From chemistry-request@server.ccl.net Thu May 11 01:21:55 2000 Received: from nmr-v.ioc.ac.ru (root@nmr-v.ioc.ac.ru [193.233.3.213]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA16991 for ; Thu, 11 May 2000 01:21:54 -0400 Received: from cacr.ioc.ac.ru (val@localhost [127.0.0.1]) by nmr-v.ioc.ac.ru (8.9.3/8.9.3) with ESMTP id JAA02446 for ; Thu, 11 May 2000 09:21:17 +0400 Sender: val@nmr-v.ioc.ac.ru Message-ID: <391A434D.E96E4DF1@cacr.ioc.ac.ru> Date: Thu, 11 May 2000 09:21:17 +0400 From: Valentine Ananikov Reply-To: val@cacr.ioc.ac.ru Organization: IOC X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.13 i686) X-Accept-Language: ru, en MIME-Version: 1.0 To: CCL_post Subject: 1,3,5-cyclohexatriene Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Dear List Members, Does anybody have an information about predicted structure and stability for 1,3,5-cyclohexatriene? I mean a six-membered ring with alternating single and double C-C bonds, but without aromatic pi-electrons delocalization due to non-planar conformation (i.e. non-planar benzene isomer). Would such structure exist in principle? Thanks! Valentin. ==================================================================== , , , , Valentine 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@server.ccl.net Wed May 10 13:17:45 2000 Received: from nic.upatras.gr (nic.upatras.gr [150.140.129.30]) by server.ccl.net (8.8.7/8.8.7) with SMTP id NAA13777 for ; Wed, 10 May 2000 13:17:43 -0400 Received: (qmail 25469 invoked from network); 10 May 2000 17:16:23 -0000 Received: from pythagoras.physics.upatras.gr (150.140.159.71) by nic.upatras.gr with SMTP; 10 May 2000 17:16:23 -0000 Received: (qmail 21726 invoked by uid 1098); 10 May 2000 17:20:26 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 10 May 2000 17:20:26 -0000 Date: Wed, 10 May 2000 20:20:26 +0300 (EEST) From: Xrhstos Garoufalhs To: CHEMISTRY@ccl.net Subject: energy of initial guess Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers How can I force G94 to print out the total energy when I use the option GUESS=(READ,ONLY). In other words I want the energy of the initial guess Thanks in advance From chemistry-request@server.ccl.net Thu May 11 02:46:20 2000 Received: from hotmail.com (oe34.law3.hotmail.com [209.185.240.202]) by server.ccl.net (8.8.7/8.8.7) with SMTP id CAA17557 for ; Thu, 11 May 2000 02:46:20 -0400 Received: (qmail 67873 invoked by uid 65534); 11 May 2000 06:44:10 -0000 Message-ID: <20000511064410.67871.qmail@hotmail.com> X-Originating-IP: [161.142.78.83] From: "Yeoh Hak Koon" To: "CCL" Subject: Frontier orbital vs. reactivity Date: Thu, 11 May 2000 14:38:21 +0800 Dear Colleagues, Due to resource constraints, I could only get some old literature about Fukui's frontier orbital theory in predicting chemical reactivity. (He won the 1981 Nobel prize for this work, but that was 19 years ago.) My questions : (a) Is his theory still valid, i.e. not overtaken by another better theory? (b) What improvements had gone into the treatment of superdelocalizability? (c) Has this theory been successful in more complicated molecules like metal complex catalysts? Any help or reference is much appreciated. Thank you. Best regards, H. K. Yeoh (Mr.) 11 May 2000 From chemistry-request@server.ccl.net Thu May 11 09:06:22 2000 Received: from Kitten.mcs.net (Kitten.mcs.com [192.160.127.90]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA20163 for ; Thu, 11 May 2000 09:06:22 -0400 Received: from oemcomputer (P48-Chi-Dial-1.pool.mcs.net [205.253.224.48]) by Kitten.mcs.net (8.9.3/8.9.3) with SMTP id IAA09081; Thu, 11 May 2000 08:05:41 -0500 (CDT) (envelope-from rone@mcs.net) Message-ID: <003001bfbb48$a0d33960$30e0fdcd@oemcomputer> From: "Rebecca Rone" To: "Giulio Vistoli" , "CCL" Subject: Re: CCL:CHARMM .ENE file Date: Thu, 11 May 2000 07:58:38 -0500 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 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Dear Giulio, I believe that Quanta has a option whereby you can skip records. Since you wanted every 1000 steps recorded and got every 300 steps instead, you might want to try to tell QUANTA to read every 4th record or every 1200 steps. I don't know which menu item to point you to as I no longer have a copy of QUANTA or a manual, but if you look in the manual index for dynamics, playback, step, or record you should find it. Good luck. Becky Rone Dr. Rebecca Rone Rone Biotechnology Consulting -----Original Message----- From: Giulio Vistoli To: CCL Date: Wednesday, May 10, 2000 4:47 AM Subject: CCL:CHARMM .ENE file >Dear CClers, >I performed a molecular dynamic with Quanta/CHARMM using the following >parameters: > >Total number of steps: 4.000.000 (4 ns) >Time step: 1 fs >Temperature: 300 K >Frame stored every 1000 step (1 ps) > >Opening the resulting .ENE file, I found that energy refresh is every 300 >steps instead of 1000. Analyzing the dynamics with Qunata, I'm afraid it >could read only the first 4.000 records and indeed the Quanta textport shows >the following warning message: >"Energy file read is being truncated ..." >This problem was shown using both the Quanta graphical interface and the >CHARMM script language. >It's all right ? >Thank you for your attention. > > > Giulio Vistoli > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Thu May 11 10:19:10 2000 Received: from chazin.structbio.vanderbilt.edu (root@chazin.structbio.Vanderbilt.Edu [160.129.248.64]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA20499 for ; Thu, 11 May 2000 10:19:10 -0400 Received: from structbio.vanderbilt.edu (IDENT:jsmith@chazin [160.129.248.64]) by chazin.structbio.vanderbilt.edu (8.9.3/8.9.3) with ESMTP id JAA25892; Thu, 11 May 2000 09:26:38 -0500 Sender: jsmith@chazin.structbio.vanderbilt.edu Message-ID: <391AC31E.512FD9CE@structbio.vanderbilt.edu> Date: Thu, 11 May 2000 09:26:38 -0500 From: Jarrod Smith Organization: Vanderbilt University X-Mailer: Mozilla 4.6 [en] (X11; I; Linux 2.2.5-22 i686) X-Accept-Language: en MIME-Version: 1.0 To: Fenglou Mao CC: CHEMISTRY@server.ccl.net Subject: Re: CCL:Superpose algrithm? References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Fenglou Mao wrote: > > Hi, all, > Who introduce some superpose algrithm or some > reference? Here's one: Kearsley, Simon K; "An Algorithm for the Simultaneous Superposition of a Structural Series"; J. Comp. Chem., 11, 1187-1192 (1990). -- Jarrod A. Smith, Ph.D. Assistant Director, Center for Structural Biology Molecular Graphics and Computation Vanderbilt University jsmith@structbio.vanderbilt.edu From chemistry-request@server.ccl.net Thu May 11 12:35:33 2000 Received: from zeta.qmw.ac.uk (zeta.qmw.ac.uk [138.37.6.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA21167 for ; Thu, 11 May 2000 12:35:32 -0400 Received: from alpha.qmw.ac.uk ([138.37.6.1]) by zeta.qmw.ac.uk with esmtp (Exim 3.02 #1) id 12pvvh-0003T6-00 for chemistry@ccl.net; Thu, 11 May 2000 17:35:17 +0100 Received: from mendelevium.chem.qmw.ac.uk ([138.37.52.101] helo=mendelevium) by alpha.qmw.ac.uk with smtp (Exim 3.12 #1) id 12pvvi-0002E5-00 for chemistry@ccl.net; Thu, 11 May 2000 17:35:18 +0100 Message-Id: <3.0.6.32.20000511173827.0087f5f0@alpha.qmw.ac.uk> X-Sender: ugca921@alpha.qmw.ac.uk X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Thu, 11 May 2000 17:38:27 +0100 To: chemistry@ccl.net From: Romano Kroemer Subject: Search in Cambridge Crystallographic Database Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear all, Given the three-dimensional description of a pharmacophore (e.g. xyz coordinates of some atoms or functional groups, or some kind of vector representation thereof), are there any programs that can be used to search for such a pharmacophore in the Cambridge Crystallographic Database? Thank you very much for your help. I'll summarise. Best regards, Romano Kroemer ============================================================================ Dr. Romano T. Kroemer Department of Chemistry Queen Mary & Westfield College University of London | Tel.: ++44-(0)20-7882 3265 Mile End Road | Fax: ++44-(0)20-7882 7794 London E1 4NS, UK | Email: R.T.Kroemer@qmw.ac.uk ============================================================================ From chemistry-request@server.ccl.net Thu May 11 13:26:03 2000 Received: from qtp.ufl.edu (zwart.qtp.ufl.edu [128.227.89.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA21544 for ; Thu, 11 May 2000 13:26:02 -0400 Received: from pc1 (pc1 [128.227.192.187]) by qtp.ufl.edu (8.9.1a/8.9.1) with SMTP id NAA11862; Thu, 11 May 2000 13:25:51 -0400 (EDT) Message-ID: <036301bfbb6e$28122e20$bbc0e380@qtp.ufl.edu> From: "Stefan Fau" To: "Xrhstos Garoufalhs" Cc: References: Subject: Re: CCL:energy of initial guess Date: Thu, 11 May 2000 13:27:17 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi Xrhstos, you can use guess=read and scf(maxcyc=1) together with #p. This would read your guess and perform a single scf cycle with that density. In that way you get the SCF energy of your guess and a new trial wavefunction/density. #p increases the detail of your output, including SCF energies every cycle. It might be a good idea to make a copy of the file containing your guess before feeding it to Gaussian. Stefan ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu Quantum Theory Project | (352) 392-6714 University of Florida Gainesville, FL 32611-8435 From chemistry-request@server.ccl.net Thu May 11 14:37:55 2000 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.18.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA21891 for ; Thu, 11 May 2000 14:37:55 -0400 Received: from syr.edu (syru33-243.syr.edu [128.230.33.243]) by mailbox.syr.edu (8.9.2/8.9.2) with ESMTP id OAA29155 for ; Thu, 11 May 2000 14:37:52 -0400 (EDT) Message-ID: <391AFF87.CF657060@syr.edu> Date: Thu, 11 May 2000 14:44:23 -0400 From: Damian Allis Reply-To: dgallis@syr.edu X-Mailer: Mozilla 4.7 (Macintosh; I; PPC) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: CI Calculations on Charged Molecules Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Greetings, all! I as hoping someone could point me to a good reference on dealing with CI calculations on charged molecules. I'm currently using the ZINDO engine in CAChe, and end up with molecules with ground state dipole moments of zero (and I know these systems have them), and non-zero x,y,z dipole vectors for the excited states. Having already worked through a previous discussion on CCL concerning the dipole moments of charged molecules, I'm trying to figure out how to deal with the next step, namely, using the CI output with whatever dipole moment I calculate by hand for the ground state. Would the resulting excited state dipole moments I'm getting simply be the difference between the ground state dipole moments with an origin yielding 0 Debye and the actual excited state dipole moments calculated with this same origin? I'm trying to develop first hyperpolarizability values for these systems using the two-state approximation, and would like to have more to go on than fitting my results to ab initio values and, using the energies and oscillator strengths I calculate, finding out where ZINDO might have put the origin of the molecule! thanks in advance, Damian Allis ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Home Address: | Chemistry Address: 349 Buckingham Ave. | 2-023 Center for Sci&Tech Syracuse, NY 13210 | Syracuse University email: dgallis@syr.edu | Syracuse, NY 13244 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#8^(= -)*-+-< everything about me: web.syr.edu/~dgallis/ Nanoworks, Inc.: www.nanoworksinc.com/ CSIR: www.csir.org/ Cornucopia Music: www.cornucopiamusic.com/