From bartberg@chem.ufl.edu Fri Jun 20 02:50:12 1997 Received: from mailey for bartberg@chem.ufl.edu by www.ccl.net (8.8.3/950822.1) id CAA19340; Fri, 20 Jun 1997 02:00:13 -0400 (EDT) Received: from localhost by mailey (SMI-8.6/4.11) id AAA14330; Fri, 20 Jun 1997 00:59:39 -0500 Date: Fri, 20 Jun 1997 01:59:39 -0400 (EDT) From: "Michael D. Bartberger" X-Sender: bartberg@mailey Reply-To: "Michael D. Bartberger" To: Computational Chemistry List Subject: BSSE in cyclophanes? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings: I am currently investigating the thermodynamics of formation for a series of substituted para-cyclophanes, of the general type CH2---Ph---CH2 | | | | CH2---Ph---CH2 /CH=CH\ as formed from their xylylene "monomers": 2 CH2=C C=CH2 \CH=CH/ (pardon the ASCII artwork!) Methodology so far has been as follows: geometry optimizations and frequencies/ZPE determination at RHF/3-21G (I'd like to go larger but I have other substituted systems where the number of heavy atoms gets quite large) with single-point energies at MP2/6-31G* and B3LYP/6-31G* on the RHF/3-21G geometries. I've been worrying about BSSE. As far as I've determined from following various threads of discussion on this list, BSSE manifests itself when determining energetics of interacting vs. isolated "monomers", where a superposition of molecule A's basis functions onto molecule B (and vice versa) occurs. I can see the ramifications of this, in, say, a case such as the acetic acid dimer, for instance. Where I'm unsure is when the "dimer" is formally bound, such as above. Should one account for BSSE effects in such a case? Surely some superposition of basis functions onto adjacent/nearby nuclei occurs (?)- if so, then it most certainly does so in just about any other organic system (again, ??) :) Pardon me, I don't mean to get too philosophical.......and I hope the question is not ridiculous. The burning question is the following: where does one draw the line when deciding to incorporate BSSE effects? Intuitively, I'd imagine one does not include them in a case like this, a formally it (the dimer) is a single molecule........ otherwise, BSSE would become a factor in, for example, [4+2] or other cycloadditions, or for that matter, any other reaction where bonds are being formed. Am I thinking too hard about this???? :) Sorry, it's late..... I'll certainly summarize responses- I'd greatly appreciate any insight the community might be able to lend. Thanks very much! Best Regards, -Michael ________________________________________________________________________________ Michael D. Bartberger bartberg@chem.ufl.edu TEL: (352) 392-3580 Department of Chemistry bartberg@qtp.ufl.edu FAX: (352) 846-0296 University of Florida Gainesville, FL 32611 USA ________________________________________________________________________________ From toukie@zui.unizh.ch Fri Jun 20 04:04:01 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id CAA20149; Fri, 20 Jun 1997 02:53:44 -0400 (EDT) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA07645; Fri, 20 Jun 1997 08:53:17 +0200 Message-Id: <1.5.4.32.19970620065528.0067dd04@highdent.zzmk.unizh.ch> X-Sender: toukie@highdent.zzmk.unizh.ch (Unverified) X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 20 Jun 1997 08:55:28 +0200 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: MOPAC7 Cc: toukie@zui.unizh.ch Dear Colleagues; I'm sure that we've all heard the dire warnings from Dr. J. Stewart re applying MOPAC7 to experimental work. In view of these warnings, I'd be grateful to hear from persons who have had an opportunity to compare "challenging" calculations using both MOPAC7 and one of the versions of MOPAC93 and are willing to share their experiences and opinions with me. I'd also like to know if anyone knows of any _published_ references to experimental work performed using MOPAC7. If so, kindly send me the citations. Thanks in advance to all responders. Sincerely, S. Shapiro toukie@zui.unizh.ch From lestaw.k.bieniasz@uni-tuebingen.de Fri Jun 20 04:04:12 1997 Received: from outmail.zdv.uni-tuebingen.de for lestaw.k.bieniasz@uni-tuebingen.de by www.ccl.net (8.8.3/950822.1) id DAA20349; Fri, 20 Jun 1997 03:36:09 -0400 (EDT) Received: from echem5.orgchemie.chemie (echem5.orgchemie.chemie.uni-tuebingen.de) by outmail.zdv.uni-tuebingen.de (4.1/ZDV-Uni-Tuebingen-1.0) id AA16595; Fri, 20 Jun 97 09:36:03 MES Date: Fri, 20 Jun 1997 09:35:11 +0200 (W. Europe Daylight Time) From: "Lestaw K. Bieniasz" To: chemistry@www.ccl.net Subject: CC semantics Message-Id: X-X-Sender: coibi01@mailserv.uni-tuebingen.de Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Tuebingen, 20.06.97 Dear Drs. Buyong Ma and Prem Yadav, I wonder how you would classify the following types of evidently chemical and computational research: 1) computer modelling of combustion phenomena (hundreds of species and reactions, highly nonlinear systems of ODEs or PDEs, intractable by analytical approaches), 2) computer modelling of spatio-temporal nonlinear dynamic effects in chemical reaction-diffusion systems by cellular automata methods, 3) computer modelling of electrochemical microelectrode assemblies in two or three-dimensional geometry (complex PDE systems with sophisticated boundary conditions, over non-trivial space domains. 4) investigations of the chemical inference rules for automating analytical chemistry measurement systems, and their practical implementation in the form of expert systems. None of these examples is molecular modelling, but I daresay all of them are computational chemistry. Sincerely, L.Bieniasz *-------------------------------------------------------------------* | Dr. Leslaw Bieniasz | | temporary address: (3rd April 1997 - 31st August 1997) | | Institut fuer Organische Chemie, Universitaet Tuebingen | | Auf der Morgenstelle 18, 72076 Tuebingen, Germany. | | E-mail: lestaw.k.bieniasz@uni-tuebingen.de | *-------------------------------------------------------------------* | permanent address: | | Institute of Physical Chemistry of the Polish Academy of Sciences,| | Molten Salts Laboratory, ul. Zagrody 13, 30-318 Cracow, Poland. | | E-mail: nbbienia@cyf-kr.edu.pl | *-------------------------------------------------------------------* From mzloh@ulsop.ac.uk Fri Jun 20 10:50:14 1997 Received: from chemb.pharm.lon.ac.uk for mzloh@ulsop.ac.uk by www.ccl.net (8.8.3/950822.1) id KAA22383; Fri, 20 Jun 1997 10:20:13 -0400 (EDT) Received: from localhost (mzloh@localhost) by chemb.pharm.lon.ac.uk (8.6.9/8.6.9) with SMTP id PAA17319 for ; Fri, 20 Jun 1997 15:24:22 GMT X-Authentication-Warning: chemb.pharm.lon.ac.uk: mzloh owned process doing -bs Date: Fri, 20 Jun 1997 15:24:21 +0000 (GMT) From: Mire Zloh X-Sender: mzloh@chemb To: CHEMISTRY@www.ccl.net Subject: Help with X-PLOR Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I have tried recently to do molecular dynamics with saving the trajectory. I am getting the following error message: %WRITEV-ERR: invalid logical unit on three different versions of X-PLOR, under the LINUX and SUN OS operating systems. I have been using the following dynamics statement. dynamics verlet trajectory=loop23_sol.dcd nsavv=10 nstep=$steps timestep=0.001 iasvel=maxwell firstt=$init_t tcoupling=true tbath=$init_t nprint=25 iprfrq=0 rbuf=27 end All other protocols (DG, SA) are working fine. Please, could anybody point the mistake(s) I am making? Yours, ========================================================== Mr Mire Zloh | School of Pharmacy | e-mail: mzloh@ulsop.ac.uk 29 Brunswick Square | Tel: + 44 171 753 5804 London WC1N 1AX | Fax: + 44 171 278 1939 ========================================================== "There are many paths leading to the top of Mount Fuji, but there is only one summit ..." "The Art of Peace" by Morihei Ueshiba ==========================================================