From chemistry-request@server.ccl.net Tue Jan 18 00:55:39 2000 Received: from mcmail.cis.McMaster.CA (mattacf@mcmail.CIS.McMaster.CA [130.113.64.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA03140 for ; Tue, 18 Jan 2000 00:55:39 -0500 Received: from localhost (mattacf@localhost) by mcmail.cis.McMaster.CA with SMTP id XAA13032; Mon, 17 Jan 2000 23:50:11 -0500 (EST) Date: Mon, 17 Jan 2000 23:50:10 -0500 (EST) From: "C.F. Matta" To: "Robert E. Harris" cc: chemistry@server.ccl.net Subject: Re: CCL:Pseudorotation? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr. Harris, You may try: [1] D.Cremer & J.A.Pople "A general definition of rung puckering coordinates" J.Am.Chem.Soc 97 (1975) 1354-1358. [2] D.Cremer & J.A.Pople "Molecular orbital theory of the electronic structure of organic compounds. XXIII. Pseudorotation in saturated five-membered ring compounds. J.Am.Chem.Soc 97 (1975) 1358-1367. (and references theirein). Take care C.F.Matta ....................................................................... Cherif F. Matta tel. (905) 525-9140 ext. 22502 Chemistry Department fax (905) 522-2509 McMaster University Hamilton, Ontario, CANADA L8S 4M1. ....................................................................... On Mon, 17 Jan 2000, Robert E. Harris wrote: > Can anyone refer me to papers discussing the small barrier motions in small > ring systems that Bill Gwinn and coworkers described as "pseudorotation" > about 35 years ago? What I am looking for is methods of calculating > contributions to thermodynamic properties (energy, entropy) from such > motions. > REH > > Robert E. Harris Phone: 573-882-3274 Fax: 573-882-2754 > Department of Chemistry, University of Missouri-Columbia > Columbia, Missouri, USA 65211 > > > > -= 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 > > > > > > From chemistry-request@server.ccl.net Tue Jan 18 03:40:06 2000 Received: from mail.rdc1.ne.home.com (imail@ha1.rdc1.ne.home.com [24.2.4.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA03778 for ; Tue, 18 Jan 2000 03:40:05 -0500 Received: from computer2 ([24.0.178.63]) by mail.rdc1.ne.home.com (InterMail v4.01.01.00 201-229-111) with SMTP id <20000118073432.MITN21641.mail.rdc1.ne.home.com@computer2> for ; Mon, 17 Jan 2000 23:34:32 -0800 Message-ID: <00cf01bf6186$760404b0$0201010a@home.local> From: "Bradley A. Smith" To: References: <00ec01bf5d34$7c975bc0$0201010a@home.local> Subject: xvibs Version 5.1 Date: Mon, 17 Jan 2000 23:34:31 -0800 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 Thanks to Leif Laaksonen, a several bugs have been fixed, and thanks to Arlen Viste, xvibs has been extended to read PC GAMESS output. The new version 5.1 is available at http://members.home.net/yeldar/xvibs. Thanks, Bradley From chemistry-request@server.ccl.net Tue Jan 18 04:49:40 2000 Received: from daisy.imc.cas.cz (daisy.imc.cas.cz [147.231.112.129]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA04176 for ; Tue, 18 Jan 2000 04:49:38 -0500 Received: from localhost (saturka@localhost) by daisy.imc.cas.cz (8.9.3/8.9.3) with SMTP id JAA32404; Sat, 18 Dec 1999 09:41:52 +0100 (CET) Date: Sat, 18 Dec 1999 09:41:52 +0100 (CET) From: Martin Saturka To: Eugene Leitl cc: rasmol@lists.umass.edu, chemistry@ccl.net Subject: Re: CCL:RasMol-2.6b2 In-Reply-To: <14467.48504.630388.351449@lrz.uni-muenchen.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 17 Jan 2000, Eugene Leitl wrote: > eugene.leitl@lrz:~/download/rasmol/RasMol-2.6b2 > make > gcc -O2 -fno-strength-reduce -I/usr/X11R6/include -Dlinux -D__i386__ -D_POSIX_C_SOURCE=199309L -D_POSIX_SOURCE -D_XOPEN_SOURCE=500L -D_BSD_SOURCE -D_SVID_SOURCE -DFUNCPROTO=15 -DNARROWPROTO -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT -c rasmol.c -o rasmol.o > rasmol.c:52: sys/termio.h: No such file or directory > make: *** [rasmol.o] Error 1 > it just means, that you haven't got file /usr/include/sys/termio.h. it's obsolete file, try either to overwrite #include to #include or to #include in your source code of rasmol or copy /usr/include/sys/termio.h to /usr/include/sys/termios.h or into directory you have permissions for /home/guy/include/sys/termio.h and (in the last case) add directive -I/home/guy/include to your compilation or add that directory into your makefile. I hope, it will work. PS what experiences do you have with such (virtual reality) devices under linux box (including SGI dials and others) - applications, prices, ...? Thank you, Martin Saturka From chemistry-request@server.ccl.net Tue Jan 18 06:15:54 2000 Received: from yogi.pc1.uni-duesseldorf.de (root@yogi.pc1.uni-duesseldorf.de [134.99.152.44]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA04495 for ; Tue, 18 Jan 2000 06:15:53 -0500 Received: from yogi.pc1.uni-duesseldorf.de (IDENT:jochen@localhost.localdomain [127.0.0.1]) by yogi.pc1.uni-duesseldorf.de (8.9.3/8.9.3) with SMTP id LAA01128; Tue, 18 Jan 2000 11:16:19 +0100 From: Jochen Kuepper Organization: Heinrich-Heine-Universität To: "Robert E. Harris" , chemistry@server.ccl.net Subject: Re: CCL:Pseudorotation? Date: Tue, 18 Jan 2000 11:09:37 +0100 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain References: In-Reply-To: MIME-Version: 1.0 Message-Id: <00011811161600.01112@yogi.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id GAA04496 On Die, 18 Jan 2000 Robert E. Harris wrote: >Can anyone refer me to papers discussing the small barrier motions in small >ring systems that Bill Gwinn and coworkers described as "pseudorotation" What exactly do you mean by pseudo-rotation. Pseudorotation like Na_3 pseudo-rotation, or ringpuckering (e.g. 5-membered rings), or ... ? Anyway, Jon Hougen comes to mind,also Laane. For ringpuckering look for Laane's publications, the last I saw where on 1,3-Benzodioxole - JACS 121(1999), 5056 >about 35 years ago? What I am looking for is methods of calculating >contributions to thermodynamic properties (energy, entropy) from such >motions. Good luck :-) -- Jochen Heinrich-Heine-Universität, Institut für Physikalische Chemie I Universitätsstr. 1, Geb. 26.43.02.29, 40225 Düsseldorf, Germany phone 02118113681 fax 02118115195 -- www-public.rz.uni-duesseldorf.de/~jochen Jochen@Uni-Duesseldorf.de -- Jochen.Kuepper@FernUni-Hagen.de -- Kuepper@ACM.org From chemistry-request@server.ccl.net Tue Jan 18 10:59:31 2000 Received: from ccshst04.cs.uoguelph.ca (ccshst04.cs.uoguelph.ca [131.104.96.17]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA06741 for ; Tue, 18 Jan 2000 10:59:31 -0500 Received: from ccshst01 (ccshst01.cs.uoguelph.ca [131.104.96.81]) by ccshst04.cs.uoguelph.ca (8.9.3/8.9.3) with SMTP id JAA10269; Tue, 18 Jan 2000 09:53:47 -0500 (EST) Date: Tue, 18 Jan 2000 09:53:46 -0500 (EST) From: WeiQuan Tian X-Sender: wtian@ccshst01 To: "Bradley A. Smith" cc: chemistry@ccl.net Subject: Re: CCL:xvibs Version 5.1 In-Reply-To: <00cf01bf6186$760404b0$0201010a@home.local> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, xvibs looks good! I am wondering it can give any graphic output to print out. Does it have such ability or will it? Does anybody know any free program can print out the vibration vector? ( for example in postscript format) I know Molekel can display the mode and its vector, but I still haven't succeeded in printing it out, also it's for SGI only. Also Molden can display the vibrational motion, but no vectors displayed. Thanks for any information and I will do the summary if anyone interested! Wei Quan Tian Univ. of Guelph Canada On Mon, 17 Jan 2000, Bradley A. Smith wrote: > Thanks to Leif Laaksonen, a several bugs have been fixed, and thanks to > Arlen Viste, xvibs has been extended to read PC GAMESS output. > > The new version 5.1 is available at http://members.home.net/yeldar/xvibs. > > Thanks, > Bradley > > > > > -= 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 > > > > > From chemistry-request@server.ccl.net Tue Jan 18 11:21:17 2000 Received: from cosmos.cosm.sc.edu (cosmos.cosm.sc.edu [129.252.40.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA06960 for ; Tue, 18 Jan 2000 11:21:17 -0500 Received: (from jorge@localhost) by cosmos.cosm.sc.edu (8.9.3/8.9.3) id KAA49509; Tue, 18 Jan 2000 10:12:42 -0500 (EST) From: Jorge Seminario Message-Id: <200001181512.KAA49509@cosmos.cosm.sc.edu> Subject: Re: CCL:GA & Chemistry Mailing Lists? To: rajarshi@presidency.com (Rajarshi Guha) Date: Tue, 18 Jan 2000 10:12:41 -0500 (EST) Cc: chemistry@ccl.net (CCL) In-Reply-To: from "Rajarshi Guha" at Jan 18, 2000 09:06:57 AM X-Mailer: ELM [version 2.5 PL2] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Helpful Web site: www.genetic-programming.org (has tutorials, etc.) Also check Al GLobus webpage at MoffetField (NASA) Jorge ================================= Jorge M. Seminario Department of Chemistry and Biochemistry University of South Carolina Columbia, South Carolina 29208 Tel: 803-777-9567 Fax: 803-777-9521 email: jorge@mail.chem.sc.edu URL: http://www.cosm.sc.edu/~jorgemgr ===================================== > > Hi, > does anybody know of mailing lists/electronic magazines etc regarding > genetic algorithms and applications to chemistry? > > TIA, > > ------------------------------------------------------------- > Rajarshi Guha | ..but there was no one > Dept Of Chemistry | in it.....! > IIT Kharagpur | > | RG. > email: rajarshi@presidency.com | > Web : www.psynet.net/jijog | > ------------------------------------------------------------- > > > -= 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 > > > > > From chemistry-request@server.ccl.net Tue Jan 18 10:52:22 2000 Received: from igc.phys.chem.ethz.ch (igc.ethz.ch [129.132.102.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA06667 for ; Tue, 18 Jan 2000 10:52:21 -0500 Received: from igc.phys.chem.ethz.ch (sulfid.ethz.ch [129.132.126.45]) by igc.phys.chem.ethz.ch (8.8.8/8.8.8) with ESMTP id PAA16118 for ; Tue, 18 Jan 2000 15:47:54 +0100 (MET) Sender: nuran@igc.phys.chem.ethz.ch Message-ID: <38847BC1.B8338BDE@igc.phys.chem.ethz.ch> Date: Tue, 18 Jan 2000 15:42:09 +0100 From: Nuran Elmaci Organization: ETH To: "CHEMISTRY@server.ccl.net" Subject: opt.at exc.st, mopac Dear CCL Members, I have a couple of questions about excited state calculations using MOPAC. I would like to do geometry optimization at the first excited state. I think EXCITED keyword or C.I.=n ROOT=2 can be used for this. But they give different geometry with different energies. If I use CI, the first root is the correction for the ground state energy, and second one is for the first excited state state and so on. is that correct? I will be very greatful if somebody can give me informations in details about excited state optimization with MOPAC or some helpful references. thanks in advance Nuran From chemistry-request@server.ccl.net Tue Jan 18 11:08:55 2000 Received: from glycine.jouy.inra.fr (glycine.jouy.inra.fr [138.102.88.135]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA06845 for ; Tue, 18 Jan 2000 11:08:54 -0500 Received: from glycine.jouy.inra.fr (localhost.inra.fr [127.0.0.1]) by glycine.jouy.inra.fr (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id QAA17351 for ; Tue, 18 Jan 2000 16:01:50 -0800 Sender: gillet@glycine.jouy.inra.fr Message-ID: <3884FEED.FF36466@glycine.jouy.inra.fr> Date: Tue, 18 Jan 2000 16:01:50 -0800 From: Alexandre Gillet Organization: inra To: chemistry@ccl.net Subject: Amber parameters I would like to know where I can find Amber force field parameters for a S-FE bond. I need to run a simulation an the cytochrome P450 bm3 in which a cystein is bond to the Fe of a haem. Getting this information will help me a lot. -- Alexandre Gillet graduate student ( University of Paris,France) gillet@glycine.jouy.inra.fr From chemistry-request@server.ccl.net Tue Jan 18 12:51:47 2000 Received: from ysbl.york.ac.uk (batman.chem.york.ac.uk [144.32.72.190]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA07410 for ; Tue, 18 Jan 2000 12:51:45 -0500 Received: from yorvic.york.ac.uk (pingu [144.32.72.76]) by ysbl.york.ac.uk (8.9.3/8.8.7) with ESMTP id QAA115940 for ; Tue, 18 Jan 2000 16:46:09 GMT Sender: caves@ysbl.york.ac.uk Message-ID: <388498D1.CBD91DC2@yorvic.york.ac.uk> Date: Tue, 18 Jan 2000 16:46:09 +0000 From: Leo Caves Organization: University of York To: chemistry@ccl.net Subject: 00.04.05 MGMS Meeting: Modelling Biomolecular Mechanism I hope this meeting is of interest to CCL'ers. Please note the calibre of the invited speakers on this important theme. Best wishes, Leo Caves -- Leo Caves Structural Biology Laboratory, Dept. of Chemistry, University of York York, YO10 5DD, UK tel:(+44)1904 434521 fax:(+44)1904 410519 =========================================== http://www.mgms.org/york2000 18th International Meeting of the Molecular Graphics and Modelling Society. Modelling Biomolecular Mechanism: From States to Processes at the Atomic Level April 5-8, 2000 at the University of York, UK * Further Details & Information Meeting Web Site at http://www.mgms.org/york2000 Information on the Scientific Programme, Contributions, Registration and Travel available on the Web site * Meeting Agenda The meeting focuses on the study of biomolecular processes incuding chemical reactions, protein folding, transport & diffusion and energy transduction. The meeting showcases advances in theoretical and computational approaches to studying biomolecular processes as well as powerful single molecule and time-resolved experimental techniques. With contributions from leading international researchers, the meeting provides an important and timely opportunity to review and stimulate discussion across the many disciplines addressing the mechanistic aspects of structure-function relationships in biological processes at the atomic level. * Scientific Programme (see http://www.mgms.org/york2000/programme.htm) -- Sessions Include: Pathway Methods; Enzyme Reactions; Transport & Diffusion; Folding; Manipulation; Energy Transfer & Transduction; Solution Dynamics -- Confirmed Invited Speakers and Titles: HJC Berendsen, Univ. of Groningen "Diffusion-limited enzyme catalysis: Lecithin into phospholipase A2" Bernie Brooks, NIH (Title TBA) Charlie Brooks, TSRI "Protein Folding Landscapes, Mechanism and Kinetics: Insights from Theory and Simulation" Leonor Cruzeiro-Hansson, Herriot-Watt Univ. "Vibrational energy transfer as the first step in protein function" Ron Elber, Cornell "Long time dynamics of biomolecules using the stochastic path approach" Stefan Fischer, Univ. of Heidelberg "Molecular kinematics: essential motion and energetics of slow (>1us) processes in proteins." Hans Frauenfelder, Los Alamos Natl Laboratory "Complexity in protein dynamics and protein reactions." Hermann Gaub, Univ. of Munich (Title TBA; topic on AFM-related work) Ian Hillier, Univ. of Manchester "What can QM/MM calculations tell us about enzyme reactions?" Martin Karplus, Univ. of Strasbourg/Harvard "Free energy simulations in the new millennium" Peter Kollman, UCSF "Molecular dynamics simulations on protein and nucleic acid systems: Entering the era of structure and free energy" Andy McCammon, UCSD "Dynamics of Molecular Recognition" Justin Molloy, Univ. of York "Use of optical techniques to probe the mechanism of energy transduction of single molecular motors" David Perahia, CNRS Orsay "Study of conformational pathways in proteins: methods and applications" Simon Phillips, Univ. of Leeds "Towards a movie of catalysis in copper amine oxidases" Rudolf Rigler, Karolinska Institute "Spectroscopy of Single Biomolecules: The fluctuating enzyme" Benoit Roux, Univ. of Montreal "Simulating the Flow of Ions across Membrane Channels" Klaus Schulten, Univ. of Illinois "Steered Molecular Dynamics to Study Biopolymer Association and Stretching" Lorna Smith, Univ. of Oxford "Characterisation of denatured and partially folded protein conformations" John Straub, Boston Univ. "Direct computation of long time processes in peptides and proteins" Michael Schaefer, Univ. of Strasbourg "Structural and thermodynamic characterization of polypeptides by computer simulation: Helices, beta-hairpins, and chameleons." Wilfred van Gunsteren, ETH Zurich "Computer simulation of the reversible folding of peptides" RJP Williams, Univ of Oxford "Coupling between electron and proton energies in Proteins" Peter Wolynes, Univ. of Illinois "Pure and Applied Protein Folding Kinetics." ----- http://www.mgms.org/york2000 From chemistry-request@server.ccl.net Tue Jan 18 15:07:46 2000 Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA00620 for ; Tue, 18 Jan 2000 15:07:42 -0500 Received: from localhost (fgonzale@localhost) by lauca.usach.cl (8.9.1b+Sun/8.9.2) with ESMTP id QAA11619 for ; Tue, 18 Jan 2000 16:03:14 -0300 (CDT) Date: Tue, 18 Jan 2000 16:03:14 -0300 (CDT) From: Fdo Danilo Gonzalez Nilo To: chemistry@ccl.net Subject: MO/G98 in GopenMol Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all! Any body know how can I display the molecular orbital obtained from G98 in GopenMol or Chem3D?, using only the checkpoint file. Thanks a lot! Danilo/// ************************************************************************* Danilo Gonzalez N. University of Santiago de Chile Faculty of Chemistry and Biology, Computational Chemistry Lab. Casilla 40, Correo 33, Santiago, Chile Fono: (562) 681 1542 Anexo:799 E-mail : fgonzale@lauca.usach.cl Fax : (562) 681 2108 ************************************************************************** From chemistry-request@server.ccl.net Tue Jan 18 16:58:15 2000 Received: from chem.boisestate.edu (chem10.boisestate.edu [132.178.209.9]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA01898 for ; Tue, 18 Jan 2000 16:54:35 -0500 Received: from chemlab53 (CHEMLAB53.boisestate.edu [132.178.213.119]) by chem.boisestate.edu (8.8.5/8.8.5) with SMTP id NAA26236; Tue, 18 Jan 2000 13:50:45 -0700 Message-Id: <3.0.6.32.20000118140148.0092dd90@chem.boisestate.edu> X-Sender: bmoritz@chem.boisestate.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Tue, 18 Jan 2000 14:01:48 -0700 To: chemistry@ccl.net, bmoritz@chem10.boisestate.edu From: Benjamin Joesph Moritz Subject: Freqchk Errors Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Netters, I am having a problem obtaining thermo values from my freqchk calculations. I am trying to calculate some thermo parameters from a perfluoro-2-azopropene (PAP) molecule. When I run freqchk on my completed jobs I'm getting some weird output files. In some of the freqchk output files only the frequencies are displayed and no thermochemistry information. While in other freqchk output files I'm getting a NaN reading for my S values. I've been using Gaussian 94 and 98. To see some output files I have loaded them onto my webpage at... http://chem.boisestate.edu/~bmoritz If you could help me in determining what I'm doing wrong, I'd gladly appreciate it. Thank you Ben Moritz Boise State University 1909 Tendoy Dr. Boise, Id 83705 bmoritz@chem.boisestate.edu ph. # 208-433-1579 From chemistry-request@server.ccl.net Tue Jan 18 18:13:30 2000 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.18.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA02977 for ; Tue, 18 Jan 2000 18:13:30 -0500 Received: from syr.edu (curie.syr.edu [128.230.187.116]) by mailbox.syr.edu (8.9.2/8.9.2) with ESMTP id RAA00463; Tue, 18 Jan 2000 17:09:19 -0500 (EST) Sender: desingh@mailbox.syr.edu Message-ID: <3884E5B5.5D506020@syr.edu> Date: Tue, 18 Jan 2000 17:14:13 -0500 From: Deepak Singh Organization: Birge Group, Dept. Of Chemistry, Syracuse Univ. X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Nuran Elmaci CC: "CHEMISTRY@server.ccl.net" Subject: Re: CCL:opt.at exc.st, mopac References: <38847BC1.B8338BDE@igc.phys.chem.ethz.ch> Content-Type: text/plain; charset=iso-8859-15 Content-Transfer-Encoding: 7bit Hi Nuran, I would recommend using the keywords CISD and C.I.=4. I have found thse to work verk very well with correlated systems. The results are even better than 6-31G** HF calculations in some cases. I hope you are trying to calculate the excited state levels using mopac? It does a terrible job. The CI works well only for ground state optimization. cheers Deepak. Nuran Elmaci wrote: > Dear CCL Members, > > I have a couple of questions about excited state calculations using > MOPAC. I would like to do geometry optimization at the first excited > state. I think EXCITED keyword or C.I.=n ROOT=2 can be used for this. > But they give different geometry with different energies. If I use CI, > the first root is the correction for the ground state energy, and second > one is for the first excited state state and so on. is that correct? > > I will be very greatful if somebody can give me informations in details > about excited state optimization with MOPAC or some helpful references. > > thanks in advance > > Nuran > > -= 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 -- ********************************************************************** Deepak Singh Tel : (315)443 1739 (w) Graduate Student (315)472 9659 (h) Dept. of Chemistry Fax : (315)443 4070 Syracuse University email : desingh@syr.edu 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh NY 13244 "Violence is the last refuge of the incompetent." --- Salvor Hardin ********************************************************************** From chemistry-request@server.ccl.net Tue Jan 18 18:15:48 2000 Received: from unicorn.it.wsu.edu (voleti@unicorn.it.wsu.edu [134.121.1.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA03010 for ; Tue, 18 Jan 2000 18:15:47 -0500 Received: from localhost (voleti@localhost) by unicorn.it.wsu.edu (8.9.3/8.9.3) with ESMTP id OAA30818 for ; Tue, 18 Jan 2000 14:11:40 -0800 (PST) Date: Tue, 18 Jan 2000 14:11:40 -0800 (PST) From: "sreedhara v. rao" X-Sender: voleti@unicorn.it.wsu.edu To: chemistry@ccl.net Subject: size consistency in solvents Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL members, This question is regarding calculation of activation barrier in solvents for a bimolecular reaction and about a possible existance of size-consistency. Is it acceptable to calculate the energy differences of the transition state-in-solvent with respect to the sum of the energies of individual reactants-in-solvents? These bimolecular reactions are radical-molecule type reactions in gas-phase and the overall charge of the reaction is zero. Calculations are single-point SCRF PCM/MP2/6-31+G** for all reactants and the hydrogen-abstraction transition states Any reference, comment and/or suggestions are highly appreciated. Thank you, Sreedhara Dr. Sreedhara V Rao Dept. of Chem., WSU, Pullman, WA-99163. voleti@wsunix.wsu.edu or voleti@wsu.edu From chemistry-request@server.ccl.net Tue Jan 18 19:44:19 2000 Received: from ivory.trentu.ca (trentu.ca [192.75.12.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA03581 for ; Tue, 18 Jan 2000 19:44:18 -0500 Received: from el1 ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #29543) with SMTP id <01JKUYYPJ4XO001MFE@trentu.ca> for chemistry@ccl.net; Tue, 18 Jan 2000 18:40:09 EST Date: Tue, 18 Jan 2000 18:43:46 -0500 From: Errol Lewars Subject: program to handle clusters of 10-100 atoms To: chemistry@ccl.net Message-id: <3884FAB2.52C@trentu.ca> Organization: Trent University MIME-version: 1.0 X-Mailer: Mozilla 3.01Gold (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit 2000 Jan 18 Hello, A colleague in my Department has looked at the mass spectra of clusters consisting of one K+ surrounded by several KCl molecules (or ion-pairs, if you prefer), and clusters of one Cl- surounded by several KCl molecules (this latter with _negative_-ion mass spec). I think these can be thought of as K+ solvated with KCl, and Cl- solvated with KCl. He's found that some clusters are particularly prominent, as if there were certain magic numbers of stable KCl "solvent" molecules (a bit reminiscent of prominent clusters in Cn mixtures, where a big C60 peak led to the hypothesis of buckminsterfullerene). QUESTION: Is there a program that will handle from a few up to about 100 KCl molecules plus a K+ or Cl- ion? Please note that these clusters may not be simple periodic systems like a KCl crystal. I don't know if they can even be viewed as doped KCl crystal. We are looking for a rationalization of the fact that clusters of certain sizes seem to be favored. Thanks E. Lewars ========== From chemistry-request@server.ccl.net Tue Jan 18 19:28:20 2000 Received: from mtiwmhc01.worldnet.att.net (mtiwmhc01.worldnet.att.net [204.127.131.36]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA03398 for ; Tue, 18 Jan 2000 19:28:19 -0500 Received: from nt ([12.67.3.209]) by mtiwmhc01.worldnet.att.net (InterMail v03.02.07.07 118-134) with SMTP id <20000118232152.HOJE5516@nt> for ; Tue, 18 Jan 2000 23:21:52 +0000 Message-Id: <3.0.32.20000118162543.00926100@postoffice.worldnet.att.net> X-Sender: mrmopac@postoffice.worldnet.att.net X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Tue, 18 Jan 2000 16:27:30 -0700 To: CHEMISTRY@ccl.net From: "James J. P. Stewart" Subject: opt.at exc.st, mopac Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" In MOPAC, the keyword EXCITED is now redundant, and is not recommended. See http://home.att.net/~mopacmanual/node176.html The reason is that the old (pre 1993) definitions used in MOPAC for excited states were ambiguous. This is the precise problem that Nuran Elmaci has encountered. For a discussion on this, see http://home.att.net/~mopacmanual/node500.html Jimmy Stewart