From chemistry-request@www.ccl.net Fri Nov 27 02:34:36 1998 Received: from phys.uni.torun.pl (deneb@class1.phys.uni.torun.pl [158.75.5.35]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id CAA21813 Fri, 27 Nov 1998 02:34:27 -0500 (EST) Received: (from deneb@localhost) by phys.uni.torun.pl (8.8.7/8.8.8/rchk1.20) id IAA16841 for chemistry@www.ccl.net; Fri, 27 Nov 1998 08:33:47 +0100 (MET) From: Robert Jankowski Message-Id: <199811270733.IAA16841@phys.uni.torun.pl> Subject: Question: computer models of water To: chemistry@www.ccl.net Date: Fri, 27 Nov 1998 08:33:47 +0100 (MET) X-Mailer: ELM [version 2.4ME+ PL40 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear Netters, I am looking for a paper with a comparison of different computer models of water used in MD simulations, e.g TIP3, TIP4, SPC, etc. Could you please, help me? I will summarize responses. Yours sincerely, Robert Jankowski, PhD student --------------------------------------- e-mail: deneb@phys.uni.torun.pl Molecular Biophysics Group, Institute of Physics, N.Copernicus Univ., 87-100 Torun, Poland ul. Grudziadzka 5 From chemistry-request@www.ccl.net Fri Nov 27 03:09:41 1998 Received: from hartree.chem.kuleuven.ac.be (hartree.quantchem.kuleuven.ac.be [134.58.49.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA21902 Fri, 27 Nov 1998 03:09:38 -0500 (EST) Received: from localhost (steven@localhost) by hartree.chem.kuleuven.ac.be (8.9.0/8.9.0) with ESMTP id JAA20106 for ; Fri, 27 Nov 1998 09:09:17 +0100 Date: Fri, 27 Nov 1998 09:09:17 +0100 (NFT) From: Steven Creve To: Computational Chemistry List Subject: CCL:ECP introduction Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, can anyone point me to a good introduction on the basic theory of ECP's, and their use. I'm especially interested to see some working equations of their implemantation in HF theory. thanks, Steven -------------------------------------------------------------------------- Steven Creve steven.creve@chem.kuleuven.ac.be Labo Quantumchemie Celestijnenlaan 200F 3001-HEVERLEE tel: (32) (16) 32 73 93 BELGIUM fax: (32) (16) 32 79 92 From chemistry-request@www.ccl.net Fri Nov 27 03:25:59 1998 Received: from hermes.bmc.uu.se (hermes.bmc.uu.se [130.238.39.159]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA21988 Fri, 27 Nov 1998 03:25:58 -0500 (EST) Received: from alpha2.bmc.uu.se ([130.238.37.65]) by hermes.bmc.uu.se (post.office MTA v2.0 0813 ID# 0-17733) with SMTP id AAA1609; Fri, 27 Nov 1998 09:22:18 +0100 Received: from munch.bmc.uu.se by alpha2.bmc.uu.se; (5.65v3.2/1.1.8.2/30Jan97-1111AM) id AA21645; Fri, 27 Nov 1998 09:25:53 +0100 Date: Fri, 27 Nov 1998 09:25:53 +0100 (MET) From: David van der Spoel X-Sender: spoel@munch.bmc.uu.se To: Robert Jankowski Cc: chemistry@www.ccl.net Subject: Re: CCL:Question: computer models of water In-Reply-To: <199811270733.IAA16841@phys.uni.torun.pl> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 27 Nov 1998, Robert Jankowski wrote: >I am looking for a paper with a comparison of different computer >models of water used in MD simulations, e.g TIP3, TIP4, SPC, etc. >Could you please, help me? I will summarize responses. > We have just published a systematic comparison of such models: @Article{Spoel98a, author = {D. van der Spoel and P. J. van Maaren and H. J. C. Berendsen}, title = {A systematic study of water models for molecular simulation}, year = 1998, journal = BTjcp, volume = 108, pages = {10220-10230} } furthermore you should have a look at the excellent review by Zhu et al which has 500+ references: @Article{Zhu94, author = {S-B. Zhu and S. Singh and G. W. Robinson}, title = {Field-Perturbed Water}, journal = BTacp, year = 1994, volume = 85, pages = {627-731} } Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@www.ccl.net Fri Nov 27 05:03:27 1998 Received: from melba.fkem2.lth.se (melba.fkem2.lth.se [130.235.27.82]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id FAA22380 Fri, 27 Nov 1998 05:03:26 -0500 (EST) Received: from texugo (fb.fkem2.dial.lth.se [130.235.237.95]) by melba.fkem2.lth.se (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id LAA04783; Fri, 27 Nov 1998 11:16:58 +0100 Message-Id: <199811271016.LAA04783@melba.fkem2.lth.se> From: "Fernando Luis Barroso da Silva" To: Cc: " Subject: Re: CCL:Question: computer models of water Date: Fri, 27 Nov 1998 10:58:55 +0100 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit > Dear Netters, > > I am looking for a paper with a comparison of different computer > models of water used in MD simulations, e.g TIP3, TIP4, SPC, etc. > Could you please, help me? I will summarize responses. > > Yours sincerely, > > Robert Jankowski, PhD student Hello Robert! I good start point is: W.L.Jorgensen et al, "Comparison of simple potential functions for simulating liquid water", JCP 79(2) 926, 1983. There is a useful table about this comparison in a paper written by M.Levitt. The reference is Chemica Scripta 29A, 197 (1989). Best regards, Fernando. -- Fernando Luis Barroso da Silva Physical Chemistry II - Chemical Center POB 124 - Lund University Fax: +46 (46) 2224543 S-221 00 Lund, Sweden Phone: +46 (46) 2228241 (lab) E-mail: fernando@melba.fkem2.lth.se +46 (46) 2220381 (office) Fernando_Luis.Barroso_da_Silva@fkem2.lth.se http://www.fkem2.lth.se/personnel/fernando/dasilva.html http://idefix.ffclrp.usp.br/barroso/fernando.html From chemistry-request@www.ccl.net Fri Nov 27 05:32:18 1998 Received: from moorea.uni-muenster.de (MOOREA.UNI-MUENSTER.DE [128.176.126.33]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA22475 Fri, 27 Nov 1998 05:32:11 -0500 (EST) Received: from localhost (chan@localhost) by moorea.uni-muenster.de (8.8.7/8.7.5) with ESMTP id KAA23178 for ; Fri, 27 Nov 1998 10:31:31 GMT Date: Fri, 27 Nov 1998 11:31:28 +0100 (MEZ) From: "Jerry C.C. Chan" To: CHEMISTRY@www.ccl.net Subject: CCL:fortran to C problem (solved) In-Reply-To: <365DAC12.2721BF2A@netgenics.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I am grateful to all of you who answered my post. As pointed out by many of you, the three functions f01ajf, x02ajf and f02amf come from the commercial Numerical Algorithm Group's (NAG) Fortran Library, http://www.nag.co.uk/numeric/FLOLCH.html, and equivalent Lapack codes can be obtained freely at http://www.netlib.org. Thanks a lot, Jerry ****************************************************************** * Jerry Chun Chung CHAN chan@uni-muenster.de * * Universitaet Muenster phone: 0049-251-83-29156 * * Institut fuer Physikalische Chemie fax: 0049-251-83-29159 * * Schlossplatz 4-7 * * D-48149 Muenster * * Germany * ****************************************************************** ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@www.ccl.net Fri Nov 27 05:45:35 1998 Received: from idun.phc.chalmers.se (idun.phc.chalmers.se [129.16.97.44]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA22594 Fri, 27 Nov 1998 05:45:33 -0500 (EST) Received: from fkrs2.phc.chalmers.se (fkrs2.phc.chalmers.se [129.16.97.48]) by idun.phc.chalmers.se (8.8.8/8.8.7) with ESMTP id LAA23825; Fri, 27 Nov 1998 11:45:32 +0100 Received: (from svedung@localhost) by fkrs2.phc.chalmers.se (8.8.8/8.8.8) id LAA15126; Fri, 27 Nov 1998 11:45:31 +0100 Date: Fri, 27 Nov 1998 11:45:29 +0100 (MET) From: Harald Svedung To: Robert Jankowski cc: chemistry@www.ccl.net Subject: Re: CCL:Question: computer models of water In-Reply-To: <199811270733.IAA16841@phys.uni.torun.pl> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII There is a study of the energy transfer between water molecules in gas phase using different potentials ( RWK2, MCY, LJC... ) by Liu Ming et al, J.Chem. Phys., Vol. 104, 9001. /Harald On Fri, 27 Nov 1998, Robert Jankowski wrote: > Dear Netters, > > I am looking for a paper with a comparison of different computer > models of water used in MD simulations, e.g TIP3, TIP4, SPC, etc. > Could you please, help me? I will summarize responses. > > Yours sincerely, > > Robert Jankowski, PhD student > --------------------------------------- > e-mail: deneb@phys.uni.torun.pl > > > Molecular Biophysics Group, > Institute of Physics, > N.Copernicus Univ., 87-100 Torun, Poland > ul. Grudziadzka 5 > Harald Svedung (M.Sc.) phone: +46-31-7722816 Department of Chemistry fax: +46-31-167194 Physical Chemistry home phone: +46-31-240897 Goeteborg University home e-mail: harald.svedung@svedung.pp.se SE-412 96 Goeteborg, Sweden www.che.chalmers.se/~svedung/ From chemistry-request@www.ccl.net Fri Nov 27 09:54:15 1998 Received: from bastion.nmrc.ucc.ie (nmrc.ucc.ie [143.239.64.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA23575 Fri, 27 Nov 1998 09:54:04 -0500 (EST) Received: from odessa.nmrc.ucc.ie (odessa.nmrc.ucc.ie [143.239.64.65]) by bastion.nmrc.ucc.ie (8.9.1a/8.9.1) with ESMTP id OAA13434 for ; Fri, 27 Nov 1998 14:55:06 GMT From: Michael Nolan Message-Id: <199811271454.OAA28265@rennes.nmrc.ucc.ie> Subject: force-field for semiconductors To: chemistry@www.ccl.net (ccl) Date: Fri, 27 Nov 1998 14:54:16 +0000 (GMT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Hi all, I have a quick question for you all... My boss is doing lattice calculations on GaAs using force-field calculations within Cerius2. The only FF which we expect any kind of results from is the Universal FF (Goddard and co-workers). So does anyone know (i)if this FF gives good results for such systems (also of interest would be Si-Ge or Si etc etc)? (ii) if not are there any other FFs we could use? Thank you in advance for your time Michael ************************************************************************** Mr. Michael Nolan Materials Modelling Section, Advanced Materials and Technologies Group National Microelectronics Research Centre Lee Maltings, Prospect Row Cork IRELAND mail: mnolan@nmrc.ucc.ie Tel: + 353 21 90 4113 http://nmrc.ucc.ie/projects/ape/ http://nmrc.ucc.ie/groups/AMT/modellingRes.html EMRS Call for papers: http://nmrc.ucc.ie/groups/AMT/SympMain.html **************************************************************************** From chemistry-request@www.ccl.net Fri Nov 27 12:47:24 1998 Received: from Sun.Farlep.Net (Sun.Farlep.Net [208.244.48.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA24302 Fri, 27 Nov 1998 12:47:22 -0500 (EST) Organization: Farlep-Internet Received: from farlep.net (L103.Farlep.Net [208.244.49.229]) by Sun.Farlep.Net (8.9.1/8.9.0/Farlep-Mail-2.0) with ESMTP id TAA20289; Fri, 27 Nov 1998 19:46:54 +0200 (EET) Message-ID: <365EE2CE.92927113@farlep.net> Date: Fri, 27 Nov 1998 19:35:10 +0200 From: Alexander Herega X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: "jkl@ccl.net" , "chemistry@www.ccl.net" Subject: Thanks References: <35E7E771.DFDB1B56@farlep.net> Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Hello. I'd like to liquidate my subscribtion for the conference for a certain time. Thank you very much for cooperation. Alexander Herega From chemistry-request@www.ccl.net Fri Nov 27 14:31:15 1998 Received: from mail-d.bcc.ac.uk (mail-d.bcc.ac.uk [144.82.100.24]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA25532 Fri, 27 Nov 1998 14:31:15 -0500 (EST) Received: from xtallography (actually host xtallography.geol.ucl.ac.uk) by mail-d.bcc.ac.uk with SMTP (XT-PP); Fri, 27 Nov 1998 19:31:15 +0000 Message-Id: <3.0.6.32.19981127193158.007b4220@pop-server.ucl.ac.uk> X-Sender: ucfbaro@pop-server.ucl.ac.uk X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Fri, 27 Nov 1998 19:31:58 +0000 To: "CHEMISTRY@www.ccl.net" From: "Artem R. Oganov" Subject: Image capturing software In-Reply-To: <36321F73.52BD4D8@ust.hk> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi, Does anybody know any free image capturing programs (PZP or something else, but better if it works with Win95)? Also, does anybody know where can I find FORTRAN77 compiler for DOS? Cheers, Artem. ---------------------------------------------- Artem R. Oganov, Affiliate Research Student, University College London, Gower Street, WC1E 6BT, London, UK From chemistry-request@www.ccl.net Tue Nov 24 05:15:18 1998 Received: from techunix.technion.ac.il (chrmiri@techunix.technion.ac.il [132.68.1.28]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA00729 Tue, 24 Nov 1998 05:15:01 -0500 (EST) Received: (from chrmiri@localhost) by techunix.technion.ac.il (8.9.1/8.8.5) id MAA24818; Tue, 24 Nov 1998 12:14:30 +0200 (IST) Date: Tue, 24 Nov 1998 12:14:30 +0200 (IST) From: Miri Karni To: chemistry@www.ccl.net cc: molecular-dynamic-news@mailbase.ac.uk Subject: Symposium on "Frontiers in Electronic Structure Calculations" Message-ID: ------------------------------------------------------------- The Institute for Advanced Studies in Theoretical Chemistry ********** The Lise Meitner - Minerva Center for Computational Chemistry ------------------------------------------------------------- "Frontiers in Electronic Structure Calculations" Department of Chemistry, Lecture Hall Number 1 Technion - Israel Institute of Technology, Haifa, Israel http://www.technion.ac.il/technion/chemistry/IASTC/Ap 13th December, 1998 09:00 - 09:30 Registration & Welcome Drinks 09:30 - 09:50 Welcome Greetings Chairperson: N. Moiseyev 09:50 - 10:40 Keiji Morokuma: "The ONIOM (our Own N-layered Integrated molecular Orbital and Molecular Mechanics) Method and its Applications to Accurate Calculations of Large Molecular Systems" 10:40 - 11:10 Roi Baer: "Electronic Structure of Large Systems: Towards an order-N ab initio Density Functional Theory" 11:10 - 11:30 Coffee Break Chairperson: D. Kost 11:30 - 12:20 Martin Head-Gordon: "Electron Correlation and Nonorthogonal Orbitals" 12:20 - 13:10 Uzi Kaldor: "High-accuracy Calculations for Heavy and Superheavy Atoms and Molecules" 13:10 - 15:00 Lunch Chairperson: B. Gerber 15:00 - 15:50 Richard A. Friesner: "Scalable Correlated Ab Initio Quantum Chemical Calculations: From Small Molecules to Proteins" 15:50 - 16:40 Sason Shaik: "Some Attempts at "Marrying" VB and DF Theories" 16:40 - 17:20 Coffee Break Chairperson: A. Goldblum 17:20 - 18:00 Frank Weinhold: "NBO/NRT Analysis of Main Group and Transition Metal Ions: Bond Ionicity, Electronegativity, and Ionic-Covalent Transitions" 18:00 - 19:45 POSTER SESSION & Coffee Break 20:00 Conference Dinner 14th December, 1998 Chairperson: R. Pauncz 09:00 - 09:50 Sigrid D. Peyerimhoff: "Spectroscopy of Molecules and Clusters by Computational Methods" 09:50 - 10:40 Joachim Sauer: "Combining Quantum Mechanics and Interatomic Potential Functions for Structure, Spectroscopy and Reactivity of Large Systems" 10:40 - 11:10 Coffee Break Chairperson: S. Shaik 11:10 - 12:00 Jurgen Gauss - The Lise Meitner Lecture: "Spin-restricted Coupled-cluster Theory for the Treatment of Open-shell Systems" Chairperson: S. Hoz 12:00 - 12:30 Uri Peskin: "Models for Nearest Neighbour Effects on Proton Transfer Rates in a Crystalline Environment: A Combined Experimental and Theoretical Approach" 12:30 - 13:00 Andreas Dreuw: "Free Stable Mixed Silicon-carbon Dianions" 13:00 - 14:30 Lunch Chairperson: A. Pross 14:30 - 15:20 Harold Basch: "Theoretical Reaction Mechanisms in Catalytic and Enzymatic Systems" 15:20 - 16:10 Wolfram Koch: "Transition Metal Compounds: Accurate Calculations and Mechanistic Studies" 16:10 - 16:40 Coffee Break Chairperson: B. Fuchs 16:40 - 17:10 Jan M. L. Martin: "Benchmark ab initio Thermochemistry for First- and Second-row Molecules by Means of Systematic Basis Set Extrapolations" 17:10 - 18:00 Helmut Schwarz: "Theory-enforced Re-investigation of the Origin of Unprecedently Large Metal-carbon Bond Strength in [Pd-CH2I]+" 18:00 - 18:30 Closing Comments ****************************************************************************** Dr. Miri Karni Department of Chemistry Technion - Israel Institute of Technology Haifa 32000 Israel e-mail: chrmiri@tx.technion.ac.il FAX:972-4-8233735 PHONE:972-4-8293056 ****************************************************************************** From chemistry-request@www.ccl.net Tue Nov 24 10:31:06 1998 Received: from mailbox.univie.ac.at (mailbox.univie.ac.at [131.130.1.26]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA02849 Tue, 24 Nov 1998 10:30:59 -0500 (EST) Received: from barolo.itc.univie.ac.at (barolo.itc.univie.ac.at [131.130.39.19]) by mailbox.univie.ac.at (8.8.4/8.8.4) with SMTP id QAA48798 for ; Tue, 24 Nov 1998 16:30:57 +0100 Message-ID: <365AD11F.1D13@univie.ac.at> Date: Tue, 24 Nov 1998 16:30:39 +0100 From: Werner Jakubetz Reply-To: werner.jakubetz@univie.ac.at Organization: Theoretical Chemistry/University of Vienna X-Mailer: Mozilla 3.0Gold (Win95; I) To: chemistry@www.ccl.net Subject: Workshop announcement ___________________________________ WINTER-WORKSHOP "REACTION DYNAMICS" MARIAPFARR (AUSTRIA) ___________________________________ The annual Theoretical Chemistry Winter-Workshop of the Austrian Chemical Society in Mariapfarr (a resort in the Austrian Alps) will take place from 16 to 19 February 1999. The 1999 workshop is dedicated to reaction dynamics. Invited Lecturers are G.G. Balint-Kurti (Bristol), G.D. Billing (Copenhagen), R. Jaquet (Siegen) and U. Manthe (Freiburg). Workshop language is English. For the full program, informations on the scope and format of the workshop and on Mariapfarr, and for all matters related to registration please visit the Mariapfarr-Homepage at http://www.kfunigraz.ac.at/tchwww/sax/mariapfarr/index_eng.html Werner Jakubetz _______________________________________________ Prof. Werner Jakubetz Institute for Theoretical Chemistry and Radiation Chemistry University of Vienna, Austria Address: Währingerstrasse 17 A-1090 Wien Austria Phone: +43-1-4277-52758 Fax: +43-1-4277-9527 email: werner.jakubetz@univie.ac.at _______________________________________________ From chemistry-request@www.ccl.net Wed Nov 25 07:04:43 1998 Received: from Raven.und.ac.za (Raven.und.ac.za [146.230.128.50]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA11219 Wed, 25 Nov 1998 07:04:17 -0500 (EST) Received: from gwise-smtp.und.ac.za (GWise-SMTP.und.ac.za [146.230.128.63]) by Raven.und.ac.za (8.8.3/8.7.3) with SMTP id OAA01279 for ; Wed, 25 Nov 1998 14:03:48 +0200 (SAT) Received: from Routing-Domain-Message_Server by gwise-smtp.und.ac.za with Novell_GroupWise; Wed, 25 Nov 1998 14:03:47 +0200 Message-Id: X-Mailer: Novell GroupWise 5.2 Date: Wed, 25 Nov 1998 13:37:21 +0200 From: "Gert Kruger" To: chemistry@www.ccl.net Subject: The use of ONLY p-orbitals in Gaussian calculation Dear CCL, I would like to experiment with the basis sets in Gaussian (purely for educational purposes). Can one specify the basis set in such a way using only p-orbitals for a specific calculation? Any references/pointers would be welcome. Gert Kruger ___________________________________ Dr HG Kruger, Chemistry, University of Natal P.O. box 18091, Dalbridge 4014 Durban, South Africa. tel: +27-31-2603090 fax: +27-31-2603091 email: kruger@scifs1.und.ac.za ___________________________________ From chemistry-request@www.ccl.net Wed Nov 25 08:31:50 1998 Received: from bastion.nmrc.ucc.ie (nmrc.ucc.ie [143.239.64.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA11723 Wed, 25 Nov 1998 08:31:46 -0500 (EST) Received: from odessa.nmrc.ucc.ie (odessa.nmrc.ucc.ie [143.239.64.65]) by bastion.nmrc.ucc.ie (8.9.1a/8.9.1) with ESMTP id NAA09646 for ; Wed, 25 Nov 1998 13:32:48 GMT From: Michael Nolan Message-Id: <199811251332.NAA27323@rennes.nmrc.ucc.ie> Subject: peptide rotation barrier To: chemistry@www.ccl.net (ccl) Date: Wed, 25 Nov 1998 13:32:00 +0000 (GMT) X-Mailer: ELM [version 2.4 PL25] Hello all, Thank you to all who amswered my question about rotation about a peptide link. I had thought that estimating the barrier using only single point calcs would not be valid. In particular, starting at the trans conformation and stepping along the torsion mentioned below, at 45^{o} one finds a barrier of over 700kCal/Mol, which indicates a poor geometry (B-LYP/6-31G*). With PCFF it is even worse...... However that was the only set of calculations I had the resources to carry out (we have one SGI O2 with a MIPS R10K 174MHz processor and it runs flat out 24 hours a day) Original Question.... Dear all, I'm studying the link formed between p-aminophenol (AP) and p-hydroxybenzoic acid (HBA). The bond formed between the two molecules is the peptide link X O \ / \ / N-----C / \ / \ H X Now according to the biochemists the most stable conformation is the trans configuration (steric reasons etc etc) We computed a rotational barrier (trans->cis for HBA-AP), simply by stepping 15 degree incremenets along the torsion X-N-C-O and calculating single point energies (our resources are so meagre that we cannot do optimisations for each structure). We used B-LYP/6-31G* and also the PCFF force-field. B-LYP gave a large barrier (hundreds of kCal/mol) and the FF gave ridiculous results. At least we could see that the barrier to rotation from trans to cis is very high, which I guess you would expect. I have a couple of questions.... 1: Would it be in people's opinion valid to use PCFF for MD simulations of this system? Bearing in mind for HBA we used the PCFF force-field successfully and I guess we would like to be consistent in our use of force-field. 2: Is it valid to estimate the barrier to rotation around the peptide link only from single point calculations? 3: Has anyone looked at this barrier before? I have looked at a number of databases for AP and only got rubbish and a chemical abstracts search was none too successful. I would appreciate any refs. at all Summary as usual Thanking you for your time Michael **************************************************************************** Answer 1: >From strasner@chem.ucla.edu Thu Oct 29 13:46:56 1998 Dear Micheal, a couple of years ago I was interested in peptides and computed rotational barriers. They are only semiempirical and there should be newer ab initio calculations. But it might give you an idea: "A semiempirical AM1, MNDO and PM3 study of the rotational barriers of various ureas, thioureas, amides and thioamides", M. Feigel, T. Strassner, J. Mol. Structure, 283 (1993) 33 - 48. Additionally concerning your questions: Single points are not acceptable, because you create unreasonable geometries. This is also the reason for the high barrier you got. The above mentioned paper gives you some idea about experimental gas phase NMR data of amides. The CAS search you mentioned should have provided above mentioned paper. Thomas Answer 2: >From spoel@xray.bmc.uu.se Thu Oct 29 15:59:48 1998 Hi Michael, I've just been busy studying omega angles from MD simulations, and found in our force field (GROMOS) that the angles are roughly a gaussian distribution around 180 (sigma=16), with min and max roughly 120 to 240 degrees. I think this distribution maybe slightly too wide however. The transition from trans to cis is possible in the testtube however, especially for proline, but I think there are also some other examples of cis peptide bonds in the protein database (Ala?). Here are some refs: @Article{Ramachandran68, author = {G. N. Ramachandran and V. Sasisekharan}, title = {Conformation of Polypeptides and Proteins}, journal = {Advan. Protein Chem.}, year = 1968, volume = 23, pages = {283-437} } @Article{Eggleton85, author = {D. S. Eggleton and D. J. Hodgson}, title = {Intramolecular water bridge and a distorted trans peptide bond in the crystal structure of {$\alpha$}-{L}-glutamyl-{L}-aspartic acid hydrate}, journal = {Intern. J. Pept. Prot. Res.}, year = 1985, volume = 26, pages = {509-517} } @Article{HeadGordon91a, author = {T. Head-Gordon and M. Head-Gordon and M. J. Frisch and C. L. {Brooks III} and J. A. Pople}, title = {Theoretical study of blocked glycine and alanine peptide analogues}, journal = {J.Am. Chem.Soc.}, year = 1991, volume = 113, pages = {5989-5997} } @Article{Burton93a, author = {N. A. Burton and S. {S-L}. Chiu and M. M. Davidson and D. V. S. Green and I/ A/ Hillier and J. J. W. {McD}ouall}, title = {Rotation about the {C_N} bond in formamide: {A}n ab initio Molecular Oribital study of structure and Energetics in the gas phase and in solution}, journal = {J.Chem.Soc.Far.Trans}, year = 1993, volume = 89, pages = {2631-2635} } @Article{MacArthur96a, author = {M. W. Mac{A}rthur and J. M. Thornton}, title = {Deviations from Planarity of the Peptide Bond in Peptides and Proteins}, journal = {J.Mol.Biol.}, year = 1996, volume = 264, pages = {1180-1195} } Please post your results. Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Answer 3: >From harrison@physics.phy.uab.edu Thu Oct 29 16:44:36 1998 Mr. Nolan, I recall having done something similar for peroxynitrite (OONO) some years back and found that the barrier obtained by just stepping through torsion angle was much larger (seem to recall an order of magnitude) than what we finally found by a transition state calculation. What seemed to be the culprit for the misleading result was that as one would go through various torsion angles, some of the other bond lengths would change when actual relaxation of the structure was allowed. In our case the extremely small cis-trans barrier was key to understanding some of the kinetics and the overall role of superoxide dismutase in ALS. See for example, J. M. Tsai, et.al. JACS 116, 4145(1994). Best Regards, Joe Harrison Dept. of Physics Univ. of Alabama at Birmingham Answer 4: >From asmellie@combichem.com Thu Oct 29 16:57:02 1998 I see one problem immediately with this approach: As you step the torsions, one might expect internal bond angles to change. In particular, as VDW interactions rise as 1 / R^12, as two atoms get closer during the torsion rotation, internal bond angles are likely to open to relieve the VDW energy. Look at the example of the central torsion of butane: C1---C--(T)--C---C2 If T = 180, C1 and C2 are maximally distant and VDW energy in minimized If T = 0, C1 and C2 are closest and one or more of the internal C-C-C bond angles opens to relieve the strain. Hope this helps, --andrew Dr. Andrew Smellie, CombiChem Inc. 1804 Embarcadero Road, Palo Alto, CA 94303 Phone: (650)-842-0560 FAX: (650-842-0575 email: asmellie@combichem.com Answer 5: >From soperpd@esvax.email.dupont.com Thu Oct 29 17:08:17 1998 Michael, Optimizing with PCFF in the trans position gives an energy of -46 kcal/mol and a C-N-C-C dihedral of 179 deg. Simply changing that dihedral to 0 deg and reoptimizing gives an energy of -44 kcal/mol and a dihedral of 21 deg. If the dihedral is constrained to zero degrees with a 1000 kcal/mol quadratic restraint the potential energy is still -44 kcal/mol. The phenyl rings must be free to rotate relative to the peptide bond. Paul Soper Answer 6: >From fau@mailer.uni-marburg.de Fri Oct 30 16:56:24 1998 Dear Michael, concerning your 2nd question I think that single-point calcs on dihedrally modified geometries will lead to poor results. Due to the changing interaction of the CO-pi-bond with the N-lone-pair (and the NX and NH antibonding orbitals) I expect the molecular geometry to change substantially in NC bond length and to a lesser degree in: * CO bond length * XNC, HNC, NCO and NCX' bond angles Therefore I would prefer to do partial optimizations of the dihedrally modified geometries, thereby optimizing a few important geometry variables. To my limited knowledge force fields are parametrized against (typically experimental) minima and are therefore of limited use for non-minimum structures. To get an idea of the accuracy of your dihedrally modified geometry approach, you could compare the geometries and energies of a cis-conformer created by dihedral modification of the FF-optimized trans-conformer and a FF-optimized cis-conformer. Just my 0.02$, Stefan Stefan Fau Fachbereich Chemie der Philipps-Universität Marburg 35032 Marburg, Deutschland From chemistry-request@www.ccl.net Wed Nov 25 10:28:39 1998 Received: from mail1.cityweb.de (mail1.cityweb.de [193.189.224.217]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA12587 Wed, 25 Nov 1998 10:28:35 -0500 (EST) Received: from cityweb.cityweb.de (ess8-m154-58.pool.cww.de [62.52.154.58]) by mail1.cityweb.de (8.9.1/8.9.1/powered by Telemedia) with SMTP id QAA15107 for ; Wed, 25 Nov 1998 16:28:02 +0100 (MET) Message-ID: <001901be1888$23776a40$3a9a343e@cityweb.cityweb.de> From: "Klaus-D. Warzecha" To: Subject: Correct representation of carbanions in HyperChem MM+ Date: Wed, 25 Nov 1998 16:27:29 +0100 Dear all, concerning the proper handling of tertiary alkyl carbanions in force field calculations (HyperChem MM+), I would like to ask for some advice. Taking methyl cyclohexane as a model, removal of the hydrogen from the tertiary carbon changes the atom type of the latter from C4 (sp3) to CR (radical, sp2). Adding a charge of -1 to this centre then gives a first representation of the carbanion. This simple model however fails to reproduce the expected pyramidal geometry of the carbanionic centre. Which modifications would necessary to obtain a more accurate representation (still in HyperChem's MM+): 1. Changing the type of the negatively charged carbon from CR to C4 or, 2. Addition of a lone pair, or 3. A combination of both ? Would this refined approach allow to calculate the relative energies of two conformers emerging from the "umbrella effect" of a carbanion ? (The rate for "flipping the carbanion" certainly is much higher than for chair-chair-interconversion of a cyclohexane and thus for any given ring conformer, two "anion conformers" should be in equilibrium.) It's rather meaningless in the the case of the methyl cyclohexane anion but might be interesting for higher substituted cyclohexanes. In that cases, these energies might be taken to explain possible stereoselectivity in the protonation of the respective species. I'm looking forward to your hints and comments. If you feel that the problem shouldn't be handled at all using a force field model, don't hesitate to suggest alternative approaches. However please notice that I'm not a theoretical chemist and thus would prefer the most simple model, rather than the most complex but more accutate one. Regards, Klaus-D. Warzecha From chemistry-request@www.ccl.net Fri Nov 27 23:57:20 1998 Received: from send106.yahoomail.com (send106.yahoomail.com [205.180.60.43]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id XAA27603 Fri, 27 Nov 1998 23:57:19 -0500 (EST) Message-ID: <19981128045719.26414.rocketmail@send106.yahoomail.com> Received: from [129.6.31.30] by send106.yahoomail.com; Fri, 27 Nov 1998 20:57:19 PST Date: Fri, 27 Nov 1998 20:57:19 -0800 (PST) From: anstrom nanometer Subject: TINKER->Distance Geometry->Docking To: CHEMISTRY@www.ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear all, Has anyone ever used TINKER's distance geometry function to docking application? I will be grateful to receive any input files template to work as an example to me. Thanks ! Hongyu Zhang CARB, University of Maryland _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com