From chemistry-request@server.ccl.net Fri Jun 25 01:02:25 1999 Received: from mail.chat.ru (gnu.chat.ru [212.24.32.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA05153 for ; Fri, 25 Jun 1999 01:02:22 -0400 Received: from [62.76.10.102] (helo=chat.ru) by mail.chat.ru with smtp (Exim 2.12 #3) id 10xO4t-000L53-00 for CHEMISTRY@ccl.net; Fri, 25 Jun 1999 08:59:05 +0400 Date: Fri, 25 Jun 1999 10:56:05 +0500 From: "Qadir K. Timerghazin" X-Mailer: The Bat! (v1.036) S/N F16EAEA6 Reply-To: "Qadir K. Timerghazin" Organization: Qadir K. Timerghazin Priority: Normal Message-ID: <12455.990625@chat.ru> To: CHEMISTRY@ccl.net Subject: NBO visualization Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CClers, I need program for visualization of NBOs, preferably for Win95/NT Any suggestions? Thanks in advance, Qadir Timergahzin mailto:qt@chat.ru From chemistry-request@server.ccl.net Fri Jun 25 08:39:50 1999 Received: from LMSMRM ([202.127.25.133]) by server.ccl.net (8.8.7/8.8.7) with SMTP id IAA10960 for ; Fri, 25 Jun 1999 08:39:35 -0400 Received: from LMSMRM (localhost [127.0.0.1]) by LMSMRM (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id UAA10393 for ; Fri, 25 Jun 1999 20:32:02 +0900 Sender: user@iris.sipp.ac.cn Message-ID: <377368B2.41C6@iris.sipp.ac.cn> Date: Fri, 25 Jun 1999 20:32:02 +0900 From: maoxiang Organization: iris.sipp.ac.cn X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@ccl.net Subject: ? do normal node calculation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, everyone: Does anyone know how to do normal mode calculation wiht GAMESS-UK, I can not find it in the manual, Maybe I missed it. Hope to hear from you soon. Thanks in advance. Regards, Mao ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Mao Xiang | | Lab of Molecular Regulation for Microbial Secondary Metabolism | | Shanghai institute of Plant Physiology, Academia Sinica | | 300 Fenglin Road, Shanghai, China, 200032 | | Tel: +86-21-64042090-4791 | | Fax: +86-21-64042385 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Fri Jun 25 08:42:19 1999 Received: from mserv.rug.ac.be (mserv.rug.ac.be [157.193.40.37]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA11030 for ; Fri, 25 Jun 1999 08:42:18 -0400 Received: from elptrs3.rug.ac.be (elptrs3.rug.ac.be [157.193.113.1]) by mserv.rug.ac.be (8.9.0/8.9.0) with SMTP id OAA03192 for ; Fri, 25 Jun 1999 14:38:22 +0200 (MET DST) Received: from lptpc66.rug.ac.be by elptrs3.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA28276; Fri, 25 Jun 1999 15:41:18 +0200 Received: by localhost with Microsoft MAPI; Fri, 25 Jun 1999 14:41:06 +0200 Message-Id: <01BEBF18.C21AA900.mark.saeys@rug.ac.be> From: Mark Saeys To: "'chemistry@ccl.net'" Subject: Defining a new method (e.g. G3, CBS-RAD) in g98 Date: Fri, 25 Jun 1999 14:41:04 +0200 Organization: Universiteit Gent X-Mailer: Microsoft Internet-e-mail/MAPI - 8.0.0.4211 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear, We are using g98 on a pentium with RedHat 6.0 linux for the calculation of accurate themochemical data. I would like to use models like the new Gaussian-3 and CBS-RAD method. These methods are a combination of several single point calculations. Is it possible to define new keywords, so that if I use the keyword G3 or CBS-RAD in the route section, g98 preforms a series of predefined calculations - as it now does with the G2, G2MP2 and CBS-like keys? Which modifications should I make in certain links in order to do that? Thanks, Mark Saeys University Gent Belgium From jkl@ccl.net Tue Jun 22 20:51:31 1999 -0400 Received: from feldmann.nist.gov (feldmann.nist.gov [129.6.178.78]) by email.nist.gov (8.9.3/8.9.3) with ESMTP id TAA00153; Tue, 22 Jun 1999 19:48:48 -0400 (EDT) Received: from localhost (chem@localhost) by feldmann.nist.gov (8.8.8+Sun/8.8.8) with SMTP id TAA12601; Tue, 22 Jun 1999 19:37:01 -0400 (EDT) Date: Tue, 22 Jun 1999 19:37:01 -0400 (EDT) From: Steve Heller To: ACSMEDI@LISTS.WAYNE.EDU, amber@cgl.ucsf.EDU, APPLSPEC@listserv.uga.edu, cache@pacificu.edu, CHEMCHAT@UAFSYSB.UARK.EDU, CHEME-L@ULKYVM.LOUISVILLE.EDU, CHEMED-L@atlantis.UWF.EDU, CHEMIG@LIST.NIH.GOV, CHEMISTRY@www.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, ICS-L@UMDD.UMD.EDU, isisforum-l@mdli.com, ISOGEOCHEM@LIST.UVM.EDU, listproc@msi.com Subject: ACS President candidtae Message-ID: I want to direct the attention to a webpage: http://www.pavlath.org which I think you would find interesting. It is the webpage of Attila Pavlath, who is one of the two candidates for the ACS presidency in the Fall election. Attila is involved for almost 30 years in various ACS activities to improve the Society. The webpage gives a very detailed description about his background as a scientist and an ACS activist. It describes his views through the many guest editorials in Chemical & Engineering New and the views of others about his activities. I urge you to view the website and if you like it alert others to its existence Steve Heller, Guest Researcher NIST/SRD, Mail Stop: 820/113 820 Diamond Avenue, Room 101 Gaithersburg, MD 20899-2310 USA E-mail: chem@feldmann.nist.gov From chemistry-request@server.ccl.net Fri Jun 25 04:19:24 1999 Received: from ifp.ifp.fr (ifp.ifp.fr [156.118.212.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA07590 for ; Fri, 25 Jun 1999 04:19:23 -0400 Received: from irsil145.ifp.fr (irsil145.ifp.fr [156.118.20.20]) by ifp.ifp.fr (8.9.3/8.9.3) with ESMTP id KAA12042; Fri, 25 Jun 1999 10:15:15 +0200 (MET DST) Received: from ifp.fr (localhost [127.0.0.1]) by irsil145.ifp.fr (8.8.5/8.8.5) with ESMTP id KAA11315; Fri, 25 Jun 1999 10:13:10 +0200 (MDT) Sender: toulhoat@ifp.fr Message-ID: <37733A15.A4590543@ifp.fr> Date: Fri, 25 Jun 1999 10:13:09 +0200 From: Herve Toulhoat Organization: Institut Francais du Petrole X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX64 6.5 IP30) MIME-Version: 1.0 To: chemistry@ccl.net CC: Herve TOULHOAT , CSC-list@msi.com Subject: Vibrational entropy of a transition state Content-Type: multipart/alternative; boundary="------------265CF2C97919BCFE75CEA954" --------------265CF2C97919BCFE75CEA954 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, The transition state theory (TST) allows to relate in principle the rate constant of a reaction to the variation in free energy between reactant(s) and the transition state. Of specific interest is the variation of entropy between reactant(s) and TS, which relates to the so-called pre-exponential factor of the rate equation. The entropy change for a gas phase reaction will be dominated by the vibrational component. The vibrational entropy of a molecular species can be evaluated from the set of vibrational normal modes. A TS however corresponds to a saddle point of the PES, and exhibits therefore one imaginary frequency (one negative eigenvalue in the hessian matrix). This imaginary frequency cannot be included in the statistical mechanical calculation of the vibrational entropy. Is it legitimate to simply forget about it? More generally, is there a rigourous procedure for evaluating the vibrational entropy of a TS? I will summarize the replies. Yours sincerely, -- Dr Herve TOULHOAT Directeur de Recherche Associe Group Leader, Molecular Modeling and Computational Chemistry Div. Computer Science and Applied Mathematics, IFP Director, Groupement de Recherches CNRS G1209: Dynamique Moleculaire Quantique Appliquee a la Catalyse Research Group CNRS G1209 Ab Initio Molecular Dynamics Applied to Catalysis (Scientific Partners: CNRS, IFP, Total, University of vienna, TU Eindhoven) INSTITUT FRANCAIS DU PETROLE Tel: +33-01-47-52-73-50 1 & 4 Avenue de Bois-Preau Fax: +33-01-47-52-70-22 92852 RUEIL-MALMAISON Cedex FRANCE E-mail: herve.toulhoat@ifp.fr Visit IFP Website at http://www.ifp.fr --------------265CF2C97919BCFE75CEA954 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hello,

The transition state theory (TST) allows to relate in principle the rate constant of a reaction to the variation in free energy between reactant(s) and the transition state. Of specific interest is the variation of entropy between reactant(s) and TS, which relates to the so-called pre-exponential factor of the rate equation.

The entropy change for a gas phase reaction will be dominated by the vibrational component. The vibrational entropy of a molecular species can be evaluated from the set of vibrational normal modes. A TS however corresponds to a saddle point of the PES, and exhibits therefore one imaginary frequency (one negative eigenvalue in the hessian matrix). This imaginary frequency cannot be included in the statistical mechanical calculation of the vibrational entropy. Is it legitimate to simply forget about it?

More generally, is there a rigourous procedure for evaluating the vibrational entropy of a TS?

I will summarize the replies.

Yours sincerely, 

-- 
Dr Herve TOULHOAT

Directeur de Recherche Associe
Group Leader, Molecular Modeling and Computational Chemistry    
Div. Computer Science and Applied Mathematics, IFP
Director, Groupement de Recherches CNRS G1209: 
Dynamique Moleculaire Quantique Appliquee a la Catalyse
Research Group CNRS G1209
Ab Initio Molecular Dynamics Applied to Catalysis
(Scientific Partners: CNRS, IFP, Total, University of vienna, TU Eindhoven)
        
INSTITUT FRANCAIS DU PETROLE                    Tel: +33-01-47-52-73-50
1 & 4 Avenue de Bois-Preau                      Fax: +33-01-47-52-70-22
92852 RUEIL-MALMAISON Cedex FRANCE       E-mail: herve.toulhoat@ifp.fr

Visit IFP Website at http://www.ifp.fr
  --------------265CF2C97919BCFE75CEA954-- From chemistry-request@server.ccl.net Fri Jun 25 12:24:35 1999 Received: from pregrado.ciencias.uchile.cl (maleiva@[146.83.21.47]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA14687 for ; Fri, 25 Jun 1999 12:24:29 -0400 Received: from localhost (maleiva@localhost) by pregrado.ciencias.uchile.cl (8.9.1a/8.9.1/Debian/GNU) with ESMTP id NAA16059 for ; Fri, 25 Jun 1999 13:24:35 GMT Date: Fri, 25 Jun 1999 13:24:35 +0000 (GMT) From: Andres Leiva To: chemistry@ccl.net Subject: ZINDO Free Code Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL'ers, I am very interested in a free source code for the ZINDO program. Known any one if such a copy is available for the public domain? Thanks in advance, M. Leiva From chemistry-request@server.ccl.net Fri Jun 25 15:45:32 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA17915 for ; Fri, 25 Jun 1999 15:45:31 -0400 Received: from wotan.duch.udel.edu (wotan.duch.udel.edu [128.175.54.25]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id PAA24229 for ; Fri, 25 Jun 1999 15:41:33 -0400 (EDT) Received: from localhost (sbennett@localhost) by wotan.duch.udel.edu (8.9.3/8.9.3) with ESMTP id PAA15569 for ; Fri, 25 Jun 1999 15:42:47 -0400 (EDT) Date: Fri, 25 Jun 1999 15:42:45 -0400 From: Steve Bennett To: CCL Users Subject: NBO analysis and dative bonds Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII CCL, I was wondering if anyone had any experience looking at or for dative bonds using Gaussian and the NBO analysis. thanks in advance. Steven D. Bennett University of Delaware Department of Chemistry 304A Drake Hall (302) 831-8720 sbennett@wotan.duch.udel.edu (302) 737-8485 http://udel.edu/~sbennett/ "X rays are a hoax" Lord Kelvin