From chemistry-request@www.ccl.net Wed Jan 6 03:43:36 1999 Received: from dreamon.oxmol.co.uk (dreamon.oxmol.co.uk [193.132.141.15]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA16314 Wed, 6 Jan 1999 03:43:33 -0500 (EST) Received: from oxmol.co.uk (bludgeon.oxmol.co.uk [193.132.141.84]) by dreamon.oxmol.co.uk (8.9.0/8.9.0/7) with ESMTP id IAA12964; Wed, 6 Jan 1999 08:42:57 GMT Message-ID: <369320EE.9CD54AAA@oxmol.co.uk> Date: Wed, 06 Jan 1999 08:38:06 +0000 From: Rob Williams Organization: Oxford Molecular Group X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: Re: CCL:QSAR References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > > Hi, > > could anyone point me to software packages (both commercial and > non-commercial) for performing QSAR analysis. > > thank you. > > steven Hi Steve, Oxford Molecular have a comprehensive QSAR product called Tsar (Tools for Structure Activity Relationships). Visit our web site at http://www.oxmol.co.uk/ if you would like more information. The Tsar user interface is based around an intuitive spreadsheet display that allows you to easily bring together and manipulate both structural and property data. As well as the normal spreadsheet functionality that you would expect, its range of analysis tools include: - 2D/3D/4D graph plotting - Univariate data analysis - Correlation matrices - Principal components analysis - Non-linear mapping - ReNDeR and forward feed neural networks - cluster (including Ward) and cluster significance analysis - discriminant analysis - multiple regression - partial least squares - FIRM (a recursive partitioning algorithm) In addition, the same spreadsheet environment can be used to derive calculated properties of loaded molecules, including: - Molecular mass, surface area and volume - R-group analysis with Verloop calculation - Moments of inertia - Dipole moments - logP and molar refractivity - Rotatable bond count - Kier and Hall (and similar) indices - Autocorrelograms - Atom and ring counting - Hydrogen bond donor/acceptor counting - Substructure counting - Lipinski's rules for screening for "drug-like" compounds It also has interfaces to other software packages: - Corina, for fast 1D/2D to 3D structure conversion - Charge, for fast partial charge derivation - Cosmic, for fast structure optimisation - Asp, for shape and electrostatic similarity calculations - Vamp, fast QM package for optimisation and property calculations - Topkat, toxicity prediction system - RS3, our Oracle based informatics framework Hope this has been of some use, Rob From chemistry-request@www.ccl.net Wed Jan 6 10:46:08 1999 Received: from mail.matav.hu (mail.matav.hu [145.236.224.244]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA17905 Wed, 6 Jan 1999 10:46:00 -0500 (EST) Received: (qmail 14138 invoked from network); 6 Jan 1999 16:45:30 +0100 Received: from unknown (HELO inhale) (195.70.54.253) by mail.matav.hu with SMTP; 6 Jan 1999 16:45:30 +0100 Message-ID: <369384E9.24EE747D@chemaxon.com> Date: Wed, 06 Jan 1999 16:44:41 +0100 From: Ferenc Csizmadia Organization: ChemAxon X-Mailer: Mozilla 4.01 [en] (WinNT; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: New year -> new ideas for chemistry software X-Priority: 3 (Normal) Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit A few weeks ago I posted the following letter to CCL: ===== I would like to know your opinion about future trends in chemical software development. What will be the hottest topics in the near future? What are the areas that need new approaches from program developers? ===== Thank you for the contributions. Here are the answers I received so far. 1. ===== I would like to submit an idea which is based on the article of Mok, Neumann and Handy, J. Phys. Chem. 1996, 100, 6225-6230. Precise calculations (approaching FCI-quality) should be quite possible, at a cost scaling as CASSCF, if one were to include only excitations corresponding to nondynamical correlation in a CASSCF calculation, and afterwards using a correlation functional fittet to only dynamical correlation (He or Ne) in a DFT calculation based on densities from the CASSCF calculation. Thomas Bligaard Pedersen University of Strasbourg and Technical University of Denmark 2. ===== It seems nearest future trends in chemistry are more or less visible. To make it short: Biology, Biochemistry and related topics. >From the clear domination of physics up to the middle of our century scientific world is moving into "the living cell". You can proof it by analyzing the number of publications, impact-factors of various journals, the number of grants in difference fields of chemistry, and activity of funding organizations in general. Even in this List, proteins and DNA modeling and visualization, docking, MD, structure determination, ..., are the topics discussed quite often. Significant contribution and support are coming from the medicine related applications, i.e., QSAR, screening, drug design, etc. I am not to say that I like the situation, but one has to accept obvious things. Concerning the possible arias of software development, very likely it could be a structure calculation, refinement, prediction and analyzing programs for the most important biological molecules like proteins, DNA, etc. Of course all of the above with up to date Graphics User Interface. So, if you are going to start new software project, try to collect more info about structural biochemistry stuff. Valentin P. Ananikov NMR Group ND Zelinsky Institute of Organic Chemistry 3. ===== It would be nice to have a Windows program that would calculate the enthalpy of formation at 0K and at 298.15 K, and a program that would calculate rate constants. You would take the output file from a Gaussian 94 or Gaussian 98 calc and drag it into the Chemaxon window, click Start, and the program would calculate heats of formation or rate. For heat of formation the Gaussian output might be a G2, G2(MP2) or CBS job. The algorithm could be bases onA. Nicolaides, A. Rauk, M. N. Glukhovtsev, L. Radom, JPC, 1996, 100, 17460. for rate constants, methods might come from standard books on statistical thermodynamics (e.g. Steinfeld, Francisco and Hase). E. Lewars 4. ===== How to determine crystal structures from powder diffraction data is still hot topic. The 5 last years have seen the emergence of many ways of locating optimally a molecular model inside a cell (Monte Carlo, simulated annealing, genetic algorithm, packing considerations, optimized grid search,...). It seems that developers believe that pharmaceutical companies are, or will be interested. You cannot find any of these new softwares in the public domain, nor in the commercial one ! See http://www.cristal.org/iniref.html for more details Structure/properties prediction is the way to continue to explore, not really new, but not really successful till now. Armel Le Bail - Université du Maine, Laboratoire des Fluorures 5. ===== In my humble opinion, linear scaling SCF theory will continue to get hotter, as applications become more wide spread and algorithms get more robust. Matt Challacombe Los Alamos National Laboratory Theoretical Division email: mchalla@t12.lanl.gov 6. ===== I think that some of the types of calculations that exist, but are seldom done, will become more widely used. Here are some of my picks. relativistic calculations solvent effects band structure calculations mesoscale calculations synthesis route prediction ab initio molecular dynamics Dave Young 7. ===== I am just reading -- again -- a very nice and very general article by Martin Head-Gordon that appeared in the centennial issue of J. Phys. Chem. He lists a lot of trends and challenges for electronic structure theory, and almost all of them are longer term, and still valid today. The reference is J. Phys. Chem. 1996, 100, 13213. In fact, the entire issue is worth a look as it contains various general reviews. Georg Schreckenbach 8. ===== I think the new ideas for chemistry software is: 1. Better organized interface. It is easy to learn. 2. Moved to cheaper but hign performance PC. FengLou Mao Peking University 9. ===== I think that simulation using virtual reality in all branches of chemistry. Jorge Arce Molina Instituto Superior Minero Metalurgico Las Coloradas s/n. 10. ===== I think we dont really need a lot of _new_ programmes; rather, we need a lot of extant programmes/source codes to be ported into Win95/WinNT executables. Now that the price of RAM is so low and we will soon have PCs with clock speeds exceeding 500 MHz, we should be able to run a lot of programmes on the PC that heretofore have been restricted to Unix workstations. For example, so far as I know, there is no simple, stand-alone programme for the PC that will calculate the molecular volume or solvent-accessible surface of a macromolecule (or even of a small molecule) from its .ent or .mol2 file. This would be a very useful tool for the community of PC computational chemists. Whilst MOPAC and AMPAC have been ported to DOS/Win, I know of no DOS/Win programme that can perform a conformational search in order to identify the (most likely) global energy minimum of a molecule _in an aqueous environment_. I believe that MacroModel contains a module which does this, so in principle it is possible to obtain a DOS/Win executable that can also do this. So far as I am aware, there are no publically-available DOS/Win programmes that use genetic algorithms for optimal selection of variables for linear regression analysis. Neither, so far as I know, does there exist a recent version of GOLPE that runs under DOS/Win. These would be very valuable chemometric tools for the PC compurtational chemist. Around April 1999 the C source code for the programme LigBuilder should be released. When it is, it will be a very useful addition to the PC computational chemistry armamentarium, if only someone would port it to a DOS/Win executable. The JPC solvent version was recently described [J. Chem. Phys. 109(1): 260 (98)]. However, there is no DOS/Win-compatible release of this method; such a release would be a valuable addition to the PC computational chemists methodological arsenal. And there are other programmes so far available only for Unix which ought to be made available to PC users: PARM and GRID are two which spring to mind at the moment. And, of course, there remains a need for new and better ways of quickly calculating log P, log D, pKa, aqueous solubility, &., &c. S. Shapiro ===== The discussion is still open. If anyone would like to contribute please send a letter in the subject to me or CCL. Ferenc ~~~~~~ Ferenc Csizmadia, Ph.D. ChemAxon Ltd. Valyog u. 7, H-1032 Budapest, Hungary http://www.chemaxon.com T:+3620 9570988 mailto:fcsiz@chemaxon.com From chemistry-request@www.ccl.net Thu Jan 7 12:11:19 1999 Received: from ned1.sims.nrc.ca (ned1.sims.nrc.ca [132.246.108.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA00050 Thu, 7 Jan 1999 12:11:18 -0500 (EST) Received: (from ramos@localhost) by ned1.sims.nrc.ca (8.8.8/8.8.8) id MAA22180; Thu, 7 Jan 1999 12:11:18 -0500 (EST) Date: Thu, 7 Jan 1999 12:11:17 -0500 (EST) From: Antonio Fernandez-Ramos To: CCL Subject: Onsager model Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters: I am using the Onsager model to taken into account the solvent effects.It happens that two structures invert their stabilities when the polarization energy is included. I know that the polarization is not included in SCF procedure and the manual looks like that the energy to be considered is the SCF one. My question is: what does it happen with the polarization energy? Should I include that in my final result, or not? My best regards, Antonio Fernandez-Ramos Room 2013; SIMS National Research Council 100 Sussex Drive Ottawa, ON, K1A-0R6 FAX :613-947-2838 Phone: 613-990-0982 From chemistry-request@www.ccl.net Fri Jan 8 09:08:08 1999 Received: from lrz.uni-muenchen.de (root@dialc099.ppp.lrz-muenchen.de [129.187.26.99]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA10222 Fri, 8 Jan 1999 09:08:01 -0500 (EST) Received: from localhost (root@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) with SMTP id WAA00844; Mon, 4 Jan 1999 22:10:23 +0100 Date: Mon, 4 Jan 1999 22:10:23 +0100 (CET) From: Eugene Leitl To: Chemistry@www.ccl.net Subject: Re: CCL:Re: CCL:G:Cerius2/Gaussview In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Are there any free tools for GAMESS visualization? Regards, Eugene On Thu, 31 Dec 1998, Ohyun Kwon wrote: > Dear Dr. Xie; > I think molden is pretty nice and you don't have to pay. You can download > it form the following > website(http://www.caos.kun.nl/~schaft/molden/molden.html) freely. From chemistry-request@www.ccl.net Fri Jan 8 09:37:42 1999 Received: from mailrelay.wiley-vch.de ([195.110.5.164]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA10459 Fri, 8 Jan 1999 09:37:41 -0500 (EST) From: niskanen@cc.wiley-vch.de Received: from wnt009.cc.wiley-vch.de ([195.110.10.199]) by mailrelay.wiley-vch.de (Post.Office MTA v3.5 release 215 ID# 0-0U10L2S100) with SMTP id de for ; Fri, 8 Jan 1999 15:36:24 +0100 Received: by wnt009.cc.wiley-vch.de(Lotus SMTP MTA v4.6.2 (693.3 8-11-1998)) id C12566F3.00503EFC ; Fri, 8 Jan 1999 15:36:30 +0100 X-Lotus-FromDomain: WILEY To: Chemistry@www.ccl.net Message-ID: Date: Fri, 8 Jan 1999 15:36:25 +0100 Subject: Chemical Concepts' News Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Chemical Concepts and LabControl are pleased to announce that we have agreed a long-term strategic partnership. For Chemical Conseps' SpecInfo customers we can now offer PC client Spectacle XS, developed by LabControl for Windows NT/95/98 with comprehensive optical spectroscopy tools including spectra processing, quantitative analysis, easy report generation and GLC conformant data handling. The easy-to-handle Web client SpecSurf will be available in the beginning of this year. For further information, please, visit our home pages: http://www.chemicalconcepts.com/ http://www.labcontrol.com/ From chemistry-request@www.ccl.net Fri Jan 8 11:48:12 1999 Received: from mailhost.lanl.gov (mailhost.lanl.gov [128.165.3.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA11469 Fri, 8 Jan 1999 11:48:11 -0500 (EST) Received: from [128.165.22.209] (machgs.lanl.gov [128.165.22.209]) by mailhost.lanl.gov (8.9.1a/8.9.1/(cic-5, 7/9/98)) with SMTP id JAA22595 for ; Fri, 8 Jan 1999 09:48:09 -0700 X-Sender: schrecke@t12mail.lanl.gov Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 8 Jan 1999 09:51:11 -0600 To: CHEMISTRY@www.ccl.net (CCL) From: schrecke@t12.lanl.gov (Georg Schreckenbach) Subject: Summary: G94/98: How to skip SCF completely? Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id LAA11470 Dear CCL, this is the summary for my earlier query on how to use input ("guess") MOs to calculate properties like nmr in G94/98. The essential answer is, it doesn't work (cf. the comments by Mike Frisch -- and he should know ...). Quite a few people suggested the keywords "Guess=(Read,Only)". It is possible to calculate population stuff and related properties with this feature, but it is impossible to go into the CPHF equations (l1002). Further, I'd like to single out the response by Rene Fournier: when posting my question, I was hoping for something along the lines of his suggestion. In this respect, all I found in the code is the old link 503 that seems to do the direct minimazation that Rene suggested. However, it is, apparently, restricted to 256 basis functions (I have a lot more), and I don't really know how to use it anyways. Finally, I wish to pass on the comment by Marta ForÈs i Bocsh : She had posted -- and summarized -- a related question some weeks ago. You can search the CCL archives, or get her summary from me. Thanx to all who took the time to reply! And, please feel free to comment on this further. Best regards, Georg -- Dr. Georg Schreckenbach Tel: (USA)-505-667 7605 Theoretical Chemistry T-12 FAX: (USA)-505-665 3909 M.S. B268, Los Alamos National E-mail: schrecke@t12.lanl.gov Laboratory, Los Alamos, New Mexico, 87545, USA Internet: http://www.t12.lanl.gov/~schrecke/ ============================ Here are the detailed answers: ============================ Original question: Dear CCL, here is a GAUSSIAN related question: I would like to calculate some properties (like forces or NMR) based solely on the "input guess". How ~is this best done? (Or is it possible at all in GAUSSIAN?) More specifically, I imagine to have some input MOs using the "Guess=Read" command. I would specify a certain DFT method, say, and then go on to calculate the desired properties. What I have tried so far is the following. A) specify a "non-standard route" that resembles a standard route but contains no 500 links. Didn't work because the subsequent links requested some files that had not been written. Perhaps one can do this in a more clever way? B) Specify "SCF(MaxCycle=1)" as well as the appropriate flags to avoid the error termintation due to incomletely converged SCF. These flags are IOp(8/7=1,5/13=1). This procedure comes close to what I want, in particular if I use SCF=QC. However, the one SCF cycle is still too much because it does modify the input MOs as is clearly visible from the output. Hence, I would want to avoid it! Any comments or suggestions? -- I will summarize as usual. Thank you very much! Georg ============================ 1) response by Mike Frisch: From: frisch@lorentzian.com (Mike Frisch) You could probably hack the program to do this, but all of the properties in Gaussian are based on derivative expressions which are derived assuming that the appropriate SCF equations have been solved. In order to use orbitals and or a density that comes from somewhere else, the CPHF/CPKS equations and possibly other terms would need to be modified to reflect how the density was determined and how it changes in response to the perturbations of interest. Mike ============================ 2) response by Rene Fournier: From: Rene Fournier Hello, In most programs the obvious way would be to use simple mixing convergence procedure with a mixing parameter equal to zero. Can you do that in Gaussian? -------------------------------------------------------------------- | Rene Fournier | Bureau/Office 303 Petrie | | Chemistry Dpt, York University | (416) 736 2100 Ext. 30687 | | 4700 Keele Street, Toronto | FAX: (416) 736-5936 | | Ontario, CANADA M3J 1P3 | e-mail: renef@yorku.ca | -------------------------------------------------------------------- ============================ 3) One example of a response suggesting Guess=(Read,Only): (Quite a few people proposed the same thing.) From: Darko Babic Dear George, This is what I've found in the G98 manual: "Guess(Only,Read): May also be used to produce population and other post-calculation analyses from the data in a checkpoint file. For example, these options alone will produce a population analysis using the wavefunction in the checkpoint file. Guess(Only,Read) Prop will cause electrostatic properties to be calculated using the wavefunction in the checkpoint file." I hope this helps. If it doesn't, I am afraid that there is no simple way to achieve this. Please, let me know if this happens. Sincerely, Darko Babic Institute "Rudjer Boskovic" HR-10001 Zagreb, P.O.B. 1016 Croatia ============================ 4) Response by Neil Henson: From: Neil Henson What does it do with "SCF(MaxCycle=0)"? [Comment by G.S.: It goes to the default] How about setting the SCF convergence criteria to something ridiculous so that it is already converged before it starts? [Comments by G.S.: a) there is some maximum possible value for the convergence criteria, and it is still to low. b) it should do one cycle anyhow] Neil. -- * Neil Henson Hartlepool Renaissance: a marina, * * neil.henson@lanl.gov/chimera@hubwest.com a hung monkey and much much more * * http://www.t12.lanl.gov/~njh Tel: 505-667-7795 Fax: 505-665-3909 * * Group T-12, Mail Stop B268, Los Alamos National Laboratory, NM 87545, USA * From chemistry-request@www.ccl.net Fri Jan 8 17:49:55 1999 Received: from achilles.noc.ntua.gr (achilles.noc.ntua.gr [147.102.222.210]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA16320 Fri, 8 Jan 1999 17:49:52 -0500 (EST) Received: from hermes.central.ntua.gr (hermes.central.ntua.gr [147.102.240.3]) by achilles.noc.ntua.gr (8.8.8/8.8.8) with ESMTP id AAA03485 for ; Sat, 9 Jan 1999 00:49:53 +0200 (EET) Received: by hermes.central.ntua.gr with SMTP id AAA19876 ; Sat, 9 Jan 1999 00:45:48 +0200 (EET) Message-ID: <004601be3b58$dea579e0$1bdf6693@titanfocalpoint> From: "Nick Fotopoulos" To: "Computational Chemistry List" Subject: Computational solid state graduate exercise theme ... Date: Sat, 9 Jan 1999 00:47:27 +0200 Dear CCLer's, I am seting up an exercise for engineering students that will present = them with the current achievements of computational chemistry = (especially in the solid state field as many of them follows electrical = engineering). The final target is to stimulate and prepare them to use = the readily available s/w tools or at least be able to operate in = interdisciplinary projects. The exercise approach is molecule --> supermolecular aggr. --> = macromolecules ---> solid state I have already finalized the first 3 phases using freely available s/w = PCGAMESS-US, Hyperchem 5.0 (almost), and Molden.on WIN95 platform, = explaining the various uses of CompChem at differenr levels of theory. I am also aware of BiconEdit program capabilities for DOS and Brillouin = zones prediction at EHMO level. Could you suggest me solid state systems and/or other material that = would be relevant to form a good teaching basis ? Also, are you aware of software capable for solid state calculations at = a level of theory greater than EHMO? I will summarise to the list. Best regards and wishes for a happy & fruitful new year, Dr. Nick Fotopoulos National Technical Univ. of Athens From chemistry-request@www.ccl.net Sun Jan 10 10:49:16 1999 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA22607 Sun, 10 Jan 1999 10:49:15 -0500 (EST) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id KAA14581 for chemistry@www.ccl.net; Sun, 10 Jan 1999 10:49:14 -0500 (EST) Date: Sun, 10 Jan 1999 10:49:14 -0500 (EST) From: "E. Lewars" Message-Id: <199901101549.KAA14581@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: SUMMARY OF RATE/ACTIVATION ENERGY FRIDAY 1999 JAN 8 SUMMARY OF ANSWERS TO ACTIVATION ENERGY/RATE CONSTANT QUESTION Thanks very much to all who replied to my question. Reply #11 is specifically to an earlier question about how to calculate in a simple way a unimolecular rate constant. I now think that the rate constant depends not just on the barrier (TS energy minus reactant energy), but on the *shape* of the transition-state (activated complex) region, the saddle-shaped part of the potential energy surface. So if you fire reactant molecules toward the saddle in a molecular dynamics simulation, they pass more easily over a flat saddle than a steep one, even if the TS's have the same energy. I've never seen it expressed like this, but I think it gives a good pictorial representation of the situation (one could even build a mechanical model to illustrate this). (I see how the shape of the PES can be represented by an analytic function fit to a set of computed (e.g. ab initio)points, but not how partition functions account for the shape) Thanks again to all who helped. E. Lewars ----------- QUESTION 1998 Dec 22, Tuesday True or false: Two reactions with exactly the same free energies of activation (delta G of activation, not Arrhenius activation energy) _must_ have the same rate constants (at the same temperature). E. Lewars =========================== RATE CONSTANT AND BARRIER-QUESTION #1 (From M. J. Kotelyanskii) False, there is a "fundamental frequency" and "transition factor" in front of the exponent.... ------------------------------------------------------------------------------- Michael J. Kotelyanskii Phone (814) 863 43 81 Polymer Science Program FAX (814) 865 29 17 Department of Materials Science and Engineering kotelyan@plmsc.psu.edu Pennsylvania State University http://www.plmsc.psu.edu/~kotelyan University Park, PA 16802, USA -------------------------------------------------------------------------------- =========================== #2 (From A. Bagatur'yants) Certainly false! BTW, what do you mean under "activation energy", next, what kind of reaction (mono-, bi-, etc. molecular). The preexponential factor is important anyway. Best wishes and Happy New Year! Yours Prof. Alexander Bagatur'yants Photochemistry Center, Russian Academy of Sciences ul. Novatorov 7a, Moscow, 117421 Russia Phone: (007-095)-936-2588 Fax: (007-095)-936-1255 E-mail: sasha@icp.rssi.ru Home page: http://www.icp.rssi.ru/eng/bagat/bagat.htm ============ #3 (From J. Villa) As soon as these two reactions are both unimolecular or both bimolecular this is true. However, the problem with the molecularity will be only in the units you w ill use. On the other hand your statement is only true if you do not take into account tunneling corrections or recrossing corrections to the rate constant. This is, t he sentence is only completely true if working in the framework of transition state theory (or variational transition state theory), without any additional correcti on. Jordi Jordi Vill`a Research Group on Medical Informatics Carrer del Doctor Aiguader 80 E-08003 Barcelona Tlf: 34-93-2211009 Fax: 34-93-2213237 jvilla@imim.es http://www1.imim.es/~jvilla ============== #4 (From T. Soelling) Hi, That has to be true (cf. the transition state theory expressions for the rate constant). All the best and happy new year. Theis Soelling ** ** ** ** Mr. Theis Ivan Solling ** ** ** ** ** Department of Chemistry ****** ****** University of Copenhagen ** ** ** DK-2100 Copenhagen ** ** ** Ph. 45-3532-0187/Fax. 45-3532-0212 theis@kalium.kiku.dk ============= #5 >From: IN%"sichelj@Umoncton.ca" "J. Sichel" I can think of two reasons why not. 1. The transition-state-theory expression for k includes a barrier transmission coefficent (denoted by kappa) which may vary between reactions. 2. Transition-state theory may not be exact for the reactions in question. John-M. Sichel Dept. de chimie et biochimie Universite de Moncton Moncton NB, Canada ================ #6 (From Peter Shenkin) >From: IN%"shenkin@still3.chem.columbia.edu" To: IN%"elewars@alchemy.chem.utoronto.ca" "E. Lewars", IN%"sichelj@umoncton .ca" "J. Sichel" > I can think of two reasons why not. > 1. The transition-state-theory expression for k includes a barrier > transmission coefficent (denoted by kappa) which may vary between > reactions. > 2. Transition-state theory may not be exact for the reactions in question. It is partly a matter of definition. If one accepts the definition: k_rate = ( k_boltz * T / h_bar ) exp( -DG_act / RT ) then, by definition, k_rate and DG_act are functionally related and of course any two reactions with the same DG_act must have the same k_rate. I think this is the answer most people would accept. In this picture, DG_act is the value the activation free energy would have if the theory were valid. If the theory is invalid, then the underlying physical picture would be misleading. For instance, if T-variation studies were performed in which DG_act were dissected into a DH_act and a DS_act, the DH_act would not really correspond to the enthalpy difference between reactants and transition state on some PE surface. OTOH, if DG_act is computed by some other means, such as by an exact classical calculation on an exactly correct potential-energy surface, then in fact the above equation will be correct only to the extent that transition-state theory (or, ahem, activated-complex theory) is applicable. For example, where tunnelling is important, the k_rate calculated from the computed DG_act would be much smaller than the experimental k_rate. -P. *** "Freedom's just another word for nothing left to lose." (B. Yeltsin)*** *Peter Shenkin; Chemistry, Columbia U.; shenkin@columbia.edu (212)854-5143* * MacroModel URL: http://www.cc.columbia.edu/cu/chemistry/mmod/mmod.html * ============ #7 (From Christopher Cramer) Depends on whether you consider quantum effects (e.g., tunneling) to be included in a phenomenological free energy of activation or to be part of the prefactor kappa. If you are DEFINING a model where the only prefactor to the exponential of -deltaG(dubdag)/RT is k(B)T/h, then your statement is true, trivially. CJC Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 Phone: (612) 624-0859 || FAX: (612) 626-2006 cramer@pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer ========== #8 (From Alan Shusterman) False. The preexponential term is usually written kT/h but I think the correct term is kT^n/h where "T^n" depends on the kinetic = line 1 [h for help]order of the reaction. If this is correct, then two reactions could = have identical delta G* but different rate constants because of = different kinetic orders. Alan (Let me know if I've screwed this up.) Alan Shusterman Department of Chemistry Reed College Portland, OR www.reed.edu/~alan ============ #9 (From Alexei Kubasov) Subject: Re: CCL:RATE CONSTANT AND BARRIER-QUESTION Date: Wed, 30 Dec 1998 09:31:44 +0300 I think that answer is no. The full expression for k according the transition-state-theory includes coefficient the value of which depends on probability of a) non-adiabatic processes and b) tunnel effects. Besides this the transition-state-theory can not describe some processes (monomolecular ones for example). Alexei A.Kubasov Moscow State University ================ #10 (Sorry--lost name) Subject: Re: CCL:RATE CONSTANT AND BARRIER-QUESTION Date: Thu, 31 Dec 1998 12:23:31 EST False. Sould consider how many molecules are involved in the reactions. ================ #11 Wei-To Chan chan@ihamilton.wlu.ca Sat Jan 9 18:32:37 EST 04:52:59 -0500 (EST) Hi, this is a response to your enquiry about rate constant calculation for HNC/HCN isomerisation posted to CCL before christmas. It may be kind of late to reply now but perhaps it is because HNC/HCN is a subject (my entire phd thesis is about this single reaction) that has haunted me to this date I can't seem to let go your enquiry. I must note that I am writing this comment on your request and others' comments from memory and so my account may not address the issue precisely. The HNC/HCN isomerisation was actually used as an example to illustrate simple rate constant calculation in Gilbert and Smith's book "Theory of unimolecular and recombination reations" on pg 39-41. I also remembered seeing a end-of-the chapter question from Steinfeld, Franciso and Hases "chemical reaction and dynamics" on evaluation of HNC/HCN reaction based on ab initio results. Assuming you have run an ab initio calculation of the equilibrium HNC structure and the HNC/HCN isomerisation transition state you can simply plug several set of data from each of the molecules into the transition state theory formulae. If you obtained the results from say gaussian (or possibly GAMESS) you will obtain the vibrational, rotational and entropies of the structure from a harmonic vibration calculation. You then simply substitute the data from gaussian into the formulae K_{uni} = A * exp(-E/kT) = (kT/h)*(Q^(ts)/Q^HNC)*exp(-E/kT) where K_{uni} is the high pressure unimolecular rate constant (low pressure value has to be evaluated with RRKM master equation method) k is the boltzman constant, Q^(ts) is the total entropy of the transition state. The total entropy is obtained from multiplication of rotatonal entropy and vibrational entropy. For unimolecular reaction the translation entropy of both the TS and the reactant are identical and you can ignore it. The total vibrational entropy of the TS must *NOT* include the single imaginary frequency corresponding to the motion in the direction of the reaction path. With gaussian 9x and possibly GAMESS exclusion of the imaginary frequency from the printed values. E is the critical energy (or zero-temperature barrier height) evaluated as the difference in the zero-point energies (zpe) of HNC and the TS. With gaussian 9x you simply subtract the printed out value of the total energy (zpe included) for HNC from that of the TS. Note that if your reaction is a bimolecular rather than unimolecular reaction E will have to be evaluated as an enthalpy (H). If your ab initio program only evaluate the harmonic vibrations for you then you have to take the trouble of turning to you calculator and evaluate the vibrational and rotational entropy from the computed harmonic vibrations and rotational constants. The relevant equations can be found handily from Gilbert and Smith or from Steinfeld et. al. This is not a diffcult task for HNC/HCN. But for large molecules you may want to use a program like UNIMOL which is part of Gilbert and Smith's book to avoid tedious evaluation of vibrational entropy from tens of harmonic vibrations. If you can't even compute the vibrational and rotational entropies from molecular orbital calculations then you have to 'guess' their values. Experimental values may be available for the reactant for the TS you may use methods as described in "Thermochemical kinetics: methods for the estimation of thermochemical data and rate parameters" by Sidney Benson I also feel compeled to comment several CCLers' commetns. One fellow CCLer urged to compute the barrier height to the highest degree of accuracy possible. While an accurate estimate certainly is desirable you must note that the energy barrier determined from the transition state formulae K_{uni} = A * exp(E/kT) is *NOT* the barrier height evaluated from the ab initio method. Even precluding the limitation of transition state theory itself substitution of an EXACT ab initio barrier height (and exact entropy values) into the above formulae won't get you the exact rate constant. chemical kineticist determine the barrier height by fitting the measured rate data into the above equation to obtain E. But the equation is to some degree emperical. A theorist shouldn't equate the experimental barrier height with the ab initio value. It is true that the rate constant is so sensitive to the barrier height that it is not likely that you would be lucky to get an estimate of the rate to within a factor of three. But it is quite possible to get a reasonably accurate value of the frequency factor using DFT. For the purpose of kinetic modelling and evaluation of trend of reactivities across a series of related molecules tansition state theory could be a useful tool. Someone recommend you using Don Truhlar's program POLYRATE. I've never used Truhlar's program but I know it specialize in microcanonical variational transition state theory and tunneling rate coefficent. Such method is required for reaction without a sharp barrier (like some dissociation reactions) or low-temperature reactions that involve proton transfer. Such method is terribly time consuming (it requires caculation of a reaction pathyway and a number of hessian along the pathway) and require quite a bit of expertise. Truhlar's program is an inappropriate................. recommendation for evaluation of rate for isomerisation and most reactions with a barrier height. Someone also pointed out that it is very unlikely to obtain meaningful rate constant from transition state theory. You certainly can't expect TST to be a quantitative tool like ab initio method. TST used as a semi-quantitative is a very valuable tool. For instance experimentalist can deduce the nature of the reactant from the value of A (Gilbert and smith pg 7-8). Drawing from my own recent experience I was led by invoking TST to understand why is it that rate of reaction for certain intramolecular nucleophilic addition reaction via formation of 3-membered ring TS actually can be substanitally faster than same reaction via formation of less strained 4 and 5-membered ring. It turned out that entropy of the TS is significantly sensitive to the ring size in these reactions. By using TST to examine rate of reactions acrossing a series of reaction valuable insight can be gained. Wai-To Chan Department of Chemistry York University, Toronto =================== From chemistry-request@www.ccl.net Sun Jan 10 14:30:12 1999 Received: from inorg.chem.ethz.ch (elwood.ethz.ch [129.132.65.20]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA23174 Sun, 10 Jan 1999 14:30:11 -0500 (EST) Received: from [192.33.93.28] (dynppp28.dialup.ethz.ch [192.33.93.28]) by inorg.chem.ethz.ch (8.8.8/8.8.8) with ESMTP id VAA17492 for ; Sun, 10 Jan 1999 21:40:00 +0100 X-Sender: senn@elwood.ethz.ch Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Sun, 10 Jan 1999 20:29:57 +0100 To: chemistry@www.ccl.net From: Hans Martin Senn Subject: RE:SUMMARY OF RATE/ACTIVATION ENERGY A very recent paper which is related to this question: B.K. Carpenter, "Dynamic Behavior of Organic Reactive Intermediates", Angew. Chem. Int. Ed. 1998, 38, No. 24, 3340-3350. (Full text available as PDF file at http://www.Wiley-VCH.de/contents/jc_2002/199824.html; some nice animations from Carpenters group can be seen at http://www.chem.cornell.edu/~bkl1/dynamics.html) It discusses problems and limitations of the commonly used statistical approaches. Regards Hans Martin Senn ........................................................................... Hans Martin Senn Swiss Federal Institute of Technology (ETH) Phone +41 (0)1 632 4460 Laboratory of Inorganic Chemistry Fax +41 (0)1 632 1310 ETH Zentrum, CAB C20 E-Mail senn@inorg.chem.ethz.ch Universitaetstrasse 6 CH-8092 Zuerich, Switzerland From chemistry-request@www.ccl.net Sun Jan 10 22:37:13 1999 Received: from smtp.263.net ([202.96.44.19]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id WAA24571 Sun, 10 Jan 1999 22:37:07 -0500 (EST) Message-Id: <199901110337.WAA24571@www.ccl.net> Received: (fmail 4423 invoked from network); 11 Jan 1999 11:34:17 -0000 Received: from unknown (HELO luoxch) (166.111.11.167) by 202.96.44.19 with SMTP; 11 Jan 1999 11:34:17 -0000 Date: Mon, 11 Jan 1999 11:38:3 +0800 From: lvtun Reply-To: lvtun@263.net To: ccl discution Subject: Cacu metal chelating clusters,use what software X-mailer: FoxMail 2.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear CCLs: I want to caculat the energy of thiol-metal chelating cluster.It include six CH3CH2S and two Zn++ or Cd++ formed two metal chelating cluster,I want to caculate the change of potential of this structure with regard to the distance between sulphur atom to the metal ion and the distance between the two metal ions,can you suggest me what kinds of method and what software is most perfect,a shared software is best. Thank you. sincerely yours LVTUN Dept.Biosci&Biotech Tsinghua University Beijing,10084 P.R.China