From chemistry-request@ccl.net Wed Aug 13 12:06:07 2003 Received: from mx3.trentu.ca (mx3.trentu.ca [192.75.12.4]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h7DG6798002890 for ; Wed, 13 Aug 2003 12:06:07 -0400 Received: (qmail 19287 invoked by uid 504); 13 Aug 2003 16:06:21 -0000 Received: from elewars)at(trentu.ca by mx3.trentu.ca by uid 501 with qmail-scanner-1.16 ( Clear:. Processed in 0.078811 secs); 13 Aug 2003 16:06:21 -0000 X-Qmail-Scanner-Mail-From: elewars)at(trentu.ca via mx3.trentu.ca X-Qmail-Scanner: 1.16 (Clear:. Processed in 0.078811 secs) Received: from unknown (HELO trentu.ca) (209.42.101.30) by mx3.trentu.ca with SMTP; 13 Aug 2003 16:06:21 -0000 Message-ID: <3F3A62B9.F354A7C)at(trentu.ca> Date: Wed, 13 Aug 2003 12:09:32 -0400 From: elewars X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: wangyan , chemistry)at(ccl.net Subject: Re: CCL:the meanings of the magnitude of the imaginary frequency? References: <200308130806.h7D86Fl04530)at(smtp.dicp.ac.cn> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit 2003 August 13 Hello, Re "...any meaning for the magnitude of the imaginary frequency at the transition state." The magnitude of a frequency is an indication of the curvature of the PES along the direction corresponding to the normal-mode vibration for the freq. If the curvature is strong, you can expect a large freq, if it is gentle (PES along that direcvtion almost flat) you can expect a low freq. The imag. freq. corresponds to the curvature in the transition state region along the reaction coordinate. In the reaction A--> TS -->B, a low A --> B barrier tends to correspond to a small curvature along the reaction coord. in the region of the TS, and so the imag. freq. will be likely to be small. Conversely, a big A --> B barrier tends to correspond to a large reaction coord. curvature near the TS, and to a large imag. freq. But since vibrational freqs. are the *mass-weighted* eigenvalues of the force constant matrix (second deriv. matrix, "curvature matrix") the masses of the atoms involved in the vibration also affect the freqs. A freq. (imaginary or otherwise) corresponding to movement of an H atom will be bigger than almost any other freq. (look at the equation for a simple harmonic oscillator). You could do a few calculations on TSs for reactions of known activation E to check out the truth of the above. People sometimes try to judge the stability of a potentially kinetically unstable molecule (with no imaginary freqs) from the value of the lowest-frequency vibration corresponding to a decomposition mode. In a very rough way (i.e. other things being about equal) a lower imag. freq probably corresponds to a smaller barrier. Thus the B3LYP/6-31G* freq for cyclic-C6H6--> 3 HCCH is 617i cm-1, while that for cyclic-N6 --> 3N2 is 323i cm-1 (barriers ca. 740 and 1 kJ mol-1). E. Lewars =========== wangyan wrote: > Dear ccler, > > I want to know whether there is any meanings for the > magnitude of the imaginary frequency at the transition > state. It is well known that the more the stretching > frequency of the zeolitec OH group, the stronger the > O-H bond. Is it still suitable for the imaginary > frequency ? Does it mean that the transition state > which have higher imaginary frequency is more stable > than that which have low imaginary frequency ? > > any information is welcome. thanks in advance. > > best regards > > wangyan > > !!!!!!!!!!!!!!!!wangyan > !!!!!!!!!!!!!!!!wangyanemail)at(dicp.ac.cn > !!!!!!!!!!!!!!!!!!!!2003-08-13 > > -= This is automatically added to each message by 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 Wed Aug 13 10:29:27 2003 Received: from mail.cybermesa.com (mail.cybermesa.com [198.59.109.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7DETR98032127 for ; Wed, 13 Aug 2003 10:29:27 -0400 Received: from dave (qwest45-dsl3.cybermesa.com [216.84.163.45]) by mail.cybermesa.com (8.11.6/8.11.6) with SMTP id h7DETZ727940 for ; Wed, 13 Aug 2003 08:29:35 -0600 (MDT) From: "David Miller" To: Subject: ChemTK Freeware issues Date: Wed, 13 Aug 2003 08:31:15 -0600 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" 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 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 Two issues have arisen with regard to the just-released ChemTK Lite freeware package: 1. Installation. If the InstallShield wizard complains about a lack of required permissions, users may now download the executable file and all data files directly from: http://www.sageinformatics.com/lite/install_files/install2.html 2. SD file format. A user has noticed that SD files having a particular type of line ending could not be opened by the application. This problem has been fixed, and the patched version is now available for download on the website. Best Regards, David W. Miller, Ph.D. Sage Informatics LLC dmiller)at(sageinformatics.com From chemistry-request@ccl.net Thu Aug 14 09:39:00 2003 Received: from mail.interware.hu ([195.70.32.156]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7EDcx98032182 for ; Thu, 14 Aug 2003 09:38:59 -0400 Received: from caracas-0373.adsl.interware.hu ([213.178.101.117] helo=cthulhu) by mail.interware.hu with smtp (Exim 4.20 #1 (Debian)) id 19nIJu-0005kn-Rz for ; Thu, 14 Aug 2003 15:39:14 +0200 Message-ID: <000501c36271$e02b81c0$0200a8c0@cthulhu> From: "Tamas E. Gunda" To: References: <000401c360db$911c2130$402b258a@Ruzhen> <3F3944E4.477DFA21..at..cornell.edu> Subject: Re: CCL:question about BABEL + autoexec.bat Date: Wed, 13 Aug 2003 18:08:25 +0100 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 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 It must be. But under WinXP it is usually already only a null file. You should add a new entry to the PATH variable by editing it in My Computer/Properties....Environment variables tab (this will be permanent) or after opening a command window, by entering path=%path%;c:\fii\foo\babel or whatever (this will be temporal). Regards Tamas E. Gunda tamasgunda..at..tigris.klte.hu ----- Original Message ----- From: "Dr. Richard L. Wood" To: "Ru-Zhen Li" Cc: Sent: Tuesday, August 12, 2003 20:50 PM Subject: CCL:question about BABEL > Hi all > > Shouldn't the autoexec.bat file be in the root directory of the c:\ > drive? Mine is. > > Richard > > Ru-Zhen Li wrote: > > > [Image] > > Dear all Thank you for all the kind people reply to me, and now, I > > have done it again from the very beginning, the problem still > > exist. 1)I downloaded the babel106.zip from > > ftp://www.ccl.net/pub/chemistry/software/UNIX/babel/ 2)I unziped it > > and copied the BABEL.EXEL, ELEMENT.LIS, TYPES.LIS to C:\BABEL 3)I add > > the SET BABEL_DIR=C:\BABEL to the AUTEXEC.BAT file which is in > > C:\Documents and Settings\ezw079.MATDOM\My Documents\My Received > > Files\winxpbootdisk\winxpbootdisk\HPWinXPbootdisk\WindowsXP&(&;+&\ 4)I > > copied the 1N5U.pdb into C:\BABEL 5)and then I entered the C:\BABEL > > under dos typed babel -ip 1N5U.pdb -ocache output.csf nothing > > happened, no error, no warning, no output file. and I tried the Open > > Babel, but seems that it is under UNIX, not DOS or Windows Thank you > > in > > advance! regards,Ru-Zhen ********************************************************************** > > > > Ms Ru-Zhen Li 0044-020-78826327 > > r.li..at..qmul.ac.uk > > Materials Department > > Queen Mary > > University of London > > E1 4NS > > -- > Richard L. Wood, Ph. D. > Physical/Computational Chemist > > > > -= This is automatically added to each message by 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 Thu Aug 14 09:39:00 2003 Received: from mail.interware.hu ([195.70.32.156]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7EDcx98032181 for ; Thu, 14 Aug 2003 09:38:59 -0400 Received: from caracas-0373.adsl.interware.hu ([213.178.101.117] helo=cthulhu) by mail.interware.hu with smtp (Exim 4.20 #1 (Debian)) id 19nIJu-0005kn-EV for ; Thu, 14 Aug 2003 15:39:14 +0200 Message-ID: <000401c36271$dfeb1d60$0200a8c0@cthulhu> From: "Tamas E. Gunda" To: References: <000401c360db$911c2130$402b258a@Ruzhen> Subject: Re: CCL:question about BABEL Date: Wed, 13 Aug 2003 17:52:21 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Dear Ru-Zhen, Download Mol2Mol 5.1.1 from http://web.interware.hu/frenzy/mol2mol/ You can interconvert from pdb to cache or xyz formats (and many other) without problems and you don't have to struggle with problems you had mentioned. Tamas tamasgunda..at..tigris.klte.hu ----- Original Message ----- From: "Ru-Zhen Li" To: Sent: Monday, August 11, 2003 15:21 PM Subject: CCL:question about BABEL Fiesta Dear all Thank you for all the kind people reply to me, and now, I have done it again > from the very beginning, the problem still exist. 1)I downloaded the babel106.zip from ftp://www.ccl.net/pub/chemistry/software/UNIX/babel/ 2)I unziped it and copied the BABEL.EXEL, ELEMENT.LIS, TYPES.LIS to C:\BABEL 3)I add the SET BABEL_DIR=C:\BABEL to the AUTEXEC.BAT file which is in C:\Documents and Settings\ezw079.MATDOM\My Documents\My Received Files\winxpbootdisk\winxpbootdisk\HPWinXPbootdisk\WindowsXP&(&;+&\ 4)I copied the 1N5U.pdb into C:\BABEL 5)and then I entered the C:\BABEL under dos typed babel -ip 1N5U.pdb -ocache output.csf nothing happened, no error, no warning, no output file. and I tried the Open Babel, but seems that it is under UNIX, not DOS or Windows Thank you in advance! regards, Ru-Zhen ********************************************************************** Ms Ru-Zhen Li 0044-020-78826327 r.li..at..qmul.ac.uk Materials Department Queen Mary University of London E1 4NS From chemistry-request@ccl.net Thu Aug 14 19:34:24 2003 Received: from sentinel.ucr.edu (sentinel.ucr.edu [138.23.226.228]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7ENYO98012269 for ; Thu, 14 Aug 2003 19:34:24 -0400 Received: from dopetec (dunn4470.ucr.edu [138.23.156.82]) by sentinel.ucr.edu (Mirapoint Messaging Server MOS 3.2.1-GA) with ESMTP id AOW03009 for ; Thu, 14 Aug 2003 16:34:41 -0700 (PDT) Reply-To: From: "Donald Keidel" To: Subject: CCL: Are there alternatives to GOLPE for 3D-QSAR studies Date: Thu, 14 Aug 2003 16:34:38 -0700 Organization: UCR Message-ID: <000001c362bc$a0d652c0$529c178a@dopetec> 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 10.0.3416 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Hello CCL, I am looking into starting some 3D-QSAR studies and I have read many papers that use GOLPE for their Linear PLS Estimations. I am wondering if anyone knows of other software, free or not, that can do what GOLPE does? I will summarize results if anyone is interested. Thank you in advance for all replies. Don ------------------------------------------------------------------------ --------------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dopetec^at^dslextreme.com webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm From jkl@ccl.net Thu Aug 14 09:13:23 2003 -0400 From: fred.roozeboom^at^philips.com To: fred.roozeboom^at^philips.com Subject: 04.05.09 ADVANCED SHORT-TIME THERMAL PROCESSING FOR Si-BASED CMOS DEVICES II Message-ID: Date: Thu, 14 Aug 2003 15:12:13 +0200 Dear colleagues, Please find attached the CALL FOR PAPERS for the annual symposium on "ADVANCED SHORT-TIME THERMAL PROCESSING FOR Si-BASED CMOS DEVICES, II", at the 205th Electrochemical Society Meeting in San Antonio, Texas (USA), May 9-14, 2004. This symposium will cover the latest developments in Rapid Thermal Processing and other short-time processing technologies such as Atomic Layer Deposition, with emphasis on CMOS gate stack, source/drain and channel engineering. Please note, that the deadline for submission of abstract is 15 NOVEMBER 2003. Please read the instructions in the attachment for the correct submission of your abstract(s). We are looking forward to receiving your abstracts. Publication of a Proceedings Volume is planned to be available at the meeting. All authors accepted for presentation are obligated to submit a camera-ready Proceedings Volume manuscript. For review purposes the electronic version of this manuscript should be sent by Email to the symposium organizers before December 15, 2003. Instructions for preparing the manuscript will be sent out by the symposium organizers after the official notification of acceptance is distributed by the ECS Headquarters Office. For more information: http://www.electrochem.org/meetings/future/205/meeting.htm and ecs^at^electrochem.org The Electrochemical Society Inc., 65 South Main Street, Pennington, NJ 08534-2896, USA Phone 609-737-1902 , fax 609-737-2743 Kind regards, on behalf of all symposium organizers, Fred ==================================== Dr. Fred Roozeboom Philips Research Labs, WA14 Prof. Holstlaan 4, 5656 AA Eindhoven The Netherlands phone *31-40-2742767; fax *31-40-2743352 mailto: Fred.Roozeboom^at^philips.com