From fredrik@donau.kemi.uu.se Wed Aug 14 04:17:27 1996 Received: from akka.kemi.uu.se for fredrik@donau.kemi.uu.se by www.ccl.net (8.7.5/950822.1) id EAA29634; Wed, 14 Aug 1996 04:10:14 -0400 (EDT) Received: from donau.kemi.uu.se by akka.kemi.uu.se with SMTP id AA02876 (5.67a8/IDA-1.5 for ); Wed, 14 Aug 1996 09:54:04 +0200 Received: by donau.kemi.uu.se; (5.65/1.1.8.2/06Jul95-0509PM) id AA14006; Wed, 14 Aug 1996 10:10:37 +0200 Date: Wed, 14 Aug 1996 10:10:37 +0200 From: Fredrik B|kman Message-Id: <9608140810.AA14006@donau.kemi.uu.se> To: chemistry@www.ccl.net Subject: Fenske-Hall calculations Cc: fredrik@donau.kemi.uu.se Dear CCL fellows, In some publications, both recent and old, Fenske-Hall calculations are used, e.g. for correlating electronic struture and XPS binding energy shifts. Is there a public domain Fenske-Hall code out out there somewhere? Or a program to be obtained for a few bucks? And are you aware of any recent reviews on/including Fenske-Hall calculations? Thanks in advance, Fredrik Bokman Dept of Organic Chemistry email: Fredrik.Bokman@kemi.uu.se Uppsala University phone: +46/18/183794 P.O. Box 531 fax: +46/18/508542 S-75121 Uppsala Sweden From fredrik@donau.kemi.uu.se Wed Aug 14 04:31:12 1996 Received: from akka.kemi.uu.se for fredrik@donau.kemi.uu.se by www.ccl.net (8.7.5/950822.1) id EAA29656; Wed, 14 Aug 1996 04:11:09 -0400 (EDT) Received: from donau.kemi.uu.se by akka.kemi.uu.se with SMTP id AA02896 (5.67a8/IDA-1.5 for ); Wed, 14 Aug 1996 09:55:03 +0200 Received: by donau.kemi.uu.se; (5.65/1.1.8.2/06Jul95-0509PM) id AA14000; Wed, 14 Aug 1996 10:11:37 +0200 Date: Wed, 14 Aug 1996 10:11:37 +0200 From: Fredrik B|kman Message-Id: <9608140811.AA14000@donau.kemi.uu.se> To: chemistry@www.ccl.net Subject: Transition metals / semiempirical parametrizations Cc: fredrik@donau.kemi.uu.se Dear CCL fellows, I am interested in the recent developments in semiempirical parametrizations for transition metal atoms. E.g., Spartan (Wavefunction) has included Thiel's MNDO/d and Ampac (Semichem) has Dewar's SAM1. The incorporation of these features is a strong argument in selling the programs to organometallic chemists (for example), but I find that there is rather little documentation on the performance of the transition metal parametrizations. Do you know of any published evaluations? By the way, do you know of any other recent (or old) parametrizations of the 3d-, 4d-, or 5d elements? Thanks in advance, Fredrik Bokman Dept of Organic Chemistry email: Fredrik.Bokman@kemi.uu.se Uppsala University phone: +46/18/183794 P.O. Box 531 fax: +46/18/508542 S-75121 Uppsala Sweden From demaria@sissa.it Wed Aug 14 08:17:28 1996 Received: from shannon.sissa.it for demaria@sissa.it by www.ccl.net (8.7.5/950822.1) id IAA00642; Wed, 14 Aug 1996 08:14:22 -0400 (EDT) Received: (from demaria@localhost) by shannon.sissa.it (8.7.3/8.7.1) id OAA20539 for chemistry@www.ccl.net; Wed, 14 Aug 1996 14:14:21 +0200 From: Leonardo Demaria Message-Id: <199608141214.OAA20539@shannon.sissa.it> Subject: LCAOSCF : how to get self-consistency ? To: chemistry@www.ccl.net (ccl) Date: Wed, 14 Aug 1996 14:14:21 +22310718 (MET_DST) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Hi everybody, I'm doing some CNDO/2 calculations for solid carbon and fullerenes. I've found some problems with the convergence of the itera- tive solutions of the Roothaan equations. There are some cases in wich the density matrix doesn't converge but oscillates and finally diverges. Is there any body out there who can tell me about some technical referen- ces about how to deal with the convergence of such equations? I've been using only the previous step density matrix in order to compute the next one but I know that relaxation techniques can be used. Can somebody tell about relaxation techniques in the solution of the SCFLCAO equations? I thank you very much in advance and I hope somebody is still at work somewhere. Bye, -- Leonardo De Maria SISSA | Universita di Trieste Scuola Internazionale | Dipartimento di Fisica Teorica Superiore di Studi Avanzati | Strada Costiera 11 via Beirut 2-4, Grignano | Miramare-Grignano I-34014 - Trieste | I-34014 - Trieste tel: +39 40 3787506 | tel: +39 40 224265 fax: 3787528 | fax: 224601 e-mail:demaria@sissa.it | e-mail : demaria@ts.infn.it From eldbjorg@chem.uit.no Wed Aug 14 09:17:31 1996 Received: from kvikk.uit.no for eldbjorg@chem.uit.no by www.ccl.net (8.7.5/950822.1) id JAA00991; Wed, 14 Aug 1996 09:09:21 -0400 (EDT) Received: from trypsin.chem.uit.no (trypsin.Chem.Uit.No [129.242.24.101]) by kvikk.uit.no (8.7.3/8.7.1) with SMTP id PAA03723 for ; Wed, 14 Aug 1996 15:09:19 +0200 (METDST) Received: by trypsin.chem.uit.no (911016.SGI/ABaa-2.0mini) id AA07136; Wed, 14 Aug 96 14:19:32 GMT Date: Wed, 14 Aug 96 14:19:32 GMT From: eldbjorg@chem.uit.no (Eldbjoerg S. Heimstad) Message-Id: <9608141419.AA07136@trypsin.chem.uit.no> To: chemistry@www.ccl.net Subject: Poisson-Boltzman calculations Cc: eldbjorg@chem.uit.no We are interested in information concerning Poisson-Boltzman calculations - does it exist a stand-alone program, how successful is the method ? -the limits/pitfalls etc. All replies will be helpful -thanks. Regards, Elle ####################################################### # Eldbjoerg Sofie Heimstad # # Protein Crystallography Group # # University Of Tromsoe, IMR # # 9037 Tromsoe, NORWAY phone: +47-776-45706 # # +47-776-44737 # # fax : +47-776-44765 # # E-mail: Eldbjorg.Heimstad@chem.uit.no # # URL: http://www.chem.uit.no/KJEMI/heimstad.html # ####################################################### From Kirk_A_Peterson%~WHC304@ccmail.pnl.gov Wed Aug 14 10:17:29 1996 Received: from pnl.gov for Kirk_A_Peterson%~WHC304@ccmail.pnl.gov by www.ccl.net (8.7.5/950822.1) id JAA01380; Wed, 14 Aug 1996 09:59:23 -0400 (EDT) From: Received: from ccmail.pnl.gov by pnl.gov (PMDF V4.3-13 #6012) id <01I899MBYP1S8WVYNC@pnl.gov>; Wed, 14 Aug 1996 06:59:17 -0700 (PDT) Date: Wed, 14 Aug 1996 06:54 -0700 (PDT) Subject: Re: CCL:Transition metals / semiempirical parametrizations To: chemistry@www.ccl.net, ng570@talisker.pnl.gov Cc: fredrik@donau.kemi.uu.se Message-id: <01I899MD48P68WVYNC@pnl.gov> MIME-version: 1.0 Content-transfer-encoding: 7BIT Rerouted to correct addressee ______________________________ Reply Separator _________________________________ Subject: CCL:Transition metals / semiempirical parametrizations Author: fredrik@donau.kemi.uu.se at -SMTPlink Date: 8/14/96 1:11 AM Dear CCL fellows, I am interested in the recent developments in semiempirical parametrizations for transition metal atoms. E.g., Spartan (Wavefunction) has included Thiel's MNDO/d and Ampac (Semichem) has Dewar's SAM1. The incorporation of these features is a strong argument in selling the programs to organometallic chemists (for example), but I find that there is rather little documentation on the performance of the transition metal parametrizations. Do you know of any published evaluations? By the way, do you know of any other recent (or old) parametrizations of the 3d-, 4d-, or 5d elements? Thanks in advance, Fredrik Bokman Dept of Organic Chemistry email: Fredrik.Bokman@kemi.uu.se Uppsala University phone: +46/18/183794 P.O. Box 531 fax: +46/18/508542 S-75121 Uppsala Sweden -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: fredrik@donau.kemi.uu.se -- Original Sender From: Address: fredrik@donau.kemi.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 From echamot@xnet.com Wed Aug 14 10:22:27 1996 Received: from mail.xnet.com for echamot@xnet.com by www.ccl.net (8.7.5/950822.1) id JAA01287; Wed, 14 Aug 1996 09:39:20 -0400 (EDT) Received: from echamot.xnet.com by mail.xnet.com (8.7.5/XNet-2.1R) with SMTP id IAA25703; Wed, 14 Aug 1996 08:38:08 -0500 (CDT) Message-ID: Date: Wed, 14 Aug 96 08:38:15 +0100 From: "Ernest Chamot" Subject: Re: CCL:Transition metals / semiempirical parametrizations To: "Fredrik B|kman" , chemistry@www.ccl.net X-Mailer: VersaTerm Link v1.1.6 Hi Fredrik, I, too, am: >. . . interested in the recent developments >in semiempirical parametrizations for >transition metal atoms. E.g., Spartan >(Wavefunction) has included Thiel's MNDO/d >and Ampac (Semichem) has Dewar's SAM1. I would add PM3(tm) (also in Spartan) and the DFT methods in general as exciting developments for transition metals. I have heard both Andy Holder and Warren Hehre present results of validation testing at ACS meetings to establish the accuracy of their parameterizations for transition metals. The current status seems to be that: MNDO/d parameterization is focused on main group elements rather than transition metals; PM3(tm) is adding transition metals rapidly, but is focused on good geometries rather than energies; and SAM1 is progressing slower, but is focused on being theoretically consistent and may give better energies. New atom parameters may announced at the upcoming ACS meeting, but the atoms parameterized (or at least announced as parameterized) that I know of to date are: MNDO/d - Ne - Cl Li - F Al - Cl Cr, Zn, Ge, Br Sn, I Hg, Pb PM3(tm) - Ti, Cr, Mn, Fe, Co, Ni, Cu Zr, Mo, Ru, Rh, Pd Hf - W Gd SAM1 - H C - F Si - Cl Fe, Cu, Br I So far, as you say, there is: >rather little documentation on the performance >of the transition metal parametrizations. >Do you know of any published evaluations? Outside of preprints and literature from Wavefunction (http://wavefun.com) and Semichem (email: aholder@vax1.unkc.edu) there are a couple of publications. Take a look at: Liljfors, et. al., J. Comp. Chem., 17(4), 429-49 (1996). W. Thiel & A. Voityuk, J. Phys. Chem., 100, 616-26 (1969). EC --- Chamot Laboratories, Inc. 530 E. Hillside Rd. Naperville, Illinois 60540 Phone/Fax: (630) 637-1559 echamot@xnet.com http://www.xnet.com/~chamotlb From Kirk_A_Peterson%~WHC304@ccmail.pnl.gov Wed Aug 14 10:26:25 1996 Received: from pnl.gov for Kirk_A_Peterson%~WHC304@ccmail.pnl.gov by www.ccl.net (8.7.5/950822.1) id JAA01384; Wed, 14 Aug 1996 09:59:51 -0400 (EDT) From: Received: from ccmail.pnl.gov by pnl.gov (PMDF V4.3-13 #6012) id <01I899MBYP1S8WVYNC@pnl.gov>; Wed, 14 Aug 1996 06:59:15 -0700 (PDT) Date: Wed, 14 Aug 1996 06:52 -0700 (PDT) Subject: Re: CCL:M:Normal Coordinate Visualisation To: Jeffrey.Gosper@brunel.ac.uk, bennett@ubeclu.unibe.ch, ng570@talisker.pnl.gov Cc: CHEMISTRY@www.ccl.net Message-id: <01I899MC3HEQ8WVYNC@pnl.gov> MIME-version: 1.0 Content-transfer-encoding: 7BIT Rerouted to correct addressee ______________________________ Reply Separator _________________________________ Subject: CCL:M:Normal Coordinate Visualisation Author: Jeffrey.Gosper@brunel.ac.uk at -SMTPlink Date: 8/13/96 10:28 PM > I am wondering if anyone has a simple program for drawing normal > coordinates on molecules once a frequency calculation has been done. Some > nice graphics programs such as Spartan can animate the normal vibrational > modes, but this is of little use for preparing static documents for example. > I guess that something that could simply draw mass weighted cartesian > coordinate arrows would be brilliant. > > Ciao At present Re_View ( a Windows pogram) will animate MOPAC normal modes but not draw arrows. The new version Re_View2 dows both. I will be releasing a test version of Re_View2 shortly so you may be interested in contacting me and acting as a beta tester. See Re_View's URL for further details. /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://http1.brunel.ac.uk:8080/~castjjg Re_View's home page (molecular animations or Chem-4D): http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: Jeffrey.Gosper@brunel.ac.uk -- Original Sender From: Address: Jeffrey.Gosper@brunel.ac.uk 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 From Kirk_A_Peterson%~WHC304@ccmail.pnl.gov Wed Aug 14 10:29:22 1996 Received: from pnl.gov for Kirk_A_Peterson%~WHC304@ccmail.pnl.gov by www.ccl.net (8.7.5/950822.1) id KAA01414; Wed, 14 Aug 1996 10:05:42 -0400 (EDT) From: Received: from ccmail.pnl.gov by pnl.gov (PMDF V4.3-13 #6012) id <01I899U3QIB48WVYNC@pnl.gov>; Wed, 14 Aug 1996 07:05:31 -0700 (PDT) Date: Wed, 14 Aug 1996 06:55 -0700 (PDT) Subject: Re: CCL:G:Book on comp. chem. To: aeleen@netcom.com, chemistry@www.ccl.net, ng570@talisker.pnl.gov Message-id: <01I899U3SHW28WVYNC@pnl.gov> MIME-version: 1.0 Content-transfer-encoding: 7BIT Rerouted to correct addressee ______________________________ Reply Separator _________________________________ Subject: CCL:G:Book on comp. chem. Author: aeleen@netcom.com at -SMTPlink Date: 8/13/96 3:11 PM The second edition of Exploring Chemistry with Electronic Structure Methods, by James B. Foresman and AEleen Frisch, has just been published. It is a thoroughly revised and expanded version of the previous work (354 pages). For this second edition, the authors have expanded the previous text and added new material throughout the book. They have also added many new exercises to most chapters covering advanced aspects of the current topic. This material constitutes an advanced track through the work. Experienced researchers may wish to examine the advanced track even in the earlier, more elementary chapters where the basic concepts are very familiar. New topics covered include the following: * Predicting NMR properties * New methods for geometry optimizations * Locating transition structures * Available methods, from semi-empirical through QCISD * Density functional theory * Gaussian-2 theory and variations * Complete Basis Set (CBS) methods * Relative accuracies and costs of various model chemistries * CASSCF calculations of excited state systems * New SCRF solvation models * SCF and DFT stability calculations Published by Gaussian, Inc., Pittsburgh, PA, USA. email: info@gaussian.com Soft cover: $ 42.00 ISBN 0-9636769-3-8 Hard cover: $100.00 ISBN 0-9636769-4-6 [available 9/96] Note: Previous purchasers of Gaussian 94 and G94W will be sent a soft cover copy automatically. -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: aeleen@netcom.com -- Original Sender From: Address: aeleen@netcom.com 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 From hobina@dmu.ac.uk Wed Aug 14 11:17:30 1996 Received: from macondo.dmu.ac.uk for hobina@dmu.ac.uk by www.ccl.net (8.7.5/950822.1) id KAA01591; Wed, 14 Aug 1996 10:34:47 -0400 (EDT) Received: from brains.eng.dmu.ac.uk (brains.eng.dmu.ac.uk [146.227.22.1]) by macondo.dmu.ac.uk (8.6.12/8.6.11) with ESMTP id PAA13381; Wed, 14 Aug 1996 15:38:35 +0100 Received: from shore.dmu.ac.uk (shore [146.227.22.9]) by brains.eng.dmu.ac.uk (8.6.12/8.6.12) with ESMTP id PAA26328; Wed, 14 Aug 1996 15:33:06 +0100 Received: from shore by shore.dmu.ac.uk (SMI-8.6/SMI-SVR4) id PAA29898; Wed, 14 Aug 1996 15:34:26 +0100 Sender: hobina@dmu.ac.uk Message-ID: <3211E3F1.357F@dmu.ac.uk> Date: Wed, 14 Aug 1996 15:34:25 +0100 From: Hobina Rajakaruna X-Mailer: Mozilla 2.0 (X11; I; SunOS 5.5 sun4m) MIME-Version: 1.0 To: chemistry@www.ccl.net CC: hobina@dmu.ac.uk Subject: function to calc. Cp of C12H26 X-URL: http://www.ccl.net/ccl/welcome.html#3 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello ; Can some one provide me with a function to calculate isobaric specific heat capacity of C12H26 as in the form: aT+bT2+cT3... accurate between 700K-3000K Regrads; ************************************** * Hobina Rajakaruna * * Research student * * De Montfort University * * Dept. of Mech. and Manf. Eng. * * Queens Building * * Leicester * * +44 166 2577096 * ************************************** From owner-chemistry@ccl.net Wed Aug 14 12:17:38 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id LAA02018; Wed, 14 Aug 1996 11:50:52 -0400 (EDT) Received: from SIUCVMB.SIU.EDU for TAPASKAR@SIUCVMB.SIU.EDU by bedrock.ccl.net (8.7.5/950822.1) id LAA00300; Wed, 14 Aug 1996 11:50:50 -0400 (EDT) Message-Id: <199608141550.LAA00300@bedrock.ccl.net> Received: from SIUCVMB.SIU.EDU by SIUCVMB.SIU.EDU (IBM VM SMTP V2R2) with BSMTP id 8630; Wed, 14 Aug 96 10:50:00 CST Date: Wed, 14 Aug 96 10:46:47 CST From: "Tapas Kar" To: chemistry@ccl.net Subject: HNO-HON surface Hi, I am looking for higher level ab initio results (relative energy, barrier height etc) of HNO-HON system. Thanks, Tapas From topper@cooper.edu Wed Aug 14 12:22:55 1996 Received: from magnum.cooper.edu for topper@cooper.edu by www.ccl.net (8.7.5/950822.1) id LAA02063; Wed, 14 Aug 1996 11:56:14 -0400 (EDT) Received: from zeus.cooper.edu by magnum.cooper.edu with SMTP id AA20585 (5.65c/IDA-1.4.4 for ); Wed, 14 Aug 1996 11:58:02 -0400 Received: by zeus.cooper.edu id AA03898 (5.67b/IDA-1.5 for CHEMISTRY@www.ccl.net); Wed, 14 Aug 1996 11:54:25 -0400 From: TOPPER ROBERT Message-Id: <199608141554.AA03898@zeus.cooper.edu> Subject: CCL:M:Normal Coordinate Visualisatio To: CHEMISTRY@www.ccl.net Date: Wed, 14 Aug 1996 11:54:25 -0400 (EDT) Cc: topper@cooper.edu (TOPPER ROBERT) X-Mailer: ELM [version 2.4 PL24alpha3] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit With respect to the question about drawing normal-mode vectors; XMol 1.3.1, which is freeware for XWindows >from the Minnesota Supercomputer Center, Inc., has this capability. See http://www.msc.edu/msc/docs/xmol/ftp.html Compiled versions are available for a variety of platforms. Best to all, rqt ************************************************************************ Robert Q. Topper email: topper@cooper.edu Asst. Prof. of Chemistry phone: (212) 353-4378 The Cooper Union FAX: (212) 353-4341 51 Astor Place subway: take the 6 to Astor Place New York, NY 10003 USA or the N/R to 8th St/NYU http://www.cooper.edu/engineering/chemechem/depts_info/topper.html ************************************************************************ Check out the Molecular Monte Carlo home page! http://www.cooper.edu/engineering/chemechem/monte.html ************************************************************************ From Jeffrey.Gosper@brunel.ac.uk Wed Aug 14 12:26:00 1996 Received: from etamin.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.7.5/950822.1) id LAA01961; Wed, 14 Aug 1996 11:43:58 -0400 (EDT) Received: from ccsc-10 (actually ccsc-10.brunel.ac.uk) by etamin.brunel.ac.uk with SMTP (PP); Wed, 14 Aug 1996 16:43:21 +0100 Date: Wed, 14 Aug 1996 16:43:18 BST From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: Re: CCL:M:Normal Coordinate Visualisation To: Jeffrey Gosper cc: "Frederick R. Bennett" , CHEMISTRY@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII > I received a message you sent to the comp chem listserv and would like to > get in on beta testing Re_View2. I liked the first version very much. > Unfortunately, I had problems running it on Windows 95 without playing > around with memory allocations. I ended up continuing running it on a > PC with WfW 3.11. I do a lot of geometry optimizations and vibrational > frequency calculations in my work towards a PhD. I have made presentations > for national conferences and would like to help you with Re_View in any way > I can. > > *************************************************** > * Fredrick (Fred) C. Hagemeister * > * Dept. of Chemistry - Div. of Physical Chemistry * > * Purdue University * > * 1393 Brown Bldg * > * West Lafayette, IN 47907-1393 * > * ph.(317)494-7792 home/ans.machn.(317)474-2303 * > * fredhag@vm.cc.purdue.edu * > *************************************************** Thanks for your interest in testing the new version. I'm putting it though its final paces and at present there is no help file or manual. Have you been using the original version of Re_View? I would also expect a short written report with comments/bugs, etc from any beta-testers. I will have a 32 bit Windows95 (NT?) version and a Win31 version. I let the CCL know when I have a copy ready for testing. PS: I have had no problems runni9ng the original version of Re_View under Windows95 but then again I have 64 Mbytes of memory. > > > ----------------------------Original message---------------------------- > > > > I am wondering if anyone has a simple program for drawing normal > > coordinates on molecules once a frequency calculation has been done. Some > > nice graphics programs such as Spartan can animate the normal vibrational > > modes, but this is of little use for preparing static documents for example. > > I guess that something that could simply draw mass weighted cartesian > > coordinate arrows would be brilliant. > > > > Ciao > At present Re_View ( a Windows pogram) will animate MOPAC normal modes but not > draw arrows. > The new version Re_View2 dows both. I will be releasing a test version of > Re_View2 shortly so you > may be interested in contacting me and acting as a beta tester. > > See Re_View's URL for further details. > /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ > Dr. Jeff Gosper > Dept. of Chemistry > BRUNEL University > Uxbridge Middx UB8 3PH, UK > voice: 01895 274000 x2187 > facsim: 01895 256844 > internet/email/work: Jeffrey.Gosper@brunel.ac.uk > internet/WWW: http://http1.brunel.ac.uk:8080/~castjjg > Re_View's home page (molecular animations or Chem-4D): > http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/re_view.htm > \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ > > > > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: Jeffrey.Gosper@brunel.ac.uk > -- Original Sender From: Address: Jeffrey.Gosper@brunel.ac.uk > 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 /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://http1.brunel.ac.uk:8080/~castjjg Re_View's Home page (A molecular display/animation/analysis program): http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From duanx@Picard.ml.wpafb.af.mil Wed Aug 14 12:28:30 1996 Received: from riker.ml.wpafb.af.mil for duanx@Picard.ml.wpafb.af.mil by www.ccl.net (8.7.5/950822.1) id LAA02032; Wed, 14 Aug 1996 11:53:10 -0400 (EDT) Received: from picard.ml.wpafb.af.mil by riker.ml.wpafb.af.mil (5.65/Ultrix3.0-C) id AA09362; Wed, 14 Aug 1996 11:53:10 -0400 Received: by Picard.ml.wpafb.af.mil (4.1/version) id AA05565; Wed, 14 Aug 96 11:53:08 EDT Date: Wed, 14 Aug 1996 11:53:08 -0400 (EDT) From: Xiaofeng Duan To: chemistry@www.ccl.net Subject: Summary: Extended Huckel Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII My original question is: > > I was wondering where I can find codes that can do Extended Huckel > calculations on the unix machine. We have Hyperchem which can do so, > but it is on PCs. I got a few answers. Basically,there are two suggestions: Landrum's code named "YAeHMOP", and programs ICON or FORTICON from QCPE. I sincerely thank all the people who answered my question promptly. Here is the summary of the answers I got. ############################################################# >From gl19@cornell.eduWed Aug 14 10:22:04 1996 Date: Mon, 12 Aug 1996 15:51:39 -0400 From: greg Landrum To: Xiaofeng Duan Subject: Re: CCL:Extended Huckel code I have written a package of programs (called YAeHMOP) for doing extended Hueckel calculations on molecules and solids. The programs are freely available in source and executable form (for IBM, HP, and SGI workstations) at. You can find information about the package at URL: http://overlap.chem.cornell.edu:8080/yaehmop.html I hope this helps, -greg -- ---------------------------- >From john@cv1.chem.purdue.eduWed Aug 14 10:22:21 1996 Date: Mon, 12 Aug 1996 14:58:34 -0500 From: "John J. Nash" To: duanx@Picard.ml.wpafb.af.mil Subject: EHMO Dear Xiaofeng: There are two packages that you might be able to use to do EHMO on Unix machines. The first is called "FORTICON8" and can be obtained from the Quantum Chemistry Program Exchange (QCPE) in Bloomington, IN. The second package is "ARGUS". I am not sure where this can be obtained but you might try contacting the author: Mark Thompson e-mail: d3f012@pnlg.pnl.gov Hope this helps! Sincerely, John Nash Purdue University john@cv1.chem.purdue.edu -------------------------------------------------------------------------- >From b_duke@quoll.ntu.edu.auWed Aug 14 10:22:35 1996 Date: Tue, 13 Aug 1996 06:56:13 +0930 (CST) From: Brian Salter-Duke To: Xiaofeng Duan Subject: Re: CCL:Extended Huckel code You do not say what elements you want to cover and what version of EHM. There is quite a bit of stuff at QCPE. I have a simple version for teaching that just handles 1st row elements. I am happy to let you have that. It, and all the QCPE stuff, is in Fortran and should run on any unix system with Fortran. Cheers, Brian. -- Associate Professor Brian Salter-Duke (Brian Duke) School of Mathematical and Physical Sciences, Northern Territory University, Darwin, NT 0909, Australia. Phone 089-466702 e-mail: b_duke@lacebark.ntu.edu.au or b_duke@quoll.ntu.edu.au ---------------------------------------------------------------------------- >From mxm@msi.comWed Aug 14 10:23:12 1996 Date: Mon, 12 Aug 1996 14:38:06 -0700 From: Max Muir To: duanx@Picard.ml.wpafb.af.mil Subject: Re: CCL:Extended Huckel code Dear Xiaofeng Duan, ZINDO can do EHT type calculations and the version available from Molecular Simulations runs on IRIX and AIX. Best wishs, Max Muir ----------------------------------------------------------------------------- >From Steve.Bowlus@sandoz.comWed Aug 14 10:23:25 1996 Date: Mon, 12 Aug 1996 23:57:46 +0200 From: Steve.Bowlus@sandoz.com To: duanx@Picard.ml.wpafb.af.mil Subject: EHT Just about every commercial package does this. For a stand-alone program you can probably use ICON or FORTICON from QCPE. I'm not certain if there is an official port of these to a UNIX box, but this should be simple to do. sb =========================================================================== Stephen B. Bowlus, Ph.D. Computer-Aided Molecular Design Research Division e-mail: bowlus@sandoz.com Sandoz Agro, Inc. Phone: + 1 415 354 3904 975 California Ave. Fax: + 1 415 857 1125 Palo Alto, CA 94304 =========================================================================== >From P.Sherwood@dl.ac.ukWed Aug 14 10:23:52 1996 Date: Mon, 12 Aug 96 23:28:08 BST From: "P. Sherwood" To: duanx@Picard.ml.wpafb.af.mil Subject: Re: CCL:Extended Huckel code take a look at YaEHMOp - from Greg Landrum of the Hoffmann group - http://overlap.chem.cornell.edu:8080/~landrum/yaehmop.html Paul Sherwood ---------------------------------------------------------------------------- >From mbs@ceres.qc.ag-berlin.mpg.deWed Aug 14 10:24:45 1996 Date: Tue, 13 Aug 1996 09:59:28 +0000 From: Martin Braendle To: Xiaofeng Duan Subject: Re: CCL:Extended Huckel code Dear Xiaofeng, such a code is available at QCPE - the ICONC/INPUTC package QCMP #116 by G. Calzaferri and M. Braendle. It has Makefiles for MS-DOS, VMS, and UNIX. With kind regards Martin -- Dr. Martin Braendle Jaegerstrasse 10/11, Zi. 303 Max-Planck-Gesellschaft D-10117 Berlin Arbeitsgruppe Quantenchemie Tel.: (49)-(30)-20192305 an der Humboldt-Universitaet Fax.: (49)-(30)-20192302 E-mail: mbs@qc.ag-berlin.mpg.de ------------------------------------------------------------------------------ >From rytz@solar.iac.unibe.chWed Aug 14 10:24:57 1996 Date: Tue, 13 Aug 1996 14:15:46 +0200 (DFT) From: Ruedi Rytz To: Xiaofeng Duan Subject: Re: CCL:Extended Huckel code Hello We have developed an Extended Huckel package called ICON-EDiT. Besides the usual EHMO computations, ICON-EDiT performs oscillator strength (UV/VIS spectra) calculations based on EHMO wave functions. The DOS-WINDOWS binaries of ICON-EDiT along with a few example files and a short manual are available by following the URL: http://iacrs1.unibe.ch/ For UNIX or VAX systems, we refer to ICON-EDiTs predecessor ICONC&INPUTC available through QCPE (number 116). The FORTRAN77 sources are shipped along with this distribution and compile on many different platforms. Except for the oscillator strength part ICONC&INPUTC and ICON-EDiT are almost the same. As soon as possible we will start distributing the ICON-EDiT sources and a detailed manual upon request for a few dollars to cover our expenses. Enjoy the package! Ruedi Rytz -- -------------------------------------------------------------------------------- Ruedi Rytz, Department of Chemistry, University of Berne, Freiestrasse. 3, 3012 Bern, Switzerland. E-Mail: rytz@solar.iac.unibe.ch HTTP://iacrs1.unibe.ch/members/rr.html Tel. +41 31 631 42 25, Fax +41 31 631 39 94 -------------------------------------------------------------------------------- From robert@pauli.utmb.edu Wed Aug 14 12:31:22 1996 Received: from nmr.utmb.edu for robert@pauli.utmb.edu by www.ccl.net (8.7.5/950822.1) id MAA02168; Wed, 14 Aug 1996 12:17:14 -0400 (EDT) Received: from pauli.utmb.edu by nmr.utmb.edu via SMTP (931110.SGI/930416.SGI.AUTO) for bennett@ubeclu.unibe.CH id AA05644; Wed, 14 Aug 96 10:19:47 -0600 Received: (from robert@localhost) by pauli.utmb.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) id KAA02889; Wed, 14 Aug 1996 10:53:16 -0500 From: "Robert Fraczkiewicz" Message-Id: <9608141053.ZM2887@pauli.utmb.edu> Date: Wed, 14 Aug 1996 10:53:16 -0500 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: bennett@ubeclu.unibe.CH Subject: Normal Coordinate Visualisation Cc: CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Frederick, > I am wondering if anyone has a simple program for drawing normal > coordinates on molecules once a frequency calculation has been done. Some > nice graphics programs such as Spartan can animate the normal vibrational > modes, but this is of little use for preparing static documents for example. > I guess that something that could simply draw mass weighted cartesian > coordinate arrows would be brilliant. > > Ciao Molecular graphics program XMol available on variety of platforms from: http://www.msc.edu/msc/docs/xmol/ftp.html has a very nice "Extras/Animate" option that can do the trick. It can both draw the arrows and animate normal modes. Since an example is the best teacher, I am attaching one of the animation input files in XYZ format recognized by XMol. This is one of the Ag vibrational modes of 6-atom (two Cu, two S and two imidazoles as point masses) model of the active site of a metalloprotein known as CuA. To see the arrows select "Display" menu and turn the option "Vectors" on. To see animation select option "Animate" from "Extras" menu. The input is composed of 30 frames in the following format Atom_symbol Atom_X Atom_Y Atom_Z Arrow_X Arrow_Y Arrow_Z You can manipulate relative arrow coordinates to make them longer or shorter. Sincerely, Robert Fraczkiewicz University of Texas Medical Branch Galveston, TX 77555 robert@nmr.utmb.edu -------------------------------CUT HERE------------------------------------- 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU 0.00000 0.00000 0.00000 0.09497 -0.06472 0.00000 CU 2.47000 0.00000 0.00000 -0.09497 0.06472 0.00000 S 1.23500 0.00000 1.79643 0.00000 0.00000 0.20062 S 1.23500 0.00000 -1.79643 0.00000 0.00000 -0.20062 N -1.47847 1.24058 0.00000 -0.08343 0.06581 0.00000 N 3.94847 -1.24058 0.00000 0.08343 -0.06581 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU 0.01974 -0.01346 0.00000 0.07522 -0.05126 0.00000 CU 2.45026 0.01346 0.00000 -0.07522 0.05126 0.00000 S 1.23500 0.00000 1.83814 0.00000 0.00000 0.15891 S 1.23500 0.00000 -1.83814 0.00000 0.00000 -0.15891 N -1.49582 1.25426 0.00000 -0.06608 0.05213 0.00000 N 3.96582 -1.25426 0.00000 0.06608 -0.05213 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU 0.03863 -0.02632 0.00000 0.05634 -0.03840 0.00000 CU 2.43137 0.02632 0.00000 -0.05634 0.03840 0.00000 S 1.23500 0.00000 1.87803 0.00000 0.00000 0.11902 S 1.23500 0.00000 -1.87803 0.00000 0.00000 -0.11902 N -1.51240 1.26735 0.00000 -0.04949 0.03904 0.00000 N 3.98240 -1.26735 0.00000 0.04949 -0.03904 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU 0.05582 -0.03804 0.00000 0.03915 -0.02668 0.00000 CU 2.41418 0.03804 0.00000 -0.03915 0.02668 0.00000 S 1.23500 0.00000 1.91435 0.00000 0.00000 0.08270 S 1.23500 0.00000 -1.91435 0.00000 0.00000 -0.08270 N -1.52751 1.27926 0.00000 -0.03439 0.02713 0.00000 N 3.99751 -1.27926 0.00000 0.03439 -0.02713 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU 0.07057 -0.04810 0.00000 0.02439 -0.01662 0.00000 CU 2.39943 0.04810 0.00000 -0.02439 0.01662 0.00000 S 1.23500 0.00000 1.94552 0.00000 0.00000 0.05153 S 1.23500 0.00000 -1.94552 0.00000 0.00000 -0.05153 N -1.54047 1.28949 0.00000 -0.02143 0.01690 0.00000 N 4.01047 -1.28949 0.00000 0.02143 -0.01690 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU 0.08224 -0.05605 0.00000 0.01272 -0.00867 0.00000 CU 2.38776 0.05605 0.00000 -0.01272 0.00867 0.00000 S 1.23500 0.00000 1.97017 0.00000 0.00000 0.02688 S 1.23500 0.00000 -1.97017 0.00000 0.00000 -0.02688 N -1.55072 1.29757 0.00000 -0.01118 0.00882 0.00000 N 4.02072 -1.29757 0.00000 0.01118 -0.00882 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU 0.09032 -0.06155 0.00000 0.00465 -0.00317 0.00000 CU 2.37968 0.06155 0.00000 -0.00465 0.00317 0.00000 S 1.23500 0.00000 1.98723 0.00000 0.00000 0.00982 S 1.23500 0.00000 -1.98723 0.00000 0.00000 -0.00982 N -1.55781 1.30317 0.00000 -0.00408 0.00322 0.00000 N 4.02781 -1.30317 0.00000 0.00408 -0.00322 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU 0.09445 -0.06436 0.00000 0.00052 -0.00035 0.00000 CU 2.37555 0.06436 0.00000 -0.00052 0.00035 0.00000 S 1.23500 0.00000 1.99595 0.00000 0.00000 0.00110 S 1.23500 0.00000 -1.99595 0.00000 0.00000 -0.00110 N -1.56144 1.30603 0.00000 -0.00046 0.00036 0.00000 N 4.03144 -1.30603 0.00000 0.00046 -0.00036 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU 0.09445 -0.06436 0.00000 -0.18942 0.12908 0.00000 CU 2.37555 0.06436 0.00000 0.18942 -0.12908 0.00000 S 1.23500 0.00000 1.99595 0.00000 0.00000 -0.40014 S 1.23500 0.00000 -1.99595 0.00000 0.00000 0.40014 N -1.56144 1.30603 0.00000 0.16640 -0.13126 0.00000 N 4.03144 -1.30603 0.00000 -0.16640 0.13126 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU 0.09032 -0.06155 0.00000 -0.18529 0.12627 0.00000 CU 2.37968 0.06155 0.00000 0.18529 -0.12627 0.00000 S 1.23500 0.00000 1.98723 0.00000 0.00000 -0.39142 S 1.23500 0.00000 -1.98723 0.00000 0.00000 0.39142 N -1.55781 1.30317 0.00000 0.16277 -0.12840 0.00000 N 4.02781 -1.30317 0.00000 -0.16277 0.12840 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU 0.08224 -0.05605 0.00000 -0.17721 0.12077 0.00000 CU 2.38776 0.05605 0.00000 0.17721 -0.12077 0.00000 S 1.23500 0.00000 1.97017 0.00000 0.00000 -0.37436 S 1.23500 0.00000 -1.97017 0.00000 0.00000 0.37436 N -1.55072 1.29757 0.00000 0.15568 -0.12280 0.00000 N 4.02072 -1.29757 0.00000 -0.15568 0.12280 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU 0.07057 -0.04810 0.00000 -0.16554 0.11281 0.00000 CU 2.39943 0.04810 0.00000 0.16554 -0.11281 0.00000 S 1.23500 0.00000 1.94552 0.00000 0.00000 -0.34971 S 1.23500 0.00000 -1.94552 0.00000 0.00000 0.34971 N -1.54047 1.28949 0.00000 0.14543 -0.11472 0.00000 N 4.01047 -1.28949 0.00000 -0.14543 0.11472 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU 0.05582 -0.03804 0.00000 -0.15079 0.10276 0.00000 CU 2.41418 0.03804 0.00000 0.15079 -0.10276 0.00000 S 1.23500 0.00000 1.91435 0.00000 0.00000 -0.31854 S 1.23500 0.00000 -1.91435 0.00000 0.00000 0.31854 N -1.52751 1.27926 0.00000 0.13246 -0.10449 0.00000 N 3.99751 -1.27926 0.00000 -0.13246 0.10449 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU 0.03863 -0.02632 0.00000 -0.13359 0.09104 0.00000 CU 2.43137 0.02632 0.00000 0.13359 -0.09104 0.00000 S 1.23500 0.00000 1.87803 0.00000 0.00000 -0.28222 S 1.23500 0.00000 -1.87803 0.00000 0.00000 0.28222 N -1.51240 1.26735 0.00000 0.11736 -0.09258 0.00000 N 3.98240 -1.26735 0.00000 -0.11736 0.09258 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU 0.01974 -0.01346 0.00000 -0.11471 0.07817 0.00000 CU 2.45026 0.01346 0.00000 0.11471 -0.07817 0.00000 S 1.23500 0.00000 1.83814 0.00000 0.00000 -0.24233 S 1.23500 0.00000 -1.83814 0.00000 0.00000 0.24233 N -1.49582 1.25426 0.00000 0.10077 -0.07949 0.00000 N 3.96582 -1.25426 0.00000 -0.10077 0.07949 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU 0.00000 0.00000 0.00000 -0.09497 0.06472 0.00000 CU 2.47000 0.00000 0.00000 0.09497 -0.06472 0.00000 S 1.23500 0.00000 1.79643 0.00000 0.00000 -0.20062 S 1.23500 0.00000 -1.79643 0.00000 0.00000 0.20062 N -1.47847 1.24058 0.00000 0.08343 -0.06581 0.00000 N 3.94847 -1.24058 0.00000 -0.08343 0.06581 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU -0.01974 0.01346 0.00000 -0.07522 0.05126 0.00000 CU 2.48974 -0.01346 0.00000 0.07522 -0.05126 0.00000 S 1.23500 0.00000 1.75472 0.00000 0.00000 -0.15891 S 1.23500 0.00000 -1.75472 0.00000 0.00000 0.15891 N -1.46112 1.22690 0.00000 0.06608 -0.05213 0.00000 N 3.93112 -1.22690 0.00000 -0.06608 0.05213 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU -0.03863 0.02632 0.00000 -0.05634 0.03840 0.00000 CU 2.50863 -0.02632 0.00000 0.05634 -0.03840 0.00000 S 1.23500 0.00000 1.71483 0.00000 0.00000 -0.11902 S 1.23500 0.00000 -1.71483 0.00000 0.00000 0.11902 N -1.44454 1.21381 0.00000 0.04949 -0.03904 0.00000 N 3.91454 -1.21381 0.00000 -0.04949 0.03904 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU -0.05582 0.03804 0.00000 -0.03915 0.02668 0.00000 CU 2.52582 -0.03804 0.00000 0.03915 -0.02668 0.00000 S 1.23500 0.00000 1.67851 0.00000 0.00000 -0.08270 S 1.23500 0.00000 -1.67851 0.00000 0.00000 0.08270 N -1.42943 1.20190 0.00000 0.03439 -0.02713 0.00000 N 3.89943 -1.20190 0.00000 -0.03439 0.02713 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU -0.07057 0.04810 0.00000 -0.02439 0.01662 0.00000 CU 2.54057 -0.04810 0.00000 0.02439 -0.01662 0.00000 S 1.23500 0.00000 1.64734 0.00000 0.00000 -0.05153 S 1.23500 0.00000 -1.64734 0.00000 0.00000 0.05153 N -1.41647 1.19167 0.00000 0.02143 -0.01690 0.00000 N 3.88647 -1.19167 0.00000 -0.02143 0.01690 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU -0.08224 0.05605 0.00000 -0.01272 0.00867 0.00000 CU 2.55224 -0.05605 0.00000 0.01272 -0.00867 0.00000 S 1.23500 0.00000 1.62269 0.00000 0.00000 -0.02688 S 1.23500 0.00000 -1.62269 0.00000 0.00000 0.02688 N -1.40622 1.18359 0.00000 0.01118 -0.00882 0.00000 N 3.87622 -1.18359 0.00000 -0.01118 0.00882 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU -0.09032 0.06155 0.00000 -0.00465 0.00317 0.00000 CU 2.56032 -0.06155 0.00000 0.00465 -0.00317 0.00000 S 1.23500 0.00000 1.60563 0.00000 0.00000 -0.00982 S 1.23500 0.00000 -1.60563 0.00000 0.00000 0.00982 N -1.39913 1.17799 0.00000 0.00408 -0.00322 0.00000 N 3.86913 -1.17799 0.00000 -0.00408 0.00322 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU -0.09445 0.06436 0.00000 -0.00052 0.00035 0.00000 CU 2.56445 -0.06436 0.00000 0.00052 -0.00035 0.00000 S 1.23500 0.00000 1.59691 0.00000 0.00000 -0.00110 S 1.23500 0.00000 -1.59691 0.00000 0.00000 0.00110 N -1.39550 1.17513 0.00000 0.00046 -0.00036 0.00000 N 3.86550 -1.17513 0.00000 -0.00046 0.00036 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU -0.09445 0.06436 0.00000 0.18942 -0.12908 0.00000 CU 2.56445 -0.06436 0.00000 -0.18942 0.12908 0.00000 S 1.23500 0.00000 1.59691 0.00000 0.00000 0.40014 S 1.23500 0.00000 -1.59691 0.00000 0.00000 -0.40014 N -1.39550 1.17513 0.00000 -0.16640 0.13126 0.00000 N 3.86550 -1.17513 0.00000 0.16640 -0.13126 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU -0.09032 0.06155 0.00000 0.18529 -0.12627 0.00000 CU 2.56032 -0.06155 0.00000 -0.18529 0.12627 0.00000 S 1.23500 0.00000 1.60563 0.00000 0.00000 0.39142 S 1.23500 0.00000 -1.60563 0.00000 0.00000 -0.39142 N -1.39913 1.17799 0.00000 -0.16277 0.12840 0.00000 N 3.86913 -1.17799 0.00000 0.16277 -0.12840 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU -0.08224 0.05605 0.00000 0.17721 -0.12077 0.00000 CU 2.55224 -0.05605 0.00000 -0.17721 0.12077 0.00000 S 1.23500 0.00000 1.62269 0.00000 0.00000 0.37436 S 1.23500 0.00000 -1.62269 0.00000 0.00000 -0.37436 N -1.40622 1.18359 0.00000 -0.15568 0.12280 0.00000 N 3.87622 -1.18359 0.00000 0.15568 -0.12280 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU -0.07057 0.04810 0.00000 0.16554 -0.11281 0.00000 CU 2.54057 -0.04810 0.00000 -0.16554 0.11281 0.00000 S 1.23500 0.00000 1.64734 0.00000 0.00000 0.34971 S 1.23500 0.00000 -1.64734 0.00000 0.00000 -0.34971 N -1.41647 1.19167 0.00000 -0.14543 0.11472 0.00000 N 3.88647 -1.19167 0.00000 0.14543 -0.11472 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU -0.05582 0.03804 0.00000 0.15079 -0.10276 0.00000 CU 2.52582 -0.03804 0.00000 -0.15079 0.10276 0.00000 S 1.23500 0.00000 1.67851 0.00000 0.00000 0.31854 S 1.23500 0.00000 -1.67851 0.00000 0.00000 -0.31854 N -1.42943 1.20190 0.00000 -0.13246 0.10449 0.00000 N 3.89943 -1.20190 0.00000 0.13246 -0.10449 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU -0.03863 0.02632 0.00000 0.13359 -0.09104 0.00000 CU 2.50863 -0.02632 0.00000 -0.13359 0.09104 0.00000 S 1.23500 0.00000 1.71483 0.00000 0.00000 0.28222 S 1.23500 0.00000 -1.71483 0.00000 0.00000 -0.28222 N -1.44454 1.21381 0.00000 -0.11736 0.09258 0.00000 N 3.91454 -1.21381 0.00000 0.11736 -0.09258 0.00000 6 2 Ag, Cu-63 obs. 260.00 cm-1, calc. 260.17 cm-1 CU -0.01974 0.01346 0.00000 0.11471 -0.07817 0.00000 CU 2.48974 -0.01346 0.00000 -0.11471 0.07817 0.00000 S 1.23500 0.00000 1.75472 0.00000 0.00000 0.24233 S 1.23500 0.00000 -1.75472 0.00000 0.00000 -0.24233 N -1.46112 1.22690 0.00000 -0.10077 0.07949 0.00000 N 3.93112 -1.22690 0.00000 0.10077 -0.07949 0.00000 From owner-chemistry@ccl.net Wed Aug 14 15:17:31 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id PAA03460; Wed, 14 Aug 1996 15:07:05 -0400 (EDT) Received: from ccshst09.cs.uoguelph.ca for WSMITH@msnet.mathstat.uoguelph.ca by bedrock.ccl.net (8.7.5/950822.1) id PAA05667; Wed, 14 Aug 1996 15:07:03 -0400 (EDT) Received: from msnet.nw.uoguelph.ca (msnet.mathstat.uoguelph.ca) by ccshst09.cs.uoguelph.ca with ESMTP (1.40.112.3/16.2) id AA021649624; Wed, 14 Aug 1996 15:07:04 -0400 Received: from MSNET/MAILQ by msnet.nw.uoguelph.ca (Mercury 1.21); 14 Aug 96 15:11:31 GMT-5 Received: from MAILQ by MSNET (Mercury 1.21); 14 Aug 96 15:11:15 GMT-5 From: "William R. Smith" Organization: Dept. of Math & Stats. To: chemistry@ccl.net Date: Wed, 14 Aug 1996 15:11:06 EDT Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Re: CCL:function to calc. Cp of C12H26 X-Confirm-Reading-To: "William R. Smith" X-Pmrqc: 1 Priority: normal X-Mailer: Pegasus Mail v3.2 (pr2) Message-Id: <12692062AF5@msnet.nw.uoguelph.ca> Hobina Rajakaruna asked: > > Can some one provide me with a function to calculate > isobaric specific heat capacity of C12H26 as in the > form: aT+bT2+cT3... accurate between 700K-3000K For n-dodecane (C12H26) in the IG state: (this representation is usually more efficient than using polynomials) Cp = A + B*(C/T/sinh(C/T))^2 + D*(E/T/cosh(E/T))^2 (in J/kmol/K) A = 2.1295E+05 B = 6.6330E+05 C = -1715.5 D = 4.5161E+05 E = -777.5 valid over 200K - 1500K, accurate to within 1% (graph it - you might be able to extrapolate to higher T values) Best Regards, W. R. Smith Professor Dept. of Mathematics and Statistics and School of Engineering University of Guelph FAX: 519-837-0221 Guelph, Ontario Tel: 519-824-4120, ext. 3038 CANADA N1G 2W1 From doublet@gauss.lsd.univ-montp2.fr Wed Aug 14 15:30:07 1996 Received: from gauss.lsd.univ-montp2.fr for doublet@gauss.lsd.univ-montp2.fr by www.ccl.net (8.7.5/950822.1) id OAA03267; Wed, 14 Aug 1996 14:18:12 -0400 (EDT) Received: (from doublet@localhost) by gauss.lsd.univ-montp2.fr (8.7.4/8.7.3) id UAA14227 for chemistry@www.ccl.net; Wed, 14 Aug 1996 20:18:27 +0200 Date: Wed, 14 Aug 1996 20:18:27 +0200 From: Marie-Liesse Doublet Message-Id: <199608141818.UAA14227@gauss.lsd.univ-montp2.fr> To: chemistry@www.ccl.net Subject: Sunview Graphic Libraries Hi, I need to re-write a graphic code that was previously written to run on Sun sparc2 workstations using Sunview Graphic Library. I have to use the PGPLOT libraries to re-write this code for IBM/RS6000 workstations. Maybe someone could help me to find out some server addresses where I can get information about some of the graphic subroutines libraries used in the initial code i.e. : gacwk gswkwn gswn gselnt gsln gpl.... I know Sunview is a very old unix-version but I do believe that the new Solaris version is still supporting the graphic libraries of sunview... at least I hope so ! Many thanks for your help ML ************************************************************************ Dr. Marie-Liesse DOUBLET Laboratoire de Structure et Dynamique des Systemes Moleculaires et Solides Batiment 15 - Case Courrier 14 ----------- Universite des Sciences et Techniques du Languedoc tel : (33) 67 14 38 83 Place Eugene Bataillon fax : (33) 67 14 33 04 34 095 Montpellier Cedex 05 e-mail : doublet@lsd.univ-montp2.fr ************************************************************************* From pughj@ucs.exp.orst.edu Wed Aug 14 16:17:34 1996 Received: from ucs.orst.edu for pughj@ucs.exp.orst.edu by www.ccl.net (8.7.5/950822.1) id QAA03885; Wed, 14 Aug 1996 16:00:05 -0400 (EDT) Received: by ucs.orst.edu; (5.65v3.2/1.1.8.2/13Mar96-1233PM) id AA10575; Wed, 14 Aug 1996 13:00:04 -0700 Date: Wed, 14 Aug 1996 13:00:03 -0700 (PDT) From: James Pugh To: chemistry@www.ccl.net Subject: DFT single point calculations Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII CCL: I have been working on a carbene rearrangement scheme and have, after much effort, been able to complete all of the calculations at the RHF/6-31G** level. These calculations include both ground and transition state structures. Each of these has been characterized by a frequency calculation and found to be a valid point on the potential energy surface. The next step is to do single point calculations using a post-HF or correlated method. This is where I have encountered much difficulty. I have attempted MP2, MP3, MP4, MP2(full), QCIS, QCISD, and QCISDT methods, but each has either failed or was beyond the scope of the computer resources at my disposal. By failure I mean that the energy values of some of the transition states was below that of the starting material. My question is thus: I have recently been doing Density Functional Theory single point calculations on the optimized geometries at the RHF/6-31G** level. Is this a valid approach to the problem? In doing a literature search, I have never seen this used before. Researchers have either used entirely ab-initio calculations or DFT - not a mixture of both. Since the DFT single point calculations are working out nicely, I would very much like to continue. Thank you very much for any help you might offer. Jim Pugh Department of Chemistry Oregon State University e-mail: pughj@ucs.orst.edu From elewars@alchemy.chem.utoronto.ca Wed Aug 14 17:17:34 1996 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.7.5/950822.1) id RAA04599; Wed, 14 Aug 1996 17:14:15 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id RAA13354 for chemistry@www.ccl.net; Wed, 14 Aug 1996 17:14:12 -0400 (EDT) Date: Wed, 14 Aug 1996 17:14:12 -0400 (EDT) From: "E. Lewars" Message-Id: <199608142114.RAA13354@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: SINGLE-POINT DFT ON HF GEOMS Hello, Jim Pugh asked if single=point DFT calcs on structures optimized at the HF/(6-31G*?) level were valid. The short answer is that if gives the right answers it's valid: one could assemble some experimental results then compare them with relative energies calculated this way. the long answer is this: Single-point MP4 and QCISD(T) on MP2/6-31G*-opt. structures are "valid" (often give reasonable answers, I think). SP MP2 energies on HF/6-31G* geoms are often done, but I don't trust them (does any one have a compilation of these calcs, comparing them with exp. or higher-level calcs?): the geom can change too much going from the HF to the MP2 level. Thus while the MP4 and QCI pot. E surfaces are (we hope) approx. parallel to the MP2 PES, the MP2 PES may not be parallel to the HF surface. Roughly parallel PES's are needed to avoid the absurdity of a TS being lower in E than one of the two points it is supposed to connect (I found this absurdity with MP2 SP calcs on HF geom's). There is a paper by Schleyer et al, ca. 1991, "The inportance of MP2 optimizations"--- I could locate it. Errol Lewars ==== From jpcannady@dcrn.e-mail.com Wed Aug 14 17:23:11 1996 Received: from E-MAIL.COM for jpcannady@dcrn.e-mail.com by www.ccl.net (8.7.5/950822.1) id RAA04584; Wed, 14 Aug 1996 17:10:48 -0400 (EDT) From: Message-Id: <199608142110.RAA04584@www.ccl.net> Received: from dcrn.e-mail.com by E-MAIL.COM (IBM VM SMTP V2R3) with BSMTP id 8739; Wed, 14 Aug 96 17:10:38 EDT Date: Wed, 14 Aug 1996 17:10:00 EDT To: chemistry@www.ccl.net X-Sender-Info: J.Pat Cannady VOICE (517)496-6471 FAX (517)496-6243 Intermediates Expertise Center, Central R&D Mail 128 Dow Corning Corp. email = jpcannady@dcrn.e-mail.com MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Subject: NO SUBJECT In a recent note, it was stated, >I have been working on a carbene rearrangement scheme and have, after >much effort, been able to complete all of the calculations at the >RHF/6-31G** level. These calculations include both ground and transition >state structures. Each of these has been characterized by a frequency >calculation and found to be a valid point on the potential energy >surface. The next step is to do single point calculations using a >post-HF or correlated method. This is where I have encountered much >difficulty. > >I have attempted MP2, MP3, MP4, MP2(full), QCIS, QCISD, and QCISDT >methods, but each has either failed or was beyond the scope of the >computer resources at my disposal. By failure I mean that the energy >values of some of the transition states was below that of the starting >material... The poster goes on to ask about using single point DFT at RHF geometries. However, I think the point of using single point MP2 (or higher) calculations at RHF geometries needs addressing. Limited as my knowledge and experience may be, it seems that the problem is that transition state geometries can be greatly affected by inclusion of electron correlation, often more so than is the case for minima on the PES. Thus, the hoped-for cancellation of errors implied in using electron correlated energies at non-correlated geometries may not obtain for transition states as readily as for minima, leading to the problems mentioned. If the system size/computer resource combination allows, wouldn't it make sense to reoptimize all the stable points identified on the PES at a post-HF level and see if the TS energies thus obtained "behave" themselves? Pat From owner-chemistry@ccl.net Wed Aug 14 18:17:46 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id RAA04924; Wed, 14 Aug 1996 17:52:57 -0400 (EDT) Received: from gaudi.gc.cuny.edu for amasunov@email.gc.cuny.edu by bedrock.ccl.net (8.7.5/950822.1) id RAA09739; Wed, 14 Aug 1996 17:52:53 -0400 (EDT) Received: from broadway.gc.cuny.edu (broadway.gc.cuny.edu) by GAUDI.GC.CUNY.EDU (PMDF V5.0-5 #13310) id <01I89WGOZEXC005CHC@GAUDI.GC.CUNY.EDU> for chemistry@ccl.net; Wed, 14 Aug 1996 17:52:53 -0400 (EDT) Received: from localhost (amasunov@localhost) by broadway.gc.cuny.edu (8.7.5/ank-osf96) with SMTP id RAA25290 for ; Wed, 14 Aug 1996 17:52:51 -0400 (EDT) Date: Wed, 14 Aug 1996 17:52:51 -0400 (EDT) From: Artem Masunov Subject: Summary: optimization and point charges... Sender: amasunov@email.gc.cuny.edu To: Computational Chemistry List Reply-to: Artem Masunov Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT Dear All, I would like to thank Magan Govender and Sudha Srinivas for their replies, it looks like there is no existing program to perform the geometry optimization in the presence of point charges; Gaussian94 needs modification in order to read and write point charges from checkpoint file. Kitaura-Morokuma analysis is disputable and does not let you simulate molecule by point charges. NOSYMM is really necessary to perform optimization in uniform electric field, but it does not help in the case of point charges... ------------------------------------------------------------------- The original question was: To study electrostatic component of intermolecular interaction I would like to do (partial) geometry optimization in the presence of background point charges. Unfortunately, Gaussian94 does not have this option. Gaussian94 is not supposed to optimize in uniform electric field also, but in fact it does. Keeping this in mind, I run optimization with background point charges. The first step seemed to work fine, generated new geometry and derivatives, etc. Nevertheless, at the second step point charges disappeared and eventually the geometry converged back to where I started. I suspect, Gaussian94 does not pass the information about point charges to some COMMON blocks, so they do not survive at the following steps of optimization route. Is there some Gaussian94 guru who can suggest me where to look or have alternative opinion on what is happening? Any opinions/pointers on geometry optimization in the presence of background point charges will be much appreciated. ---------------------------------------------------------------- The answers were: Date: Mon, 05 Aug 1996 15:53:09 +0930 (SAST) From: Magan Govender The Morokuma Decom analysis can give you the ES component within the SCF interaction energy ... Are you imposing any symmetry to the geometry that you are optimizing?..., you could try NOSYMM, in order to prevent this collapsing into the original orientation.... Date: Wed, 7 Aug 1996 12:29:15 -0500 (CDT) From: Sudha Srinivas The background point charge is read in only in the first step of a gaussian optimization run. To get around this problem, you should specify that the background charge be read in from the checkpoint file. From Alan.Shusterman@directory.Reed.EDU Wed Aug 14 19:17:32 1996 Received: from reed.edu for Alan.Shusterman@directory.Reed.EDU by www.ccl.net (8.7.5/950822.1) id SAA05082; Wed, 14 Aug 1996 18:17:41 -0400 (EDT) Received: from isis.Reed.EDU [134.10.2.1 no identification] by reed.edu (/\oo/\ Smail3.1.29.1osf1 #29.2) id ; Wed, 14 Aug 96 15:17 PDT Message-id: <1557860@isis.Reed.EDU> Date: 14 Aug 96 15:17:42 PDT From: Alan.Shusterman@directory.Reed.EDU (Alan Shusterman) Subject: CCL:SINGLE-POINT DFT ON HF GEOMS To: chemistry@www.ccl.net Errol Lewars wrote: SP MP2 energies on HF/6-31G* geoms are often done, but I don't trust them (does any one have a compilation of these calcs, comparing them with exp. or higher-level calcs?): the geom can change too much going from the HF to the MP2 level. Response: A small compilation can be found in Practical Strategies for Electronic Structure Calculations, W.J. Hehre, Wavefunction, 1995. The upshot is that transition state geometries vary much more with the level of theory than do equilibrium geometries, but energy barriers need not. Although it is easiest to think about cancellation of errors resulting from "parallel" energy surfaces, one need not have a surface that parallels the true surface to get cancellation of errors and a reasonable energy barrier. Two examples drawn from Hehre's book (p 106-107), rearrangement of methylisocyanide to acetonitrile, and elimination of formic acid from ethyl formate, illustrate what may (?) be typical results. Single point DFT barriers calculated using either AM1, HF/3-21G, HF/6-31G*, MP2/6-31G* geometries all agreed to within 3 kcal for the first reaction and to within 7 kcal for the second (DFT//AM1 results were usually the outliers; excellent agreement was seen between DFT//HF and DFT//MP2 barriers). Single point MP2 barriers calculated using the same geometries used above were in even better agreement, i.e., choice of geometry mattered less. The differences in DFT and MP2 barriers for a given reaction and given method for obtaining geometries were larger than the differences caused by changes in geometry. In short, several energy surfaces that have their stationary points in the wrong places and which cannot, therefore, be parallel to the true surface or to each other, may still provide similar estimates of energy barriers. Alan Shusterman Department of Chemistry Reed College Portland, OR 97202 From haney@haney.hbond.com Wed Aug 14 23:17:34 1996 Received: from haney.hbond.com for haney@haney.hbond.com by www.ccl.net (8.7.5/950822.1) id XAA05782; Wed, 14 Aug 1996 23:15:19 -0400 (EDT) Received: by haney.hbond.com (940816.SGI.8.6.9/940406.SGI) id UAA05016; Wed, 14 Aug 1996 20:15:53 -0700 From: haney@haney.hbond.com (Dr. David N. Haney) Message-Id: <199608150315.UAA05016@haney.hbond.com> Subject: Re: CCL:Poisson-Boltzman calculations To: eldbjorg@chem.uit.no (Eldbjoerg S. Heimstad) Date: Wed, 14 Aug 1996 20:15:53 -0800 (PDT) Cc: CHEMISTRY@www.ccl.net In-Reply-To: <9608141419.AA07136@trypsin.chem.uit.no> from "Eldbjoerg S. Heimstad" at Aug 14, 96 02:19:32 pm Reply-To: haney@hbond.com X-Mailer: ELM [version 2.4 PL22] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Columbia develops a program called Delphi. I believe that they still offer it to academics as a standalone code. Commercial people must get it from MSI and I dont believe they offer the standalone version. See the URL: http://tincan.bioc.columbia.edu/Lab/delphi/ > > > We are interested in information concerning Poisson-Boltzman > calculations - does it exist a stand-alone program, how successful is the > method ? -the limits/pitfalls etc. > > All replies will be helpful -thanks. > > Regards, > Elle > > > ####################################################### > # Eldbjoerg Sofie Heimstad # > # Protein Crystallography Group # > # University Of Tromsoe, IMR # > # 9037 Tromsoe, NORWAY phone: +47-776-45706 # > # +47-776-44737 # > # fax : +47-776-44765 # > # E-mail: Eldbjorg.Heimstad@chem.uit.no # > # URL: http://www.chem.uit.no/KJEMI/heimstad.html # > ####################################################### > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: eldbjorg@chem.uit.no > -- Original Sender From: Address: eldbjorg@chem.uit.no > 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 > -- ************** David N. Haney, Ph.D. **************** * Haney Associates Phone - 619-566-1127 * * 12010 Medoc Ln. * * San Diego, CA 92131 Fax - 619-586-1481 * * * ************** Email - haney@hbond.com ****************