From rabe@fu-berlin.de Mon Jul 1 05:57:36 1996 Received: from ki1.chemie.fu-berlin.de for rabe@fu-berlin.de by www.ccl.net (8.7.5/950822.1) id FAA21163; Mon, 1 Jul 1996 05:38:30 -0400 (EDT) Received: by ki1.chemie.fu-berlin.de (Smail3.1.28.1) from fermi.chemie.fu-berlin.de (160.45.26.7) with smtp id ; Mon, 1 Jul 96 11:38 MEST Received: by fermi.chemie.fu-berlin.de (Smail3.1.28.1) from Fermi.Chemie.FU-Berlin.DE (127.0.0.1) with smtp id ; Mon, 1 Jul 96 11:38 MEST Sender: rabe@www.ccl.net Message-ID: <31D79C85.237C@fu-berlin.de> Date: Mon, 01 Jul 1996 11:38:13 +0200 From: Bjoern Rabenstein Organization: Freie Universitaet Berlin, Germany X-Mailer: Mozilla 2.02 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Computational Chemistry Mailing List Subject: Background Charges with SPARTAN Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi! In GAUSSIAN (92) there is an easy way of including background charges in the calculation. (simply write "CHARGE ") Does anybody know a way to do this in SPARTAN? Thanks and bye! -- Bjoern Rabenstein * Freie Universitaet Berlin * Inst. f. Biochemie Inst. f. Kristallographie * AG Knapp * Takustrasse 6 * D-14195 Berlin [Telephon] +49-30-838-3484 [Telefax] +49-30-838-3464 privat-> [Telephon] +49-30-7057858 [Telefax] +49-30-7051527 [email] rabe@fu-berlin.de [WWW] http://www.chemie.fu-berlin.de/~rabe/ From tsai@chu1.chem.nthu.edu.tw Mon Jul 1 06:57:39 1996 Received: from chu1.chem.nthu.edu.tw for tsai@chu1.chem.nthu.edu.tw by www.ccl.net (8.7.5/950822.1) id GAA21394; Mon, 1 Jul 1996 06:38:31 -0400 (EDT) Received: by chu1.chem.nthu.edu.tw (AIX 3.2/UCB 5.64/4.03) id AA23113; Mon, 1 Jul 1996 18:01:08 +0800 Date: Mon, 1 Jul 1996 18:01:08 +0800 From: tsai@chu1.chem.nthu.edu.tw (Ming-Song Tsai) Message-Id: <9607011001.AA23113@chu1.chem.nthu.edu.tw> To: CHEMISTRY@www.ccl.net Subject: DFT(B3LYP) problem Dear Netters, I got a question when I tried to run DFT(B3LYP) using gaussian 94. I ran three kinds of input as follows, (1) #n b3lyp/sto-3g iop(5/45=10000800) iop(5/46=02000720) iop(5/47=01900810) (2) #n blyp/sto-3g iop(5/45=10000800) iop(5/46=02000720) iop(5/47=01900810) (3) #n b3lyp/sto-3g Why both (1) and (2) give the same energy results but differ from that of (3)? And which input is the right one? Please e-mail me using the following e-mail adress Thanks a lot in advance. ===================================================================== May-May Lin | E-mail: ccluser@chu.chem.nthu.edu.tw Department of chemistry | National Tsing Hua University | ===================================================================== From owner-chemistry@ccl.net Mon Jul 1 07:04:20 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id GAA21356; Mon, 1 Jul 1996 06:27:40 -0400 (EDT) Received: from ns1.DKFZ-Heidelberg.de for tajkhors@mbp-sgi7.inet.dkfz-heidelberg.de by bedrock.ccl.net (8.7.5/950822.1) id GAA29036; Mon, 1 Jul 1996 06:27:32 -0400 (EDT) Received: from mbp-sgi7.inet.dkfz-heidelberg.de (mbp-sgi7.inet.dkfz-heidelberg.de [193.174.48.96]) by ns1.DKFZ-Heidelberg.de (8.7.3/DKFZ-8.6.4) with ESMTP id MAA15071 for ; Mon, 1 Jul 1996 12:24:09 +0200 (MET DST) Received: (tajkhors@localhost) by mbp-sgi7.inet.dkfz-heidelberg.de (940816.SGI.8.6.9/DKFZ-8.6.4) id MAA22296 for chemistry@ccl.net; Mon, 1 Jul 1996 12:25:12 +0200 From: "Emadeddin Tajkhorshid" Message-Id: <9607011225.ZM22294@mbp-sgi7.inet.dkfz-heidelberg.de> Date: Mon, 1 Jul 1996 12:25:12 -0600 Reply-To: E.tajkhorshid@dkfz-heidelberg.de X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@ccl.net (Computational Chemistry List) Subject: Continum model simulation Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi all I want to compare the results of vaccum calculation with that of continum solvent model of water using G94. I found different methods in using Dipole, PCM, IPCM and SCIPCM. Actually I was able to work with Dipole ( Onsager) method, but I found problems using other methods. Perhaps I do not include complete information required by the program. Could you please point me to some examples with this regard. Any other comments are greatly appreciated. Thanks in advance emad -- E. Tajkhorshid German Cancer Research Center; DKFZ Tel: +49 6221 42 2339 Dept. Molecular Biophysics (0810) FAX: +49 6221 42 2333 P.O.Box 101949 Email: E.Tajkhorshid@dkfz-heidelberg.de 69009 Heidelberg, FRG ********************************************************************** * It is nice to be important, but it is more important to be nice! * ********************************************************************** From toukie@zui.unizh.ch Mon Jul 1 10:57:40 1996 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.7.5/950822.1) id KAA22321; Mon, 1 Jul 1996 10:06:05 -0400 (EDT) Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA00839; Mon, 1 Jul 96 16:05:52 +0200 X-Nupop-Charset: Swiss Date: Mon, 1 Jul 1996 16:06:53 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <58013.toukie@zui.unizh.ch> To: chemistry@www.ccl.net Subject: 2 questions re TLC results Dear Colleagues; I have recently been performing TLC (stationary phase, silica gel) of some simple o-, m-, and p-monoalkyl- and -monoalkoxyphenols, and have obtain- ed results which I have difficulty rationalising. Perhaps someone can answer one or both of these questions for me: (i) In the case of alkoxyphenols, I find that the o-isomers have much higher Rf values than the corresponding m- or p-isomers. This is to be expected if an intramolecular hydrogen bond forms between the hydroxy H-atom and the alkoxy -O- atom in the ortho position. However, the same thing ap- pears to be true for , e.g., cresols and t-butylphenols. Since molecular mechanics studies indicate that the hydroxy H-atom is oriented trans to the ortho substituent in o-cresol and o-t-butylphenol, why should the ortho iso- mers of monoalkylphenols consistently have higher Rf values than their meta or para counterparts? (ii) For virtually all of the monoalkylphenol and monoalkoxyphenol com- pounds that I have examined, the Rf values for the meta and para isomers are very close to each other, but the meta derivative almost always has a _very slightly higher_ Rf value (usually <0.05 Rf units) than the corresponding para derivative. Can anyone suggest a reason for this very slight but ap- parently real difference in Rf value between meta and para isomers? Of course, any literatures references bearing on these two questions are extremely welcome. Thanks in advance to all responders. Sincerely, S. Shapiro H toukie@zui.unizh.ch From rosas@irisdav.chem.vt.edu Mon Jul 1 11:06:07 1996 Received: from irisdav.chem.vt.edu for rosas@irisdav.chem.vt.edu by www.ccl.net (8.7.5/950822.1) id KAA22360; Mon, 1 Jul 1996 10:23:23 -0400 (EDT) Received: by irisdav.chem.vt.edu (951211.SGI.8.6.12.PATCH1042/921111.SGI.AUTO) for chemistry@www.ccl.net id KAA20358; Mon, 1 Jul 1996 10:18:43 -0700 From: "Victor M. Rosas Garcia" Message-Id: <9607011018.ZM20356@irisdav.chem.vt.edu> Date: Mon, 1 Jul 1996 10:18:39 -0400 In-Reply-To: "Victor M. Rosas Garcia" "CCL:modeling of phosphonates..." (May 22, 1:46pm) References: <9605221346.ZM15901@irisdav.chem.vt.edu> X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Summary: CCL:modeling of phosphonates... Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi everybody, Some time ago I posted the following question: > Is there anyone out there modeling phosphonates? I'd like to discuss > some experiences (both good and bad) I've had. Comments about the > appropriateness of any method (molecular mechanics, semiempirical and ab > initio) are welcome. I'm particularly interested in modeling including solvent > effects. I got several responses that were most useful. Thanx to: Michael Colvin Christopher Cramer Beverly Bendiksen Rainer Koch and Steve Cabaniss To make a long story short: DO NOT use semiempirical methods for modeling phosphorus(V) species. They'are bad. The problem I ran into was sort of a catch-22 situation: AM1 was way off in the P-C bond length (1.63 angs vs 1.77 exp) while PM3 was pretty close (1.73 vs 1.77), but PM3 went awry when the solvent was included, probably because of the quality of the charges produced by PM3 (that's my best guess). I also got some references: Denmark, S. E.; Cramer, C. J. "The Theoretical Structures of Neutral, Anionic and Lithiated P-Allylphosphonic Diamide" J. Org. Chem. 1990, 55, 1806. Cramer, C. J.; Denmark, S. E.; Miller, P. C.; Dorow, R. L.; Swiss, K. A.; Wilson, S. R. "Structure and Dynamics of Phosphorus(V)-Stabilized Carbanions: A Comparison of Theoretical, Crystallographic, and Solution Structures" J. Am. Chem. Soc. 1994, 116, 2437. Koch, R.; Anders, E.; "Ab Initio and PM3-MO calculations of Lithiophosphonates" J. Org. Chem. 1995, 60, 5861-5866 Interesting thing: after reading a few papers, I found that the P-C bond length is very sensitive to the substituents on the P. These are the P-C bond lengths for a few P species: Phosphines: 1.81 angs Phosphonates: 1.77 angs Phosphonic diamides: 1.71 angs. Most molecular mechanics force fields have P-C parameters derived from phosphines (probably based on Allinger's original publications). I haven't found any force fields that included phosphonates in the parametrization (although I have not looked very hard on this). So, once more, participating in the CCL provided a valuable learning experience. Thank you all. Victor. -- ----------------------------------------------------------------------- Victor M. Rosas Garcia * "How can we contrive to be rosas@irisdav.chem.vt.edu * at once astonished at the Virginia Tech doesn't necessarily share * world and yet at home in it?" the opinions you just read. * G. K. Chesterton ----------------------------------------------------------------------- From P.E.Young@dl.ac.uk Mon Jul 1 11:10:00 1996 Received: from mserv1.dl.ac.uk for P.E.Young@dl.ac.uk by www.ccl.net (8.7.5/950822.1) id KAA22388; Mon, 1 Jul 1996 10:31:15 -0400 (EDT) Received: from tcxs1.dl_sun_server by mserv1.dl.ac.uk with SMTP id PAA27665 (8.6.13/5.3[ref postmaster@dl.ac.uk] for dl.ac.uk from P.E.Young@dl.ac.uk); Mon, 1 Jul 1996 15:31:03 +0100 Precedence: first-class Received: by tcxs1.dl_sun_server (4.1/SMI-4.1) id AA18516; Mon, 1 Jul 96 15:29:52 BST Date: Mon, 1 Jul 96 15:29:52 BST From: P.E.Young@dl.ac.uk (P. Young) Message-Id: <9607011429.AA18516@tcxs1.dl_sun_server> To: chemistry@www.ccl.net Subject: CCP1 Study Weekend CCP1 Study Weekend Topic Quantum Theory of Large Systems Date: Dinner Fri. 20 Sept. to Lunch Sun. 22 Sept. 1996 Application and Registration: Deadline 1 Sept 1996 Venue: Daresbury Laboratory, Daresbury, Warrington UK Scope of Meeting: Approximately every two years, the UK CCP1 (Collaborative Computational Project 1: Electronic Structure Methods) organises a "Study Weekend". These are very informal meetings (maximum 40 participants) that are organised around topics that may form the basis of future collaborative work in CCP1. The previous meeting was organized on Hybrid methods. The meeting this year at Daresbury is focussed on methods (mainly ab initio) for studying large molecules. Thus the scope of the meeting includes DFT theory, the coulomb problem, fast multipole methods, distributed multipole methods and related techniques. Speaker Topic P. Gill Circumventing the Coulomb Problem (Cambridge) G. Scuseria Linear Scaling Electronic Structure Methods (Rice Univ. Houston) for Large Molecules T. Ziegler Beating the Heavy Metal Blues with DFT (Calgary) N. Burton Molecular Electronic Structure Calculations (Manchester) Employing a Plane-Wave Basis: A Comparison With Gaussian Basis Calculation I. Gould Modelling Chlorophyll in solution: Experiment (Imperial College) and Theory in Unison M. Guest The Treatment of Large Molecular Systems; (Daresbury) NWchem and Fully Distributed Parallel Applications C. Reynolds Theoretical and Experimental Studies on (Essex) Cobalt-Based Bioreductive Anti-Cancer Agents V. Saunders Hartree-Fock Theory for Crystals of Large (Daresbury) Unit Cell. A. Stone Intermolecular Forces between Large Molecules (Cambridge) There will also be an "informal" poster session. Please send a title with your registration if you wish your poster title to appear in the programme. Accomdation will be in the Park Royal International Hotel in Stretton near Warrington. The hotel is located 12 minutes from Manchester Airport, 1 minute from Junction 10 of the M56, 5 minutes from Junction 20 of the M6 and midway between the cities of Chester, Liverpool and Manchester. The attendance fee is 110 pounds which includes accomodation, meals and transport to and from Daresbury Laboratory to the hotel. For those who do not require accomodation, the attendance fee is 15 pounds or 30 pounds if you wish to attend the evening meal on the Saturday. Registration enquiries and application forms to be sent to Dr. Phill Young, Daresbury Laboratory, Daresbury, Warrington, WA4 4AD e-mail p.e.young@dl.ac.uk phone +44-(0)1925-603657 fax +44-(0)1925-603634 Informal enquiries to Professor M. A. Robb, Chemistry Department,King's College London, Strand, London WC2R 2LS e-mail m.a.robb@kcl.ac.uk phone +44-(0)171-873-2098 fax +44-(0)172-873-2810 ------------------------------------------------------------------------------- R E G I S T R A T I O N F O R M Name: _____________________________________________________________________ Address: __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ Email: _________________________________ I will require accomodation at the hotel. (110 pounds) (Yes/No)* I will attend the workshop during the day only (15 pounds) (Yes/No)* I will attend the workshop during the day and wish to attend the evening meal on Saturday (30 pounds) (Yes/No)* Total amount enclosed:________________________ (Please make cheques payable to DARESBURY LABORATORY) Please indicate any dietary requirements below. _____________________________________________________________________ _____________________________________________________________________ From toukie@zui.unizh.ch Mon Jul 1 11:57:50 1996 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.7.5/950822.1) id LAA22586; Mon, 1 Jul 1996 11:21:32 -0400 (EDT) Received: from rzurs3.unizh.ch by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA05682; Mon, 1 Jul 96 17:21:26 +0200 Received: by rzurs3.unizh.ch (AIX 3.2/UCB 5.64/4.03) id AA79158; Mon, 1 Jul 1996 17:21:25 +0200 From: toukie@zui.unizh.ch (Hr Dr. S. Shapiro) Message-Id: <9607011521.AA79158@rzurs3.unizh.ch> Subject: 2 Questions re TLC To: chemistry@www.ccl.net Date: Mon, 1 Jul 1996 17:21:25 +0200 (MEST) X-Mailer: ELM [version 2.4 PL24 PGP2] Content-Type: text Dear Colleagues; I have recently performed TLC (stationary phase = silica gel) of some simple o-, m-, and p-monoalkyl- and o-, m-, and p-monoalkylphenols, and have obtained results that are a bit puzzling. Perhaps someone can answer one or both of these questions: (i) In the case of alkoxyphenols I find that the o-isomers have much higher Rf values than the corresponding m- or p-isomers. This is to be expected if an intramolecular hydrogen bond exists between the hydroxy H-atom and the alkoxy -O- atom in the ortho position. However, the same thing happens with, e.g., cresols and t-butylphenols. Since molecular mechanics studies indicate that the hydroxy H-atom is oriented trans to the ortho substituent in o-cresol or o-tert-butylphenol, why should the ortho isomers of monoalkylphenols con- sistently have higher Rf values than their meta or para counterparts? (ii) For virtually all of the monoalkylphenol and monoalkoxyphenol compounds I have examined the Rf values for the meta and para isomers are very close to each other, but the meta derivative almost always has a _very slightly higher_ Rf value (usually < 0.05 Rf units) than the corresponding para derivative. Can anyone suggest a reason for this very slight but apparently real difference in Rf value between meta and para isomers? Of course, any literature references bearng on these two questions are extremely welcome. Thanks in advance to all responders. Sincerely, S. Shapiro ZH toukie@zui.unizh.ch From CALEF@CMS1.llnl.gov Mon Jul 1 12:57:45 1996 Received: from ICDC.LLNL.GOV for CALEF@CMS1.llnl.gov by www.ccl.net (8.7.5/950822.1) id MAA23380; Mon, 1 Jul 1996 12:49:23 -0400 (EDT) From: Received: from DECNET-MAIL (CALEF@CMS1) by icdc.llnl.gov (PMDF V5.0-4 #9419) id <01I6JYN660YO934T1F@icdc.llnl.gov> for chemistry@www.ccl.net; Mon, 01 Jul 1996 09:49:09 -0700 (PDT) Date: Mon, 01 Jul 1996 09:49:09 -0700 (PDT) Subject: MD/MM Session at the West Coast ACS in SF To: chemistry@www.ccl.net Message-id: <01I6JYN6864I934T1F@icdc.llnl.gov> X-VMS-To: ICDC::IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT I have been asked by the local ACS to see if there is enough interest to hold a a session on molecular dynamics/molecular modeling at the ACS West Coast region al meeting in San Francisco. This would be a "special session" which means the abstract deadline has been extended to July 31.The meeting is at the Cathedral Hill Hotel in SF on October 300 - November 2 , 1996. We would need ~6 20 minute papers for a half day session. Graduate students and post-doc's often find these meetingsare a good vehicle for preparing themselves for other, more crucial, presentations. Interested individuals should contact me calef1@llnl.gov calef@cms1.llnl.gov 510-422-7797 voice 510-422-6363 fax There is a specific form for the abstract that is available >from http://www.acs .org/memgen.meetings/absdown.htm and I alsohave a few paper copies I can mail to interested parties. Dan Calef Lawrence Livermore National Laboratory L-325 P.O. Box 808 Livermore CA 94550