From chemistry-request@ccl.net Mon Nov 17 16:36:17 2003 Received: from smtp3.Stanford.EDU (smtp3.Stanford.EDU [171.67.16.117]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAHLZjRW003896 for ; Mon, 17 Nov 2003 16:35:45 -0500 Received: from webmail2.Stanford.EDU (webmail2.Stanford.EDU [171.64.14.89]) by smtp3.Stanford.EDU (8.12.10/8.12.10) with ESMTP id hAHLZgOR024467; Mon, 17 Nov 2003 13:35:43 -0800 Received: (from web@localhost) by webmail2.Stanford.EDU (8.12.10/8.12.10) id hAHLZgiu002157; Mon, 17 Nov 2003 13:35:42 -0800 Received: from 171.64.125.56 ([171.64.125.56]) by webmail.stanford.edu (IMP) with HTTP for ; Mon, 17 Nov 2003 13:35:42 -0800 Message-ID: <1069104942.3fb93f2e8bc9d.-at-.webmail.stanford.edu> Date: Mon, 17 Nov 2003 13:35:42 -0800 From: "S. I. Gorelsky" To: freddie salsbury Cc: chemistry.-at-.ccl.net Subject: Partial density of states plots References: <17210524676.20031115184415.-at-.joyie.com> <3FB8DC40.2050003.-at-.wfu.edu> <3FB8DD35.6010204.-at-.wfu.edu> In-Reply-To: <3FB8DD35.6010204.-at-.wfu.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.1 X-Authenticated-User: gorelsky X-Originating-IP: 171.64.125.56 X-Spam-Status: No, hits=-2.3 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES,REPLY_WITH_QUOTES, USER_AGENT_IMP version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) You can also check the AOMix program (http://www.obbligato.com/software/NP/2003-AO.html). It creates the partial-density-of-states plots. S.G. Quoting freddie salsbury : > I sent this message with an incorrect subject, so I'm resending it. > > sorry > Fred > > Hello -- > > We are using Gaussian 03 with periodic boundary conditions to model > an > organic material. We would like to do a partial density of states > analysis, does anyone know how to obtain the necessary info from > gaussian? > > thanks > Fred Salsbury > > > > > -= 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) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > -- Department of Chemistry, Stanford University, Box 155, Mudd Bldg., 333 Campus Drive, Stanford, CA 94305-5080 U.S.A. Fax: (650)723-0553 From chemistry-request@ccl.net Mon Nov 17 16:33:16 2003 Received: from dep.chem.rug.nl (dep.chem.rug.nl [129.125.7.81]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAHLWiRW003831 for ; Mon, 17 Nov 2003 16:32:45 -0500 Received: (from uucp@localhost) by dep.chem.rug.nl (8.9.3/8.9.3/Debian 8.9.3-21) id WAA32743 for chemistry[at]ccl.net; Mon, 17 Nov 2003 22:32:44 +0100 X-Authentication-Warning: dep.chem.rug.nl: uucp set sender to spoel[at]rugmd64.chem.rug.nl using -f Received: from rugmd64.chem.rug.nl by dep.chem.rug.nl (AvMailGate-2.0.1.7) id 16610-1C36484C; Mon, 17 Nov 2003 22:32:44 +0100 Received: from localhost (spoel@localhost) by rugmd64.chem.rug.nl (SGI-8.9.3/8.9.3) with ESMTP id WAA55117 for ; Mon, 17 Nov 2003 22:31:10 +0100 (MET) Date: Mon, 17 Nov 2003 22:31:10 +0100 From: David van der Spoel To: chemistry[at]ccl.net Subject: opteron performance Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-AntiVirus: checked by AntiVir MailGate (version: 2.0.1.7; AVE: 6.22.0.1; VDF: 6.22.0.39; host: dep.chem.rug.nl) X-Spam-Status: No, hits=-1.6 required=7.0 tests=EMAIL_ATTRIBUTION,QUOTED_EMAIL_TEXT,SIGNATURE_LONG_DENSE, USER_AGENT_PINE,X_AUTH_WARNING version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) On Mon, 2003-11-17 at 19:35, pderosa-Latech wrote: > Dear all: > > Can any of you give me your opinion about AMD Opteron. They > are intended to run Gaussian 03, MD simulations, and a cellular > simulator. I believe Opteron do not have the problem associated with > 32 bit processors that cannot handle files larger than 2 GB. But how > they perform compared to Alpha?, how are they for integer > operations?. Opteron is much cheaper than alphas, thus I can take > some loss in performance, but not too much. > > I apologize if this issue was already treated in CCL, I tried > to check the CCL archives but they seem to be unavailable at this > moment. > > Thanks, Since you ask, I recently did some tests with the GROMACS MD package (http://www.gromacs.org), see below. Hi, FYI, I've done some benchmarks on our new 2 GHz Opterons. I have two dual machines which are connected directly by a Gbit ethernet cable running at full duplex. The numbers are the regular gromacs benchmarks run using grompp -shuffle -sort. For comparison results on our Dual 2.2 GHz Xeon are given as well. Results in ps/day (higher is better!) natoms Delta t 1 CPU 2 CPU 4 CPU 2Xeon Villin 9389 2 fs 9340 18180 19190 13280 LZM 23207 4 fs 2541 5080 7200 3756 LZM-PME 23207 4 fs 1600 3086 3756 1920 DPPC 121856 2 fs 185 419 702 330 Polymer 6000 2 fs 4192 7714 9394 5268 Conclusion: scaling to 2 CPUs is excellent, four CPU's is only worth it for DPPC. Furthermore the Opterons are quite a bit faster (35%) than the Xeons, this might be due in part to the larger cache (1 Mb iso 512 kb). The Opterons are more expensive than the Xeons, but their GROMACS speed at 2 GHz is roughly comparable to a 3 GHz Xeon. Preliminary tests imply that similar GROMACS performance can also be obtained on a 900 MHz Itanium. The LZM-PME result on 2 Opterons is roughly 0.12s per integration step, which compares favorably to the recently posted PMEMD and NAMD results (PMEMD at 0.43 s per integration step on 2 x 1 GHz Alpha processors). One should be careful interpreting these results however, because simulation systems and parameters were not completely identical. Obviously GROMACS scaling (with PME) is still a problem. Hope this helps... > > Pedro > -- David. ________________________________________________________________________ David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel[at]xray.bmc.uu.se spoel[at]gromacs.org http://xray.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@ccl.net Mon Nov 17 15:52:14 2003 Received: from smtp2.es.uci.edu (smtp2.es.uci.edu [128.200.80.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAHKphRW000558 for ; Mon, 17 Nov 2003 15:51:43 -0500 Received: from 128.200.204.154 (dhcp-204154.bio.uci.edu [128.200.204.154]) by smtp2.es.uci.edu (8.12.8/8.12.8) with ESMTP id hAHKpdol014786 for ; Mon, 17 Nov 2003 12:51:39 -0800 Date: Mon, 17 Nov 2003 13:50:37 -0800 From: John Lee X-Mailer: The Bat! (v1.62r) Reply-To: John Lee X-Priority: 3 (Normal) Message-ID: <1923790408.20031117135037[at]joyie.com> To: chemistry[at]ccl.net Subject: scaling factor for B3LYP/6-311++G** MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-UCIRVINE-MailScanner: No viruses found X-Spam-Status: No, hits=0.7 required=7.0 tests=FROM_ENDS_IN_NUMS version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi CCLers, Does anybody knows the scaling factor for B3LYP/6-311++G**, especially when calculating water cluster using G03? Thanks. -- Best regards, John From chemistry-request@ccl.net Mon Nov 17 15:41:56 2003 Received: from smtp.goldrush.com (smtp.goldrush.com [206.171.171.11]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAHKfORW032174 for ; Mon, 17 Nov 2003 15:41:24 -0500 Received: from goldrush.com (x2-04b-20.goldrush.com [64.162.11.20]) by smtp.goldrush.com (8.12.8/8.12.8) with ESMTP id hAHKfJ6w011228 for ; Mon, 17 Nov 2003 12:41:19 -0800 Date: Mon, 17 Nov 2003 12:40:26 -0800 Mime-Version: 1.0 (Apple Message framework v551) Content-Type: text/plain; delsp=yes; charset=US-ASCII; format=flowed Subject: CCL:How to calculate the Verloop STERIMOL parameters? From: Stephen Bowlus To: chemistry~at~ccl.net Content-Transfer-Encoding: 7bit Message-Id: <46077D56-193E-11D8-A88F-000393D4953A~at~goldrush.com> X-Mailer: Apple Mail (2.551) X-MailScanner: Found to be clean X-MailScanner-SpamCheck: not spam (whitelisted), SpamAssassin (score=-4.9, required 4.2, BAYES_00 -4.90) X-Spam-Status: No, hits=-0.5 required=7.0 tests=QUOTED_EMAIL_TEXT,USER_AGENT_APPLEMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) > I made a conversion of the STERIMOL program to PC from the original > VAX version. The program is officially and rapidly available from > QCPE ... or you can wait while I grub around through my files and find > my copy. The advantage of the QCPE copy is that you get all the > documentation. > > Cheers, > Steve > > > On Sunday, November 16, 2003, at 12:32 AM, Jinsong Zhao wrote: > >> Dear all, >> >> I wonder whether there is an free routine or program >> that could be used to calculate the Verloop STERIMOL >> parameters. >> >> Thanks in advance! >> >> Best wishes, >> >> Jinsong >> >> __________________________________________________ >> Do You Yahoo!? >> Tired of spam? Yahoo! Mail has the best spam protection around >> http://mail.yahoo.com >> >> >> -= 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 Tue Nov 18 05:47:20 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 hAIAkmRW008991 for >ccl.net>; Tue, 18 Nov 2003 05:46:48 -0500 Received: by smtp2.ruc.dk (Postfix, from userid 504) id 4636A173F1BE; Tue, 18 Nov 2003 11:46:47 +0100 (CET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id C5F48173F1B4; Tue, 18 Nov 2003 11:46:43 +0100 (CET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 18 Nov 03 11:46:43 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 18 Nov 03 11:46:34 +0100 From: "Jens Spanget-Larsen" >virgil.ruc.dk> Organization: Roskilde Universitetscenter To: John Lee >joyie.com> Date: Tue, 18 Nov 2003 11:46:29 +0100 Subject: Re: CCL:scaling factor for B3LYP/6-311++G** Reply-To: spanget<>ruc.dk Cc: chemistry<>ccl.net Message-ID: <3FBA0698.1693.152A2077@localhost> Priority: normal In-reply-to: <1923790408.20031117135037<>joyie.com> 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-Status: No, hits=-0.6 required=7.0 tests=IN_REP_TO,MAILTO_TO_SPAM_ADDR,QUOTED_EMAIL_TEXT version=2.55 John Lee >joyie.com>: > Does anybody knows the scaling factor for B3LYP/6-311++G**, > especially when calculating water cluster using G03? Thanks. Do you mean the scaling factor that converts computed harmonic wavenumbers into 'experimental scale'? - The factor alpha = 0.98 was found for B3LYP/6-311++G** in calculations on malonaldehyde enol: J. Spanget-Larsen, Chem. Phys. 240, 51-61 (1999) Yours, 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<>ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@ccl.net Tue Nov 18 14:09:06 2003 Received: from cornell.edu (cornell.edu [132.236.56.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAIJ8YRW028168 for ; Tue, 18 Nov 2003 14:08:35 -0500 Received: from cornell.edu (fili.ccmr.cornell.edu [128.84.241.145]) by cornell.edu (8.9.3p2/8.9.3) with ESMTP id OAA13629 for ; Tue, 18 Nov 2003 14:08:34 -0500 (EST) Message-ID: <3FBA6E32.3050804~at~cornell.edu> Date: Tue, 18 Nov 2003 14:08:34 -0500 From: Connie Chang User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4) Gecko/20030703 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry~at~ccl.net Subject: CCL: G03 and negative frequencies Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.6 required=7.0 tests=FROM_ENDS_IN_NUMS,USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi -- I just had a job finish and it ended up giving me all negative frequencies. My job is with PM3. I have several questions: 1) Is there a way to tell if a job will give negative frequencies before it completes? This job took 5 full days, so it would be nice to know a little more beforehand that a job will yield negative frequencies 2) I know that negative frequencies usually means that I'm not at a minimum but rather am at a saddle point. But I optimized first using PM3 and then did a freq calculation. Are there other things I can do to ensure that I am at a true minimum and not a saddle point before proceeding? 3) Other suggestions? Thanks, Connie From chemistry-request@ccl.net Tue Nov 18 13:40:52 2003 Received: from copland.udel.edu (copland.udel.edu [128.175.13.92]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAIIeKRW027706 for ; Tue, 18 Nov 2003 13:40:21 -0500 Received: from [128.175.138.90] ([128.175.138.90]) by copland.udel.edu (8.12.10/8.12.10) with ESMTP id hAIIeJbk026782 for ; Tue, 18 Nov 2003 13:40:19 -0500 (EST) Message-Id: <200311181840.hAIIeJbk026782{at}copland.udel.edu> X-Mailer: Microsoft Outlook Express Macintosh Edition - 4.5 (0410) Date: Tue, 18 Nov 2003 13:32:56 -0500 Subject: Re:imaginary frequencies in cycloaddition's TS From: "Olga Dmitrenko" To: chemistry{at}ccl.net Mime-version: 1.0 X-Priority: 3 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-Spam-Score: 0.9 DEAR_SOMEBODY,SPAM_PHRASE_00_01 X-Scanned-By: MIMEDefang 2.37 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) Dear Alessandro, What do you mean by syncronous or asyncronous exactly? Anyway, we started to use imaginary freq vibration visualization pictures in our publications to demonstrate the degree of hidrogen transfer involvement during OH or oxygen transfer reactions. You may have a look at our recent paper: Electronic Requirements for Oxygen Atom Transfer from Alkyl Hydroperoxides. Model Studies on Multisubstrate Flavin-Containing Monooxygenases Bach, R. D.; Dmitrenko, O.; J. Phys. Chem. B. ; (Article); 2003; 107(46); 12851-12861. See figures 4 and 5 there. Best regards, Olga >Hi, >This could be a naive question, but I'd like to ask if is it possible to >state if a cycloaddition reaction proceeds by a syncronous or asyncronous >mechanism by visual inspection of the TS' imaginary frequency. >Any suggestion or litt. ref. will be appreciated. >Thanks a lot >Alessandro From chemistry-request@ccl.net Tue Nov 18 13:13:26 2003 Received: from mail1.engr.sc.edu (mail1.engr.sc.edu [129.252.21.14]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAIICtRW027030 for ; Tue, 18 Nov 2003 13:12:55 -0500 Received: from yayay ([129.252.22.24]) by mail1.engr.sc.edu with Microsoft SMTPSVC(5.0.2195.6713); Tue, 18 Nov 2003 13:12:54 -0500 Message-ID: <019501c3adff$9645d310$1816fc81@yayay> From: "Liuming Yan" To: References: <3FBA0698.1693.152A2077@localhost> Subject: Textbook of Fortan 95! Date: Tue, 18 Nov 2003 13:12:54 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-OriginalArrivalTime: 18 Nov 2003 18:12:54.0798 (UTC) FILETIME=[96651AE0:01C3ADFF] X-Spam-Status: No, hits=-0.5 required=7.0 tests=REFERENCES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear all, I want to find a textbook for Fortran 95 (if there is PPT edition, it is much better). This course is for the science and engineering students with a goal of numerical calculation. Thanks ********************************************* Dr. Liuming Yan Electrical Engineering Department University of South Carolina Columbia, SC29208 Phone: 803-777-0392 e-mail: yanli:at:engr.sc.edu From chemistry-request@ccl.net Tue Nov 18 07:49:52 2003 Received: from web20208.mail.yahoo.com (web20208.mail.yahoo.com [216.136.226.63]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hAICnLRW014017 for ; Tue, 18 Nov 2003 07:49:21 -0500 Message-ID: <20031118124920.45101.qmail$at$web20208.mail.yahoo.com> Received: from [212.98.201.1] by web20208.mail.yahoo.com via HTTP; Tue, 18 Nov 2003 04:49:20 PST Date: Tue, 18 Nov 2003 04:49:20 -0800 (PST) From: Hatice Can Subject: Free Fortran code for Radial Distribution Function To: chemistry$at$ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=0.7 required=7.0 tests=FROM_ENDS_IN_NUMS version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear All, If someone sent to me free Fortran code or the webpage for calculating the radial distribution function, I would be so appriciated. Kind regrads and many thanks, H.Can __________________________________ Do you Yahoo!? Protect your identity with Yahoo! Mail AddressGuard http://antispam.yahoo.com/whatsnewfree From chemistry-request@ccl.net Tue Nov 18 02:55:24 2003 Received: from sungod.ccs.yorku.ca (sungod.ccs.yorku.ca [130.63.236.104]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAI7srRW032458 for ; Tue, 18 Nov 2003 02:54:53 -0500 Received: from curl.gkcl.yorku.ca (curl.gkcl.yorku.ca [130.63.232.224]) by sungod.ccs.yorku.ca (8.12.10/8.12.8) with ESMTP id hAI7sqYU000121 for ; Tue, 18 Nov 2003 02:54:52 -0500 (EST) Received: (from chan@localhost) by curl.gkcl.yorku.ca (8.10.0/8.10.0) id hAI7nlJ04635 for chemistry*at*ccl.net; Tue, 18 Nov 2003 02:49:47 -0500 (EST) From: Wai-To Chan Message-Id: <200311180749.hAI7nlJ04635*at*curl.gkcl.yorku.ca> Subject: imaginary frequencies in cycloaddition's TS To: chemistry*at*ccl.net Date: Tue, 18 Nov 2003 02:49:47 -0500 (EST) X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit 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) In the case of the reaction of ozone + ethene/propene which I've studied the structural difference between the TSs for the concerted cycloaddition and the stepwise pathway is so obvious that not even a visualization of their imaginary vibrations are required. It could be easier if you differentiate the two TS structures in terms of their activation entropies. The looser structure of the asyncronous-path TS implicates a higher entropy than the syncronous TS which is expected to have a more compact ring-like structure for cycloaddition. The magnitude of the Arrhenius factor of the asyncronus pathway is likely to be significantly greater than that of the syncronous pathway. In fact the A-factor is one important quantity for the experimentalists to deduce qualitatively the structure of a TS. In case this is of interest this paper "Mechanisms for the ozonolysis of ethene and propene: Reliability of quantum chemical predictions", J. Chem. Phys., 118, 1688-1701 (2003) reports a comparison between theoretically calculated A-factors for the concerted and stepwise pathway of the ozone+alkene reactions and experimental values. Both calculated A-factors and imaginary frequencies for the asyncronous TSs are greater. Wai-To Chan <<<<<<<<<<<<<<<<<<<<<< Hi, This could be a naive question, but I'd like to ask if is it possible to state if a cycloaddition reaction proceeds by a syncronous or asyncronous mechanism by visual inspection of the TS' imaginary frequency. Any suggestion or litt. ref. will be appreciated. Thanks a lot Alessandro >>>>>>>>>>>>>>>>>>>>>>>>>>.. From chemistry-request@ccl.net Tue Nov 18 15:03:04 2003 Received: from hellmouth3.gatech.edu (hellmouth3.gatech.edu [130.207.165.163]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAIK2XRW030710 for ; Tue, 18 Nov 2003 15:02:33 -0500 Received: from hellmouth3.gatech.edu (localhost [127.0.0.1]) by hellmouth3.gatech.edu (Postfix) with SMTP id 1783C221169 for ; Tue, 18 Nov 2003 15:02:33 -0500 (EST) (envelope-from ok16=at=mail.gatech.edu) Received: from acmex.gatech.edu (acmex.prism.gatech.edu [130.207.171.14]) by hellmouth3.gatech.edu (Postfix) with ESMTP id 8612522117A for ; Tue, 18 Nov 2003 15:01:02 -0500 (EST) (envelope-from ok16=at=mail.gatech.edu) Received: by acmex.gatech.edu (Postfix, from userid 11564) id 4AA661DFAC; Tue, 18 Nov 2003 15:01:02 -0500 (EST) Received: from localhost (localhost [127.0.0.1]) by acmex.gatech.edu (Postfix) with ESMTP id 2C01D1F17D for ; Tue, 18 Nov 2003 15:01:02 -0500 (EST) (envelope-from ok16=at=mail.gatech.edu) Date: Tue, 18 Nov 2003 15:01:01 -0500 (EST) From: Ohyun Kwon X-X-Sender: Reply-To: Tommy Ohyun Kwon To: Subject: energy decomposition method Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.7 required=7.0 tests=FROM_ENDS_IN_NUMS,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCLers; Would you please give me some information about energy decomposition method and QM softwares for the energy decomposition analysis? Thank you very much for your kind attention. Yours, Tommy Ohyun Kwon, Ph.D School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta Georgia, 30332 Email: ohyun.kwon=at=chemistry.gatech.edu From chemistry-request@ccl.net Tue Nov 18 16:39:41 2003 Received: from ms1.usu.edu (ms1.usu.edu [129.123.104.11]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAILdARW001297 for ; Tue, 18 Nov 2003 16:39:10 -0500 Received: from pc3 (pc3.chem.usu.edu [129.123.3.37]) by ms1.usu.edu (8.12.8/8.12.8) with SMTP id hAIKq0Fr031032; Tue, 18 Nov 2003 13:52:00 -0700 Reply-To: From: "Tapas Kar" To: "Ohyun Kwon" , Subject: RE: energy decomposition method Date: Tue, 18 Nov 2003 13:47:54 -0700 Message-ID: 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 IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal In-reply-to: X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-USU-MailScanner-Information: Please contact the USU HelpDesk for more information (http://helpdesk.usu.edu) X-USU-MailScanner: Found to be clean X-USU-MailScanner-SpamCheck: not spam (whitelisted), SpamAssassin (score=0, required 5) X-Spam-Status: No, hits=-1.4 required=7.0 tests=IN_REP_TO,MSGID_GOOD_EXCHANGE,ORIGINAL_MESSAGE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, One such possibility is Gamess(USA) for Morokuma energy decomposition scheme. Thanks, Tapas -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request(at)ccl.net]On Behalf Of Ohyun Kwon Sent: Tuesday, November 18, 2003 1:01 PM To: chemistry(at)ccl.net Subject: CCL:energy decomposition method Dear CCLers; Would you please give me some information about energy decomposition method and QM softwares for the energy decomposition analysis? Thank you very much for your kind attention. Yours, Tommy Ohyun Kwon, Ph.D School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta Georgia, 30332 Email: ohyun.kwon(at)chemistry.gatech.edu -= 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 Tue Nov 18 16:43:59 2003 Received: from col-msxproto2.col.missouri.edu (col-msxproto2.col.missouri.edu [128.206.3.152]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAILhSRW001450 for ; Tue, 18 Nov 2003 16:43:28 -0500 Received: from mizzou.edu ([128.206.124.129]) by col-msxproto2.col.missouri.edu over TLS secured channel with Microsoft SMTPSVC(5.0.2195.6673); Tue, 18 Nov 2003 15:43:26 -0600 Message-ID: <3FBA929F.4090402(at)mizzou.edu> Disposition-Notification-To: Lorant Janosi Date: Tue, 18 Nov 2003 15:43:59 -0600 From: Lorant Janosi User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en, ro, hu MIME-Version: 1.0 To: Computational Chemistry List Subject: ZINDO method related questions Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-OriginalArrivalTime: 18 Nov 2003 21:43:26.0144 (UTC) FILETIME=[FF438C00:01C3AE1C] X-Spam-Status: No, hits=-0.1 required=7.0 tests=USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Using g98 revision A11: I used ZINDO method to compute the excited states for a chlorophyll molecule. Everything worked just fine. But when I included point charges around it, everything went totally wrong. No SCF convergence or, if I removed some of the point charges, there was an SCF convergence but the excited levels were completely wrong and unreal. My questions are: 1) Why is this happening? 2) How can it be fixed? (using ZINDO of course) 3) How is the Hamiltonian computed when point charges are included? 4) Why is ZINDO so sensitive (even to symmetry)? Using g03: All results computed with ZINDO for the chlorophyll molecule are exactly the same with or without point charges included. It's like they are completely ignored by g03. My questions are: 1) Can anyone explain that to me? 2) Why is this happening? 3) Is it possible at all to use ZINDO and include point charges in the system? Thank you. Lori.