From joubert@ext.jussieu.fr Fri Mar 22 04:18:04 1996 Received: from shiva.jussieu.fr for joubert@ext.jussieu.fr by www.ccl.net (8.7.1/950822.1) id DAA23192; Fri, 22 Mar 1996 03:33:25 -0500 (EST) Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.7.3/jtpda-5.2) with ESMTP id JAA13372 for ; Fri, 22 Mar 1996 09:33:25 +0100 (MET) Received: from [134.157.11.17] by idf.ext.jussieu.fr (8.6.10/jtpda-4.0) with SMTP; Fri, 22 Mar 1996 09:33:23 +0100 Date: Fri, 22 Mar 1996 09:33:23 +0100 X-Sender: joubert@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: joubert@ext.jussieu.fr (laurent JOUBERT) Subject: SUMMARY "ECP FOR DFT" A few days ago, I put this question on the ccl : "Does anyone know special ECP (for lanthanides and actinides) developped for DFT methods ? Do the Hartree-Fock's ECP work correctly with DFT ?" I thank you very much all who replied. Here are their answers : *************************************************** MAREK SIERKA *************************************************** Hi, You can try: T.V. Russo, R.L. Martin, P.J. Hay, "Effective Core Potentials for DFT Calculations" J. Phys. Chem. 1995, 99, 17085-17087. Marek Sierka. -- "Politics consists in the art of taking votes from the poor and money from the rich under the pretext of protecting each from the other." Marek Sierka e-mail: mas@gea.qc.ag-berlin.mpg.de ************************************************************************ MARTIN KAUPP ************************************************************************ We have used ab initio ECPs (i.e. those obtained from a fit to Hartree-Fock or quasirelativistisc SCF all-electron data) in our DFT studies on transition metal systems. While the emphasis has been mainly on NMR-Properties, which adds some more aspects to the problem, we also optimized structures and looked at energies and vibrational frequencies. For the usual 'small-core' ECPs, the transferability of these ECPs in DFT applications is excellent, and I expect similar accuracy for lanthanide and actinide systems. Similar experience has also been made by others (e.g.: C. van W\"ullen Int. J. Quant. Chem., in press. T. V. Russo, R. L. Martin, P. J. Hay J. Phys. Chem. 1995, 99, 17085. See also the work of H. Schwarz and W. Koch and their groups in Berlin. As far as I remember, they also looked at some lanthanide systems using hybrid DFT/HF methods). Some of our own results may be found, e.g. in: J. Am. Chem. Soc. 1995, 117, 1851; ibid 1995, 117, 8492. Chem. Phys. Lett. 1995, 235, 382. Chem. Eur. J. 1996, 2, 24. Chem. Eur. J. 1996, 2, 194. A particularly nice example is the unusual structure of W(CH3)6, where e.g. DFT and MP2 calcs. with ECPs give virtually identical results (M. Kaupp, JACS, in press). We have also tested to what extent ECPs for main-group atoms may be transferred (M. Kaupp, H.-J. Flad, A. K\"oster, H. Stoll, D. R. Salahub, manuscript in preparation). The answer depends on the core size. Thus, e.g., I do not recommend to transfer a 1-valence-electron ECP for Na or K, or a 3-valence-electron ECP for Ga, but smaller cores, such as e.g. for the halogens look fine. Hope this helps, Martin Kaupp ------------------------------------------------------------------ | Dr. Martin Kaupp | | Max-Planck-Institut fuer Festkoerperforschung, | | Heisenbergstrasse 1, D-70569 Stuttgart, Germany, | | Tel.: country-code+711/689-1532 | | Fax.: country-code+711/689-1562 | | email: kaupp@vsibm1.mpi-stuttgart.mpg.de | | | | and Institut fuer Theoretische Chemie, Universitaet Stuttgart, | | Pfaffenwaldring 55, D-70569 Stuttgart, Germany | | Tel.: country-code+711/685-4399 | | Fax.: country-code+711/685-4442 | | http://www.theochem.uni-stuttgart.de/~kaupp/ | ------------------------------------------------------------------ ********************************************************************** FRED.P.ARNOLD ********************************************************************** Hello. laurent JOUBERT (joubert@ext.jussieu.fr) wrote asking about ECPs for lanthanides for use in DFT calculations, and whether or not the HF ECPs work correctly. I cannot address the first question, but the second one was addressed in the recent paper by Hay and coworkers Russo, T. V.; Martin, R. L.; Hay, P. J., J. Phys. Chem., 1995, 99, 17085. The basic consesus of the paper is that while the ECP itself may be used with good reliability, at least when compared to all electron calculations, the HF basis set is probably not reliable with DFT calculations. -fred arnold ******************************************************************* SORRY, THE TWO NEXT ANSWERS ARE IN FRENCH. I CAN TRANSLATE THEM FOR THOSE WHO ARE INTERESTED ******************************************************************* ******************************************************************************* FREDERIC BOUYER ******************************************************************************* Salut Laurent, En general, les orbitales HF peuvent marcher pour des calculs DFT, mais il existe des problemes de BSSE (Basis Set Superposition Error) Typiquement, si tu dissocies par exemple une molecule, H2O, il serait bon, lorsque que tu augmentes une distance O-H (chemin de dissociation), de retrouver pour une grande distance, la somme des energies OH(-) et H(+). Generalement, avec les orbitales HF, ca ne marche pas, et les orbitales DFT (celles de DMol ou celles de DGauss/deMon) sont faites pour la methodologies DFT, de facon a supprimer les pb de BSSE. Tu peux voir la reference: N. Godbout, D.R. Salahub, J. Andzelm et E. Wimmer, Can. J. Chem., 70, 560, 1992. pour les orbitales DFT (DGauss/deMon) pour la methodologie LCGTO-MCP (Linear Combination of Gaussian-Type Orbitals-Model Core Potential). Pour celles de DMol, tu peux regarder la doc. sur DMol. Sinon, si tu as des infos sur des ECP (avec effet relativiste), sur des actinides/lanthanides, je suis preneurs. En esperant que cela t'aide, Amicalement, Frederic -- /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Frederic Bouyer Groupe Chimie Corrosion - RNE-EMA EDF-DER Les Renardieres Tel: (33) 1-60-73-69-65 Route de Sens, Ecuelles, BP1 Fax: (33) 1-60-73-68-89 77250 MORET-SUR-LOING - FRANCE Email: Frederic.Bouyer@der.edfgdf.fr \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ *************************************************************************** GABRIELE VALERIO *************************************************************************** En generale les ECP HF (ex: Hay and Wadt '85) peuvent etre utilises aussi pour des calculs DFT. Je suis en train de les utiliser sur des clusters de palladium et les resultats semblent tres bons et coherents. C'est quand meme vrai que si tu peut utiliser des ECP developpes pour la DFT (et fiables) alors cela pourrait etre encore mieu. Bon courage, Gabriele gabriel.valerio@ifp.fr ****************************************************************************** Laurent JOUBERT ------------------------------------------------------------------ Laurent JOUBERT Ecole Nationale Superieure de Chimie de Paris Laboratoire d'Electrochimie et de Chimie Analytique 11, rue Pierre et Marie Curie 75231 PARIS CEDEX 05- FRANCE Tel : 44-27-66-94 Fax : 44-27-67-50 E-Mail : joubert@ext.jussieu.fr WWW site : http://www.enscp.jussieu.fr ------------------------------------------------------------------ From d.w.price@reading.ac.uk Fri Mar 22 07:18:00 1996 Received: from sussdirt.rdg.ac.uk for d.w.price@reading.ac.uk by www.ccl.net (8.7.1/950822.1) id GAA24909; Fri, 22 Mar 1996 06:24:28 -0500 (EST) Received: from INDIGOH (actually host indigoh.chemistry.rdg.ac.uk) by sussdirt.rdg.ac.uk with SMTP - Local (PP); Fri, 22 Mar 1996 11:18:08 +0000 Received: from INDIGOH by INDIGOH via SMTP (940816.SGI.8.6.9/930416.SGI) for id LAA07662; Fri, 22 Mar 1996 11:17:53 GMT Sender: dave@reading.ac.uk Message-ID: <31528C60.41C6@reading.ac.uk> Date: Fri, 22 Mar 1996 11:17:52 +0000 From: Dave Price Organization: none-what-so-ever X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP20) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: HELP: Gometry optimisation with ADF Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Comp Chem Listers, I am ahving trouble with a geometry optimisation of a Rhodium complex containing a chelate ring and a pair of functionalised ethylene molecules. The problem is that after starting with the geometry optimised bis-ethylene complex and replacing the ethylenes with the functionlised equivalents the calculation will not converge on an energy minimum. Rather, it reaches a minimum then over shoots, viz- 5 E-test: old,new= -5.85880, -5.85899 hartree Minimum 6 E-test: old,new= -5.85899, -5.85884 hartree 7 E-test: old,new= -5.85884, -5.85824 hartree 8 E-test: old,new= -5.85824, -5.85780 hartree 9 E-test: old,new= -5.85780, -5.85727 hartree 10 E-test: old,new= -5.85727, -5.85694 hartree 11 E-test: old,new= -5.85694, -5.85687 hartree 12 E-test: old,new= -5.85687, -5.85671 hartree I am using ECPs for all atoms except H, double zeta valence orbitals and GGA rather than LDA. Any help? ------------------------------------------------------------------------ Dr. David W. Price, Tel: +44 (0)1734 875123 extn 7415 Department of Chemistry, Fax: +44 (0)1734 311610 University of Reading, e-mail: d.w.price@reading.ac.uk Whiteknights, W.W.W.: READING HTTP://www.chem.rdg.ac.uk/g50/mmrg/dave/dave.html RG6 2AD U.K. ------------------------------------------------------------------------ From herbert.homeier@rchs1.chemie.uni-regensburg.de Fri Mar 22 09:18:12 1996 Received: from comsun.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by www.ccl.net (8.7.1/950822.1) id IAA27290; Fri, 22 Mar 1996 08:53:33 -0500 (EST) Received: from rchs1.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA16379 (5.65c/IDA-1.4.4 for ); Fri, 22 Mar 1996 14:52:57 +0100 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA03974; Fri, 22 Mar 96 14:54:25 +0100 Date: Fri, 22 Mar 96 14:54:25 +0100 From: Herbert Homeier t4720 Message-Id: <9603221354.AA03974@rchs1.chemie.uni-regensburg.de> To: ariane@WAPinorg.chemie.uni-halle.de, CHEMISTRY@www.ccl.net Subject: Re: CCL:How to get information Content-Type: text/plain Mime-Version: 1.0 X-Mailer: NCSA Mosaic 2.6 on Sun X-Url: http://rchs1.chemie.uni-regensburg.de/%7Emaillist/data/0674.html Ariane, please have a look at http://www.chemie.uni-regensburg.de/external.html especially http://www.chemie.uni-regensburg.de/external.html#j You might also try the Uncover service. (See external.html). Best regards Herbert --------------------------------------------------------------- Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX : +49-941-943 2305 email: na.hhomeier@na-net.ornl.gov HOMEPAGE --------------------------------------------------------------- From consult@betacyte.pt Fri Mar 22 09:43:28 1996 Received: from tirith.esoterica.pt for consult@betacyte.pt by www.ccl.net (8.7.1/950822.1) id IAA27151; Fri, 22 Mar 1996 08:21:49 -0500 (EST) Received: from lisslip3.esoterica.pt by mail.esoterica.pt with smtp (Linux Smail3.1.29.1 #2) id m0u06rR-000zepC; Fri, 22 Mar 96 14:26 GMT+0100 Message-Id: Date: Fri, 22 Mar 96 14:26 GMT+0100 X-Sender: betacyte@mail.esoterica.pt X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: BetaCyte Consultants Subject: WWW possiblities Dear CCL'ers, With the arrival of Chemical MIME, JAVA, JavaScript and soon Microsoft's Visual Basic script, a lot is now possible on the WWW. For the chemical community, the WWW has become a very handy tool. Literature research and finding chemical resources is becoming much easier. But to aid the chemical industry, much more is POSSIBLE. We are interested in any hearing what kind of applications chemist would like to see to help them in their research, production, customer relations, marketing etc.. Any comments will be much appreciated. If desired, the ideas remain confidential and perhaps we can implement your suggestions to help your company. thanks for your bandwidth, Patrick P.S. We won't have a stand at the ACS meeting, but you can drop by our virtual booth (http://www.betacyte.pt) any time! +-----------------------------------------------------+ | Patrick M. van der Valk, M.Sc. | | Technical Director, BetaCyte Consultants | | Complete Internet Service for the Chemical Industry | +-----------------------------------------------------+ | Rua Joao Luis Ricardo 65, suite 4b | | 2775 Parede, Portugal | | tel: +351 (1) 456.42.98 | | fax: +351 (1) 458.07.91 | | email: consult@betacyte.pt | | WWW: http://www.betacyte.pt | +-----------------------------------------------------+ From owner-chemistry@ccl.net Fri Mar 22 09:56:50 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id JAA27361; Fri, 22 Mar 1996 09:13:10 -0500 (EST) Received: from krakow.ccl.net for jkl@ccl.net by bedrock.ccl.net (8.7.1/950822.1) id JAA25819; Fri, 22 Mar 1996 09:13:08 -0500 (EST) From: Jan Labanowski Received: for jkl@ccl.net by krakow.ccl.net (8.6.10/920428.1525) id JAA00686; Fri, 22 Mar 1996 09:13:07 -0500 Date: Fri, 22 Mar 1996 09:13:07 -0500 Message-Id: <199603221413.JAA00686@krakow.ccl.net> To: chemistry@ccl.net Subject: CCL changes rules Cc: jkl@ccl.net Dear Netters, Looking at the contents of communication in the last week or so, and the angry letters in my mailbox, I made changes to the CCL rules. The portions of CCL rules which were affected are given below. Some will be sorry, and some will be happy, but it is a good occasion to remind ourself what is suitable and what is not suitable on CCL. The complete help file for CCL can be retrieved by sending a message help chemistry to MAILSERV@www.ccl.net or via our home page: http://www.ccl.net/chemistry.html Jan Labanowski Trying to cope... jkl@ccl.net --------------------------------------------------------------------------- Topics which may appear on the list include: o Reporting bugs in chemistry software and possible work- arounds o New chemistry software announcements o Announcements of computational chemistry-related workshops and symposia o New methods and techniques in computational chemistry o Questions and answers about solving computational chemistry problems o Programs and utilities o Information on the availability of particular software, data, etc. o Hardware-related issues relevant to the computational chemistry community o Opinions about services and products Topics which may not appear on this list include: o Personal attacks o Topics unrelated to computational chemistry o Announcements of "vaporware" o Commercial "Meet us at the booth" announcements o Announcements of job openings or CV's. (These are handled off line-- see Section 5 for more information). o Address inquiries, unless you have exhausted all other options. Before posting an address inquiry, you should try looking in the ACS Directory of Chemistry Departments in your library, searching the archives of CCL (especially the lists of addresses), using netfind, contacting CCL's list coordinator at jkl@ccl.net, contacting the Postmaster at the target machine, and tried everything suggested in this file on finding e-mail addresses. --------------------------------------------------------------- 4. Commercial Software Announcements ==================================== "Commercial software" is defined as any software that was sold to anyone for more than the cost of handling and documentation. A "commercial post" is defined as commercial software advertisements posted by the people who develop or sell the software. Posts responding to user questions, as well as bug reports, requests for comments, and tips on efficient software use are not considered commercial postings and are highly encouraged. Commercial software reviews or evaluations conducted or posted by people not associated with the software vendor/developer are also encouraged. Those wishing to submit commercial posts to the list must abide by the following rules. Short (25 lines or less) commercial postings are allowed. They should include a straightforward subject line. Reposts are not allowed unless new features/releases become available. Announcements of "vaporware" (software that is not yet working or available), and invitations to expositions and trade shows at meetings are not allowed. You can submit commercial postings of any length to the list administrators at chemistry-request@www.ccl.net which will made available in the CCL software archives for downloading. ---------------------------------------------------------------------- From ragno@serifos.caspur.it Fri Mar 22 10:18:02 1996 Received: from serifos.caspur.it for ragno@serifos.caspur.it by www.ccl.net (8.7.1/950822.1) id KAA28066; Fri, 22 Mar 1996 10:10:42 -0500 (EST) Received: by serifos.caspur.it; id AA15800; Fri, 22 Mar 1996 16:10:27 +0100 Date: Fri, 22 Mar 1996 16:10:27 +0100 (MET) From: Gianluca Sbardella To: chemistry@www.ccl.net Subject: CCL : DMSO Toxicity ?? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, we're going to find out news about cellular toxicity of DMSO in vitro. Does anybody have references about this topic ? Many thanks Dr. Antonello Mai Dr. Gianluca Sbardella P.S. We're not in the CCL, yet. So, please, respond directly. Thank you again ! ***************************************************************** * * * Dr. Gianluca Sbardella E-mail: ragno@kea.caspur.it * * Dip. Studi Farmaceutici ragno@serifos.caspur.it * * Universita' "La Sapienza" Phone: 39-6-49913814 * * P.le A. Moro, 5 Fax: 39-6-491491 * * 00185 Roma * * ITALY * ***************************************************************** From owner-chemistry@ccl.net Fri Mar 22 17:18:05 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id QAA05678; Fri, 22 Mar 1996 16:33:54 -0500 (EST) Received: from ns-1.csn.net for craig@SoftShell.com by bedrock.ccl.net (8.7.1/950822.1) id QAA07430; Fri, 22 Mar 1996 16:33:52 -0500 (EST) Received: from zazu.softshell.com by ns-1.csn.net with SMTP id AA18263 (5.65c/IDA-1.4.4 for ); Fri, 22 Mar 1996 14:33:52 -0700 Message-Id: Date: 22 Mar 1996 14:25:21 -0700 From: "Craig Shelley" Subject: SoftShell New Products + To: chemistry@ccl.net X-Mailer: Mail*Link SMTP-QM 3.0.2 Subject: Time: 2:20 PM OFFICE MEMO SoftShell New Products + Date: 3/22/96 ===> NEW: SoftShell Press Releases announce new products ChemWindow DB (structure drawing and database), SymApps (3-D rendering), SoftShell Properties (logP, Molar Refractivity, Henry's Constant), etc. Introductory pricing through April of: ChemWindow DB: $298 ($799 after April) SymApps: $198 ($499 after April), $99 Academic, $49 Student SoftShell Properties $198 ($499 after April) http://www.softshell.com/SSO_HTML/PressBin/Releases.html -------------------------------------------------------- ===> IS "CHEMWINDOW DB" AN UPGRADE? 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From Y0H8797@ACS.TAMU.EDU Fri Mar 22 17:49:45 1996 Received: from VMS1.TAMU.EDU for Y0H8797@ACS.TAMU.EDU by www.ccl.net (8.7.1/950822.1) id RAA05895; Fri, 22 Mar 1996 17:14:32 -0500 (EST) Date: Fri, 22 Mar 1996 16:13:53 -0600 (CST) From: YONG HUANG To: CHEMISTRY@www.ccl.net Message-Id: <960322161353.22a125b9@ACS.TAMU.EDU> Subject: Summary: structure-kinetics correlation On March 7, I posted a message about the correlation of structure - kinetics. I received 3 responses. Many thanks to Drs. Michael Chabinyc, John Liebeschuetz and James Verth. The summary below is followed by a little additional correspondence with Dr. Liebeschuetz. Yong Huang (y0h8797@acs.tamu.edu) -------------------------------------------------------------------------------- From: SMTP%"Y0H8797@ACS.TAMU.EDU" 7-MAR-1996 22:51:24.14 Subj: CCL:reference on structure-kinetics relationship Can anybody recommend some literature (books, papers) on the relationship between kinetics and molecular structure? The reason is as follows. It seems easier to make a guess of stability, acidity or basicity etc. by looking at the structure of a molecule than make a guess of how fast it would react with other molecules. In other words, the relationship between thermodynamics and structure is more straightforward than that between kinetics and structure. However, the Hammett equation, as well as other physico-organic equations, shows correlation between sigma (substituent parameter, a structural parameter) and K, where this K can be either equilibrium constant or rate constant. This implies thermodynamics goes the same way as kinetics in those series of compounds. In my mass spectrometry experiment, it seems compounds of even similar structure show different thermodynamic trend (acidity in my case) than kinetic trend.* I think the bridge between thermodynamics and kinetics is the stability of reaction intermediate or activated complex. But I'm not successful in making use of this knowledge to explain my experiments. Any help will be appreciated. Yong ________________________ *E.g., in the chart of degree of proton transfer vs. acidity, sinapic acid and caffeic acid lie on the same line while 4-OH-cinnamic acid and ferulic acid on the other line. The 2 lines may suggest 2 activation energies. -------------------------------------------------------------------------------- From: SMTP%"chabinml@chem.Stanford.EDU" 7-MAR-1996 22:38:44.18 Subj: Re: CCL:reference on structure-kinetics relationship I saw your message and thought I'd send you a note. One recent paper to look at is "Intrinsic Structure-Reactivity Relationships in Gas-Phase SN2 reactions: Identity Exchange Reactions of Substituted Benzyl Chlorides with Chloride Ion" - B.D. Wladkowski, J.L. Wilbur, J. I. Brauman JACS 116 2471-2480 1994 There are lots of papers out on this topics many from our group - just do a lit. search on John Brauman. Terry MacMahon, and Kebarble have also done some work in this area. The paper I mentioned has a good review of the literature also. Some issues to worry about are complexation energies of your reactants and competing reaction channels. If you want more info send me a specific area of interest. Michael -------------------------------------------------------------------------------- From: SMTP%"johnL@proteus.co.uk" 8-MAR-1996 06:53:15.14 Subj: structure-kinetics A correlation between kinetic rate and thermodynamic stability is not suprising for a single step reaction. The height of the free energy `hill' between reactant and product is not independant of the relative free energy between these species. This will be especially true if the transition state is `late' on the reaction coordinate i.e. product resembling. Where you get two classes of molecules, each of which show a different linear relationship between kinetics and thermodynamics, then the liklehood is that you are seeing two different reaction mechanisms. I don't know much about the sort and the conditions of reaction you are looking at but is it possible that in one of your classes some sort of intramolecular proton transfer is occuring as part of your reaction and in your other class it is not ? Regards John -------------------------------------------------------------------------------- From: SMTP%"JVSQUARE%canisius.BITNET@UBVM.cc.buffalo.edu" 9-MAR-1996 01:42:38.59 Subj: thermodynamics vs. kinetics See J. Org. Chem. 1995, 60, 3452-3458 for a related study. > *E.g., in the chart of degree of proton transfer vs. acidity, sinapic acid and > caffeic acid lie on the same line while 4-OH-cinnamic acid and ferulic acid > on the other line. The 2 lines may suggest 2 activation energies. James E. Van Verth Department of Chemistry jvsquare@canisius.edu Canisius College, Buffalo, NY 14208 -------------------------------------------------------------------------------- From: SMTP%"johnL@proteus.co.uk" 11-MAR-1996 04:18:48.96 Subj: Re: structure-kinetics On Mar 8, 10:13am, YONG HUANG wrote: > Subject: RE: structure-kinetics > John, thank you for your comment. The proton transfer IS inter-molecular in > all cases. The experiment is MH(NH3)n cluster (MH is the acid) photoinduced > intra-cluster proton transfer. Here I say intra-cluster because MH + nNH3 > forms the cluster. > > Although the molecules MH are very similar (cinnamic acid derivatives, OH > and/or OCH3 attaching to benzene ring), we do suspect two mechanisms as you > mentioned. I'm working on the effect of variable reaction time on the extent > of proton transfer. Preliminary results indicate all show more proton transfer > but only 4-OH-cinnamic acid increases A LOT. > Why do you say the energy of the transition state is not independent of the > reactant and product ESPECIALLY when it's closer to the product? How about > closer to the reactant? Thanks vey much. > > Yong >-- End of excerpt from YONG HUANG Yong, The reason that the transition state energy (and hence rate of reaction) is often closely related to the Free Energy of the reaction when the transition state is close in nature to the product is simply due to the fact that species close to each other on the reaction coordinate are liable to have closely linked energies, the energy function being continuous. Therefore the energy change between the reactant and transition state closely parallels that between reactant and product. This is embodied in what I believe is called the Bell-Evans-Polanyi principle which describes why the product distribution of some irreversible reactions is determined by the relative stability of the products (I'll try to get a ref. for you). If the transition state is early on the reaction coordinate then the transition state energy will be linked to that of the reactant rather than the product and therefore is less likely to be related to the Free Energy change for the reaction. I suppose another possibility you might have, other than two different mechanisms, is different electron distributions in the transition state which would imply different molecular orbitals are involved in stabilising the developing anion in both cases. That would be interesting. I guess to explore that possibility you'd have to do some fairly extensive high level MO calculations. Looks as though you've got an exciting bit of research going on ! John John W. Liebeschuetz Ph.D. | johnl@proteus.co.uk [Yong's words: Later I tried to find the transition state by CAChe MOPAC of the reaction: MH...NH3 -> M-...NH4+, where MH is the simplest molecule in my experiment, 4OH-cinnamic acid. The TS is extremely close to the reactant. I tried the same calculation on the reverse reaction and the TS was very different. I was advised to use a keyword LST. But I don't see it in the MOPAC manual. This work is temporarily set aside. All the advice I've got so far is very much appreciated.] From shubin@email.unc.edu Fri Mar 22 18:18:19 1996 Received: from login0.email.unc.edu for shubin@email.unc.edu by www.ccl.net (8.7.1/950822.1) id RAA06067; Fri, 22 Mar 1996 17:45:05 -0500 (EST) Received: (from shubin@localhost) by login0.email.unc.edu (8.6.12/8.6.12) id RAA140687; Fri, 22 Mar 1996 17:45:01 -0500 Date: Fri, 22 Mar 1996 17:45:00 -0500 (EST) From: Shubin Liu To: CHEMISTRY@www.ccl.net cc: CHEMISTRY@www.ccl.net Subject: CCL: How to get Ex and J values from G9X? In-Reply-To: <01I2IOY5W2EQ0019AA@aardvark.ucs.uoknor.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all CCLers: Can you tell me how to extract the exchange energy Ex and the classical Coulomb repulsion energy J from Gaussian 9X runs? Thanks for your attention! Shubin From ascanio@salve3.salve.edu Fri Mar 22 18:31:05 1996 Received: from SALVE3.SALVE.EDU for ascanio@salve3.salve.edu by www.ccl.net (8.7.1/950822.1) id RAA06108; Fri, 22 Mar 1996 17:55:16 -0500 (EST) From: Received: by salve3.salve.edu (MX V3.2) id 3377; Fri, 22 Mar 1996 17:53:09 EST Date: Fri, 22 Mar 1996 17:53:07 EST To: chemistry@www.ccl.net Message-ID: <0099FBA0.E43443E0.3377@salve3.salve.edu> Subject: DIS-secting CON-form-er Colleagues: I am a con-FORM-ist that talks about CON-form-ers It depends on the starting point. "Con" words of two or three syllables in "The American Heritage Dictionary" The New Edition(1978) are usually accented on the second syllable; hence con-FORM(a verb, con-FORM-ist, etc. Four syllable words, e.g. CON-fron_TA-tion, CON-for-MA-tion(generally nouns) have two accents on CON and the third syllable. The same exists for in-FORM-er and IN-form-A-tion. CON-for-mer is a word synthesized by scientists to lazy(or busy) to keep repeating "CON-for-MAY-tion-al ISOmers". This is now like re-DOX rather than RED-ox (reduction-oxidation) although we normally say oxidation-reduction (OX-red is yuk). Since the word is synthetic the pronunciation can be arbitray. A greater problem is the DI-SSEASE DIS-ease. Many who are now CON-form-ing or co-FORM-ing are probably also DI-ssecting rather than DIS-secting con-form-er. Their women are probably attended to by a GUY-nee-cologist rather than a JEAN-a-cologist. Do these same people go to the GUYM to play basketball. The problem is that we have neglected the classic education. DIS-sect from SECARE(to cut, early Italian(Latin?) and DIS(apart). DIS-sect, to cut apart. there is no word in any language that begins with two esses ! yet most people still say, wrongly, Di- ssect. The Greek word for woman is yeh-ne-ka. Because it starts with gamma doesn't mean it is pronounced GUY. Or, did this develop because most JEAN-a-col-o-gistswer are GUYS ? The proper pronunciation of these, and other, words is grounded in established languages and we should correct these, whenever possible. Words are beautiful and I enjoy creating them. Getting them accepted is another matter. We are chemists. Try this at some meeting. "Let us not do this in a "hemionic" fashion " Does this mean half (hemi) ionic(involving ions" with the elision of the i's or hemi and onic(Greek, onus = donkey) Ergo, "let us not proceed in a half- donkey fashion" :-) ********* Happy St. Patrick's Day ************* Ciao Fr. Ascanio, C.H.S.