From chemistry-request@ccl.net Thu Jun 2 09:54:41 2005 Received: from web14427.mail.yahoo.com (web14427.mail.yahoo.com [216.136.175.204]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j52Dscaq015621 for ; Thu, 2 Jun 2005 09:54:39 -0400 Received: (qmail 14174 invoked by uid 60001); 2 Jun 2005 12:54:38 -0000 DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=Message-ID:Received:Date:From:Subject:To:MIME-Version:Content-Type:Content-Transfer-Encoding; b=zAiiYB+ZQ6g0f7M6RLZbntyUNzJGDSaSDIT/mROg2+56TR6YNbOBIeeHZRaQOkMTTPC3I8nJr3nbMUpUClGykA46RQqABCVafz6OFJZgvIwWqCs26bPVXYBQ5RFyDfgBYIXOV901oP6d7LMKGsHVLxl4uvJcOC9ZEf0gKzQWmf0= ; Message-ID: <20050602125438.14172.qmail-.at.-web14427.mail.yahoo.com> Received: from [139.184.30.17] by web14427.mail.yahoo.com via HTTP; Thu, 02 Jun 2005 05:54:38 PDT Date: Thu, 2 Jun 2005 05:54:38 -0700 (PDT) From: Ricardo Oliveira Subject: TDDFT on G03: negative transition energies To: chemistry-.at.-ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=1.8 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST autolearn=no version=3.0.3 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net I have done some B3lyp TDDFT calculations on some transition metal complexes and I have obtained some negative excitation energies . Does it make sense or it is an error of the code? Has anyone come across the same problem? __________________________________ Discover Yahoo! Use Yahoo! to plan a weekend, have fun online and more. Check it out! http://discover.yahoo.com/ From chemistry-request@ccl.net Thu Jun 2 09:44:01 2005 Received: from web14425.mail.yahoo.com (web14425.mail.yahoo.com [216.136.174.229]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j52DhtRR015068 for ; Thu, 2 Jun 2005 09:43:55 -0400 Received: (qmail 80159 invoked by uid 60001); 2 Jun 2005 12:43:53 -0000 DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=Message-ID:Received:Date:From:Subject:To:In-Reply-To:MIME-Version:Content-Type:Content-Transfer-Encoding; b=u/srDe6n8mqNMPrajf8rQPpsbqsszNYbcYGV7JlOGO++hvjwdZZTMq8nhfJhoGp/jtWnRcZiSs9CZwIfUfufV5p2BnmZmivkw3cgqpW2o9AJTK69uupYIBC+zLh82/2cZy0I7q+vAruAHopqMhvwcrjN1N+UMmedeZIa0ArMOkU= ; Message-ID: <20050602124353.80157.qmail-.at.-web14425.mail.yahoo.com> Received: from [139.184.30.17] by web14425.mail.yahoo.com via HTTP; Thu, 02 Jun 2005 05:43:53 PDT Date: Thu, 2 Jun 2005 05:43:53 -0700 (PDT) From: Ricardo Oliveira Subject: Re: CCL:TDDFT calculations using Gaussian To: chemistry-.at.-ccl.net In-Reply-To: <6.0.0.22.2.20050525101414.01ca7538-.at.-mail.bucknell.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=1.8 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST autolearn=no version=3.0.3 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hi Brian, the keyword you need is : TD. If you want x excited states you may use td(nstates=x) best wishes Ricardo Esplugas Sussex University email: r.o.esplugas-.at.-susx.ac.uk --- Brian Williams wrote: > Greetings- > > I am an experimentalist attempting to learn how to > use Gaussian in order to > calculate molecular properties. I wish to calculate > vertical excited > electronic states using TDDFT, starting with an > optimized ground state > geometry calculated using B3LYP 6-31(d). I have not > been able to locate an > example of how to set up the keywords to carry this > out- Foresman's book > mainly discusses CIS. Thanks for any help. > > Brian Williams, Chemistry, Bucknell University > > > > -= This is automatically added to each message by > the mailing script =- > To send e-mail to subscribers of CCL put the string > CCL: on your Subject: line > and send your message to: CHEMISTRY-.at.-ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST-.at.-ccl.net > HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to > spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > __________________________________ Discover Yahoo! Get on-the-go sports scores, stock quotes, news and more. Check it out! http://discover.yahoo.com/mobile.html From chemistry-request@ccl.net Thu Jun 2 09:50:34 2005 Received: from smtp1.hws.edu (smtp1.hws.edu [66.153.24.60]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j52DoTvn015397 for ; Thu, 2 Jun 2005 09:50:29 -0400 Received: from bexs2.hws.edu ([172.30.10.172]) by smtp1.hws.edu (SMSSMTP 4.1.0.19) with SMTP id M2005060208404714455 ; Thu, 02 Jun 2005 08:40:47 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.0.6603.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8" Subject: Fourth MERCURY Conference for Undergraduate Computational Chemistry Date: Thu, 2 Jun 2005 08:41:08 -0400 Message-ID: <8E787FB50F0F274B85D1FDF398918B77241407-.at.-bexs2.hws.edu> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Fourth MERCURY Conference for Undergraduate Computational Chemistry Thread-Index: AcVncFlPt0N6ORb2TWWX1ltd+cqg7A== From: "Parish, Carol" To: Cc: X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id j52DoYvm015404 Dear Colleagues, We are pleased to announce the Fourth MERCURY Conference for Undergraduate Computational Chemistry. The Conference will be held July 27-29th, 2005, at Hamilton College, in Clinton, NY. The conference will feature plenary lectures by Igor Alabugin, Florida State University; Emily Carter, Princeton University; Anna Krylov, University of Southern California; Ann Mattsson, Sandia National Laboratories; Adrian Roitberg, University of Florida; Ilja Siepmann, University of Minnesota; and John Tully, Yale University. In addition mainstays of the conference include an Undergraduate Poster Session and evening social sessions. This conference represents an excellent forum for undergraduates to present their work and to learn from experts in the field, allowing them to put their own research in perspective. It is equally valuable as a network for faculty working with undergraduates. Undergraduates from all institutions are invited to come present their work. Conference Fees are $200 for faculty, postdocs, or graduate students, and $100 for undergraduates, and include registration, housing, and meals. Details of the conference and information on registration and submission of Abstracts can be found on our web site: http://mercury.chem.hamilton.edu/conference/2005/index.html Carol Parish, on behalf of MERCURY, the Molecular Education and Research Consortium in Undergraduate computational chemistRY Carol Parish, Ph.D. Associate Professor Department of Chemistry Gottwald Science Center, C-209 University of Richmond 28 Westhampton Way Richmond, VA 23173 Phone: 804-484-1548 Fax: 804-287-1897 http://oncampus.richmond.edu/~cparish/ From chemistry-request@ccl.net Thu Jun 2 08:11:49 2005 Received: from localhost.localdomain (leitl.org [213.239.210.243]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j52CBinc011444 for ; Thu, 2 Jun 2005 08:11:45 -0400 Received: by localhost.localdomain (Postfix, from userid 1000) id 1F2B610380C9; Thu, 2 Jun 2005 12:11:35 +0200 (CEST) Date: Thu, 2 Jun 2005 12:11:35 +0200 From: Eugen Leitl To: chemistry[at]ccl.net Subject: [geoff[at]geoffhutchison.net: [Open Babel] Open Babel test file repository 2005-06-01 Message-ID: <20050602101135.GX4197[at]leitl.org> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.9i X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net ----- Forwarded message from Geoff Hutchison ----- From: Geoff Hutchison Date: Wed, 1 Jun 2005 21:29:33 -0400 To: openbabel-discuss list , openbabel-repository[at]lists.sourceforge.net Cc: cdk , jmol-developers[at]lists.sf.net, Warren DeLano , octet-devel[at]lists.sourceforge.net, joelib Subject: [Open Babel] (no subject) X-Mailer: Apple Mail (2.730) I'm happy to announce the release of the first public snapshot of the Open Babel test file repository 2005-06-01. This repository is an open resource for the purposes of test molecules, scripts and results in various chemical file formats. Releases are expected several times a year. The test set includes 39 "canonical" files (including 20 formats) and 47 additional files. Many file formats have formal specifications (e.g., CML or PDB) but realistically, such specifications evolve, many files are passed around which do not adhere to these specifications, and without example reference files, the details of file format specifications are not always clear. Importantly these files can be used for testing import/export routines in many chemical programs, not just Open Babel. By providing such a resource, we hope that developers of chemical software will minimize bugs when translating chemical and molecular data between different file formats and different representations. Additionally, we hope to encourage the community of chemical software developers to support open, well-defined file formats to facilitate interconversion and collaboration in the chemical sciences. * For more information, check: * To download the release: * To discuss the release (openbabel-repository[at]lists.sourceforge.net): Please consider contributing files: http://sourceforge.net/tracker/? atid=740158&group_id=40728&func=browse Cheers, -Geoff (Please distribute this announcement as you see fit to chemistry/ cheminformtics software developers, etc.) ------------------------------------------------------- This SF.Net email is sponsored by Yahoo. Introducing Yahoo! Search Developer Network - Create apps using Yahoo! Search APIs Find out how you can build Yahoo! directly into your own Applications - visit http://developer.yahoo.net/?fr=offad-ysdn-ostg-q22005 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss[at]lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ----- End forwarded message ----- -- Eugen* Leitl leitl ______________________________________________________________ ICBM: 48.07100, 11.36820 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE From chemistry-request@ccl.net Thu Jun 2 13:46:38 2005 Received: from smtp3.Stanford.EDU (smtp3.Stanford.EDU [171.67.16.138]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j52HkXNa026963 for ; Thu, 2 Jun 2005 13:46:34 -0400 Received: from cardinal4.Stanford.EDU (cardinal4.Stanford.EDU [171.64.15.252]) by smtp3.Stanford.EDU (8.12.11/8.12.11) with ESMTP id j52H9sC1007118; Thu, 2 Jun 2005 10:09:54 -0700 Date: Thu, 2 Jun 2005 10:09:54 -0700 (PDT) From: "S.I.Gorelsky" To: Ricardo Oliveira cc: chemistry /a\ ccl.net Subject: Re: CCL:TDDFT on G03: negative transition energies In-Reply-To: <20050602125438.14172.qmail /a\ web14427.mail.yahoo.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net > I have done some B3lyp TDDFT calculations on some > transition metal complexes and I have obtained some > negative excitation energies . Does it make sense or > it is an error of the code? Has anyone come across the > same problem? This means that what you have got as a reference state in your calculation is THE EXCITED STATE, and there is at least one lower-energy electronic state (the TRUE ground state) at the given level of theory. Regards, S. Gorelsky ---------------------------------------------------------------- Dr S.I. Gorelsky, Department of Chemistry, Stanford University Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA Phone: (650) 723-0041. Fax: (650) 723-0852. ---------------------------------------------------------------- From chemistry-request@ccl.net Thu Jun 2 17:46:53 2005 Received: from moria.cc.vt.edu (moria.cc.vt.edu [198.82.160.19]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j52Lkm3D007503 for ; Thu, 2 Jun 2005 17:46:48 -0400 Received: from rivendell.cc.vt.edu ([198.82.160.18]) by moria.cc.vt.edu with Microsoft SMTPSVC(5.0.2195.6713); Thu, 2 Jun 2005 16:59:21 -0400 Received: weboutlook.vt.edu 198.82.160.18 from 198.82.160.23 198.82.160.23 via HTTP with MS-WebStorage 6.0.6249 Received: 198.82.160.23 198.82.160.23 from via HTTP with MS-WebStorage 6.0.6249 User-Agent: Microsoft-Entourage/11.1.0.040913 Date: Thu, 02 Jun 2005 16:59:21 -0400 Subject: Re: CCL:TDDFT on G03: negative transition energies From: "T. Daniel Crawford" To: "S.I.Gorelsky" , Ricardo Oliveira CC: Message-ID: In-Reply-To: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-OriginalArrivalTime: 02 Jun 2005 20:59:21.0838 (UTC) FILETIME=[F349F8E0:01C567B5] X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net It should be noted that, in the TD-DFT framework (which is closely related to RPA), the response matrix cannot technically have negative eigenvalues. I would speculate that the eigenvalues reported by the code as negative are actually pure imaginary. This does indicate an "instability" in the response matrix, which you could perhaps interpret as a lower-energy state. -Daniel On 6/2/05 1:09 PM, "S.I.Gorelsky" wrote: > >> I have done some B3lyp TDDFT calculations on some >> transition metal complexes and I have obtained some >> negative excitation energies . Does it make sense or >> it is an error of the code? Has anyone come across the >> same problem? > > This means that what you have got as a reference state in your calculation > is THE EXCITED STATE, and there is at least one lower-energy electronic > state (the TRUE ground state) at the given level of theory. > > Regards, > > S. Gorelsky > > ---------------------------------------------------------------- > Dr S.I. Gorelsky, Department of Chemistry, Stanford University > Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA > Phone: (650) 723-0041. Fax: (650) 723-0852. > ---------------------------------------------------------------- > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY!at!ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST!at!ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > -- T. Daniel Crawford Department of Chemistry crawdad!at!vt.edu Virginia Tech www.chem.vt.edu/faculty/crawford.php Voice: 540-231-7760 FAX: 540-231-3255 -------------------- PGP Public Key at: http://www.chem.vt.edu/chem-dept/crawford/publickey.txt From chemistry-request@ccl.net Thu Jun 2 18:17:28 2005 Received: from prserv.net (asmtp2.prserv.net [32.97.166.52]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j52MHPZV008414 for ; Thu, 2 Jun 2005 18:17:25 -0400 Received: from [127.0.0.1] (cpe-65-29-74-171.indy.res.rr.com[65.29.74.171]) by prserv.net (asmtp2) with ESMTP id <2005060222172325203te86se> (Authid: jmmckel); Thu, 2 Jun 2005 22:17:23 +0000 Message-ID: <429F8596.3050900 :: attglobal.net> Date: Thu, 02 Jun 2005 17:17:58 -0500 From: John McKelvey User-Agent: Mozilla Thunderbird 1.0.2 (Windows/20050317) X-Accept-Language: en-us, en MIME-Version: 1.0 To: "T. Daniel Crawford" CC: "S.I.Gorelsky" , Ricardo Oliveira , chemistry :: ccl.net Subject: Re: CCL:TDDFT on G03: negative transition energies References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net This comment is strongly tied to the Thouless instability condition [see copious work by Paldus and Cizek in the 60's.] Negative eigenvalues were discussed as a direction in which to improve the reference wavefunction, usually the ground state. Rolf Seeger et. al. placed such code in Gxy for HF wave functions, I believe... John McKelvey T. Daniel Crawford wrote: >It should be noted that, in the TD-DFT framework (which is closely related >to RPA), the response matrix cannot technically have negative eigenvalues. >I would speculate that the eigenvalues reported by the code as negative are >actually pure imaginary. This does indicate an "instability" in the >response matrix, which you could perhaps interpret as a lower-energy state. > >-Daniel > > >On 6/2/05 1:09 PM, "S.I.Gorelsky" wrote: > > > >>>I have done some B3lyp TDDFT calculations on some >>>transition metal complexes and I have obtained some >>>negative excitation energies . Does it make sense or >>>it is an error of the code? Has anyone come across the >>>same problem? >>> >>> >>This means that what you have got as a reference state in your calculation >>is THE EXCITED STATE, and there is at least one lower-energy electronic >>state (the TRUE ground state) at the given level of theory. >> >>Regards, >> >>S. Gorelsky >> >>---------------------------------------------------------------- >> Dr S.I. Gorelsky, Department of Chemistry, Stanford University >> Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA >> Phone: (650) 723-0041. Fax: (650) 723-0852. >>---------------------------------------------------------------- >> >> >> >> >> >>Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST :: ccl.net >>HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs >> >>use the Web based form from CCL Home Page >> >> >> >> >> >> >> > > >