From chemistry-request@ccl.net Fri Nov 21 08:11:57 2003 Received: from GWIA.HSC.WVU.EDU (gateway.hsc.wvu.edu [157.182.105.18]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hALDBPRW030553 for ; Fri, 21 Nov 2003 08:11:26 -0500 Received: from HSC-DOM5-MTA by GWIA.HSC.WVU.EDU with Novell_GroupWise; Fri, 21 Nov 2003 07:55:08 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.5.1 Date: Fri, 21 Nov 2003 07:54:56 -0500 From: "Peter Gannett" To: , Subject: Re: CCL:Nanotechnology course Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Tapas: I, too, am interested in this and would appreciate it if you would forward an responses that don't get posted to the list. As a start, you may want to contact NBTC at Cornell University. Pete Gannett >>> "Tapas Kar" 11/20/03 05:19PM >>> Hi, We are planning to introduce Nanotechnology Courses at undergraduate and graduate levels. Like to know how many universities offer such courses and some information on course materials. This will help us to develop such course. I appreciate your help to direct me related websites also. Thanks, Tapas *********************************************** "We owe a lot to the Indians, who taught us how to count, without which no worthwhile scientific discovery could have been made." - Albert Einstein - ---------------------------------------------------------------------------- ---- Tapas Kar, Ph. D Department of Chemistry & Biochemistry Utah State University Logan, UT 84322-0300 Tel: 435-797-7230 Fax: 435-797-3390 Email: tapaskar!at!cc.usu.edu Web:http://www.chem.usu.edu/faculty/Tapas/index.html From chemistry-request@ccl.net Fri Nov 21 09:18:35 2003 Received: from web12902.mail.yahoo.com (web12902.mail.yahoo.com [216.136.174.69]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hALEI2RW000866 for ; Fri, 21 Nov 2003 09:18:03 -0500 Message-ID: <20031121141802.40469.qmail!at!web12902.mail.yahoo.com> Received: from [216.126.217.163] by web12902.mail.yahoo.com via HTTP; Fri, 21 Nov 2003 06:18:02 PST Date: Fri, 21 Nov 2003 06:18:02 -0800 (PST) From: Mitch Miller Subject: Symposium Update -- ACS, Anaheim To: chemistry!at!ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Colleagues, I am pleased to announce that the symposium entitled The Bigger Picture: Linking Bioinformatics to Cheminformatics at the next ACS National Meeting (Anaheim March 28 - April 1, 2004), has been designated a plenary session with the confirmation of a talk by Christopher A. Lipinski, Adjunct Senior Research Fellow, Pfizer Global R&D, Groton Labs (retired). Dr. Lipinski will speak on Technical and people disconnects hindering knowledge exchange between chemistry and biology. The tentative date for this symposium is Sunday, March 28, 2004. You are invited to submit an abstract to help complete the symposium! > From a previous announcement: Theme: Most life-science research organizations have information systems for sequence data and for compound data. This symposium will explore what is being done to bridge these two types of systems and provide an integrated view that facilitates faster compound discovery. We welcome talks about information systems in production, development, or planning. You can even talk about what you wish you could build if you could... Here are the details: - The best way to submit an abstract is on-line using OASYS(http://oasys.acs.org/) - Please e-mail or call me if you have trouble with OASYS. - The deadline for submissions is 1 December 2003. (You can submit an abstract now and then make changes until 1 December.) - Target presentation length is 20 minutes, with 5 minutes for questions. Please let me know if you need more time. - We especially welcome presentations from research organizations working with bioinformatics and cheminformatics. - When planning your presentation, consider a back-up person from your organization who could deliver your talk if for any reason you cannot make it to the meeting. Questions are welcome! Regards, Mitch 801 569 1390 ===== Mitchell Miller, Ph.D. Cheminformatics Consultant ChemMitch!at!yahoo.com __________________________________ Do you Yahoo!? Free Pop-Up Blocker - Get it now http://companion.yahoo.com/ From chemistry-request@ccl.net Fri Nov 21 03:43:43 2003 Received: from crane2.cf.ac.uk (crane2.cf.ac.uk [131.251.0.25]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAL8hCRW020338 for ; Fri, 21 Nov 2003 03:43:12 -0500 Received: from thor.cf.ac.uk ([131.251.0.1]) by crane2.cf.ac.uk with esmtp (Exim 4.24) id 1AN6si-00075G-0q; Fri, 21 Nov 2003 08:43:12 +0000 Received: from localhost (sacjap@localhost) by thor.cf.ac.uk (8.8.8/8.6.12) with ESMTP id IAA04206; Fri, 21 Nov 2003 08:43:11 GMT Date: Fri, 21 Nov 2003 08:43:11 +0000 (GMT) From: Jamie Platts X-X-Sender: sacjap@thor To: Alan Shusterman cc: chemistry!at!ccl.net Subject: Re: CCL:AIM software In-Reply-To: <17707700!at!rosencrantz.reed.edu> Message-ID: References: <17707700!at!rosencrantz.reed.edu> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-2.5 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi Alan - the main programs for performing AIM that I'm aware of are: Bader's AIMPAC (http://www.chemistry.mcmaster.ca/aimpac/), Popelier's MORPHY (http://morphy.ch.umist.ac.uk/), Biegler-Konig's AIM2000 (http://www.aim2000.de/), Gaussian98/03 (http://www.gaussian.com) To my mind, all have their own strengths. AIMPAC has all the experience of Bader's group behind it, and is very flexible and widely used across the world. MORPHY has had a lot of effort put into making it very robust and rigorous. It is an excellent program in my opinion, and still very much supported and actively being developed. AIM2000 takes a different approach, with a very easy to use and attractive GUI - an excellent entry point to the whole method, but perhaps not as flexible or widely used as those above, and will only run under Windoze. In my experience, the Gaussian implementation is disappointing - it is very slow compared to the above, and seems to fail far too often for my liking. On the plus side, it's almost completely automatic, so when it does work it's very straightforward. It also has no graphics capability that I'm aware of, unlike all others above. Hope this is useful, Jamie ---------------------------------------------------------- Jamie Platts Dept. of Chemistry Phone: +44 (0) 2920 874950 Cardiff University Email: platts!at!cf.ac.uk P.O. Box 912 FAX: +44 (0) 2920 874030 Cardiff CF10 3TB www.cf.ac.uk/chemy On Thu, 20 Nov 2003, Alan Shusterman wrote: I am interested in obtaining software (free or commercial) to perform Atoms-in-Molecules analyses on electron density distributions and convert some of the results into graphical images. I'm using Spartan04(W2000) and Jaguar (Linux) to calculate wave functions, so I figure I'll probably have to do some file conversion to create the necessary input. Can anyone recommend Windows/Linux software that they *currently/recently* use that might be appropriate for this? By the same token, can anyone warn me about software that would be too difficult/out-of-date to use? I have just visited the Morphy98 and AIM2000 web pages, but I can't tell if these programs are still being maintained (the web pages haven't changed for a year or more!?). > > -Alan > > ==== > > Alan Shusterman > Department of Chemistry > Reed College > 3203 S.E. Woodstock Blvd. > Portland, OR 97202-8199 > 503-517-7699 > > > > -= 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 mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl!at!ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Fri Nov 21 02:58:58 2003 Received: from smtp2.ruc.dk (smtp2.ruc.dk [130.225.220.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAL7wQRW018418 for ; Fri, 21 Nov 2003 02:58:27 -0500 Received: by smtp2.ruc.dk (Postfix, from userid 504) id 9710F17A27C5; Fri, 21 Nov 2003 08:58:26 +0100 (CET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 8081C17A27C1; Fri, 21 Nov 2003 08:58:22 +0100 (CET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 21 Nov 03 08:58:22 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 21 Nov 03 08:58:12 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "Olga Dmitrenko" , chemistry!at!ccl.net Date: Fri, 21 Nov 2003 08:57:51 +0100 Subject: CCL:protonation/deprotonation at the excited state: computational evidence Reply-To: spanget!at!ruc.dk Message-ID: <3FBDD390.24849.2D90DB@localhost> Priority: normal In-reply-to: <200311191755.hAJHt8bk017956!at!copland.udel.edu> X-mailer: Pegasus Mail for Windows (v4.01) X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) X-Spam-Report: X-Spam-Status: No, hits=-1.0 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT version=2.55 X-Spam-Level: "Olga Dmitrenko" : > I would like to suggest in my paper that nitrogen atom in my molecule > (urocanic acid) becomes more basic upon excitation. Is it enough to > demonstrate that a particular atom, in my case nitrogen, has > significantly increased electron density at the excited state when > comparing HOMO and LUMO molecular orbital pictures? I did literature > search - not much outcome. Any references would be of great help - > thanks in advance. Bests, Olga Dear Olga, increased electron density on the basic nitrogen center is certainly an important indication, but it is not generally sufficient to predict increased basicity. Poor correlations have been found between calculated nitrogen electronic populations and pKa values (e.g., pyridine, pyrimidine, s- triazine [1]). These publications may be of interest to you: [1] J. Spanget-Larsen, "A Structure-Reactivity Relationship for the Basicity of Aza-arenes", J. Chem. Soc. Perkin Trans II, 417-419 (1985) [2] J. Waluk, W. Rettig, J. Spanget-Larsem, "Ground and Excited-State Protonation of Aminoquinoxalines", J. Phys. Chem. 92, 6930-6935 (1988) [3] J. Spanget-Larsen, "Structure-Reactivity Correlations for Aza-arenes. Proton Affinities, pKa Values, Hydrogen-Deuterium Exchange Rates, and Radical Induced 13C Shifts", J. Phys. Org. Chem. 8, 496-505 (1995) [4] E. Sikorska, H. Szymusiak, I.V. Khmelinskii, A. Koziolowa, J. Spanget-Larsen, M. Sikorski, "Spectroscopy and Photophysics of Alloxazines Studies in Their Ground and First Excited States", J. Photochem. Photobiol. A 158, 45-53 (2003) Good Luck, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget!at!ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@ccl.net Fri Nov 21 09:57:46 2003 Received: from helix.nih.gov (helix.nih.gov [128.231.2.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hALEvERW002635 for ; Fri, 21 Nov 2003 09:57:14 -0500 Received: from helix.nih.gov (localhost [127.0.0.1]) by helix.nih.gov (8.11.7-8.359.2.8/8.11.6) with SMTP id hALEvDO50636533; Fri, 21 Nov 2003 09:57:13 -0500 (EST) Received: from 129.43.27.155 (SquirrelMail authenticated user kmgreen) by helix.nih.gov with HTTP; Fri, 21 Nov 2003 09:57:13 -0500 (EST) Message-ID: <2221.129.43.27.155.1069426633.squirrel_at_helix.nih.gov> Date: Fri, 21 Nov 2003 09:57:13 -0500 (EST) Subject: Re: CCL:Nanotechnology course From: "Karen M. Green" To: In-Reply-To: References: X-Priority: 3 Importance: Normal Cc: Reply-To: kmgreen_at_helix.nih.gov X-Mailer: SquirrelMail (version 1.2.11) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=-2.0 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES,REPLY_WITH_QUOTES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, Tapas, You might want to go to the Institute for Nanotechnology at Northwestern University -- they offer some short courses (NSF Summer Institute for Nano Mechanics and Materials). There are links from: http://www.nanotechnology.northwestern.edu/calendar.htm to the contact information of the instructors. Karen > Hi, > We are planning to introduce Nanotechnology Courses at undergraduate and > graduate levels. > Like to know how many universities offer such courses and some > information on course materials. This will help us to develop such > course. > I appreciate your help to direct me related websites also. > Thanks, > Tapas > *********************************************** > "We owe a lot to the Indians, who taught us how to count, without > which no worthwhile scientific discovery could have been made." > - Albert Einstein - > ---------------------------------------------------------------------------- > ---- > Tapas Kar, Ph. D > Department of Chemistry & Biochemistry > Utah State University > Logan, UT 84322-0300 > > Tel: 435-797-7230 > Fax: 435-797-3390 > Email: tapaskar_at_cc.usu.edu > Web:http://www.chem.usu.edu/faculty/Tapas/index.html From chemistry-request@ccl.net Fri Nov 21 13:59:36 2003 Received: from wanderer.mr.itd.umich.edu (wanderer.mr.itd.umich.edu [141.211.93.146]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hALIx4RW012761 for ; Fri, 21 Nov 2003 13:59:05 -0500 Received: from Garfield (pcp05005614pcs.sanarb01.mi.comcast.net [68.40.225.128]) by wanderer.mr.itd.umich.edu (smtp) with ESMTP id hALIx1sN030044 for ; Fri, 21 Nov 2003 13:59:04 -0500 From: "Joslyn Kravitz" To: Subject: CCL:D orbitals in Gaussian Date: Fri, 21 Nov 2003 13:59:03 -0500 Message-ID: <001101c3b061$881f8830$80e12844@Garfield> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 In-Reply-To: <20031121141802.40469.qmail(at)web12902.mail.yahoo.com> Importance: Normal X-Spam-Status: No, hits=-0.5 required=7.0 tests=IN_REP_TO version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello, For some time I have been trying to use Gaussian to calculate the molecular orbitals for some vanadyl compounds. I want to see which atomic orbitals from the V are contributing to the homo, somo and lumo. I have obtained lovely pictures of the MO's but I want to be able to quantify the atomic orbital contributions. According to an e-mail I received from the help line at Gaussian the orbitals are numbered like this: d0 = z^2 (really 3z^2-r^2) d+1 = xz d-1 = yz d+2 = x^2 - y^2 d-2 = xy Unfortunately, since Gaussian puts the molecules into the standard orientation the atomic orbital names in the output no longer correspond to the ones you normally think of based on symmetry. That is, you would expect the dz^2 to be oriented along the V=O bond and all the others to fall in place around it, but that doesn't seem to be true. The dz^2 orbital is oriented along whatever random direction is designated the z axis in the "standard orientation" and then the other orbitals fall in around that. Unfortunately, that makes interpreting the results a little difficult, especially when different compounds are oriented differently, so that the atomic orbitals are not named consistently between compounds. I have tried using input coordinates that place the V=O bond along a z-axis and setup the equatorial plane in an appropriate way and then running a "NoSymm" calc, but that doesn't seem to help at all. Does anyone know how I can convert my calculated orbitals to more "chemically intuitive" ones, or at the very least, force Gaussian to not reorient the molecule? Thank you, Joslyn Kravitz Depart. Of Chem. University of Michigan From chemistry-request@ccl.net Fri Nov 21 15:41:27 2003 Received: from casbah.it.northwestern.edu (casbah.it.northwestern.edu [129.105.16.52]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hALKeuRW016860 for ; Fri, 21 Nov 2003 15:40:56 -0500 Received: (from mailnull@localhost) by casbah.it.northwestern.edu (8.12.10/8.12.10) id hALKeuYX002738 for ; Fri, 21 Nov 2003 14:40:56 -0600 (CST) Message-Id: <200311212040.hALKeuYX002738-.at.-casbah.it.northwestern.edu> Received: from casbah.it.northwestern.edu (localhost [127.0.0.1]) by casbah.it.northwestern.edu via smap (V2.0) id xma002321; Fri, 21 Nov 03 14:40:47 -0600 Content-Type: text/plain Content-Disposition: inline Content-Transfer-Encoding: binary X-Mailer: EMUmail 5.1 X-Originating-Ip: 12.247.24.182 Priority: 3 (Normal) X-Webmail-User: wjp207@localhost To: chemistry-.at.-ccl.net X-Priority: 3 (Normal) MIME-Version: 1.0 X-Http_host: casbah.it.northwestern.edu From: pfaendtner-.at.-northwestern.edu Subject: G98 QCISD/MP4 calculations Date: Fri, 21 Nov 2003 14:40:47 CST Reply-To: pfaendtner-.at.-northwestern.edu X-Spam-Status: No, hits=1.2 required=7.0 tests=MSG_ID_ADDED_BY_MTA_2,NO_REAL_NAME version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi all, I am trying to do several G3//B3LYP calculations with G98. I am using a Rocks cluster. All calculations are using 1 node only and 12, 2GB readwrite files on that node. The molecules are alkylbenzene radicals. On many of the calculations, probably half or greater, the system is crashing with this message at the end of the logfile: Error termination in NtrErr: NtrErr called from FIOCnC. The crashes are almost always during QCISD or MP4 calculations. I ensured I am not running out of hard-disk space so that is not the issue. I thought the issue might have been writing files if two of my jobs are launching on the same node but using different processors. I think this is not the case based on some trials I have done. I can t pinpoint the crashes to an individual node either. The crashes are seemingly random. These are my command lines for the calculations, does anyone know if I can modify them in any way that might stop the crashing? #MP4/6-31G(2df,p) geom=allcheck guess=read #QCISD(T,E4T)/6-31G(d) geom=allcheck guess=read any thoughts are most appreciated! Jim From chemistry-request@ccl.net Fri Nov 21 19:04:55 2003 Received: from webmail.mta.ca (postal.mta.ca [138.73.1.51]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAM04ORW023148 for ; Fri, 21 Nov 2003 19:04:24 -0500 Received: from nobody by webmail.mta.ca with local (Exim 4.20) id 1ANLEg-0001IA-A8 for chemistry~at~ccl.net; Fri, 21 Nov 2003 20:02:50 -0400 Received: from 156.34.176.192 ( [156.34.176.192]) as user kgdct~at~mailserv.mta.ca by webmail.mta.ca with HTTP; Fri, 21 Nov 2003 20:02:50 -0400 Message-ID: <1069459370.3fbea7aa45e9a~at~webmail.mta.ca> Date: Fri, 21 Nov 2003 20:02:50 -0400 From: Katie Doucet To: CCL Subject: Optimization aborted.-- Gradient out of range.-- Maximum allowed force = ******** MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Originating-IP: 156.34.176.192 X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) I was wondering if anyone knew what this Gaussian 98 error message means and how to solve the problem? I am running an IRC for a degradation pathway Berny optimization. Internal Forces: Max nan RMS -nan Search for a local minimum. Step number 68 out of a maximum of 100 All quantities printed in internal units (Hartrees-Bohrs-Radians) R1 R2 R3 R4 R5 -DE/DX nan nan nan nan nan R6 R7 R8 R9 R10 -DE/DX nan nan nan nan nan R11 A1 A2 A3 A4 -DE/DX nan nan nan nan nan A5 A6 A7 A8 A9 -DE/DX nan nan nan nan nan A10 A11 A12 A13 D1 -DE/DX nan nan nan nan nan D2 D3 D4 D5 D6 -DE/DX nan nan nan nan nan D7 D8 D9 -DE/DX nan nan nan Optimization aborted. -- Gradient out of range. -- Maximum allowed force = ******** Error termination via Lnk1e in /programs/g98/l103.exe. Job cpu time: 0 days 0 hours 0 minutes 59.4 seconds. File lengths (MBytes): RWF= 18 Int= 0 D2E= 0 Chk= 13 Scr= 1 thank you K.Doucet