From chemistry-request@www.ccl.net Sat Mar 6 11:15:45 1999 Received: from snake.npac.syr.edu (snake.npac.syr.edu [128.230.162.60]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA02531 Sat, 6 Mar 1999 11:15:44 -0500 (EST) Received: from localhost (bernhold@localhost) by snake.npac.syr.edu (950413.SGI.8.6.12/8.6.6) with SMTP id LAA02737; Sat, 6 Mar 1999 11:15:41 -0500 Message-Id: <199903061615.LAA02737@snake.npac.syr.edu> X-Authentication-Warning: snake.npac.syr.edu: Host localhost didn't use HELO protocol Reply-to: bernhold@npac.syr.edu To: "Andruski, Stephen W." cc: "'CCL'" cc: bernhold@npac.syr.edu Subject: Re: CCL:MIF format In-reply-to: Message from "Andruski, Stephen W." of "Fri, 05 Mar 1999 08:41:32 EST." <80F79FF3ECD6D1119D9000805FCC602A309C18@Ntsvexch> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-ID: <2731.920736940.1@snake.npac.syr.edu> Date: Sat, 06 Mar 1999 11:15:40 -0500 From: "David E. Bernholdt" It strikes me that the "right" way to do something like this these days is to use XML. Chemical Markup Language (CML) was one of the very first XML applications (having started development before XML itself. It is certainly not as complete as CIF or (what I recall of) MIF, but it could be a useful starting point or at least a source of ideas. I think XML offers a huge potential to standardize the input and output of many comp. chem. applications -- if people think it is useful enough to agree to/help develop the standards. -- David E. Bernholdt | Email: bernhold@npac.syr.edu Northeast Parallel Architectures Center | Phone: +1 315 443 3857 111 College Place, Syracuse University | Fax: +1 315 443 1973 Syracuse, NY 13244-4100 | URL: http://www.npac.syr.edu From chemistry-request@www.ccl.net Sat Mar 6 14:22:40 1999 Received: from giasbma.vsnl.net.in (giasbma.vsnl.net.in [202.54.4.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA02920 Sat, 6 Mar 1999 14:22:37 -0500 (EST) Received: from giasbmc.vsnl.net.in (giasbmc [202.54.4.6]) by giasbma.vsnl.net.in (8.8.8/8.8.8) with SMTP id BAA25026 for ; Sun, 7 Mar 1999 01:01:17 +0500 (IST) Date: Sun, 7 Mar 1999 00:34:38 -0500 (GMT) From: Amit Galande To: CHEMISTRY@www.ccl.net Subject: Sampling combinatorial library Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII This is with reference to one article on www.netsci.org/Science/Screening/feature09.html which tries to answer whether random or rational approach should be used for the sampling of combinatorial library. Key equation derived by iteration is as follows n ( 1-(1-r) ) n = ------------ r(1-P) where n = number of molecules sampled. P = % overlap r = ratio of weighage of individual molecules to the weighage of entire diversity Desperately looking for discussion about this article Can anybody help ? Amit Galande From chemistry-request@www.ccl.net Thu Mar 4 08:25:38 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA21951 Thu, 4 Mar 1999 08:25:37 -0500 (EST) Received: from xray5.chem.louisville.edu (xray5.chem.louisville.edu [136.165.12.18]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id MAA15741 for ; Wed, 3 Mar 1999 12:13:34 -0500 (EST) Received: (from dew01@localhost) by xray5.chem.louisville.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) id MAA20306 for chemistry@ccl.net; Wed, 3 Mar 1999 12:13:31 -0500 From: "Donald E. Williams" Message-Id: <9903031213.ZM20304@xray5.chem.louisville.edu> Date: Wed, 3 Mar 1999 12:13:31 -0500 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@ccl.net Subject: New version of mpa Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii 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 From chemistry-request@www.ccl.net Thu Mar 4 08:36:32 1999 Received: from Raven.und.ac.za ([146.230.128.50]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA22152 Thu, 4 Mar 1999 08:35:55 -0500 (EST) Received: from gwise-smtp.und.ac.za (GWise-SMTP.und.ac.za [146.230.128.63]) by Raven.und.ac.za (8.8.3/8.7.3) with SMTP id LAA25193 for ; Wed, 3 Mar 1999 11:52:01 +0200 (SAT) Received: from Routing-Domain-Message_Server by gwise-smtp.und.ac.za with Novell_GroupWise; Wed, 03 Mar 1999 11:52:01 +0200 Message-Id: X-Mailer: Novell GroupWise 5.2 Date: Wed, 03 Mar 1999 11:51:41 +0200 From: "Gert Kruger" To: chemistry@www.ccl.net Subject: Re: Gaussian and NMR properties Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id IAA22169 Dear CCLers, 1. Is it possible to compute the NMR properties (C13 and proton data) of only a specific selection of atoms in a large molecule. Specifically a segment that you are interested in? 2. It seems not possible to use the NMR command with the ONIOM method in Guassian 98? It would have been nice to calculate the specific segment of interest at a high level and calculate the HMR properties of those atoms only (rest of the atoms at a low level and exclude that atoms from the NMR calculation). Any hints? Best wishes Gert Kruger ___________________________________ Dr HG Kruger, Chemistry, University of Natal P.O. Box 18091, Dalbridge 4014 Durban, South Africa. tel: +27-312603090, fax: +27-31-2603091 email: kruger@scifs1.und.ac.za ___________________________________ From chemistry-request@www.ccl.net Thu Mar 4 09:23:39 1999 Received: from hotmail.com (law-f66.hotmail.com [209.185.131.129]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id JAA22515 Thu, 4 Mar 1999 09:23:38 -0500 (EST) Received: (qmail 8248 invoked by uid 0); 4 Mar 1999 11:36:10 -0000 Message-ID: <19990304113610.8247.qmail@hotmail.com> Received: from 195.33.244.168 by www.hotmail.com with HTTP; Thu, 04 Mar 1999 03:36:10 PST X-Originating-IP: [195.33.244.168] From: "Sonat Biray" To: chemistry@www.ccl.net Subject: Fortran downloading Date: Thu, 04 Mar 1999 03:36:10 PST Mime-Version: 1.0 Content-type: text/plain Hi everybody, Where can I download free Fortran 77 or the last version of Fortran? Cheers... Sonat Biray ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From chemistry-request@www.ccl.net Thu Mar 4 10:53:57 1999 Received: from jmlopez.fam.cie.uva.es (jmlopez.fam.cie.uva.es [157.88.38.56]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA23518 Thu, 4 Mar 1999 10:52:40 -0500 (EST) Received: (from aguado@localhost) by jmlopez.fam.cie.uva.es (8.9.1/8.9.1) id NAA12399 for chemistry@www.ccl.net; Wed, 3 Mar 1999 13:19:03 +0100 Date: Wed, 3 Mar 1999 13:19:03 +0100 From: Andres Aguado Message-Id: <199903031219.NAA12399@jmlopez.fam.cie.uva.es> To: chemistry@www.ccl.net Subject: WORDtoLaTeX summary Hi all, Few days ago I posted an e-mail to CCL asking for some program able to convert a WORD file into a LaTeX file. Below is the summary of the responses I have received. I recommend to anyone that is interested in such software to have a look at http://www.kfa-juelich.de/isr/1/texconv/pctotex.html And thanks a lot for all your help!! Best regards, Andres Aguado. ........................................................................ Hi, try this site: They have an rtf2latex converter http://www.primate.wisc.edu/software/RTF/ suerte a. -- Adrian E. Roitberg ======================================================================== NIST | Phone: (301) 975-4469. 100 Bureau Drive, Stop 8311 | Fax (301) 975-5449 Gaithersburg, MD 20899-8311 | E-mail : adrian@nist.gov ======================================================================== .......................................................................... Dear Andres: I don't know of any software that can make this conversion (doesn't mean that such a program does not exist) but I know a program that can help. The program is call Scientific Word, This program has an environment similar to any windows-base word processor (it is actually one of them) but it save in your disk a latex type file, (this program also include a compiler with their own styles). I used to use this software before and whenever I needed a latex version of a word file, I just copied the text in the WORD window and pasted in the Scientific word window, the formula and special characters are not recognized and you need to go over the text a correct them, but anyway, if you don't have to many formula, you save a lot of time (the text can be fixed using the spelling corrector). Now if you save the document you will have a latex document, you can even use your own style just editing this ascii file and copying anything between /begin{document} and /end{document}. I know this is not and standart procedure but works, of course in case you don't have access to scientific word, just delete this message and I am sorry for the time you spent reading it. regards, Pedro Derosa -- ******************************** Dr. Pedro A. DEROSA Dept of Chemical Engineering University of South Carolina Off 2A01H Ph. (1-803) 777-0611 FAX (1-803) 777-8265 e-mail: pedro@sun.che.sc.edu ******************************** ........................................................................ see for example links in http://bolug.uni-bonn.de/wissen/robin/latex.html http://www.kfa-juelich.de/isr/1/texconv/pctotex.html can be found by a search on altavista.com Martin -- Dr. Martin Braendle Lab. fuer Anorg. Chemie Tel. (+41) 1/ 632 2894 ETH Zentrum CAB B17 Fax (+41) 1/ 632 1149 Universitaetstr. 6 E-mail braendle@inorg.chem.ethz.ch CH-8092 Zuerich http://www.inorg.chem.ethz.ch/group/braendle.html ........................................................................ Hello Andres, Check the following URL: http://www.kfa-juelich.de/isr/1/texconv/pctotex.html You may also want to check www.ctan.org -- Jesus M. Castagnetto - "Ken Zen Ichi-nyo" Program Project: http://www.scripps.edu/research/metallo/ Metalloprotein DB: http://metallo.scripps.edu/ Pilot Stuff: http://www.geocities.com/ResearchTriangle/Lab/1059/ ......................................................................... Not directly a Word file, but an RTF file, which is easy to create >from Word. But it's text only, no formulas. You can find the program (rtf2latex or something similar) on any CTAN server, e.g. ftp.dante.de. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@www.ccl.net Thu Mar 4 11:12:04 1999 Received: from dqo.fcq.unc.edu.ar (diego@dqo.fcq.unc.edu.ar [200.16.18.55]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA23799 Thu, 4 Mar 1999 11:12:02 -0500 (EST) Received: from localhost (diego@localhost) by dqo.fcq.unc.edu.ar (8.8.7/8.8.7) with ESMTP id KAA28769 for ; Thu, 4 Mar 1999 10:15:48 -0300 Date: Thu, 4 Mar 1999 10:15:48 -0300 (ART) From: "Diego S. Pedrosa" To: Computational Chemistry List Subject: Structure Drawing Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL'ers: Thanks to Meike and Reinaldo, for their answears, they will help a lot. This time I'm looking for a Structure Drawing soft (like ChemWindow or ChemOffice) for linux, I'm writeing a document and need that soft. If someone knows about that, please let me know quick. Thanks. Diego. From chemistry-request@www.ccl.net Thu Mar 4 12:09:17 1999 Received: from gatekeeper2.novartis.com (gatekeeper2.novartis.com [194.191.169.74]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA25026 Thu, 4 Mar 1999 12:09:15 -0500 (EST) From: takanori.kanazawa@pharma.Novartis.com Received: from mta3.is.chbs (mail.novartis.com [192.37.10.59]) by gatekeeper2.novartis.com (8.9.0/8.9.0) with ESMTP id DAA09555 for ; Thu, 4 Mar 1999 03:31:33 +0100 (MET) Received: from nts1.novartis.com ([192.168.50.131]) by mta3.is.chbs (8.8.5/8.8.5) with SMTP id DAA28205 for ; Thu, 4 Mar 1999 03:34:59 +0100 (MET) Received: by nts1.novartis.com(Lotus SMTP MTA v1.2 (600.1 3-26-1998)) id 4125672A.000DD505 ; Thu, 4 Mar 1999 03:31:04 +0100 X-Lotus-FromDomain: PH@N1 To: chemistry@www.ccl.net Message-ID: <4925672A.000D2CEE.00@nts1.novartis.com> Date: Thu, 4 Mar 1999 11:33:08 +0900 Subject: help:NAMD2 Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Dear CCLers, Could someone help me to solve a problem with a MD simulation using namd2. I downloaded namd2.0b3(binary) from the namd homepage and installed on my SGI machine(octance R10000 250MHz, 2cpu, IRIX6.4). When I ran a MD simulation with a periodic boundary condition, the job stopped with the following messages. ..... Info: **************************** Info: STRUCTURE SUMMARY: Info: 1012 ATOMS Info: 11 BONDS Info: 18 ANGLES Info: 16 DIHEDRALS Info: 2 IMPROPERS Info: 0 EXCLUSIONS Info: 3033 DEGREES OF FREEDOM Info: 1005 HYDROGEN GROUPS Info: ***************************** Info: Entering startup phase 0 Info: Entering startup phase 1 Info: Entering startup phase 2 Info: Entering startup phase 3 Info: PATCH GRID IS 69 (PERIODIC) BY 69 (PERIODIC) BY 69 (PERIODIC) Info: REMOVING COM VELOCITY ( -0.1068, 0.0186864, -0.00757281) Info: 1012 atoms assigned to node 0 ID's not allocated in ComputeMap::storeCompute(). ############### END of the log-file ############### The sample job attached to the program(MD of alanine oligopeptide) runs without any problem. Any comments or suggestions are appreciated. Thanks in advance, Takanori Kanazawa *************************************************************** Takanori Kanazawa E-mail : takanori.kanazawa@pharma.novartis.com Drug Discovery Group / CAMM Takarazuka Research Institute Novartis Pharma K.K. 10-66 Miyuki-cho, Takarazuka, Hyogo 665 JAPAN *************************************************************** From chemistry-request@www.ccl.net Thu Mar 4 13:00:56 1999 Received: (from ccl@localhost) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) id NAA25715 Thu, 4 Mar 1999 13:00:55 -0500 (EST) Message-ID: X-Mailer: XFMail 1.3 [p0] on Solaris X-Priority: 3 (Normal) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit MIME-Version: 1.0 Resent-Date: Tue, 02 Mar 99 18:10:26 +0100 Resent-Message-Id: <9903021710.AA00539@leonardo.biomed.unipr.it> Resent-From: A.Romani@leonardo.biomed.unipr.it Resent-To: chemistry-request@www.ccl.net Date: Thu, 04 Mar 1999 13:00:54 -0500 (EST) Reply-To: chemistry-request@www.ccl.net Organization: Ohio Supercomputer Center/CCL Sender: ccl@www.ccl.net From: ccl@www.ccl.net To: chemistry@www.ccl.net Subject: FW: Heat protein denaturation -----FW: <9903021710.AA00539@leonardo.biomed.unipr.it>----- Date: Tue, 02 Mar 99 18:10:26 +0100 From: A.Romani@leonardo.biomed.unipr.it To: chemistry-request@www.ccl.net Subject: Heat protein denaturation Dear netters, I apply to your kind attention to obtain, if possible, some informations and suggestion about this problem. I have to simulate the heat protein denaturation (from room temperature to 45 Celsius degrees).There is someone that has just faced this problem? How can I solve it? Is AMBER 5.0 able to do it? Is there a dedicated software that can do it? I find also articles or reviews that explain this problem. Examples or script file are appreciated. Thanking in advance for what you can do about it. Yours faithfully Antonello Romani ___________________________________________ Antonello Romani Istituto di Patologia Generale Plesso Biotecnologico Integrato Facolta' di Medicina e Chirurgia Universita' degli Studi di Parma via Volturno 39 43100 Parma Tel : +39 0521 903 764 Fax : +39 0521 903 742 E-Mail : A.Romani@leonardo.biomed.unipr.it ___________________________________________ --------------End of forwarded message------------------------- ---------------------------------- E-Mail: ccl@www.ccl.net Date: 04-Mar-99 Time: 12:59:03 This message was sent by XFMail ---------------------------------- From chemistry-request@www.ccl.net Thu Mar 4 14:06:00 1999 Received: from nmr-v.ioc.ac.ru (root@nmr-v.ioc.ac.ru [193.233.3.213]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA26210 Thu, 4 Mar 1999 13:59:47 -0500 (EST) Received: from cacr.ioc.ac.ru (val@localhost [127.0.0.1]) by nmr-v.ioc.ac.ru (8.8.7/8.8.7) with ESMTP id VAA05400 for ; Thu, 4 Mar 1999 21:41:50 +0300 Sender: val@nmr-v.ioc.ac.ru Message-ID: <36DED3EE.6ADB7A45@cacr.ioc.ac.ru> Date: Thu, 04 Mar 1999 21:41:50 +0300 From: val Reply-To: val@cacr.ioc.ac.ru Organization: IOC X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.30 i686) X-Accept-Language: en MIME-Version: 1.0 To: CCL_post Subject: SUMMARY: TS imaginary freq. value Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCL'ers, The original question and the replies received up to now are shown below. My big thanks to to Stefan Fau, Alexander Bagatur'yants, Marcel Swart and E. Lewars. best regards, Valentin. --------------------------------------------------q--- I have got a Transition State (TS) structure with unusually low imaginary frequency value, about 17 CM**-1. However, the gradient convergence criterion is satisfied, Hessian is correct (only one imaginary freq.), visualization of the normal mode gives right picture and Intrinsic Reaction Coordinate optimization connects the TS to reactants and products. Is this enough to proof that the saddle point is true TS of the reaction of interest? Does it make any sense to take into account the value of the imaginary frequency? In what range should it be for the most common cases? Any references on TS imaginary frequency value interpretation are really welcome. Thanks in advance, I will summarize as usual. sincerely yours, Valentin. ------------------------------------------------------ --------------------------------------------------r1-- Dear Valentin, I think you did anything to ensure that your structure IS a TS connecting your educts and products. You certainly did more than some people do in recent publications. If you are interested in exact values for the lower frequencies, you need a geometry that is very good, i.e. the displacements should be inside the limits, too. (With Gaussian DFT you can increase the integration grid to "ultrafine". A subsequent optimization with this grid needs only a few cycles to converge.) The absolute value of your imaginary frequency is quite low, most bond breaking processes have values in the range of hundreds i cm^-1. We know values of 20i cm^-1 from rotations of M-CH3 or M-PH3 bonds, but since you did the IRC you are on the safe side. The value of the imaginary frequency gives you information about the curvature of the potential energy surface at the TS along the imaginary mode. It is a local quantity that may be used to guess the shape of the "energy wall" separating educts and products, but the energies of the optimized points of your IRC give the same information quantitatively. In my view an imaginary frequency of 17i cm^-1 is not very different from a "normal" frequency of 17 cm^-1. It is just imaginary instead of real. Stefan ______________________________________________________________________ Dr. Stefan Fau Fachbereich Chemie, AK Frenking Philipps-Universität Marburg 35032 Marburg, Germany fau@chemie.uni-marburg.de ------------------------------------------------------ --------------------------------------------------r2-- Dear Valentin, Certainly, this is the correct TS that correspond to the reaction that you are interested in. The region of TS is a domain of strong anharmonicity. In addition, the nature of your TS may be different. For example, two valleys can differ only in the conformation(s) of the reacting molecule(s). The other reason for the extreme flattnes of your PES in the TS region can be associated with a low activation barrier, at least on the one side of your reaction. Anyway, there is no apparent restriction on the value of the imaginary frequency characterizing a TS as well as in the case of a real frequency of a minimum (or a TS). Best wishes, Yours Prof. Alexander Bagatur'yants Photochemistry Center, Russian Academy of Sciences ul. Novatorov 7a, Moscow, 117421 Russia Phone: (007-095)-936-2588 Fax: (007-095)-936-1255 E-mail: sasha@icp.rssi.ru Home page: http://www.icp.rssi.ru/eng/bagat/bagat.htm ------------------------------------------------------ --------------------------------------------------r3-- A normal imaginary frequency is of the range of 300 - 800 CM**-1, but the value depends much on the QM method you use. Do you use semi-empirical (i.e. AM1/PM3) methods ? This because I have some limited experience with TS's in MOPAC93, and if I remember correctly, the TS frequency was smaller than with ab initio methods. Sincerely, Marcel Swart. ============================================================== Marcel Swart Theoretical Chemistry (MSC) Molecular Dynamics (GBB) University of Groningen Chemistry Department Room 18.45 Nijenborgh 4 9747 AG Groningen The Netherlands tel : 31 - (0)50 - 3634377 fax : 31 - (0)50 - 3634441 E-mail : m.swart@chem.rug.nl WWW: http://theochem.chem.rug.nl/~marcel/ ============================================================== ------------------------------------------------------ --------------------------------------------------r4-- 1999 Feb 23 REPLY TO VALENTIN ANANIKOV, Re IMAG FREQ (BELOW) Hello, If you have an imaginary frequency (one and only one), then *at that level of theory* the species is a transition state (a first-order saddle point). So your structure is indeed a TS (at that level of theory). QED. As you point out, 17i ("-17") cm-1 seems small for an imag freq. It's probably OK, however, for a low-energy rotation; you don't say what the vibration (rotation?) corresponds to--an almost free rotor (low-energy torsional barrier), or pyramidalization of a group that is barely flat? In any case the small value of the imag freq indicates the barrier to the reaction represented by the TS is very low. The reactant going to this TS hovers on the edge of existence -- at the level of theory that you used (for a rotation or pyramidalization the "reaction" is trivial and represents just a conformational change). You do say that visualization and an IRC job confirm it's the TS you want. TS freqs are commonly in the range of roughly 300i -- 1500i cm-1, with the bigger values involving H migration (as in HNC --> HCN). E. Lewars ============================== ------------------------------------------------------ ==================================================================== , , , , Valentin P. Ananikov |\\\\ ////| /////| NMR Group | \\\|/// | ///// | ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | Leninsky Prospect 47 | |===| | |===| | Moscow 117913 | | | | | | | Russia | | A | | | Z | | \ | | / | | / e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' Fax +7 (095)1355328 Phone +7 (095)9383536 ==================================================================== From chemistry-request@www.ccl.net Thu Mar 4 15:54:51 1999 Received: from ifi.unicamp.br (lua.ifi.unicamp.br [143.106.6.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA29101 Thu, 4 Mar 1999 15:54:48 -0500 (EST) Received: (from daemon@localhost) by ifi.unicamp.br (8.8.8/8.8.8) id RAA00751 for ; Thu, 4 Mar 1999 17:54:12 -0300 (BSC) Received: from cation.ifi.unicamp.br(143.106.39.135), claiming to be "cation" via SMTP by lua.ifi.unicamp.br, id smtpdaaaFma; Thu Mar 4 17:54:11 1999 Message-Id: <3.0.32.19990304175558.00928d80@lua.ifi.unicamp.br> X-Sender: dasf@lua.ifi.unicamp.br X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Thu, 04 Mar 1999 17:56:00 -0300 To: CHEMISTRY@www.ccl.net From: "=?iso-8859-1?Q?=22Dem=E9trio_A._da_Silva_Filho=22?=" Subject: First Excited State Geometry Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id PAA29104 Dear CCL readers, Does anybody knows if it's possible do calculate the geometry of the first excited state using GAMESS or GAUSSIAN? If it's possible, what keywork I must use? Thanks in advance, Demétrio Filho _____________________________________ Demetrio A. da Silva Filho UNICAMP - IFGW Prédio D - Sala 17 CEP 13083-970 C.Postal 6165 Campinas - SP - Brasil _____________________________________ From chemistry-request@www.ccl.net Thu Mar 4 17:56:35 1999 Received: from scribe.cc.purdue.edu (scribe.cc.purdue.edu [128.210.11.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA29925 Thu, 4 Mar 1999 17:56:34 -0500 (EST) Received: from marie.chem.purdue.edu by scribe.cc.purdue.edu with ESMTP; Thu, 4 Mar 1999 17:56:26 -0500 Received: from localhost (lev@localhost) by marie.chem.purdue.edu (8.8.7/8.8.7) with SMTP id RAA18323 for ; Thu, 4 Mar 1999 17:56:25 -0500 (EST) X-Authentication-Warning: marie.chem.purdue.edu: lev owned process doing -bs Date: Thu, 4 Mar 1999 17:56:25 -0500 From: Lev Gorenstein cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:Dore metall In-Reply-To: Message-Id: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 4 Mar 1999, Richard Wood from CHEM.UIC.EDU wrote: > On Wed, 3 Mar 1999, Milan Antonijevic from Serbia wrote: > > > Dear Sirs, > > Please send me some papers, abstracts, web sites and some > > other sources of informations from which I can get > > information about > > .... [skipped] > > This is not intended to be snotty or anything like that. But, doesn't > anybody know how to use a library anymore? Let me put in my $0.02 worth. I'm affraid that folks here in the States are "spoiled" by the availability of information. Sometimes people take those nice libraries with tons of different journals for granted, and don't realize that it may not be true in other countries. Being originally from Russia I could easily see that Milan Antonijevic in Serbia may have problems acessing current information on the subject. At least, MORE problems comparing to Richard Wood's trip to UIC library ;-). Actually just 2 days ago I was xeroxing about 100 pages from various papers (and another 100 is coming soon from Interlibrary Loans ;-) for a personal friend of mine who works in Siberian Branch of Russian Academy of Sciences. Just because they don't have money to subscribe for all those journals. Regards, Lev From chemistry-request@www.ccl.net Thu Mar 4 20:42:06 1999 Received: from smtp3.ny.us.ibm.com (smtp3.ny.us.ibm.com [198.133.22.42]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id UAA01067 Thu, 4 Mar 1999 20:42:05 -0500 (EST) From: whuber@almaden.ibm.com Received: from westrelay02.boulder.ibm.com (westrelay02.boulder.ibm.com [9.99.132.205]) by smtp3.ny.us.ibm.com (8.8.7/8.8.7) with ESMTP id UAA58264 for ; Thu, 4 Mar 1999 20:42:06 -0500 Received: from d53mta03h.boulder.ibm.com (d53mta03h.boulder.ibm.com [9.99.142.3]) by westrelay02.boulder.ibm.com (8.8.7/NCO v1.8) with SMTP id SAA210340 for ; Thu, 4 Mar 1999 18:41:34 -0700 Received: by d53mta03h.boulder.ibm.com(Lotus SMTP MTA Internal build v4.6.2 (651.2 6-10-1998)) id 8725672B.00094AA3 ; Thu, 4 Mar 1999 18:41:29 -0700 X-Lotus-FromDomain: IBMUS To: chemistry@www.ccl.net Message-ID: <8725672B.00094A42.00@d53mta03h.boulder.ibm.com> Date: Thu, 4 Mar 1999 17:41:20 -0800 Subject: Stability of inertial axes Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline When you define an internal coordinate system for a molecule by diagonalization of its inertial tensor, the definition obviously becomes ambiguous for degenerate eigenvalues, and it is unstable for nearly degenerate eigenvalues. Has anyone come across either (i) a criterion how to detect such an instability (that would somehow involve an error model), or (ii) even a method how to remove it (that would somehow use information beyond the inertial tensor)? Wolfgang Huber IBM Research Almaden San Jose CA, USA