program enters link 102 and prints the following > > ONIOM: calculating energy. > E123= E_1 E_scf E_3 (three real numbers) > ONIOM: extrapolated energy = (a fourth real number calculated > > as, I guess, E_scf - E_1 + E_3) > > Now my questions: > > i) Is the "oniom extrapolated energy" the valid energy in an oniom job? > ii) What does E_1 mean? I wish to thank Nicolas Ferre, Richard Hall, Stephane Humbel, and Joseph Ochterski from Gaussian for their answers. Briefly, the answer to (i) is Yes, the "oniom extrapolated energy" is the energy to take into account. For question (ii) I summarize Joseph's answer: >E_3 = lower level calculation on the whole system >E_2 = higher level calculation on the small piece (I call it E_scf) >E_1 = lower level calculation on the small piece > >extrapolated energy = E2 + (E_3 - E_1) > >which is equivalent to what you have, but I wrote it that way because it's >easier to see what's going on. The part in parentheses is the energy of the >whole system minus the energy of the inner system, at the low level. That >gets added to the energy of the inner system at the high level, giving a >total energy for the whole system. >E_1 removes the "overlapping" piece which is calculated at the low level. >It's kind of like removing a pit from an olive, and filling the hole with >something better :) Finally, the responders seem to agree in recommending the following article describing the g98's oniom implementation Dapprich and al., J.Molec.Struct.(Theochem) 461-462 (1999) 1-21 Thanks again. Regards, Reinaldo From chemistry-request@server.ccl.net Wed Jul 19 12:08:19 2000 Received: from sun1.udg.es (sun1.udg.es [130.206.45.89]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA32132 for ; Wed, 19 Jul 2000 12:08:18 -0400 Received: from xamba.udg.es (iqcxfl@xamba.udg.es [130.206.128.78]) by sun1.udg.es (8.9.3/8.9.3) with SMTP id SAA09403; Wed, 19 Jul 2000 18:04:32 +0100 (WET DST) Date: Wed, 19 Jul 2000 18:12:15 +0200 (MET DST) From: Xavier Fradera To: CHEMISTRY@ccl.net cc: jordipo@stark.udg.es Subject: IRC in Gaussian Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I'm trying to follow a reaction path with Gaussian, by means of the IRC keyword. However, in some cases, the IRC does not reach the final optimized products, and stops at an intermediate structure. Looking at the Gaussian output, I can see that the convergence criteria used for IRC are very loose, compared to the ones used usually in OPT calculations. I haven't seen any option to change these convengergence criteria. Any idea on how to do this ? Thanks, Xavier. -- Xavier Fradera Institute of Computational Chemistry University of Girona, Girona, Catalonia. e-mail: xavier@iqc.udg.es Tel: 34 972 41 83 58 Fax: 34 972 41 83 56 From chemistry-request@server.ccl.net Wed Jul 19 06:10:48 2000 Received: from mailhub2.shef.ac.uk (mailhub2.shef.ac.uk [143.167.2.154]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA29978 for ; Wed, 19 Jul 2000 06:10:47 -0400 Received: from stoat.shef.ac.uk ([143.167.2.1]) by mailhub2.shef.ac.uk with esmtp (Exim 3.02 #2) id 13EqoI-0004ai-00 for chemistry@ccl.net; Wed, 19 Jul 2000 11:10:38 +0100 Received: from li1vg (helo=localhost) by stoat.shef.ac.uk with local-esmtp (Exim 3.14 #2) id 13EqoI-0000Hd-00 for chemistry@ccl.net; Wed, 19 Jul 2000 11:10:38 +0100 Date: Wed, 19 Jul 2000 11:10:38 +0100 (BST) From: Val Gillet X-Sender: li1vg@stoat To: chemistry@ccl.net Subject: Chemoinformatics conf: Sheffield, 2001 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Call For Papers The Chemical Structure Association and the Molecular Graphics and Modelling Society announce their Second Joint Sheffield Conference on Chemoinformatics: Computational Tools for Lead Discovery. The conference will be held in Stephenson Hall, University of Sheffield, UK from 9th to 11th April 2001. Offers of papers are welcomed in all aspects of lead discovery. Possible topics include (but are not limited to): * 3D databases, including docking and pharmacophore analysis; * assay QC and its influence on data mining; * chemical data mining; * descriptor validation; * design of leadlike combinatorial libraries; * design of screening collections; * e-business to facilitate lead discovery; * novel software and hardware systems for lead discovery; * selective compound acquisition from in house and commercial suppliers; * similarity and clustering methods; * structure-activity methods for lead identification and early optimisation; * structure-based design for lead identification and early optimisation; * virtual screening; * case histories incorporating any of the above. Authors interested in submitting a paper for consideration should send a title and brief abstract to Val Gillet (v.gillet@sheffield.ac.uk) by 15th September 2000. Further details of the conference and registration information will follow later in the year and will be posted at www.shef.ac.uk/cisrg/shef2001. From chemistry-request@server.ccl.net Wed Jul 19 06:44:51 2000 Received: from fletxa.iqs.es (root@[193.145.86.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA30077 for ; Wed, 19 Jul 2000 06:44:50 -0400 Received: from millet (millet.iqs.url.es [193.145.86.12]) by fletxa.iqs.es (8.9.3/8.9.3) with SMTP id LAA02298 for ; Wed, 19 Jul 2000 11:41:15 +0200 Message-ID: <00a701bff16b$ccbe4700$0c5691c1@iqs.url.es> From: "Oscar Rey" To: Subject: porphyrin/porphycene Date: Wed, 19 Jul 2000 12:26:28 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Dear CCL members I'd like to obtein some information (bibliography, previous works) about atom types and force file parameters related to porphyrin and porfycene, specially about Weiner et al. and Cornell et al. force fields. Thanks in advance Oscar Rey Puiggròs Computational Chemistry Group (Section of Synthesis), Organic Chemistry Departament Institut Químic de Sarrià (URL) e-mail: orey@iqs.edu telf: 932 038 900 Ext.:2361 Via Augusta 390, 08017 Barcelona_CATALUNYA (Spain) _____________________________________________________________ From chemistry-request@server.ccl.net Wed Jul 19 08:35:14 2000 Received: from terra.ifi.unicamp.br (terra.ifi.unicamp.br [143.106.6.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA31339 for ; Wed, 19 Jul 2000 08:34:51 -0400 Received: from ifi.unicamp.br (lua [143.106.6.13]) by terra.ifi.unicamp.br (8.9.3/8.9.3) with ESMTP id JAA10321 for ; Wed, 19 Jul 2000 09:32:17 -0300 (BSC) Received: (from daemon@localhost) by ifi.unicamp.br (8.9.3/8.9.3) id JAA11101 for ; Wed, 19 Jul 2000 09:32:14 -0300 (BSC) Received: from giselle.ifi.unicamp.br(143.106.72.217) via SMTP by lua.ifi.unicamp.br, id smtpdAAAa002hR; Wed Jul 19 09:32:12 2000 Message-Id: <4.3.2.7.0.20000719091727.00b3a2d0@lua.ifi.unicamp.br> X-Sender: dasf@lua.ifi.unicamp.br X-Mailer: QUALCOMM Windows Eudora Version 4.3.2 Date: Wed, 19 Jul 2000 09:21:55 -0300 To: CHEMISTRY@ccl.net From: Demetrio Antonio da Silva Filho Subject: CI-Singles Summary Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id IAA31348 Original post: Dear Netters, I'm in doubt about the CI-Singles method and the number of single substitutions that this method uses on its calculation. In Pople's paper (J. B. Foresman, M. Head-Gordon, J. A. Pople and M. J. Frisch, Toward a Systematic Molecular Orbital Theory for Excited States, J. Phys. Chem. 96, 135 (1992).) the CI-Singles method is defined as configuration interaction among "all" singly substituted determinants. In Gaussian manual, there is a keyword for this method (NStates) which sets the number of states that will be solved. This keyword (Mstates) sets the number of states used in the CI expansion of the wavefunction or independent of the number used in this keyword all singly substituted determinants will be used? Thanks in advance, Demetrio FIlho Replies! =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-==-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Dear Demetrio! The Gaussian keyword CIS implies a CI-Singles calculation with inclusion of "all" singly excited configurations (however, core levels are usually not included in the CI). The NStates option specifies how many excited states should be calculated; the default value is 3. The value of NStates has no effect on the number of configurations included in the CI. Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-==-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Dear Antonio, This keyword (Mstates) sets the number of states to solve for and this does not affect the number of determinants (precisely: CSF) in the CI expansion (which is Nocc x Nvirt of course). Stefan _________________________________________________________ Prof. Dr. Stefan Grimme Organisch-Chemisches Institut (Abt. Theoretische Chemie) Westfaelische Wilhelms-Universitaet, Corrensstrasse 40 D-48149 Muenster, Tel (+49)-251-83 36512/33241/36515(Fax) Email:grimmes@uni-muenster.de http://www.uni-muenster.de/Chemie/OC/research/grimme/ _________________________________________________________ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-==-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Hello, I think that Gaussian does not diagonalize the complete CIS matrix to get the eigenvectors (and eigenvalues), but rather solve the problem iteratively for each eigenvector. Then the CIS matrix contains all singly excited determiants, but Gaussian gives you only the first "Nstates" eigenvectors. I don't know if I am right, but that the way I understand it. Hope this helps. ...Xav Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.u-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 91 21 49 Universite Henri Poincare (F) 33 3 83 91 25 30 F-54506 Nancy BP 239 http://www.lctn.u-nancy.fr =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-==-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Dear Demetrio, The Nstates keyword in gaussian determines the number of excited states whose energies and other properties are solved for using CIS. It doesn't affect the number of single excitations used in the CI. Best regards, Sam Abrash Dear Demetrio, The CIS method is indeed configuration interaction among all singly substituted determinants. That is, the electronic Hamiltonian is represented in a basis consisting of only determinants which are single orbital-substitutions away from a reference (usually the Hartree-Fock determinant). Once you have this CIS Hamiltonian, you can extract its eigenvalues, which represent energies of electronically excited states. The keyword "NStates" denotes the number of eigenvalues of the CIS Hamiltonian you wish to obtain, not the number of singly excited determinants used for the representation of H. -Daniel -- T. Daniel Crawford Department of Chemistry crawdad@vt.edu Virginia Polytechnic Institute and www.chem.vt.edu/chem-dept/crawford State University =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-==-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- _____________________________________ Demetrio A. da Silva Filho UNICAMP - IFGW Prédio D - Sala 17 CEP 13083-970 C.Postal 6165 Campinas - SP - Brasil _____________________________________ "Se não houver frutos, valeu a beleza das flores. Se não houver flores, valeu a sombra das folhas. Se não houver folhas, valeu a intenção da semente." Henfil From chemistry-request@server.ccl.net Wed Jul 19 12:49:30 2000 Received: from mailoff.mtu.edu (campus1.mtu.edu [141.219.69.101]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA32548 for ; Wed, 19 Jul 2000 12:49:30 -0400 Received: from mail.mtu.edu (campus0.mtu.edu [141.219.69.100]) by mailoff.mtu.edu (8.9.3/8.9.3) with ESMTP id MAA13995 for ; Wed, 19 Jul 2000 12:49:16 -0400 (EDT) Received: from abyss1.cee.mtu.edu (abyss1.cee.mtu.edu [141.219.57.61]) by mail.mtu.edu (8.9.3/8.9.3) with ESMTP id MAA04485 for ; Wed, 19 Jul 2000 12:49:15 -0400 (EDT) Received: from cepc17 (cepc17.cee.mtu.edu [141.219.58.71]) by abyss1.cee.mtu.edu (8.9.3+Sun/8.9.3/mturelay-2.0b) with SMTP id MAA01581 for ; Wed, 19 Jul 2000 12:49:12 -0400 (EDT) Message-Id: <3.0.6.32.20000719124914.00916280@pop.cee.mtu.edu> X-Sender: ssanongr@pop.cee.mtu.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Wed, 19 Jul 2000 12:49:14 -0400 To: chemistry@ccl.net From: Sompop Sanongraj Subject: Fatal Problem: The largest alpha MO coefficient Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi all When I ran the MP2 single point calculation with diffuse functions in a basis set using gaussian98 (A.7) e.g. # rmp2/6-31g+(d,P) maxdisk=1500mb or # rmp2/6-31g++(d) maxdisk=1500mb. I got the error message shown: **** Fatal Problem: The largest alpha MO coefficient is 0.17136284D+04 Error termination via Lnk1e in /local/gauss/g98-a7/g98/l801.exe. Could anybody tell me how to deal with this problem? Thanks sompop Sompop Sanongraj 208 Church Street Hancock MI 49930. TEL: (906) 482 9377 Sompop Sanongraj 208 Church Street Hancock MI 49930. TEL: (906) 482 9377 From chemistry-request@server.ccl.net Wed Jul 19 13:45:22 2000 Received: from qtp.ufl.edu (zwart.qtp.ufl.edu [128.227.89.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA00148 for ; Wed, 19 Jul 2000 13:45:22 -0400 Received: from pc1 (pc1 [128.227.192.187]) by qtp.ufl.edu (8.9.1a/8.9.1) with SMTP id NAA06283; Wed, 19 Jul 2000 13:44:57 -0400 (EDT) Message-ID: <022a01bff1a9$5ffb1240$bbc0e380@qtp.ufl.edu> From: "Stefan Fau" To: "Xavier Fradera" Cc: "CCL - all" References: Subject: Re: CCL:IRC in Gaussian Date: Wed, 19 Jul 2000 13:47:13 -0400 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 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi Xavier, use # ... irc(verytight, other_options) ... and have a look at http://www.gaussian.com/techinfo.htm There you'll find the online version of the G98 manual. Stefan ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu Quantum Theory Project | (352) 392-6714 University of Florida Gainesville, FL 32611-8435 From chemistry-request@server.ccl.net Wed Jul 19 13:51:00 2000 Received: from rzumail1.unizh.ch (rzumail1.unizh.ch [130.60.128.9]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA00207 for ; Wed, 19 Jul 2000 13:51:00 -0400 Received: from zisgi.unizh.ch (zisgi.unizh.ch [130.60.19.17]) by rzumail1.unizh.ch (8.9.3/8.9.3/07) with ESMTP id TAA13847 for ; Wed, 19 Jul 2000 19:50:44 +0200 (MET DST) Date: Wed, 19 Jul 2000 19:50:44 +0200 From: "Dr. Peter Burger" To: CHEMISTRY@ccl.net Subject: CCL: DFT & metal-metal bond distances Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I got a question concerning DFT & metal-metal bond distances. With both B3LYP and the BP86 functionals I do observe siginificantly longer metal-metal multiple bonds compared to the experimental data (accurate) in geometry optimizations of dinuclear (tungsten & molybdenum) complexes, which have bond orders of 2. (M-M distance 2.72 X-ray vs 2.88 A by DFT) I have done alot calculations with different ECPs, all electron basis for Mo, basis sets (double and triple zeta for the metal centers) but could not cure the problem. The complexes are dicationic and I am not including the anion so far. The calculations are done without solvation, i.e. in the gasphase. Comments? Anyone with an idea? Perhaps I should include point charges in the geom. opt. step? Many thanks in advance Peter ------------------------------------ Peter Burger University of Zuerich From chemistry-request@server.ccl.net Wed Jul 19 14:08:34 2000 Received: from rzumail1.unizh.ch (rzumail1.unizh.ch [130.60.128.9]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA00447 for ; Wed, 19 Jul 2000 14:08:34 -0400 Received: from zisgi.unizh.ch (zisgi.unizh.ch [130.60.19.17]) by rzumail1.unizh.ch (8.9.3/8.9.3/07) with ESMTP id UAA14986 for ; Wed, 19 Jul 2000 20:08:19 +0200 (MET DST) Date: Wed, 19 Jul 2000 20:08:19 +0200 From: "Dr. Peter Burger" To: CHEMISTRY@ccl.net Subject: CCL: DFT & metal metal bonds Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sorry, for wasting bandwidth, but in my last post to CCL. I forgot to mention, that if the metal-metal bond distance was fixed to the experimentally observed shorter distance, the energy was found to be ca. 5 kcal/mol higher than the geometry optimized structure with the longer M-M distance. Also, I forgot to mention that I tried polarisation functions as well (also numerical basis sets i.e. Dmol). I have not tried STO's yet. Perhaps I should give ADF a try? Peter From chemistry-request@server.ccl.net Wed Jul 19 14:44:29 2000 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA00653 for ; Wed, 19 Jul 2000 14:44:27 -0400 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id LAA04833; Wed, 19 Jul 2000 11:40:51 -0700 (PDT) Received: from unknown(146.202.29.179) by mailhost.msi.com via smap (V2.0) id xma004826; Wed, 19 Jul 00 11:40:35 -0700 Message-Id: <4.2.0.58.20000719113008.00aa16c0@146.202.6.218> X-Sender: nxg@146.202.6.218 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Date: Wed, 19 Jul 2000 11:49:48 +0100 To: "Dr. Peter Burger" , CHEMISTRY@ccl.net From: nxg Subject: Re: CCL:DFT & metal-metal bond distances In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear Peter, What you are seeing is normal when you use GGA (B3LYP, BP86, PW91...) exchange-correlation functionals. These typically overestimate bond distances for molecules and lattice constants (in the case of solids). Now you have to be careful when you use quantum chemical ECP's with these calculations. The reason being, these ECP's are normally calculated using Hartree-Fock and therefore one has an incompatibility in the exchange-correlation...i.e. you have an Hartree-Fock ECP and a GGA exch-corr in the main calculation. Its important to keep the theory levels consistent i.e. you should use a GGA optimised pseudopotential if you're using that GGA in your main calculation. You could try this. In your case where you've been using ECP's in conjunction with your DFT calculations, you should still see an over estimation. If you do get the correct answer its purely by chance. It would in some sense be the right answer for the wrong reason... Hope this helps -Niranjan At 07:50 PM 7/19/00 +0200, Dr. Peter Burger wrote: >Dear CCLers, > >I got a question concerning DFT & metal-metal bond distances. >With both B3LYP and the BP86 functionals I do observe siginificantly >longer metal-metal multiple bonds compared to the experimental data >(accurate) in geometry optimizations of dinuclear (tungsten & >molybdenum) complexes, which have bond orders of 2. (M-M distance 2.72 >X-ray vs 2.88 A by DFT) I have done alot calculations with different ECPs, >all electron basis for Mo, basis sets (double and triple zeta for the >metal centers) but could not cure the problem. The complexes are >dicationic and I am not including the anion so far. >The calculations are done without solvation, i.e. in the gasphase. > >Comments? Anyone with an idea? Perhaps I should include point charges >in the geom. opt. step? > >Many thanks in advance > >Peter >------------------------------------ >Peter Burger >University of Zuerich > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To >Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > ___________________________________ Niranjan Govind, Ph.D. Scientist, Materials Science Molecular Simulations, Inc 9685 Scranton Road, CA 92121-3752 Tel: 858-799-5337, Fax: 858-458-0136 Email: nxg@msi.com Web: http://www.msi.com From chemistry-request@server.ccl.net Wed Jul 19 15:01:29 2000 Received: from mailspool.helios.nd.edu (mailspool.helios.nd.edu [129.74.250.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA00826 for ; Wed, 19 Jul 2000 15:01:28 -0400 Received: from carbon.helios.nd.edu (carbon.helios.nd.edu [129.74.220.6]) by mailspool.helios.nd.edu (8.9.2/8.9.2) with ESMTP id OAA22935 for ; Wed, 19 Jul 2000 14:01:32 -0500 (EST) Received: from localhost (jaouad@localhost) by carbon.helios.nd.edu (8.9.1/8.9.1) with ESMTP id OAA26748 for ; Wed, 19 Jul 2000 14:01:31 -0500 (EST) X-Authentication-Warning: carbon.helios.nd.edu: jaouad owned process doing -bs Date: Wed, 19 Jul 2000 14:01:31 -0500 (EST) From: Jaouad El Bahroui X-Sender: jaouad@carbon.helios.nd.edu To: chemistry@ccl.net Subject: StepSize commands problem Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Please can some one give me any information how to use tha commands StepSize=N in gaussian, I was unable to make it working for my calculation it's always give me an error of syntax. are there any minimum limit or maximum limit? many thanks in advance, I will summarized to the list. Jaouad ///////////////////////////////////////////////////////////////////// / Jaouad El-Bahraoui, Ph.D / / University of Notre Dame / / Dpto of Chemistry & Biochemistry / / Notre Dame, Indiana 46556-5670 / / / / / / Tel: (219)-631-4007 / / Fax: (219)-631-6652 / / Tel: (Home) (219)-243-8001 / / http://www.nd.edu/~jaouad / ///////////////////////////////////////////////////////////////////// From chemistry-request@server.ccl.net Wed Jul 19 19:42:57 2000 Received: from homer.reed.edu (homer.reed.edu [134.10.15.82]) by server.ccl.net (8.8.7/8.8.7) with SMTP id TAA02756 for ; Wed, 19 Jul 2000 19:42:56 -0400 Received: from isis.reed.edu ([134.10.2.1] verified) by homer.reed.edu (Stalker SMTP Server 1.7) with ESMTP id S.0000299520; Wed, 19 Jul 2000 16:42:57 -0700 Message-id: <12566267@isis.reed.edu> Date: 19 Jul 2000 16:42:56 PDT From: Alan.Shusterman@directory.reed.edu (Alan Shusterman) Subject: CCL:Summary: Are atoms spherical? To: chemistry@ccl.net, shustermang@pdx.edu, mkellison@home.com, hemphill@TELEPORT.COM MIME-Version: 1.0 Content-Type: text/enriched Content-Disposition: inline Here is a summary of responses. Thanks to all who responded. -Alan Alan Shusterman Department of Chemistry Reed College Portland, OR, USA ---- My original question: Programs like Spartan produce nonspherical isodensity surfaces for many atoms (for example, any of the halogens). I would like to know if this outcome is physically reliable, i.e., are only some atoms spherical? I can see why the computational programs yield nonspherical electron density distributions. This is because a UHF or UDFT calculation on fluorine (5 valence p electrons) assigns 2 electrons to p_x, 2 electrons to p_y, but only 1 electron to p_z. But is this physically realistic? ---- Responses: Several of the responses I received were to a question I did not ask, namely, the shapes of atoms in molecules. My question concerns isolated atoms. Atoms in molecules do not need to be spherical because their external environment does not have spherical symmetry (but thanks anyway to all who pointed this out). As far as isolated atoms are concerned, the concensus is, "yes, atoms are spherical, even if most quantum chemical computations lead to solutions of lower symmetry". Responses are reproduced below. Thanks again to David Woon, Fred Arnold, Gijs Schaftenaar, Carlos Faerman, Scot Wherland, Artem Masunov, Christoph van Wuellen, and Douglas Smith for helping me out. 1. From David Woon: To generate the proper spherical charge distribution for an open-shell atom, one must use a multireference method that allows equal weighting of degenerate occupations. This is also true for molecules: to properly describe a Pi state in a linear molecule, one must include and equally weight the pi_x and pi_y occupations. Practically, however, the energy differences are usually small, much smaller than other sources of error present in the calculation. Dave Woon woon@hecla.molres.org 2. From Gijs Schaftenaar: Atom groundstates yield spherically symmetric electron densities. However the density is a linear combination of px(1)py(2)pz(2), px(2)py(1)pz(2), px(2)py(2)pz(1) contributions, these solutions are degenerate. However this degeneracy is lifted even at very long range proximity of other atoms. This has its manifestation in difference density plots. Gijs Schaftenaar schaft@cmbi.kun.nl 3. From Scot Wherland: In support of the "all (isoolated) atoms are spherical" position I refer students to an old letter in J Chem Ed. Irwin Cohen J. Chem. Ed. 42 397-8 (1965). The letter is in response to what he calls a "readily understandable misunderstanding" -Scot Wherland scot_wherland@wsu.edu (Alan: the first half of the letter that Scot refers to is exactly what I was looking for. Here is, in part, what I. Cohen wrote: "In contrast to the idea we may well get from the shapes of the orbitals, all isolated atoms are spherical. To explain this perhaps surprising conclusion, consider first the simplest case - an excited H atom with one 2p electron. Let us, with Johnson and Rettew [p. 145 in this Journal], place the atom in an indifferent environment, one with no selection or preference for any direction. The location of the electron in such an environment must necessarily be equally probable in any direction from the nucleus.") 4. From Christoph van Wuellen: Are atoms spherical? For an isolated atom, since the external potential is spherical, the "density" has to be spherical as well. For degenerate states, the "density" thus is the ensemble density. For an atom in an environment, there is no such argument. E.g. the density of a hydrogen atom will be deformed by the nearby presence of another hydrogen atom -- they form a bond. So, if atoms in VanDerWaals situations are nonspherical, this does not mean the "atom itself" is non-spherical. Nonspherical atoms as the result of a quantum-chemical calculations are a different topic, they mostly aris through symmetry breaking, that mostly is a defect of the chosen method. If, e.g. a fluorine atom is treated at the single-configuration level and if pz is chosen to be singly occupied, then the radial wave function of pz will be different from px and py --- no spherical density can be obtained even for an ensemble. This will change if one goes to a state-averaged calculation. -Christoph van Wuellen Christoph.van.Wuellen@ruhr-uni-bochum.de (Alan: I wrote some additional questions to Christoph, and his replies shed some more light on this question) 5. From Christoph van Wuellen: for the electronic system, the electron-nuclear attraction is the "external potential" (i.e. external to the electrons), and that is spherical. The electron-electron interaction is "internal". So if you have a nonspherical density, you can just rotate the wave function a little bit and you get a rotated density. The rotated wave function must be degenerate with the original one. In the whole set of degenerate wave functions, you can find linear combinations which are angular momentum eigenfunctions and so forth... In many-electron atoms, you will only find that the rotated wave functions form an irreducible representation of the rotation group with dimension 2L+1. Such "states" are then called S P D F .... states for L=0,1,2,3,.... If you do a calculation, you might encounter "symmetry breaking". This means that all the rotated images of your original wave function do not form an irrep of the rotation group (i.e. states higher L are mixed in). This does not happen for "true" atomic wave functions since configurations with different L are non-degenerate except for one-electron systems. Christoph van Wuellen Christoph.van.Wuellen@ruhr-uni-bochum.de