From Y0H8797@ACS.TAMU.EDU Wed Dec 4 01:51:01 1996 Received: from VMS2.TAMU.EDU for Y0H8797@ACS.TAMU.EDU by www.ccl.net (8.8.3/950822.1) id BAA19348; Wed, 4 Dec 1996 01:03:23 -0500 (EST) Date: Wed, 4 Dec 1996 0:03:19 -0600 (CST) From: YONG HUANG To: CHEMISTRY@www.ccl.net Message-Id: <961204000319.2053a6a8@ACS.TAMU.EDU> Subject: pKa in NH3 Does anybody know where I can find pKa of phenol and some carboxylic acids in non-aqueous solution such as ammonia? I spent a whole night in the library and couldn't find it. Thanks very much. Yong From Giulia.Caron@ict.unil.ch Wed Dec 4 03:51:02 1996 Received: from unilmta3.unil.ch for Giulia.Caron@ict.unil.ch by www.ccl.net (8.8.3/950822.1) id DAA19969; Wed, 4 Dec 1996 03:07:13 -0500 (EST) Received: from pcbep5008b.unil.ch by unilmta3.unil.ch with SMTP inbound; Wed, 4 Dec 1996 09:06:49 +0100 Message-Id: <2.2.16.19961204091442.08ff564e@ulys.unil.ch> X-Sender: gcaron@ulys.unil.ch X-Mailer: Windows Eudora Pro Version 2.2 (16) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: "Giulia Caron (la Perla di Losanna)" Subject: About VAMP: summary Date: Wed, 4 Dec 1996 08:06:52 +0000 Thank you very much to people who answered me! Here is the summary of mails I received! My original question was >Dear CCLers, > >I like before giving correct assignment to NMR spectra, to have predictions >of chemical shift by semi empirical methods. VAMP 5.1 (Oxford Molecular) >uses neural nets to extimate from the wave function the spectroscopic >properties of molecules but I don't know how it works. >Can you help me? > >Thank you very much! > > Giulia Answers 1. Dear Giulia, How big systems do you want to calculate? If it less than 50-80 atoms I would suggest to work with Density Functional Theory (DFT) based methods rather than with semiempirical. The results normally will be more reliable. Please, find below some references. Best regards, Vladimir Malkin REFERENCES. \item {\bf Malkin V.G., Malkina O.L, Eriksson L.A., and Salahub D.R.} "The Calculation of NMR and ESR Spectroscopy Parameters Using Density Functional Theory", in: "Modern Density Functional Theory: A Tool for Chemistry"; Theoretical and Computational Chemistry, Vol. 2, Eds. J. M. Seminario, P. Politzer, Elsevier, Amsterdam, 1995. \item {\bf Malkin V.G., Malkina O.L., and Salahub D.R.} "Calculation of Spin-Spin Coupling Constants Using Density Functional Theory", Chem. Phys. Lett. 221 (1994) 91. \item {\bf Malkin V.G., Malkina O.L., Casida M.E., and Salahub D.R.} "Nuclear Magnetic Resonance Shielding Tensors Calculated with a Sum-Over-States Density Functional Perturbation Theory", J. Am. Chem. Soc., 116 (1994) 5898. \item {\bf Kaupp M., Malkin V.G., Malkina O.L., and Salahub D.R.} "Calculation of Ligand NMR-Chemical Shifts in Transition-Metal Complexes Using ab Initio Effective-Core Potentials and Density Functional Theory.", Chem. Phys. Lett. 235 (1995) 382 . \item {\bf Kaupp M., Malkin V.G., Malkina O.L., and Salahub D.R.} "Scalar Relativistic Effects on $^{17}$O NMR Chemical Shifts in Transition-Metal Oxo Complexes. An ab Initio-ECP/DFT Study.", J. Am. Chem. Soc. 117 (1995) 1851. \item {\bf Malkin V.G., Malkina O.L., and Salahub D.R.} "Influence of Intermolecular Interactions on the NMR Shielding Tensors in Solid $\alpha$-Glycine.", J. Am. Chem. Soc. 117 (1995) 3294. \item {\bf Woolf T.B., Malkin V.G., Malkina O.L., Salahub D.R., and Roux B.} "The Backbone $^{15}$N Chemical Shift Tensor of the Gramicidin Channel: A Molecular Dynamics and Density Functional Study", Chem. Phys. Lett. 239 (1995) 186. \item {\bf Kaupp M., Malkin V.G., Malkina O.L., and Salahub D.R.} "Ab Initio ECP/DFT Calculation and Interpretation of Carbon and Oxygen NMR Chemical Shift Tensors in Transition-Metal Carbonyl Complexes", Chem. Eur. J. 2(1996)24 \item {\bf Malkin V.G., Malkina O.L., and Salahub D.R.} "Comment on Density Functional Calculation of Nuclear Magnetic Resonance Chemical Shifts", J.Chem.Phys. 104(1996)1163 \item {\bf Malkin V.G., Malkina O.L., Steinebrunner G. and Huber H.} "Solvent Effect on the NMR Chemical Shieldings in Water Calculated by a Combination of Molecular Dynamics and Density Functional Theory", Chem. Eur. J. 2(1996)452 \item {\bf Fedotov M.A., Malkina O.L. and Malkin V.G.} "$^{35/37}$Cl NMR Chemical Shifts and Nuclear Quadrupole Couplings for Some Small Chlorine Compounds: Experimental and Theoretical Study", Chem. Phys. Lett., 258(1996)330. \item {\bf Malkin V.G., Malkina O.L., and Salahub D.R.} "Spin-Orbit Correction to NMR Shielding Constants From Density Functional Theory", Chem. Phys. Lett. 261 (1996), 335. \item {\bf Godbout N., Malkin V.G., Malkina O.L., and Salahub D.R.} "Density Functional Calculations of Deuterium Nuclear Quadrupole Coupling Constants", J. Chem. Phys., submitted. \item {\bf Eriksson L.A., Malkin V.G., Malkina O.L., and Salahub D.R.} "Investigation of Moessbauer Parameters for a set of Iodine Compounds using Gradient Corrected Density Functional Theory", Int. J. Quantum Chem., in press. \item {\bf Malkina O.L., Salahub D.R., and Malkin V.G.} "NMR Spin-Spin Coupling Constants From Density Functional Theory: Problems and Results", J. Chem. Phys., 105 (1996) 8793. \item {\bf Kaupp M., Malkina O.L., Malkin V.G.} "Interpretation of $^{\bf 13}$C NMR Chemical Shifts in Halomethyl Cations. A Cautionary Note on the Importance of Spin-Orbit Coupling and Electron Correlation", Chem. Phys. Lett., submitted. ############################################################### # Dr. Vladimir G. Malkin # # Senior Research Scientist # # Institute of Inorganic Chemistry # # Slovak Academy of Sciences # # Dubravska cesta 9 malkin@savba.sk # # SK-84236 Bratislava Fax (42-7) 373-541 # # Slovakia Phone (42-7) 378-2923 # ############################################################### 2. Dear Giulia, you can find all details on the method how Vamp predicts 13C chemical shifts in: T.Clark, A.Breindl, G.Rauhut: "A Combined semiempirical MO/Neural Net Technique for Estimating 13C chemical shifts." J. Mol. Model., 1995, 1(1), 22-35. An abstract can be found at URL: http://science.springer.de/jmm/abstracts/1995/clark.html If you have any questions, problems, suggestions, etc. with Vamp, please have a look at our WWW page at: http://www.ccc.uni-erlangen.de/info/OML/Vamp/ you will find references to the literature, information on coming updates (version 6.0 should be here for Christmas), and much more. or just contact the nearest Oxford Molecular helpdesk; for Switzerland that is: me. All the best, Wolfgang Sauer -- PS: Informationen ueber OM finden Sie auch im WWW unter URL: http://www.ccc.uni-erlangen.de/info/OML/about-OML_d.html Dr. Wolfgang Sauer ------------ | ## ## ## | Oxford Molecular - CCC | ## ## ## | Naegelsbachstr. 25 | ###### | D-91052 ERLANGEN, FRG | ## | | ## | Tel : +49 9131 8796 10 | #### | Fax : +49 9131 8796 11 ------------ 3. Dear Giulia Caron, VAMP version 5.6,6.0 and the newest release 6.1 is able to estimate 13C- chemical shifts via a combination of MO-calculations and a back-propagation neural network (Lit.: T. Clark, G. Rauhut,A. Breindl J. Mol. Model.1995,1,22). Originally introduced for neutral organic compounds, this technique has been expanded to estimate carbocations and carbanions. VAMP 6.1 is available from Oxford Molecular Ltd. ( http://www.oxmol.co.uk ). your sincerely Andreas Breindl -- Meine Adresse: Dipl.-Chem. Andreas Breindl CCC ( Computer Chemie Centrum ) Institut fuer Organische Chemie I der Uni Erlangen-Nuernberg Naegelsbachstr. 25 D-91052 Erlangen Tel. 09131-85-6581 e-mail: breindl@organik.uni-erlangen.de \\|// ( @ @ ) .---------------------oOOo----(_)----oOOo-----------------------------------. | La Perla di Losanna | ICT | | Giulia Caron | Section de Pharmacie | | mail : giulia.caron@ict.unil.ch | UNIVERSITE DE LAUSANNE | | tel: ++41 21/692-4528 | BEP CH-1015 Lausanne | | fax : +41 21/692-4505 Oooo. | Switzerland | | ( ) Oooo. | | .----------------------------\ (----( )-----------------------------------. \_) ) / (_/ From kelterer@fptchbds01.tu-graz.ac.at Wed Dec 4 04:51:03 1996 Received: from fptchbds01.tu-graz.ac.at for kelterer@fptchbds01.tu-graz.ac.at by www.ccl.net (8.8.3/950822.1) id EAA20232; Wed, 4 Dec 1996 04:16:33 -0500 (EST) Received: by fptchbds01.tu-graz.ac.at (5.57/Ultrix3.0-C) id AA15610; Wed, 4 Dec 96 11:15:28 +0100 Date: Wed, 4 Dec 96 11:15:28 +0100 From: kelterer@fptchbds01.tu-graz.ac.at (M.Kelterer) Message-Id: <9612041015.AA15610@fptchbds01.tu-graz.ac.at> To: chemistry@www.ccl.net Subject: MMFF94-BatchMin-distribution adress? Cc: kelterer@fptchbds01.tu-graz.ac.at Dear Netters, I'd like to use the program MMFF94 -- either in BatchMin version 5.5 from Clark Still's group -- or the earlier Cerius2 implementation of MMFF93 from MSI. Who can help me with the email- or fax-adress of the group who is distributing these programs, the costs of the programs and/or experience with performance, handling, etc ? Kelterer Anne-Marie Institut f. Physikal.u. Theoret. Chemie TU Graz, Austria e-mail: Kelterer@fptchbds01.tu-graz.ac.at From manz@chemie.fu-berlin.de Wed Dec 4 08:51:14 1996 Received: from eagle.chemie.fu-berlin.de for manz@chemie.fu-berlin.de by www.ccl.net (8.8.3/950822.1) id IAA21221; Wed, 4 Dec 1996 08:27:37 -0500 (EST) Received: by eagle.chemie.fu-berlin.de (1.37.109.16/16.2) id AA164126008; Wed, 4 Dec 1996 14:26:48 +0100 Date: Wed, 4 Dec 1996 14:26:44 +0100 (MEZ) From: "Prof. Manz" X-Sender: manz@eagle.chemie.fu-berlin.de To: molecular-dynamics-news@mailbase.ac.uk Cc: spectroscopy-group@mailbase.ac.uk, CHEMISTRY@www.ccl.net Subject: "Hydrogen Transfer: Experiment and Theory" Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: QUOTED-PRINTABLE Deutsche Bunsen-Gesellschaft f=FCr Physikalische Chemie International Discussion Meeting "Hydrogen Transfer: Experiment and Theory" Freie Universit=E4t Berlin, September 10 - 13.1997 Organizers: H.H.Limbach and J.Manz, Freie Universit=E4t Berlin Announcement This discussion meeting will deal with all experimental and theoretical aspects of hydrogen and proton transfer dynamics in molecules embedded in different phases. The meeting will be held at the Dahlem Campus of the Fachbereich Chemie of the Freie Universit=E4t Berlin. Hotel rooms are avail= abe at a price of 80 DM/night (single room) and 110 DM/night (double room) including breakfast. A moderate registration fee will be taken. Those wishing to contribute papers should submit a brief abstract of about 200 words before April 15, 1997 as a word for windows file, either per email or diskette. Acceptance will be confirmed by 15th May 1997 and will indicate whether the paper is accepted for oral presentation or for poster presentation. The proceedings of the meeting will be published as a special issue of the Berichte der Bunsengesellschaft f=FCr Physikalische Chemie. Fo= r inclusion in these proceedings authors should submit their manuscripts not later than the conference itself. All current information concerning this conference will be announced in the Internet under http://WWW.chemie.fu-berlin.de/~htrans Correspondence should be sent to: H.H.Limbach and J.Manz, Freie Universit=E4t Berlin, Fachbereich Chemie, Takustrasse 3, D-14195 Berlin, Germany, Tel.: +49-30-838-5375, Fax :+49-30-838-5310, EMail: selim@chemie.fu-berlin.de ---------------------------------------------------------------------------= - REGISTRATION FORM FOR ALL PARTICIPANTS INCLUDING INVITED SPEAKERS Please complete and return the following form to: selim@chemie.fu-berlin.de I would like to attend the International Discussion Meeting "Hydrogen Transfer: Experiment and Theory" Freie Universit=E4t Berlin, September 10 - 13. 1997 Name: First Name: Title: Affiliation/Address: I am interested in participation at the meeting: Yes I would like to reserve room at the Studenthotel: single room for 1 person/double room for 2 persons, nights from ??? to ??? I would like to receive further circulars: Yes I would like to make a contribution: poster/oral I have been already invited for a talk: title in preliminary programme is correct/not correct Title: Authors: Affiliation: Abstract: ---------------------------------------------------------------------------= - PRELIMINARY SCHEDULE (alphabetical order of speakers) Session A: Coherent vs. Incoherent Hydrogen Dynamics 1. J.Bargon, Bonn, NMR: Ortho- and parahydrogen induced nuclear spin polarization during transition metal catalyzed reactions 2. G.Buntkowsky, Berlin: Spin quantum fynamics of D2 in transition metal complexes 3. B.Chaudret, Toulouse, France: NMR studies of transition metal hydrides 4. J.P.Daudey, Toulouse, France: Ab initio studies of transition metal hydrides 5. J.Eckert, Los Alamos, USA: Inelastic neutron scattering of transition metal hydrides 6. O.Eisenstein, Montpellier, France: Ab initio studies of transition metal hydrides 7. R.R.Ernst/R.Meyer, Z=FCrich, Switzerland: NMR hydrides and carboxylic acids 8. J.M.Lluch, Barcelona, Spain: Quantum phenomena in transition-metal polyhydride and dihydrogem complexes. Session B: Thermally Activated Proton Transfer Across or Through a Barrier 1. J.Elguero, Madrid, Spain: Proton transfer and hydrogen bonding in solid pyrazoles 2. B.Nickel, G=F6ttingen: Anomaly of triplet energy transfer from 2-(2=92-hydroxyphenyl)-benzoxazole and similar compounds exhibiting a dual phosphorescence due to intramolecular proton transfer. 3. A.J.Horsewill, Nottingham, UK: The quantum dynamics of the hydrogen Bond. 4. S.Takeda, Osaka, Japan: Proton dynamics in interacting hydrogen bonds in crystals. 5. H.P.Trommsdorf, Grenoble, France: Proton dynamics in hydrogen bonded crystals: Studies by optical spectroscopy, NMR and neutron scattering. Session C: Proton Transfer in Excited States 1. A.Douhal, Toledo, Spain: The involvement of rotational processes in the intramolecular proton or H-atom transfer cycle 2. T.Els=E4sser, Berlin, Germany: Excited state proton transfer of aromatic molecules in liquids: Femtosecond reaction dynamics, vibrational coherence and energy redistribution. 3. N.Ernsting, Berlin, Germany: ZEKE Spectroscopy of an ESIPT System: The structure of the molecular radical cation and implications for femtosecond spectroscopy. 4. R.Knochenmuss, Z=FCrich, Switzerland: Mechanistic aspects of the naphthol-to-water excited state proton transfer reaction. 5. M.Quack/M.Suhm, Z=FCrich, Switzerland: Spectroscopy and quantum dynamics of proton transfer in hydrogen fluoride complexes and their isotopomers. 6. J.Waluk, Warsaw, Poland: Excited state Proton transfer in organic molecules. Session D: Proton Dynamics and Localization in Strong Hydrogen Bonds 1. I.Alkorta, Madrid, Spain: Ab initio studies of proton transfer in condensed phase 2. G.S.Denisov/N.S.Golubev, St.Petersburg, Russia, NMR, IR, UV studies of coupled low barrier hydrogen bonded systems 3. M.M.Kreevoy, Minneapolis, USA: The Hydrogenic Potential Function in Solid Sodium Hydrogen Bis(4-nitrophenoxide) Dihydrate. 4. Ch.Perrin, San Diego, USA: Symmetries of Hydrogen Bonds in Solution. 5. J.Sauer, Berlin, Germany: Proton transfer in adsorption complexes on acidic zeolite catalysts. Ab Initio Studies. 6. S.Scheiner, Carbondale, USA: Proton transfer in electronically excited states. 7. L.Sobczyk, Wroclaw, Poland: IR, UV and NMR manifestations of proton transfer equilibria in phenols - amine systems. Session E: Proton Transfer in Complex Systems: Liquids, Surfaces, Biomolecules etc. 1. J.Brickmann, Darmstadt, Germany: Proton Migration in Water 2. M.Edgar, Berlin, Germany: Br=F6nstedt centers in surfaces 3. W.Junge, Osnabr=FCck, Germany: Rotatory Catalysis by Proton-Translocating ATP-Synthase 4. R.Hemplemann, Saarbr=FCcken, Germany: Hydrogen Diffusion Mechanism in Proton Conducting Oxides by means of Quasielastic Neutron Scattering. 5. J.T.Hynes, Boulder, USA: proton dynamics in the liquid state 6. J.Klinman, Berkeley, USA: Hydrogen Transfer in Enzyme Reactions 7. K.D.Kreuer, Stuttgart, Germany: Proton transport in oxides and hydrooxides 8. M.Parrinello, Stuttgart, Germany: Ab-initio Simulation of Proton Transfer Processes. 9. R.L.Schowen, Lawrence, USA: The Contribution of Proton Bridges to the Catalytic Power of Enzymes. From rochus@felix.anorg.chemie.tu-muenchen.de Wed Dec 4 12:51:07 1996 Received: from felix.anorg.chemie.tu-muenchen.de for rochus@felix.anorg.chemie.tu-muenchen.de by www.ccl.net (8.8.3/950822.1) id MAA22612; Wed, 4 Dec 1996 12:07:09 -0500 (EST) Received: by felix.anorg.chemie.tu-muenchen.de (940816.SGI.8.6.9/930416.SGI) for chemistry@www.ccl.net id SAA05050; Wed, 4 Dec 1996 18:06:27 +0100 From: "Rochus Schmid" Message-Id: <9612041806.ZM5048@felix> Date: Wed, 4 Dec 1996 18:06:25 +0100 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: concerted reaction/ kinetics Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear netters, Please help me with the understanding of the following problem: I can calculate the thermodynamics of a reaction cascade AB + C --> A + B + C --> AC + B The first step is the dissociation of B and the second is the association of C. The energy barrier (if association and dissociation don't have a barrier, e.g. a simple morse potential like bond breaking) is equivalent to the dissociation energy: AB --> A + B right? Now, if this reaction (or substitution) would be concerted BA + C --> [ B-A-C ]# --> B + AC the barrier is the energy between BA + C and the TS [ B-A-C ]. right? This is probably (from the point of energy) lower than the two step mechanism. However, I have the feeling, that the free energy barrier will be different, since C must "meet" BA, wich should somehow reduce the probability of the reaction. OK Am I right? Or is this stupid? And is there any possibility after calculating both barriers to estimate the free energies? In other words: if the barrier for the concerted reaction is lower, does it really happen that way? Thanx in advance for any replies. I will summarize. Rochus -- ******************************************************************************** Rochus Schmid Technische Universitaet Muenchen Tel. ++49 89 2891 3140 Lehrstuhl f. Anorganische Chemie 1 Fax. ++49 89 2891 3088 Prof. W. A. Herrmann E-mail: Lichtenbergstrasse 4 rochus@felix.anorg.chemie.tu-muenchen.de 85747 Garching ******************************************************************************** From berriz@chasma.harvard.edu Wed Dec 4 14:51:07 1996 Received: from chasma.harvard.edu for berriz@chasma.harvard.edu by www.ccl.net (8.8.3/950822.1) id OAA28436; Wed, 4 Dec 1996 14:50:03 -0500 (EST) Received: by chasma.harvard.edu (AIX 3.2/UCB 5.64/4.03) id AA01607; Wed, 4 Dec 1996 14:48:31 -0500 Date: Wed, 4 Dec 1996 14:48:31 -0500 From: berriz@chasma.harvard.edu (Gabriel Berriz) Message-Id: <9612041948.AA01607@chasma.harvard.edu> To: chemistry@www.ccl.net Subject: Advice needed: Complete overhaul of computer system Dear netters: I hope this question is not deemed inappropriate. This morning, our lab's director surprised us with the news that he intends a complete overhaul of our computer system, and I would like to ask for your advice (from end users, that is; no vendors, please). Basically, everything is up for replacement, all the way down to Unix flavor and resource management policies. As a very rough measure of what I'm talking about, we're looking at a system of about 5-10 workstations, plus peripherals. We need at least 10 *intelligent terminals*, but we are uncertain as to the best set up to simultaneously solve this requirement, and the need for raw number-crunching power. Our work consists of developing and running simulation code, as well as using some commercial packages such as CHARMM, &c. Our principal concerns are (roughly in order of preference): 1. manageability, where I include both system upkeep and resource allocation (CPU time, disk space, &c.); (we cannot afford a full-time sysadmin, so the problem of management lands on hapless graduate students, who usually have little sysadmin expertise and who'd rather spend their time finishing their dissertations.) 2. system stability (we have been burnt lately by a couple of very deluxe "crashing prima donna" workstations...). 3. performance (raw computing power, development-friendly environment, software availability, graphics). And of course: 4. cost. We would greatly appreciate to hear advice, comments, cautionary tales, raunchy jokes, &c. from anyone who has recent experience with setting up a similar system. Thank you very much. Gabriel Berriz berriz@chasma.harvard.edu Department of Chemistry and Chemical Biology Harvard University From jdurant@mephisto.ca.sandia.gov Wed Dec 4 15:13:02 1996 Received: from mephisto.ca.sandia.gov for jdurant@mephisto.ca.sandia.gov by www.ccl.net (8.8.3/950822.1) id OAA28396; Wed, 4 Dec 1996 14:38:51 -0500 (EST) Received: by mephisto.ca.sandia.gov (950413.SGI.8.6.12/890607.SGI) (for ) id TAA28699; Wed, 4 Dec 1996 19:36:46 GMT From: jdurant@mephisto.ca.sandia.gov (Joe Durant) Message-Id: <199612041936.TAA28699@mephisto.ca.sandia.gov> Subject: CCL:concerted reaction/ kinetics To: chemistry@www.ccl.net Date: Wed, 4 Dec 1996 11:36:46 -0800 (PST) Cc: rochus@felix.anorg.chemie.tu-muenchen.de X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi! Your questions seem to boil down to two fundamental ones: 1) can one calculate the "free energy of activation" for the reaction AB + C -> [B-A-C]# -> B + AC ? and 2) where is [B-A-C]# energetically located relative to the reactants? If the reaction takes place in the gas phase then the answer (with caveats) to 1 is yes. To get the free energy of activation you need to know relative energies of the species, rotational constants and vibrational frequencies. Throw in some statistical mechanics and you will have an answer. (far easier said than actually done :-)) As to the second question I would direct you back to Johnston's BEBO method. He treats this sort of a reaction, and looks at the thermodynamics as follows: in going from AB + C to [BAC] you have partially broken the AB bond, and partially made a BC bond. Additionally, you have a anti-bonding B-C interaction (assuming A is an atom), which will be repulsive. The general atom-transfer reaction treated this way will have a barrier, with the barrier height being maximum for a thermoneutral reaction, and decreasing for more exothermic reactions. If A is a polyatomic fragment the above analysis no longer holds, and you are left with the task of deciding whether a (meta)stable BAC molecule can be formed. Hope this helps. Joe -- #################################################################### # Joe Durant voice: (510) 294-3343 # # Mail Stop 9057 FAX: (510) 294-2276 # # Sandia National Laboratories jdurant@ca.sandia.gov # # Livermore, CA 94551 http://mephisto.ca.sandia.gov # #################################################################### From M.Biggs@surrey.ac.uk Wed Dec 4 17:51:10 1996 Received: from mailc.surrey.ac.uk for M.Biggs@surrey.ac.uk by www.ccl.net (8.8.3/950822.1) id RAA11015; Wed, 4 Dec 1996 17:39:59 -0500 (EST) Message-Id: <199612042239.RAA11015@www.ccl.net> Received: from surrey.ac.uk by mailc.surrey.ac.uk id <10890-0@mailc.surrey.ac.uk>; Wed, 4 Dec 1996 22:39:58 +0000 Subject: important figures to ask for To: chemistry@www.ccl.net Date: Wed, 4 Dec 1996 22:39:57 +0000 (GMT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit From: Dr Mark J Biggs Sender: M.Biggs@surrey.ac.uk Hi All! We have been fortunate enough to recieve an award to buy a mini-supercomputer and a supporting workstation. We would like to see some 3D colour graphics capabilities included in the workstation and so I have a few questions that I am sure you will be able to answer: 1. What are the important graphics benchmarks - number of shaded polygons, number of vectors and/or others ???? 2. I have noticed that one vendor mentions the size of the polygons, the type of shading, that the polygons are lit, 3D, Z-buffered (I think that is all). Is there infact any standard for garphics benchmarks or do manufactrers play with the numbers. If there is some standard, what is it????? The same goes for vectors (3D, lit (?), randomly orientated, Z-buffered and double-buffered). 3. Does double buffering allow the machine to draw an image "behind" another as one is being rendered on screen thus allowing for smooth movements on-screen ????? 4. "Alpha planes" are used for transparency I think (?), what are "stencil planes" (in bits) and "overlay planes" used for????? Many thanks to all those who respond and if there is any interest, I shall summarize to the CCL. Dr Mark Biggs Department of Chemical and Process Engineering University of Surrey From jose@zeus.uncor.edu Wed Dec 4 18:01:19 1996 Received: from zeus.uncor.edu for jose@zeus.uncor.edu by www.ccl.net (8.8.3/950822.1) id QAA06445; Wed, 4 Dec 1996 16:57:07 -0500 (EST) Received: by zeus.uncor.edu; id AA03896; Wed, 4 Dec 1996 19:02:03 -0200 Sender: jose@zeus.uncor.edu Message-Id: <32A5E6CB.237C@zeus.uncor.edu> Date: Wed, 04 Dec 1996 19:02:03 -0200 From: "Dr. Jose Santiago Duca (h)" Organization: INFIQC - Dpto Qca Organica - Facultad de Ciencias Quimicas - Universidad Nacional de Cordoba - Agencia Postal 4 - CC 61 (5016) - Cordoba - ARGENTINA - tel.: +54-51-33-4170 / +54-51-33-4173 fax: +54-51-33-4174 X-Mailer: Mozilla 3.0Gold (X11; I; OSF1 V3.0 alpha) Mime-Version: 1.0 To: chemistry@www.ccl.net Cc: jose@zeus.uncor.edu Subject: HELP: kinetics and computers Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers, I got a problem (maybe completely out of theme, if so my sincere apologies) with the following experimental system because I cannot find the corresponding global kinetic equation, k1 I0 ----> I1 + X ka I1 + Nu ----> I2 kT I2 + R1 ----> P1 + I0 k2 I3 ----> I4 + X ka I4 + Nu ----> I5 kT I5 + R2 ----> P2 + I3 K12 I0 + R2 <====> R1 + I3 (this is a fast equilibrium, K12=k12/k21) kT I5 + R1 ----> P2 + I0 kT I2 + R2 ----> P1 + I3 This system correspond to a SRN1 competition reaction of two substrates by a nucleophile, and the problem with it is that the limitant steps are those of k1 and k2 constants, which take place LATER than the fast equilibrium reaction, so P1 and P2 are linked... I know that all intermediates (I0, ...I5) can be treated as in stationary state, but... what I want to know is the expressions of dP1/dt and dP2/dt (much better (dP1/dt)/(dP2/dt) as the relative rates) as functions of the initial quantities of R1, R2 and maybe of P1 and P2 since **the only thing** I can messure is the final yield of the products P1 and P2!! I have been trying to deal with this problem with no success because I am not an expert on kinetics and I haven't found any useful example on kinetic books, so I am asking you for help. Is there any program that can manage systems like that or simulate kinetic systems in order to find the kinetic equation, or does anybody know about a reference of similar systems or something? Do there exist any people who can help me or give me some useful advice about how to solve the system? Any comments are welcome, Thank you in advance. Jose -- Dr. Jose Santiago Duca (h) e-mail: jose@zeus.uncor.edu URL: http://zeus.uncor.edu/jsd/jsd.htm From kneth@serf2.Colorado.EDU Wed Dec 4 22:51:12 1996 Received: from serf2.Colorado.EDU for kneth@serf2.Colorado.EDU by www.ccl.net (8.8.3/950822.1) id VAA18402; Wed, 4 Dec 1996 21:58:08 -0500 (EST) Received: from localhost by serf2.Colorado.EDU via SMTP (920330.SGI/911001.SGI) for chemistry@www.ccl.net id AA14447; Wed, 4 Dec 96 19:57:33 -0700 Date: Wed, 4 Dec 1996 19:57:22 -0700 (MST) From: Kenneth Geisshirt To: "Dr. Jose Santiago Duca (h)" Cc: chemistry@www.ccl.net Subject: Re: kinetics and computers In-Reply-To: <32A5E6CB.237C@zeus.uncor.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr. Duca, If you need a numerical simulation of any kinetic scheme, I might have a program that can help you. But then you need the numerical values of the rate constants and so on. The program can be downloaded from my home page at address: http://virgil.ruc.dk/~kneth/software.html - the program is called KCI. The manual is not yet completed, but some parts can the read on-line at the same address. Best wishes Kenneth +-----------------------------------------------------------------+ | Kenneth Geisshirt Ph.D.-student | | Department of Life Sciences and Chemistry, Roskilde University | | Currently at: University of Colorado at Boulder | +-----------------------------------------------------------------+ | kneth@fatou.ruc.dk http://virgil.ruc.dk/~kneth/ | +-----------------------------------------------------------------+ | Geek Code 2.1: d++h--s!gp2!aua-w+vc+U++p+L++3EN++K-W---M- | | !V-po+Y+t!5jRG?!tvb++D+B?e---u+h--grn++y+ | +-----------------------------------------------------------------+