From chemistry-request@www.ccl.net Tue Mar 9 04:37:06 1999 Received: from serenity.mcc.ac.uk (serenity.mcc.ac.uk [130.88.200.93]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA26967 Tue, 9 Mar 1999 04:37:04 -0500 (EST) Received: from nessie.mcc.ac.uk ([130.88.200.20] ident=root) by serenity.mcc.ac.uk with esmtp (Exim 1.92 #2) id 10KIwj-0004H5-00; Tue, 9 Mar 1999 09:37:06 +0000 Received: from serenity.mcc.ac.uk (serenity.mcc.ac.uk [130.88.200.93]) by nessie.mcc.ac.uk (8.8.8/8.8.8) with ESMTP id JAA00641; Tue, 9 Mar 1999 09:37:05 GMT (envelope-from mbdtsnm@mchhpf.ch.man.ac.uk) Received: from [130.88.12.28] (helo=hpf.ch.man.ac.uk) by serenity.mcc.ac.uk with smtp (Exim 1.92 #2) id 10KIwi-0004H1-00; Tue, 9 Mar 1999 09:37:04 +0000 Date: Tue, 9 Mar 1999 09:34:22 GMT Message-Id: <26869.9903090934@hpf.ch.man.ac.uk> From: "Nathaniel (noj) Malcolm" Cc: chemistry@www.ccl.net, Patrick.Bultinck@rug.ac.be In-Reply-To: <199903051713.MAA07615@robin.cooper.edu> (topper@cooper.edu) Subject: Re: CCL:Re: CCL:QC journals 'in trouble' Reply-To: Noj.Malcolm@man.ac.uk X-Beard: Beard v5.3 X-Child: Bethany in case anyone is still interested in this subject there is an amusing paper in the "new journal of chemistry" (which should be available on-line at: http://www.rsc.org/is/journals/current/newjchem/njccon.htm for those library cannot afford to stock such esoteric titles!) regarding citation data and impact factors : "Sense and nonsense of science citation analyses: comment on the monopoly position of ISI and citation inaccuracies. Risks of possible misuse and biased citation and inpact data" Jan Reedijk NEW JOURNAL OF CHEMISTRY, 1998, Vol.22, No.8, pp.767-770 noj -- Dr. Noj Malcolm Theory Group, Dept. of Chemistry, University of Manchester, Oxford Road, Manchester. M13 9PL e-mail noj.malcolm@man.ac.uk From chemistry-request@www.ccl.net Tue Mar 9 04:37:24 1999 Received: from mailgate.rz.uni-karlsruhe.de (nz40.rz.uni-karlsruhe.de [129.13.197.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA26976 Tue, 9 Mar 1999 04:37:20 -0500 (EST) Received: from tchibm3.chemie.uni-karlsruhe.de (dapprich2@tchopin.chemie.uni-karlsruhe.de [129.13.107.204]) by mailgate.rz.uni-karlsruhe.de with esmtp (Exim 2.04 #3) id 10KIve-0005lB-00; Tue, 9 Mar 1999 10:35:58 +0100 Sender: dapprich2@www.ccl.net Message-ID: <36E4EBBB.2154866C@tchibm3.chemie.uni-karlsruhe.de> Date: Tue, 09 Mar 1999 10:36:59 +0100 From: Stefan Dapprich Organization: University of Karlsruhe X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.36 i686) X-Accept-Language: German, de, en MIME-Version: 1.0 To: Sergio Emanuel Galembeck CC: chemistry@www.ccl.net Subject: Re: CCL:G:G: ONIOM using ECP References: <000701be69ae$3558f180$0100005a@ligquim.ffclrp.usp.br> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Sergio Emanuel Galembeck wrote: > I am trying to run a metal complex > job using ONIOM. In the higher layer > I am using LSDA/LANL2DZ and in > the lower HF/3-21G. The job bumps > in the beginning and presents the > following: [...] Since the low level calculation comprises the entire molecule, you might use: ONIOM(LSDA/LANL2DZ:HF/LANL2MB) or something similar. Alternatively, you could employ a nonstandard route: ONIOM(LSDA/gen:HF/gen) pseudo=read Then, of course, you need to specify basis sets and pseudopotentials explicitly. Hope this helps. Stefan -- +----------------------------------------+ Dr. Stefan Dapprich Institut fuer Physikalische Chemie Universitaet Karlsruhe D-76128 Karlsruhe Phone ++49-721-608-7229 Fax ++49-721-608-4856 +----------------------------------------+ From chemistry-request@www.ccl.net Tue Mar 9 09:35:42 1999 Received: from sheridan.dina.kvl.dk (root@sheridan.dina.kvl.dk [130.225.40.227]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA28782 Tue, 9 Mar 1999 09:35:41 -0500 (EST) Received: from dina.kvl.dk (speciale.dina.kvl.dk [130.225.40.164]) by sheridan.dina.kvl.dk (8.9.0.Beta5/8.9.0.Beta5) with ESMTP id PAA09874 for ; Tue, 9 Mar 1999 15:36:01 +0100 Message-ID: <3503FE06.1B1B14A2@dina.kvl.dk> Date: Mon, 09 Mar 1998 15:34:46 +0100 From: Lars Olsen X-Mailer: Mozilla 4.07 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Parameters for Zn and Cd using AMBER and AM1? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Everybody Do any of you know the parameters for Zn and Cd using AMBER and AM1 and how to prepare the input for Gaussian 98 using these parameters? My e-mail address is: larso@dina.kvl.dk I am very much looking forward to hearing from you. Yours, Lars Olsen (Master Student) Department of Mathematics and Physics The Royal Veterinary and Agricultural University Thorvaldsensvej 40 DK-1871 Frederiksberg C, Denmark From chemistry-request@www.ccl.net Sat Mar 6 09:55:05 1999 Received: from zzmkgtw.zzmk.unizh.ch (zzmkgtw.unizh.ch [130.60.67.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id JAA02340 Sat, 6 Mar 1999 09:55:04 -0500 (EST) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA04276; Sat, 6 Mar 1999 15:55:05 +0100 Message-Id: <3.0.3.32.19990306160032.0069e940@highdent> X-Sender: toukie@highdent (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Sat, 06 Mar 1999 16:00:32 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: GA for PLS Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleagues; Does anyone know of a DOS or Win95 executable that uses a genetic algorithm for variable selection in least squares analyses? If so, kindly send details. Thanks, S. Shapiro toukie@zui.unizh.ch From chemistry-request@www.ccl.net Mon Mar 8 03:21:15 1999 Received: from dreamon.oxmol.co.uk (dreamon.oxmol.co.uk [193.132.141.15]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA09819 Mon, 8 Mar 1999 03:21:13 -0500 (EST) Received: from oxmol.co.uk (bludgeon.oxmol.co.uk [193.132.141.84]) by dreamon.oxmol.co.uk (8.9.0/8.9.0/7) with ESMTP id IAA19169; Mon, 8 Mar 1999 08:20:10 GMT Message-ID: <36E3885C.CFD2D12A@oxmol.co.uk> Date: Mon, 08 Mar 1999 08:20:44 +0000 From: Rob Williams Organization: Oxford Molecular Group X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: "Victor E. Kuz'min" CC: Tamas Gunda , chemistry@www.ccl.net Subject: Re: CCL:CCL:Drawings--->Stuctural file References: <199903051353.IAA10441@www.ccl.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Tamas Gunda wrote: > > > > > > > Dear Colleagues, > > Whether there is a software for conversion of a graphics image of > > molecular structure ( for example: *.gif, *.jpg, .. etc) in files such > > as *.mol, *.hin, *.pdb, ..? This is a peculiar kind of OCR for the > > structural formulas. It will enable for scanned drawings to get the > > structural file. Is it possible? I shall be grateful for any guidelines > > or tips. > > > > With best regards, > > VEK > > As far as I remember, there is a program called Kekule somewhere > out there, which was designed to convert scanned structural images > to molfiles > > Hope this helps > > Tamas Kekule is supplied by Oxford Molecular. You can find more information at: http://www.oxmol.co.uk/prods/kekule/ I hope this is what you need. Thanks, Rob -- --------------------------------------------------------------------- Dr Rob Williams Tel: (+44) 1865 784600 Deputy Engineering Manager Fax: (+44) 1865 784601 Oxford Molecular Limited E-mail: rwilliams@oxmol.co.uk --------------------------------------------------------------------- From chemistry-request@www.ccl.net Mon Mar 8 06:37:40 1999 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id GAA10268 Mon, 8 Mar 1999 06:37:39 -0500 (EST) Received: by bioc1.msi.com (931110.SGI/930416.SGI) for CHEMISTRY@www.ccl.net id AA19484; Mon, 8 Mar 99 03:36:14 -0800 Received: from news.msi.com(146.202.0.224) by bioc1.msi.com via smap (V2.0) id xma019481; Mon, 8 Mar 99 03:35:45 -0800 Received: by news.msi.com (4.1/SMI-4.1) id AA01122; Mon, 8 Mar 99 03:12:59 PST Newsgroups: msi.comp-chem-list Path: uucp From: Victor Milman Subject: Re: CCL:New version of mpa X-Nntp-Posting-Host: 192.190.183.137 Content-Type: text/plain; charset=us-ascii To: "Donald E. Williams" Message-Id: <36E3B63F.72C93935@msi.com> Sender: uucp@msi.com Content-Transfer-Encoding: 7bit Organization: Molecular Simulations Inc. References: <9903031213.ZM20304@xray5.chem.louisville.edu> Mime-Version: 1.0 Date: Mon, 8 Mar 1999 11:36:31 GMT X-Mailer: Mozilla 4.03 [en] (WinNT; I) Dear Dr Williams, I am afraid the webpage you advertised is inaccessible: The requested web resource has been restricted. This could be due to one of the following conditions: 1.File Permissions on the web server do not allow for web users to view the contents of the file. 2.Access Control for the file restricts access to particular hosts on the Internet. 3.Access Control restricts access to particular userids/passwords. 4.Permissions on one of the directories within which the file resides do not allow for web users to view the contents of the directory. Any comments? Donald E. Williams wrote: > > ANNOUNCEMENT > > Mpa (molecular packing analysis) is a software program which > optimizes structures of molecular docking, molecular clusters, > crystals, and polymorphs by intermolecular force field energy > minimization. > > Version 2 of mpa is now available. This version has new features > which improve the efficiency of ab initio prediction of crystal > structures and their polymorphs. > > More information is available at http://www.louisville.edu/~dewill01, > or by email. > > -- > Dr. Donald E. Williams email:dew01@xray5.chem.louisville.edu > Department of Chemistry http://www.louisville.edu/~dewill01 > University of Louisville phone:502-852-5975 > Louisville, KY 40292 fax: 502-852-8149 > > --- > Administrivia: This message is automatically appended by the mail exploder: > 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 > --- > > ****Posts to this newsgroup leave MSI's network**** -- =================================================================== Victor Milman * Project Leader, Quantum Mechanics Molecular Simulations Inc * tel: (01223) 413300 The Quorum * fax: (01223) 413301 Barnwell Road * tel. from abroad: +44 1223 413301 Cambridge CB5 8RE, UK * e-mail: vmilman@msicam.co.uk =================================================================== From chemistry-request@www.ccl.net Mon Mar 8 08:27:51 1999 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA10949 Mon, 8 Mar 1999 08:27:49 -0500 (EST) Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id OAA04986; Mon, 8 Mar 1999 14:24:00 +0100 From: Jochen Kuepper Organization: Heinrich-Heine-Universitaet To: Sonat Biray , chemistry@www.ccl.net Subject: Re: CCL:Fortran downloading Date: Mon, 8 Mar 1999 14:22:21 +0100 X-Mailer: KMail [version 1.0.17] Content-Type: text/plain References: <19990304113610.8247.qmail@hotmail.com> MIME-Version: 1.0 Message-Id: <99030814240003.04443@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id IAA10951 On Don, 04 Mär 1999 Sonat Biray wrote: >Hi everybody, >Where can I download free Fortran 77 or the last version of Fortran? Guessing you are looking for a FORTRAN compiler ? What operating system for ? You should probably look at egcs.cygnus.com for a free C/C++/FORTRAN/... compiler suite. It's FORTRAN77 compiler is quite ok. Greetings, Jochen ----------------------------------------------------------------------- Jochen Küpper Heinrich-Heine-Universität Düsseldorf jochen@uni-duesseldorf.de Institut für Physikalische Chemie I Universitätsstr. 1, Geb 26.43 Raum 02.29 phone ++49-211-8113681 40225 Düsseldorf fax ++49-211-8115195 Germany http://www-public.rz.uni-duesseldorf.de/~jochen ----------------------------------------------------------------------- From chemistry-request@www.ccl.net Mon Mar 8 09:51:49 1999 Received: from oc30.uni-paderborn.de (oc30.uni-paderborn.de [131.234.240.90]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA11950 Mon, 8 Mar 1999 09:51:48 -0500 (EST) Received: from localhost (cpilger@localhost) by oc30.uni-paderborn.de (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id PAA11875 for ; Mon, 8 Mar 1999 15:50:09 +0100 (CET) Date: Mon, 8 Mar 1999 15:50:09 +0100 From: Christian Pilger To: chemistry@www.ccl.net Subject: conformational search on ring systems (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by www.ccl.net id JAA11951 Dear CCL'ers, one week ago, I posted a question about conformational searches on ring systems: > Dear CCL'ers, > > is anybody aware of a software package that has a conformational >search tool applicable to ring-systems ? I got several answers on this topic. Thank you very much. Many people asked me to summarize the responses: =========================================================================== From: Jonathan Brecher I believe that Conformer will do this, although I have not tried it myself. See http://www.conformer.com Jonathan Brecher CambidgeSoft Corporation jsb@camsoft.com =========================================================================== From: Ray Fort Jr. The molecular mechanics program PCModel, which runs on both PCs and UNIX boxes, has a search module called GMMX that will do what you want. It's available from Serena Software, Box 3076, Bloomington, IN 47402; telephone (812)-333-0823. While not free, it is not terribly expensive. =========================================================================== From: Curt M. Breneman For ring systems, a stochastic method of conformational searching is preferable such as the one described by Prof. Martin Saunders of Yale University. Curt Breneman RPI Chemistry =========================================================================== From: Chris Williams The Molecular Operating Environment (MOE ) from Chemical Computing Group (CCG) offers many conformational searching tools, the most relevant for your purposes being the RIPS conformational search. Check out the CCG website http: //www.chemcomp.com or contact me directly for more information. =========================================================================== From: A. Gil Santos Spartan, from Wave Function, has the possibility of conformational search applicable to ring systems. Nevertheless, version 5.1 had several problems when runing this kind of jobs. I just got today the last version of this package, with the information that a lot of things has been changed, but I hadn't the time to test them till now. I hope that this information can help you. =========================================================================== From: "[iso-8859-1] Márcio Cyrillo" I can tell you that I developed a software package for PCs that acts as an interface for the semi-empirical program MOPAC6. With this program, named Chem2Pac, you can perform conformational analysis (sistematic only) for one or two variables (bond length, angle or dihedral). It does not have a help file and I do not know if I can distribute it now, but let me know if you are interested. Grüss aus Brasilien, Marcio =========================================================================== From: Wayne Steinmetz Tripos' Sybyl offers a variety of tools that can be used in searching the conformational space of cyclic molecules. =========================================================================== From: Hr. Dr. S. Shapiro For the quality of your binding constants, check out the programme SCORE [cf. J. Mol. Model. 4: 379 ('98)]. For a programme that will do conformational searches on ring systems, check out GMMX by Serena Software. (And for an analysis of your obtained ring conformations, you can use the programme RICON, freely obtainable from Zefirov's group in Moskau.) =========================================================================== From: Mark Forster This is quite a niche topic and few if any packages address it. In terms of manual ring conformation adjustment I have used the Biopolymer module of the insightII program, this has a very neat interactive ring flipping implementation. =========================================================================== From: Paul D Soper I discussed this problem some time ago with Paul Saxe of MSI's San Diego office. He has BTCL scripts for use with Discover 3 which allow one to distort rings. His e-mail address is pws@msi.com. =========================================================================== From: Andy Holder Our AMPAC with Graphical User Interface has a simulated annealing method that has been quite successful on flexible ring systems. If you like, I'll send out some materials on this aspect of our software. Let me know. In the meantime, the following references describe the SA method. 1. Bokisch, F.; Liotard, D.; Rayez, J. C.; Duguay, B. Intl. J. Quant. Chem. 1992, 44, 619. =========================================================================== From: Patrick Bultinck Stochastic searching is implemented in MM3, obtainable from QCPE (object code). I use it very regularly on crown ethers and other macrocycles. If you want I can send a reprint (when I get them...). =========================================================================== From: Tamas Gunda If you mean on "conformational search tool applicable to ring-systems" the calculation of ring-puckering data, distances from least-square planes, torsional angles in rings, different pyramidality indices of atoms, then have a look on Mol2mol at www.compuchem.com/mol2mol.htm =========================================================================== From: Patrick Bultinck Have a look at B.P. Hay et al., J. Mol. Struct. (THEOCHEM), 337 (1995) 34-47 It nicely illustrates the use of MM3 conformational searching. MM3 can be obtained from QCPE for LOW cost, but without graphical interface, but you can check results with all kinds of graphical programs. If you want I can also send a proof of my own work, which is mainly on ab initio calculations. =========================================================================== From: Cikui Liang You can find information on CONFLEX from: http://sun.icrs.tohoku.ac.jp/~gotoh/CONFLEX/conflex_manual.htm Oxford Molecular Group (www.oxmol.com) has implemented CONFLEX with their CAChe software. It is going to be available for the next CAChe release. Hope this helps. =========================================================================== From: Chris Williams The application in MOE most suited for your problem of ring system conformational searching is the RIPS (Random Incremental Pulse Search) application. The RIPS application is based on a paper by Ferguson et.al. (J. Am. Chem. Soc., 111, p4371-4378, (1989)) The implementation of this algorithm MOE has an additional chiral constraining force than ensures the correct diastereomer of a given compound is generated upon minimization of the perturbed structure. Other conformational searching tools in MOE include molcular dynamics (MD), a hybrid MD/Monte Carlo conformational search and a fast rotatable bond search. Of these, only the fast rotatable bond search is not applicable to ring searches. If you need more specific information, please contact me at either the e-mail address or the telephone number below. =========================================================================== From: trevor.howe@pharma.Novartis.com MacroModel is excellent for this although the analysis tools are pretty hopeless but I would say this is the industry standard for ring systems. QUNATA, does a similar job with CHARMm as the force field. =========================================================================== From: Jens Sadowski the 3D-structure generator corina is capable of generating multiple conformations for ring systems up to ring size 8. Look at http://www2.ccc.uni-erlangen.de/services/3d.html =========================================================================== From: Mark Forster I'll address this in two parts 1) Code to measure ring conformation parameters. 2) Software to manipulate ring conformations interactively. 1) For six membered rings our Unix/X11 code called mdXvu is available from the Quantum Chemistry Program Exchange (QCPE) and one of its features is the measurement of the Cremer Pople ring puckering parameters. 2) The Biopolymer module of insightII (from MSI) has a nice tool for 'ring flapping' i.e. selecting two atoms in a ring and pivoting the intermediate ring atoms about the selected pair while maintaining the bond lengths and angles. This works for 5,6,7.... membered rings. =========================================================================== Regards, Christian ----------------------------------------------------------------- Dipl.-Chem. Christian Pilger Uni-GH Paderborn FB 13 - Organische Chemie Warburger Str. 100 D-33098 Paderborn/Germany Tel.: 05251-60279/-602183 Fax : 05251-603245 email: cpilger@oc30.uni-paderborn.de ----------------------------------------------------------------- From chemistry-request@www.ccl.net Tue Mar 9 11:05:10 1999 Received: from web702.mail.yahoo.com ([128.11.23.22]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA00244 Tue, 9 Mar 1999 11:05:09 -0500 (EST) Message-ID: <19990309160431.21161.rocketmail@web702.mail.yahoo.com> Received: from [129.43.6.38] by web702.mail.yahoo.com; Tue, 09 Mar 1999 08:04:31 PST Date: Tue, 9 Mar 1999 08:04:31 -0800 (PST) From: Aaron First Subject: For computational chemistry To: chemistry@www.ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, I want to continue my education in the field of computational chemistry for a Ph.D. How and where could I apply now ? Thanks Aaron _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com From chemistry-request@www.ccl.net Tue Mar 9 11:40:58 1999 Received: from tehama.criticalpath.net (tehama.paix.cp.net [209.228.15.41]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA00532 Tue, 9 Mar 1999 11:40:57 -0500 (EST) Message-Id: <199903091640.LAA00532@www.ccl.net> Received: (cpmta 17080 invoked from network); 9 Mar 1999 08:40:57 -0800 Received: from pcb4122.univ-lemans.fr (193.52.30.155) by smtp.cristal.org with SMTP; 9 Mar 1999 08:40:57 -0800 X-Sent: 9 Mar 1999 16:40:57 GMT X-Sender: pop@mail.cristal.org X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.1 Date: Tue, 09 Mar 1999 17:47:24 +0100 To: chemistry@www.ccl.net From: Armel Le Bail Subject: Re: CCL:QC journals 'in trouble' References: <199903051713.MAA07615@robin.cooper.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" At 09:34 09/03/99 +0000, Nathaniel (noj) Malcolm wrote: >in case anyone is still interested in this subject there is an >amusing paper in the "new journal of chemistry" >(which should be available on-line at: >http://www.rsc.org/is/journals/current/newjchem/njccon.htm for those >library cannot afford to stock such esoteric titles!) regarding >citation data and impact factors : > >"Sense and nonsense of science citation analyses: comment on the >monopoly position of ISI and citation inaccuracies. Risks of possible >misuse and biased citation and inpact data" > >Jan Reedijk NEW JOURNAL OF CHEMISTRY, 1998, Vol.22, No.8, pp.767-770 Just in case people try to get the ISI's most cited authors lists >from the Web address inside the above paper, they moved at : http://pcb4122.univ-lemans.fr/cit.html And, no, they will not be updated (at least not by me, ask ISI for updates). Best wishes, Armel Le Bail - Universite du Maine, Laboratoire des Fluorures, CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France http://www.cristal.org/ From chemistry-request@www.ccl.net Tue Mar 9 13:48:11 1999 Received: from servidor.unam.mx (servidor.unam.mx [132.248.10.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA02348 Tue, 9 Mar 1999 13:48:07 -0500 (EST) Received: from localhost (apisan@localhost) by servidor.unam.mx (8.8.8/8.8.8) with SMTP id MAA13068 for ; Tue, 9 Mar 1999 12:45:45 -0600 (CST) Date: Tue, 9 Mar 1999 12:45:45 -0600 (CST) From: Pisanty Baruch Alejandro-FQ To: chemistry@www.ccl.net Subject: Re: CCL:QC journals 'in trouble' (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Patrick and all, let's be brief since this is not a mainstream CCL topic. Patrick's original mail on impact factors shows the fundamental illness of bibliometric research for all its claims of objectivity. The fact is that the impact factors are skewed in favor of secondary sources which aggregate the results of a number of original papers. That is why even JACS and other major, highly respected and highly quoted journals don't make it to the top, whereas all forms of reviews do. This is not meant to disparage reviews! - just to add perspective, recognizing that some of the very major journals are also in the top. Specialized knowledge gets lost in this turmoil. Whether it be theoretical chemistry or tannery, specialized journals just don't cut it for bibliometers. Yet bibliometry is most surely here to stay and, as Patrick makes it clear, is a well established church with dogmas and rituals which will not move. So my way of thinking is along Jaime Martell's last line: tune policy, personalize assessments of researchers (we ARE persons!), and abandon all pretense of objectivity and generality coming from bibliometric research when applied to evaluating people. Alejandro Pisanty . . . . . . . . . . . . . . . . . . . . . . . . . . Dr. Alejandro Pisanty, Director General de Servicios de Computo Academico (Director, Computing Academic Services) Universidad Nacional Autonoma de Mexico (UNAM) Ciudad Universitaria, 04510 Mexico City DF MEXICO Tel. (+52-5) 622-8541, 622-8542; Fax 622-8540 . . . . . . . . . . . . . . . . . . . . . . . . . . From chemistry-request@www.ccl.net Tue Mar 9 13:49:50 1999 Received: from swan2.uspnet.usp.br (swan2.uspnet.usp.br [143.107.253.69]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA02398 Tue, 9 Mar 1999 13:49:36 -0500 (EST) Received: from ligquim ([143.107.194.89]) by swan2.uspnet.usp.br (8.9.1a/8.9.1) with SMTP id PAA22360 for ; Tue, 9 Mar 1999 15:46:15 -0300 (EST) Message-ID: <006d01be6a5d$8593a0a0$0100005a@ligquim.ffclrp.usp.br> From: "Sergio Emanuel Galembeck" To: "CCL mail list" Subject: Thermochemistry of radicals, a summary. Date: Tue, 9 Mar 1999 15:48:54 -0300 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Content-Transfer-Encoding: 7bit Dear Netters, Some weeks ago I sent the following question to CCL: What is the best method to calculate energies of reactions involving radicals? Is compound methods like CBS-Q as good choice? Thank you very much to Steen Hammerum, Paul Soper, Karl K. Irikura, Denes Szieberth and Theis Soelling. Their answers: =================================================== >From Steen Hammerum: Not an easy question to answer, inasmuch as there are not that many good numbers to calibrate against. For simple alkyl radicals, CBS-Q is not particularly successful (it gives results for the heats of formation that are up to 10 kJ/mol different from the literature values). G3 on the other hand provides very good correspondence with the currently recommended experimental heats of formation (4 kJ off for methyl, very good for ethyl, propyl, isopropyl, butyl, secbutyl, isobutyl). Radom recently described a composite method, CBS-RAD, that is supposed to be better for radicals, but it is quite demanding in terms of computer resources. Petersson's CBS-B3 (already incorporated in Gaussian 98) may also be well suited for radicals. =================================================== >From Paul Soper: I would recommend using isodesmic reactions with heats of formation for simple radicals taken from the JANAF tables. =================================================== >From Karl K. Irikura: It depends upon the accuracy you require. Radom has published a variant called "CBS-rad", or something like that, designed specifically for radicals. Computing thermochemistry for radicals is the same as for closed-shell molecules, except that spin contamination is more common. If you only need accuracy to about 25 kJ/mol, B3LYP is probably good and is far less expensive than CBS. =================================================== >From Denes Szieberth: You can find a comparison of different model chemistries in: Ochterski, Petersson, Wiberg : J. Am. Chem. Soc. 1995, 117, 11299-11308 or you can use some not so computationally demanding approaches described in e.g.: Sana, Nguyen: CPL 1992 196(3,4) 390 =================================================== >From Theis Soelling: Recently, Radom and coworkers recommeded a modified CBS procedure which is supposed to give excellent DfH of radicals. In addition, I find that the new G3-method by Curtiss et al. yields good agreement with experiment for e.g. CH3-dot, allyl-dot. References: 1) P.M. Mayer, C.J. Parkinson, D.M. Smith, L. Radom, J. Chem. Phys. 108 (1998) 604. 2) L.A. Curtiss, K. Raghavachari, P.C. Redfern, V. Rassolov, J.A. Pople, J. Chem. Phys. 109 (1998) 7764. =================================================== Best wishes, Sergio ============================================== Sergio Emanuel Galembeck Assistant Professor in Physical Chemistry Laboratorio de Modelagem Molecular Departamento de Quimica Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto Universidade de Sao Paulo fax: +55-16-633-81-51 e-mail: segalemb@usp.br =============================================== From chemistry-request@www.ccl.net Tue Mar 9 19:31:04 1999 Received: from rs6chem.chem.vill.edu (rs6chem.chem.vill.edu [153.104.73.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA07698 Tue, 9 Mar 1999 19:31:04 -0500 (EST) Received: from [153.104.73.18] (bausch.chem.vill.edu [153.104.73.18]) by rs6chem.chem.vill.edu (8.8.5/8.8.5) with ESMTP id TAA14906 for ; Tue, 9 Mar 1999 19:30:44 -0500 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 9 Mar 1999 19:34:51 -0500 To: CHEMISTRY@www.ccl.net From: "Joseph W. Bausch" Subject: getting data from vibrational frequencies I have an optimized geometry (using Gaussian94) of a highly symmetrical molecule. A frequency calculation indicates that it is a saddle point, with 4 imaginary frequencies. I have animated these frequencies using MOLDEN. I would like to reoptimize this structure "following" the changes as indicated by each of the four imaginary frequencies (I'm hoping that it will lead down to a transition state). Is there any easy way to get MOLDEN, or any other program, to give starting coordinates corresponding to the geometries just slightly perturbed from this optimized geometry? I'll summarize if there is sufficient interest, JWB bausch@chem.vill.edu --------------------