From chemistry-request@server.ccl.net Tue Jun 29 06:04:43 1999 Received: from avalon.ciam.unibo.it (root@avalon.ciam.unibo.it [137.204.214.167]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA03427 for ; Tue, 29 Jun 1999 06:04:41 -0400 Received: from gandalf.ciam.unibo.it (giampi@localhost [127.0.0.1]) by avalon.ciam.unibo.it (8.8.7/8.8.7) with ESMTP id KAA11224 for ; Tue, 29 Jun 1999 10:53:00 +0200 Sender: giampi@avalon.ciam.unibo.it Message-ID: <3778896A.FF97D00D@gandalf.ciam.unibo.it> Date: Tue, 29 Jun 1999 10:52:58 +0200 From: GP Miscione X-Mailer: Mozilla 4.07 [en] (X11; I; Linux 2.0.36 i686) MIME-Version: 1.0 To: ccl Subject: Max. numbers of atoms (G98) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, is there anyone who can tell me whether there is a maximum numbers of atoms over which the molecule cartesian coordinates are not displayed by default in the Gaussian98 output? I suppose it's 50, but I don't know how to increase it! Can anybody help me please? Thanks in advance, Gian Pietro From chemistry-request@server.ccl.net Tue Jun 29 08:39:58 1999 Received: from fsuj20.rz.uni-jena.de (fsuj20.rz.uni-jena.de [141.35.1.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA05476 for ; Tue, 29 Jun 1999 08:39:51 -0400 Received: from pc04.chemie.uni-jena.de (pc04.chemie.uni-jena.de [141.35.29.60]) by fsuj20.rz.uni-jena.de (8.9.1a/8.9.1) with SMTP id OAA03064 for ; Tue, 29 Jun 1999 14:36:17 +0200 (MET DST) Received: from pc03.chemie.uni-jena.de by pc04.chemie.uni-jena.de (5.65v3.2/1.1.10.5/28Jan98-0152PM) id AA16947; Tue, 29 Jun 1999 14:36:16 +0200 Sender: goeller@pc04.chemie.uni-jena.de Message-Id: <3778BDC0.2781@pc04.chemie.uni-jena.de> Date: Tue, 29 Jun 1999 14:36:16 +0200 From: Andreas Goeller X-Mailer: Mozilla 3.04Gold (X11; I; OSF1 V4.0 alpha) Mime-Version: 1.0 To: chemistry@ccl.net Subject: NT queueing Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, is there anybody who knows about or has something like a queueing system for W95/98/NT, something that accepts jobs, stores them and executes them one after another, like gNQS or others do in UNIX? Or, is there somebody who has ported Gamess to Linux so it works better than in NT. The PCGamess page suggests to run it under Linux in the wine emulator environment. To summarize, I look for queued execution of Gamess on PC. -- Andreas Goeller --------------------------------------------------------------- Dr. Andreas Goeller Institut fuer Physikalische Chemie Friedrich-Schiller-Universitaet Lessingstr. 10 phone: +49(0)-3641-948352 D-07743 Jena fax: +49(0)-3641-948302 (secretary) Germany email: goeller@pc04.chemie.uni-jena.de http://www.uni-jena.de/chemie/photo/goeller/goeller.html --------------------------------------------------------------- Dr. Andreas Goeller ehemals Computer Chemie Centrum email: goeller@organik.uni-erlangen.de http://www.organik.uni-erlangen.de/clark/goeller/goeller.html --------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Jun 29 08:56:22 1999 Received: from mail2.uct.ac.za (mail2.uct.ac.za [137.158.128.9]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA05640 for ; Tue, 29 Jun 1999 08:55:42 -0400 Received: from mort by mail2.uct.ac.za with local (Exim 2.01 #1) for chemistry@ccl.net id 10yxMz-0000hy-00; Tue, 29 Jun 1999 14:52:13 +0200 Received: by mail2.uct.ac.za (Mort 2.23alpha) id 538 from ACHIM@PSIPSY; Tue Jun 29 14:52:13 1999 From: "Achim Lienke" Organization: University of Cape Town To: chemistry@ccl.net Date: Tue, 29 Jun 1999 14:56:44 SAST-2 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Nucleophilic addition to a carbonyl group Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) Message-Id: Dear CCLers, is there anybody who knows a good reference for modelling transition states and relative rate constants for the addition of nucleophiles (amine) to a carbonyl group (ester, amide)? I will summarize Achim ---------------------------------------------------------------------- Achim Lienke Department of Chemistry University of Cape Town Private Bag Rondebosch 7701 South Africa Phone: ++27-21-650-2325 or -2530 Fax: ++ 27-21-689-7499 email: achim@psipsy.uct.ac.za ---------------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Jun 29 11:46:21 1999 Received: from vanilla.ice.mpg.de (root@vanilla.ice.mpg.de [195.37.47.220]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA07477 for ; Tue, 29 Jun 1999 11:46:20 -0400 Received: from ice.mpg.de (relax.ice.mpg.de [195.37.47.89]) by vanilla.ice.mpg.de (8.8.7/8.8.7) with ESMTP id RAA26971; Tue, 29 Jun 1999 17:44:56 +0200 Message-ID: <3778E96D.369F6898@ice.mpg.de> Date: Tue, 29 Jun 1999 17:42:37 +0200 From: Christoph Steinbeck Reply-To: steinbeck@ice.mpg.de Organization: Max-Planck-Institute of Chemical Ecology X-Mailer: Mozilla 4.6 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@server.ccl.NET, CHMINF-L@LISTSERV.INDIANA.EDU Subject: ANNOUCE: JChemPaint 0.3 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I'd like to announce the release of JChemPaint v0.3 JChemPaint is a 2D molecular structure editor written in Java, with a GUI based on the Swing tool kit. It is developed as an Open Source Project and released under GNU General Public License. The code should be considered pre-alpha quality, but there are enough features implemented to get an idea about where the program development is heading. JChemPaint development is coordinated by Christoph Steinbeck and his Chemical Information group (http://www.ice.mpg.de/departments/ChemInf) at the Max Planck Instiutute of Chemical Ecology (http://www.ice.mpg.de). The program currently supports: 1. A subset of the regular drawing features of commercial programs, as there are - drawing of single, double and triple bonds (no stereo descriptors yet). - deletion of bonds and atoms - one-click drawing of ring templates (3-8) - one-click spiro attachment of rings to an atom (can be member of a ring or a chain), but no condensation yet. 2. Loading and saving of structures as MDL Molfiles and in Chemical Markup Language (CML). 3. Automated Structure Layout, aka Structure Diagram Generation. More information as well as a download option can be found on http://www.ice.mpg.de/~stein/projects/JChemPaint/ People a sought to join the development of JChemPaint. JChemPaint is associated with the OpenScience project (www.openscience.org) and the 3D molecular viewer JMol (http://www.openscience.org/jmol/), both initiated by Dan Gezelter at Columbia University (http://www.chem.columbia.edu/~gezelter/). Cheers, Chris -- Dr. Christoph Steinbeck (http://www.ice.mpg.de/~stein) MPI of Chemical Ecology, Tatzendpromenade 1a, 07745 Jena, Germany Tel: +49(0)3641 643644 - Mobile: +49(0)177 8236510 - Fax: +49(0)3641 643665 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From chemistry-request@server.ccl.net Mon Jun 28 06:00:35 1999 Received: from fen.bilkent.edu.tr (leo.fen.bilkent.edu.tr [139.179.97.92]) by server.ccl.net (8.8.7/8.8.7) with SMTP id GAA10594 for ; Mon, 28 Jun 1999 06:00:32 -0400 Received: from pinar.fen.bilkent.edu.tr by fen.bilkent.edu.tr (5.65c/1.4IDA) id AA18153; Mon, 28 Jun 1999 13:01:13 +0400 Received: by pinar.fen.bilkent.edu.tr (SMI-8.6/SMI-SVR4) id MAA19622; Mon, 28 Jun 1999 12:59:51 +0300 Date: Mon, 28 Jun 1999 09:59:51 +0000 (GMT) From: Ulrike Salzner To: ccl Subject: gopenmol - printing Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I have installed GopenMol on my PC and got some really great orbital contour plots. Now I would like to print them, preferentially in black and white for use in a paper. Can anybody give me advice how to do this? Please explain it for dummies. Thanks, Uli Salzner =================================================================== Dr. Ulrike Salzner Department of Chemistry Tel.: (312) 290-2122 Bilkent University Fax.: (312) 266-5097 06533 Bilkent, Ankara e-mail: salzner@fen.bilkent.edu.tr Turkey ==================================================================== From chemistry-request@server.ccl.net Mon Jun 28 11:08:07 1999 Received: from harfang.CC.UMontreal.CA (harfang.CC.UMontreal.CA [132.204.2.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA14786 for ; Mon, 28 Jun 1999 11:08:06 -0400 Received: from balzac.CERCA.UMontreal.CA (balzac.CERCA.UMontreal.CA [132.204.150.21]) by harfang.CC.UMontreal.CA (8.8.8/8.8.8) with ESMTP id LAA17959 for ; Mon, 28 Jun 1999 11:03:32 -0400 (EDT) Received: from beckett.CERCA.UMontreal.CA (beckett.CERCA.UMontreal.CA [132.204.150.42]) by balzac.CERCA.UMontreal.CA (8.9.3/8.9.3) with ESMTP id LAA13548 for ; Mon, 28 Jun 1999 11:02:28 -0400 (EDT) From: Suzanne Sirois Received: (from siroiss@localhost) by beckett.CERCA.UMontreal.CA (980427.SGI.8.8.8/8.8.8) id LAA24764 for chemistry@ccl.net; Mon, 28 Jun 1999 11:02:27 -0400 (EDT) Message-Id: <199906281502.LAA24764@beckett.CERCA.UMontreal.CA> Subject: Database->list To: chemistry@ccl.net Date: Mon, 28 Jun 1999 11:02:27 -0400 (EDT) X-Mailer: ELM [version 2.4ME+ PL53 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CClers, I wish to extend my thanks to those people who replied to my question. My original question was: ------------ | Database | DOCK--> Known Enzyme | of all | Structure. | known drugs| ----------- I am looking for a database of all known drugs with their corresponding chemical structure. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I was overwhelm by the number of requests asking for posting the answers as compare to the number of answers itself. Here are some URLs which provide the 2D or 3D structures: http://nci3d.chemweb.com:8012/nci3d/query.html -> 126554 Records http://chem.sis.nlm.nih.gov/hsdb/ http://www.chemfinder.com/ anymore (free access)? http://www.cas.org/ information without the structure: http://toxnet.nlm.nih.gov/servlets/simple-search?1.25.0.1689 http://cri.ensmp.fr/biam/acceuil.html -> french very nice web page! site providing a list of databases links: http://www.chemweb.com/databases http://expasy.hcuge.ch/ http://www.expasy.ch/alinks.html#Proteins http://www.ncifcrf.gov/fcrdc/resources/index.html http://www.chemie.de/~knecht/englisch/dataeng.phtml http://www.chemfinder.com/siteslist.html http://www.iucr.ac.uk/sincris-top/themes/chimie/ http://www2.ccc.uni-erlangen.de/services/webmol.html http://wit.mcs.anl.gov/WIT2/ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Anyone who wants to update this list is very welcome. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Suzanne Sirois, Ph.D. From chemistry-request@server.ccl.net Tue Jun 29 07:09:08 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 HAA04897 for ; Tue, 29 Jun 1999 07:09:02 -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 NAA00688 for ; Tue, 29 Jun 1999 13:05:32 +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 NAA25859; Tue, 29 Jun 1999 13:03:18 +0200 (MDT) Sender: toulhoat@ifp.fr Message-ID: <3778A7F1.B264D7FF@ifp.fr> Date: Tue, 29 Jun 1999 13:03:15 +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: CCL CC: Herve TOULHOAT Subject: SUMMARY: Vibrational entropy of a transition state Content-Type: multipart/alternative; boundary="------------E82D31D1494BC0BABF041F13" --------------E82D31D1494BC0BABF041F13 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCL'ers, I summarize below the replies I obtained very quickly to my question. It helped a lot. CCL proved once again very effective in filling the gaps of my porous personal knowledge. I thank very much all those who supplied information. I hope this summary will be useful to others. I found thereafter that in MOPAC 6.0 the keyword TRANS=n allows to delete the first n vibrations (i.e. the negative(s) frequencies) for a thermochemical calculation. I am not sure this very useful feature is present in other "off the self" codes available (could vendors and authors manifest themselves on that point?). With my best regards, 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 My original request was: ========================================================================= 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 obtained very rapidly a clearcut answer through numerous replies: =========================================================================== >From R.A.van Santen : Dear Herve, In our book R.A. van Santen, H. Niemantsverdriet, Chemical kinetics and Catalysis we have explained why in the transition state entropy the reaction coordinate is not included. The procedure is vigorous. I hope to see you Soon. Best regards, Rutger Eindhoven University of Technology Laboratory for Inorganic Chemistry and Catalysis P.O. Box 513 5600 MB EINDHOVEN The Netherlands Tel.: +31 40 2472730 Fax: +31 40 2455054 (Comment: I have read the book some times ago, certainly not carefully enough! Indeed the answer is there page 149 for instance. Specialthanks to you Rutger). =============================================================================== >From Ned C.Haubein: Dr. Toulhoat, > This imaginary frequency cannot be included in the statistical > mechanical calculation of the vibrational entropy. Is it legitimate to > simply forget about it? yes, you should omit the contribution of the motion along the reaction coordinate. For a rigorous derivation, see "Kinetics and Mechanism" by John W. Moore and Ralph G. Pearson, 3rd ed, Wiley, 1981 pp 165,178. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ned C. Haubein Graduate Student Dept. of Chemical Engineering Northwestern University 2145 Sheridan Rd / Rm E136 Evanston, IL 60208-3120 Phone: 847-467-1402 Fax: 847-491-3728 Email: n-haubein@nwu.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ =============================================================================== >From Wayne Steinmetz : In Eyring's derivation of the TST, the contributions of the degree of freedom with an imaginary vibrational frequency is handled separately. This degree of freedom corresponds to translation in reaction space along the reaction coordinate. The particle-in-a-one-dimensional-box model is used to evaluate its partition function. The result of this calculation and the contribution of the velocity in reaction space at the transition state combine to yield the kT/h term. Therefore, in the well known result rate constant = (kT/h) x [exp(-delGact/kT)], translation in reaction space, the degree of freedom associated with the imaginary frequency, does NOT contribute to the calculation of delGact, the standard Gibbs free energy of activation. In this sense, the transition state is a peculiar species with only 3N-1 degree of freedom, not 3N as in the case of a normal molecule. A useful reference for these calculations from first principles is H. S. Johnston, Gas Phase Reaction Rate Theory, Ronald Press, New York, 1966. Johnston was the first to come up with a reaction mechanism for the destruction of stratospheric ozone. In his case, the villain was NO. His calculations were instrumental in ending the US participation in the development of the supersonic transport which would have dumped large amounts of NO in the stratosphere. Rowland later used his approach to establish that atomic chlorine would have the same effect. In the development of his model, Johnston required rate constants that had not been measured at the time. He therefore refined the use of TST to obtain reasonable estimates of the missing data. (Comment: I was delighted with this point of modern history. I suppose Concorde is to be blamed for a part of the ozone hole. I am afraid however of subsonic transport as well.) ============================================================================= >From Karl Irikura : Dear Dr. Toulhoat, I've never seen any mathematical discussion of this (but I'm not a kineticist). The quasi-equilibrium hypothesis of TST only makes sense physically if motion along one degree of freedom, the reaction coordinate, is prohibited, because any displacement in that direction would yield a molecular structure that is no considered a transition state. If you agree with this, then it's easy to accept that the (imaginary) "frequency" in the deleted coordinate should also be deleted. This is what people usually do, so the vibrational partition function includes only 3N-7 vibrational coordinates but is otherwise ordinary. If you do not agree to delete that coordinate, then clearly the "imaginary frequency" is irrelevant, since it describes only the curvature of the surface and has nothing to do with energy eigenstates (which alone determine the partition function). Instead, the energy levels on the unbound (one-dimensional) potential are a continuum of scattering states. You could work out the corresponding partition function for a model potential, e.g., U = -0.5*k*x*x (maybe this has already been done in some textbook). Perhaps the result would be similar to that for a free translation. But I wonder if this approach would be consistent with the usual simple treatment (translational or vibrational or rotational) of the reactants along all coordinates, including the special one. Please let me know if you learn whether this can be worked out consistently. Meilleurs voeux, Karl Irikura ================================================================================ >From Carlos Gonzalez : Dear Herve; Once a reacting system goes from the reactant side (a stationary point characterized by a all positive frequencies) towards the TS, one of the modes becomes a translation and this is basically why it becomes imaginary (col 1, in mathematical language). So, accordingly, this mode can not and should not be included in the zero point energy corrections for the calculation of the entropy. A similar situation arises when you step down from a TS following a reaction path toward the minima. In these cases, of course overall translations, and rotations should be projected out of the Hessian, but you also need to project out the translation along the reaction coordinate (the one that correlates with the mode that gives an imaginary frequency at the TS). This is a general procedure that is used to compute the rate constants as well as the DeltaG of activatioan along the path needed in VTST calculations. You can read Donald Truhlar's papers on this subject. I hope this little note helps you. Carlos Gonzalez. ============================================================================== >From Frank Jensen : The missing frequency is the reaction coordinate, and is part of the pre-exponential factor. So yes, it is legitimate to not include it in the entropy. And note for bimolecular reactions the translational entropy change by 30-40 eu., which usually is much larger than the vibrational component. > More generally, is there a rigourous procedure for evaluating the > vibrational entropy of a TS? Beyond the rigid rotor-harmonic frequency approximation, there are no 'standard' procedure. The next improvement could be anharmonic corrections. Try looking up some of Truhlars work. Frank ================================================================================================ >From Jordi Villa (): Dear Herve, I recommend to you to read some work from Donald G. Truhlar (http://comp.chem.umn.edu/~truhlar/) specially the following references: "The Current Status of Transition State Theory," D. G. Truhlar, W. L. Hase, and J. T. Hynes, Journal of Physical Chemistry 87, 2664-2682 (1983). Erratum: 87, 5523 (1983). "Generalized Transition State Theory," D. G. Truhlar, A. D. Isaacson, and B. C. Garrett, in Theory of Chemical Reaction Dynamics, edited by M. Baer (CRC Press, Boca Raton, FL, 1985), Vol. 4, pp. 65-137. "Transition State Theory," M. M. Kreevoy and D. G. Truhlar, in Investigation of Rates and Mechanisms of Reactions, 4th edition, edited by C. F. Bernasconi (John Wiley and Sons, New York, 1986), Part 1, pp. 13-95. [Tech. Chem. (N.Y.), 4th ed., 6/Pt. 1, 13-95 (1986)] "Dynamical Formulation of Transition State Theory: Variational Transition States and Semiclassical Tunneling," S. C. Tucker and D. G. Truhlar, in New Theoretical Concepts for Understanding Organic Reactions, edited by J. Bertrán and I. G. Csizmadia (Kluwer, Dordrecht, The Netherlands, 1989), pp. 291-346. [NATO ASI Ser. C 267, 291-346 (1989)] "Current Status of TransitionState Theory," D. G. Truhlar, B. C. Garrett, and S. J. Klippenstein, Journal of Physical Chemistry 100, 12771-12800 (1996). (Centennial Issue) and to take a look at his computer progrtam POLYRATE (http://comp.chem.umn.edu/polyrate/) Best wishes ===================================================================================== -- --------------E82D31D1494BC0BABF041F13 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers,

I summarize below the replies I obtained very quickly to my question. It helped a lot.
CCL proved once again very effective in filling the gaps of my porous personal knowledge.

I thank very much all those who supplied information. I hope this summary will be useful to others.

I found thereafter that in MOPAC 6.0 the keyword TRANS=n allows to delete the first n vibrations (i.e. the negative(s) frequencies) for a thermochemical calculation. I am not sure this very useful feature is present in other "off the self" codes available (could vendors and authors manifest themselves on that point?).

With my best regards,

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
 

My original request was:
=========================================================================
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 obtained very rapidly a clearcut answer through numerous replies:
===========================================================================
From R.A.van Santen <R.A.v.Santen@tue.nl>:

Dear Herve,

        In our book R.A. van Santen, H. Niemantsverdriet, Chemical kinetics
and Catalysis we have explained why in the transition state entropy the
reaction coordinate is not included. The procedure is vigorous. I hope to
see you Soon.

        Best regards,

                Rutger

Eindhoven University of Technology
Laboratory for Inorganic Chemistry and Catalysis
P.O. Box 513
5600 MB EINDHOVEN
The Netherlands

Tel.: +31 40 2472730
Fax:  +31 40 2455054

(Comment: I have read the book some times ago, certainly not carefully enough!
 Indeed the answer is there page 149 for instance. Specialthanks to you Rutger).
===============================================================================
From Ned C.Haubein:

Dr. Toulhoat,

> This imaginary frequency cannot be included in the statistical
> mechanical calculation of the vibrational entropy. Is it legitimate to
> simply forget about it?

yes, you should omit the contribution of the motion along the reaction
coordinate.  For a rigorous derivation, see "Kinetics and Mechanism"  by
John W. Moore and Ralph G. Pearson, 3rd ed, Wiley, 1981 pp 165,178.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Ned C. Haubein
Graduate Student
Dept. of Chemical Engineering
Northwestern University
2145 Sheridan Rd / Rm E136
Evanston, IL 60208-3120
Phone: 847-467-1402
Fax:   847-491-3728
Email: n-haubein@nwu.edu
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
===============================================================================
From Wayne Steinmetz <WSTEINMETZ@POMONA.EDU>:

In Eyring's derivation of the TST, the contributions of the degree of freedom
with an imaginary vibrational frequency is handled separately.  This
degree of freedom corresponds to translation in reaction space along the
reaction coordinate.  The particle-in-a-one-dimensional-box model is used
to evaluate its partition function.  The result of this calculation and
the contribution of the velocity in reaction space at the transition state
combine to yield the kT/h term.  Therefore, in the well known result
rate constant = (kT/h) x [exp(-delGact/kT)], translation in reaction
space, the degree of freedom associated with the imaginary frequency, does NOT
contribute to the calculation of delGact, the standard Gibbs free energy of
activation.  In this sense, the transition state is a peculiar species with
only 3N-1 degree of freedom, not 3N as in the case of a normal molecule.
A useful reference for these calculations from first principles
is H. S. Johnston, Gas Phase Reaction Rate Theory, Ronald Press, New York,
1966.  Johnston was the first to come up with a reaction mechanism for
the destruction of stratospheric ozone.  In his case, the villain was
NO.  His calculations were instrumental in ending the US participation in
the development of the supersonic transport which would have dumped
large amounts of NO in the stratosphere.  Rowland later used his approach
to establish that atomic chlorine would have the same effect.
In the development of his model, Johnston required rate  constants
that had not been measured at the time.  He therefore refined the
use of TST to obtain reasonable estimates of the missing data.

(Comment: I was delighted with this point of modern history. I suppose Concorde is to be blamed for a part of the ozone hole. I am afraid however of subsonic transport as well.)
=============================================================================

From Karl Irikura <karl.irikura@nist.gov>:
 

Dear Dr. Toulhoat,

I've never seen any mathematical discussion of this (but I'm not a kineticist).  The
quasi-equilibrium hypothesis of TST only makes sense physically if motion along one degree of
freedom, the reaction coordinate, is prohibited, because any displacement in that direction would
yield a molecular structure that is no considered a transition state.  If you agree with this, then
it's easy to accept that the (imaginary) "frequency" in the deleted coordinate should also be
deleted.  This is what people usually do, so the vibrational partition function includes only 3N-7
vibrational coordinates but is otherwise ordinary.

If you do not agree to delete that coordinate, then clearly the "imaginary frequency" is
irrelevant, since it describes only the curvature of the surface and has nothing to do with energy
eigenstates (which alone determine the partition function).  Instead, the energy levels on the
unbound (one-dimensional) potential are a continuum of scattering states.  You could work out
the corresponding partition function for a model potential, e.g., U = -0.5*k*x*x (maybe this has
already been done in some textbook).  Perhaps the result would be similar to that for a free
translation.  But I wonder if this approach would be consistent with the usual simple treatment
(translational or vibrational or rotational) of the reactants along all coordinates, including the
special one.  Please let me know if you learn whether this can be worked out consistently.

Meilleurs voeux,

Karl Irikura

================================================================================

From Carlos Gonzalez <carlos.gonzalez@nist.gov>:

Dear Herve;

Once a reacting system goes from the reactant side (a stationary point characterized by a all
positive frequencies) towards the TS, one of the modes becomes a translation and this is
basically why it becomes imaginary (col 1, in mathematical language). So, accordingly, this
mode can not and should not be included in the zero point energy corrections for the calculation
of the entropy. A similar situation arises when you step down from a TS following a reaction
path toward the minima. In these cases, of course overall translations, and rotations should be
projected out of the Hessian, but you also need to project out the translation along the reaction
coordinate (the one that correlates with the mode that gives an imaginary frequency at the TS).
This is a general procedure that is used to compute the rate constants as well as the DeltaG of
activatioan along the path needed in VTST calculations. You can read Donald Truhlar's papers
on this subject. I hope this little note helps you.
 

Carlos Gonzalez.
==============================================================================

From Frank Jensen <frj@dou.dk>:

        The missing frequency is the reaction coordinate, and is
part of the pre-exponential factor. So yes, it is legitimate
to not include it in the entropy. And note for bimolecular
reactions the translational entropy change by 30-40 eu., which
usually is much larger than the vibrational component.

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

        Beyond the rigid rotor-harmonic frequency approximation, there
are no 'standard' procedure. The next improvement could be anharmonic
corrections. Try looking up some of Truhlars work.

        Frank

================================================================================================

From Jordi Villa (<jvilla@imim.es>):

Dear Herve,

I recommend to you to read some work from Donald G. Truhlar
(http://comp.chem.umn.edu/~truhlar/)
specially the following references:

"The Current Status of Transition State Theory," D. G. Truhlar, W. L.
Hase, and J. T. Hynes, Journal of Physical Chemistry 87, 2664-2682
(1983). Erratum: 87, 5523 (1983).

"Generalized Transition State Theory," D. G. Truhlar, A. D. Isaacson,
and B. C. Garrett, in Theory of Chemical Reaction Dynamics,
     edited by M. Baer (CRC Press, Boca Raton, FL, 1985), Vol. 4, pp.
65-137.

"Transition State Theory," M. M. Kreevoy and D. G. Truhlar, in
Investigation of Rates and Mechanisms of Reactions, 4th edition,
     edited by C. F. Bernasconi (John Wiley and Sons, New York, 1986),
Part 1, pp. 13-95. [Tech. Chem. (N.Y.), 4th ed., 6/Pt. 1, 13-95
     (1986)]

"Dynamical Formulation of Transition State Theory: Variational
Transition States and Semiclassical Tunneling," S. C. Tucker and
     D. G. Truhlar, in New Theoretical Concepts for Understanding
Organic Reactions, edited by J. Bertrán and I. G. Csizmadia (Kluwer,
     Dordrecht, The Netherlands, 1989), pp. 291-346. [NATO ASI Ser. C
267, 291-346 (1989)]

"Current Status of TransitionState Theory," D. G. Truhlar, B. C.
Garrett, and S. J. Klippenstein, Journal of Physical Chemistry 100,
12771-12800
(1996). (Centennial Issue)

and to take a look at his computer progrtam POLYRATE
(http://comp.chem.umn.edu/polyrate/)

Best wishes

=====================================================================================
 
  

--
  --------------E82D31D1494BC0BABF041F13-- From chemistry-request@server.ccl.net Tue Jun 29 16:24:16 1999 Received: from ce.fis.unam.mx (ce.fis.unam.mx [132.248.33.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA11077 for ; Tue, 29 Jun 1999 16:24:13 -0400 Received: from ce.fis.unam.mx ([132.248.33.121]) by ce.fis.unam.mx with ESMTP (8.7.1/8.7.1) id PAA08281; Tue, 29 Jun 1999 15:20:02 -0700 (PDT) Message-ID: <3779387F.4232CC3F@ce.fis.unam.mx> Date: Tue, 29 Jun 1999 15:19:59 -0600 From: Max Valdez Organization: Centro de Ciencias Fisicas, UNAM X-Mailer: Mozilla 4.6 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: GP Miscione CC: ccl Subject: Re: CCL:Max. numbers of atoms (G98) References: <3778896A.FF97D00D@gandalf.ciam.unibo.it> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I use Gaussian 94 for a molecule with more than 70 atoms without any problem, are you asking about gaussian viewer?. As I know the limits of Gaussian are set in the number of basis functions, not in the number of atoms. Max Valdez GP Miscione wrote: > Hi all, > > is there anyone who can tell me whether there is a maximum > numbers of atoms over which the molecule cartesian coordinates are > not displayed by default in the Gaussian98 output? > > I suppose it's 50, but I don't know how to increase it! > > Can anybody help me please? > > Thanks in advance, > > Gian Pietro > > -= 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 Tue Jun 29 21:55:45 1999 Received: from ceniai.net.cu (ceniai.net.cu [169.158.128.142]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA13386 for ; Tue, 29 Jun 1999 21:55:41 -0400 Received: from ceniai.inf.cu ([169.158.128.138]:54537 "EHLO ceniai.inf.cu" ident: "NO-IDENT-SERVICE[2]") by ceniai.net.cu with ESMTP id <51551-176>; Tue, 29 Jun 1999 21:47:30 -0400 Received: from oc.uh.cu by ceniai.inf.cu with bsmtp (Smail3.2) id m10z9Uj-000EFqC; Tue, 29 Jun 1999 21:49:01 -0400 (CDT) Received: from nffuh.ff.oc.uh.cu (root@nffuh.ff.oc.uh.cu [169.158.202.134]) by ffuh.ff.oc.uh.cu (8.8.7/8.8.7/JP) with ESMTP id SAA08266; Tue, 29 Jun 1999 18:37:23 -0400 Received: from karin.fq.oc.uh.cu (gerardo@karin.fq.oc.uh.cu [169.158.202.18]) by nffuh.ff.oc.uh.cu (8.8.7/8.8.7/JP) with ESMTP id RAA03670; Tue, 29 Jun 1999 17:41:41 -0400 Received: from localhost (gerardo@localhost) by karin.fq.oc.uh.cu (8.9.0/8.8.7/JP) with SMTP id SAA01424; Tue, 29 Jun 1999 18:40:03 -0400 Date: Tue, 29 Jun 1999 18:40:02 -0400 (CDT) From: Gerardo =?ISO-8859-1?Q?Gonz=E1lez?= Aguilar To: Andreas Goeller cc: chemistry@ccl.net Subject: Re: CCL:NT queueing In-Reply-To: <3778BDC0.2781@pc04.chemie.uni-jena.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Andreas, During two-three months I had the same problem, but it is ease to solve, just create a batch (.BAT) file with the adecuate sequence of task you want to perform an run this file and you will obtain the desired results, you can make this file with a small program write in C, Pascal or even in Basic, collecting each input file in a given directory. for example I run my MOPAC calculations using this file (his name is mopac.bat) ECHO ***************** MOPAC RUNNING ************** mopac <--------<>------------------------------------- On Tue, 29 Jun 1999, Andreas Goeller wrote: > Dear CCLers, > > is there anybody who knows about or has something like a queueing system > for W95/98/NT, something that accepts jobs, stores them and executes > them one after another, like gNQS or others do in UNIX? > > Or, is there somebody who has ported Gamess to Linux so it works better > than in NT. The PCGamess page suggests to run it under Linux in the wine > emulator environment. > > To summarize, I look for queued execution of Gamess on PC. > -- > Andreas Goeller > > --------------------------------------------------------------- > Dr. Andreas Goeller Institut fuer Physikalische Chemie > Friedrich-Schiller-Universitaet > Lessingstr. 10 > phone: +49(0)-3641-948352 D-07743 Jena > fax: +49(0)-3641-948302 (secretary) Germany > email: goeller@pc04.chemie.uni-jena.de > http://www.uni-jena.de/chemie/photo/goeller/goeller.html > --------------------------------------------------------------- > Dr. Andreas Goeller ehemals Computer Chemie Centrum > > email: goeller@organik.uni-erlangen.de > http://www.organik.uni-erlangen.de/clark/goeller/goeller.html > --------------------------------------------------------------- > > -= 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 > > > > >