From parthi@aero.iisc.ernet.in Mon Mar 10 01:28:19 1997 Received: from milan.doe.ernet.in for parthi@aero.iisc.ernet.in by www.ccl.net (8.8.3/950822.1) id BAA07643; Mon, 10 Mar 1997 01:21:22 -0500 (EST) Received: from iisc.ernet.in by milan.doe.ernet.in (4.1/SMI-4.1) id AA14868; Mon, 10 Mar 97 11:30:18+050 Received: from aero.iisc.ernet.in by iisc.ernet.in (ERNET-IISc/SMI-4.1) id LAA05637; Mon, 10 Mar 1997 11:48:58 +0530 Received: by aero.iisc.ernet.in (ERNET-IISc/SMI-4.1) id AA10162; Mon, 10 Mar 1997 11:46:27 -0500 Date: Mon, 10 Mar 1997 11:46:27 -0500 (GMT) From: S Parthiban To: Sergey Nogaev Cc: chemistry@www.ccl.net Subject: Re: CCL:Studies on ozone In-Reply-To: <10142.l504@cacr.ioc.ac.ru> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Dear Collegues, > We have just started the studies on ozone interaction with > different molecules, mainly F- and Cl-containing, using > quantum chemical methods. This is in connection with > stratospheric ozone depletion problem. > I would be happy if somebody share his/her experience > in this field. > Any references on this subject are appreciated. > Sincerely, > Sergey Nogaev, Institute of Chemical Physics, Russia. > > The following references would be useful. S. Parthiban et al., Ab initio study of the molecular structure and vibrational spectra of dichlorine hexoxide and its significance to stratospheric ozone depletion, Chemical Physics, 199: 183-193. S. Parthiban et al., Ab initio quantum chemical calculations of geometry and vibrational frequencies of dichlorine heptoxide, Spectrochimica Acta Part A, 51: 2453-2458. S. Parthiban et al., Sturcures, energies and vibrational spectra of dinitrogen pentoxide, Journal of Molecular Structure (THEOCHEM), Vol. 367, 111-118. Sincerely S Parthiban From Patrick.Bultinck@rug.ac.be Mon Mar 10 05:28:21 1997 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.8.3/950822.1) id FAA13656; Mon, 10 Mar 1997 05:19:46 -0500 (EST) Received: from hartree1.rug.ac.be by mserv.rug.ac.be with SMTP id AA20683 (5.67b/IDA-1.5 for ); Mon, 10 Mar 1997 11:19:43 +0100 Received: by hartree1.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA06984; Mon, 10 Mar 1997 18:18:40 +0100 Date: Mon, 10 Mar 1997 18:18:39 +0100 (NFT) From: Patrick Bultinck To: CCL Subject: Pt-F binding energies Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does anybody have a reference where we could find binding energies or formation ethalpies for the formation of platinum-fluorine bonds ? Thanks in advance, Patrick Bultinck ***************************************************************************** Patrick Bultinck Ph. D. Student Quantum Chemistry Dept. Inorganic & Physical Chemistry System/Network Administrator University of Ghent Tel. Int'l code/32/9/264.44.44 Krijgslaan 281 (S-3) Fax. Int'l code/32/9/264.49.83 9000 Gent E-mail : Patrick.Bultinck@rug.ac.be Belgium http://allserv.rug.ac.be/~pbultink/ ***************************************************************************** From d3g359@fido.pnl.gov Mon Mar 10 14:28:32 1997 Received: from pnl.gov for d3g359@fido.pnl.gov by www.ccl.net (8.8.3/950822.1) id OAA16645; Mon, 10 Mar 1997 14:14:40 -0500 (EST) Received: from fido.pnl.gov by pnl.gov (PMDF V4.3-13 #6012) id <01IGC35DIEG090NXVS@pnl.gov>; Mon, 10 Mar 1997 11:14:18 -0800 (PST) Received: by fido.pnl.gov (951211.SGI.8.6.12.PATCH1042/951211.SGI.AUTO) for CHEMISTRY@www.ccl.net id LAA21414; Mon, 10 Mar 1997 11:10:30 -0800 Date: Mon, 10 Mar 1997 11:10:30 -0800 From: d3g359@fido.pnl.gov (John Nicholas) Subject: all electron basis set for Pt To: CHEMISTRY@www.ccl.net Message-id: <199703101910.LAA21414@fido.pnl.gov> Content-transfer-encoding: 7BIT Hi, Does anyone have an all-electron basis set for Pt? John ------------------------------------------------------------------------------ John Nicholas Office: (509) 375-6559 Senior Research Scientist FAX: (509) 375-6631 Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Mailstop K1-96 Richland, WA 99352 ------------------------------------------------------------------------------ From SMILLER@RARUSRAEXS1.prius.jnj.com Mon Mar 10 16:28:27 1997 Received: from smtp-internet.jnj.com for SMILLER@RARUSRAEXS1.prius.jnj.com by www.ccl.net (8.8.3/950822.1) id PAA17252; Mon, 10 Mar 1997 15:54:55 -0500 (EST) Received: by smtp-internet.jnj.com id AA25197 (InterLock SMTP Gateway 3.0 for chemistry@www.ccl.net); Mon, 10 Mar 1997 15:54:35 -0500 Received: by smtp-internet.jnj.com (Internal Mail Agent-2); Mon, 10 Mar 1997 15:54:35 -0500 Received: by smtp-internet.jnj.com (Internal Mail Agent-1); Mon, 10 Mar 1997 15:54:35 -0500 Date: Mon, 10 Mar 1997 15:56:38 -0500 From: "Miller, Susan [PRI]" Subject: QSAR To: "'chemistry@www.ccl.net'" Message-Id: Mime-Version: 1.0 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.993.5 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers' I am about to start doing some QSAR on a set of 120 compounds. How long should I expect it to take to overlay all 120 compounds and adjust their conformations, to achieve maximal overlap? A range of times or an approximate number of hours will make a fine answer. Thanks alot. Susan From s.hogg@ic.ac.uk Mon Mar 10 16:31:57 1997 Received: from romeo.ic.ac.uk for s.hogg@ic.ac.uk by www.ccl.net (8.8.3/950822.1) id PAA17151; Mon, 10 Mar 1997 15:40:05 -0500 (EST) Received: from judy.ic.ac.uk [155.198.5.5] by romeo.ic.ac.uk with esmtp (Exim 0.57 #1) id 0w4Br2-0004aa-00; Mon, 10 Mar 1997 20:39:32 +0000 Received: from mtcmsa.mt.ic.ac.uk (mtcmsag1.mt.ic.ac.uk [155.198.96.22]) by judy.ic.ac.uk (8.7.5/8.7.5) with SMTP id UAA21166 for ; Mon, 10 Mar 1997 20:39:10 GMT Received: from mtcsh.mt.ic.ac.uk by mtcmsa.mt.ic.ac.uk (5.x/4.1) id AA22541; Mon, 10 Mar 1997 20:39:09 GMT X-Received: from helen.mt.ic.ac.uk by mtcsh.mt.ic.ac.uk; Mon, 10 Mar 1997 20:39:08 GMT Message-Id: <3.0.1.32.19970310203252.006dac7c@155.198.100.1> X-Sender: seth@155.198.100.1 X-Mailer: Windows Eudora Pro Version 3.0.1 (32) Date: Mon, 10 Mar 1997 20:32:52 +0000 To: CHEMISTRY@www.ccl.net From: Simon Hogg Subject: Molecular Dynamics (non-Bio) for Win95?? Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" I now have Molgen and Mopac6 for Win95, which I am playing with to do some (very minor) work with silanes (thanks to all those who helped!!) My next problem is to find a molecular dynamics program that runs under native Win95 (no compiling, etc.) The systems I am looking at are alkyl and aryl silanes, e.g. (Ph2)MeSi.NH.SiMe(Ph2) and CF3.CF2.CF2.CF2.CH2.CH2.Si.(Me2).Cl So I want a package that can dealt with this size of molecule and these species. Any pointers?? (I've been all over www.ccl.net and spent 3 hours on AltaVista ...) -- Simon Hogg, Imperial College, London, UK Tel. +44 171 589 5111 ext. 56721 Fax. +44 171 584 3194 Owner of Glass Mailing List glass-list@ic.ac.uk PGP fingerprint NOT USED AS FROM 06-MARCH-1997 From Y0H8797@ACS.TAMU.EDU Mon Mar 10 17:28:27 1997 Received: from VMS2.TAMU.EDU for Y0H8797@ACS.TAMU.EDU by www.ccl.net (8.8.3/950822.1) id RAA17836; Mon, 10 Mar 1997 17:16:30 -0500 (EST) Date: Mon, 10 Mar 1997 16:16:31 -0600 (CST) From: YONG HUANG To: CHEMISTRY@www.ccl.net Message-Id: <970310161631.20a78d96@ACS.TAMU.EDU> Subject: Typos in COSMO paper While I'm reading the most cited paper on COSMO, a continuum type solvent simulation model, I find these errors (due to typing or not). Can anybody help me by confirming them? Thank you very much. Paper: A.Klamt and G.Schuurmann, J.Chem.Soc.Perkin Trans. 2,1993,p.799. 1. On p.800, equation (5), should be |r_i - r_j| to the power of -1, not -1/2 because this is Coulombic energy. 2. Under equation (6a), should be "a unit charge at r_i" not r_j. This is kind of trivial though. 3. Equation (11) should be "E(q*) = ..." not "E(sigma*) = ...". 4. In Figure 1., the atoms should be called alpha and beta, not A and B according to the text. Therefore all subscripts A and B should be alpha and beta (including the figure caption). The SAS (solvent accessible surface) refers to the broken line curve. R_alpha is from the center of A to the outermost solid curve. In case I'm wrong, ||a_value|| means the same as |a_value|, i.e., the absolute value of a_value, right? Thank you very much. Yong From eslone@patriot.net Mon Mar 10 18:28:27 1997 Received: from jefferson.patriot.net for eslone@patriot.net by www.ccl.net (8.8.3/950822.1) id SAA18233; Mon, 10 Mar 1997 18:21:42 -0500 (EST) Received: from eric (th-0-24.patriot.net [206.151.9.33]) by jefferson.patriot.net (8.7.4/8.7.3) with SMTP id SAA27979 for ; Mon, 10 Mar 1997 18:20:16 -0500 Message-ID: <332497F9.1B3D@patriot.net> Date: Mon, 10 Mar 1997 18:23:37 -0500 From: "J. Eric Slone" Reply-To: eslone@patriot.net Organization: Scientific Consulting Services X-Mailer: Mozilla 3.0Gold (Win95; U) MIME-Version: 1.0 To: Computational Chemistry List Subject: Molgen Program Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi again!! It's been some time since I posted Molgen to the CCL archives and entered it into the public domain. I hope that many of you are using and enjoying the program. I'd like to ask a moment of your time to answer a few questions. [1] How do you use Molgen? [2] What do you find about the program to be useful? [3] What do you think the weak points of the program are? [4] Are there any ideas you have for new modules or improvements? Thanks for your time, and if you publish an article and cite Molgen in your paper, please send me the reference! Thanks, Eric ___________________________________________________________________ J. Eric Slone Scientific Consulting Services 5500 Holmes Run Parkway, Suite 501 Alexandria, Virginia 22304-2851 Phone: (703) 461-7078 mailto:eslone@patriot.net Fax: (703) 751-6639 http://www.patriot.net/users/eslone ___________________________________________________________________ From panc@isc.kyushu-u.ac.jp Mon Mar 10 21:28:38 1997 Received: from ryugaku.isc.kyushu-u.ac.jp for panc@isc.kyushu-u.ac.jp by www.ccl.net (8.8.3/950822.1) id VAA18798; Mon, 10 Mar 1997 21:15:33 -0500 (EST) Received: from [133.5.200.108] (pestic6.ach.agr.kyushu-u.ac.jp [133.5.200.108]) by ryugaku.isc.kyushu-u.ac.jp (8.7.5/3.4W4) with SMTP id LAA24866; Tue, 11 Mar 1997 11:16:31 +0900 (JST) Message-Id: <199703110216.LAA24866@ryugaku.isc.kyushu-u.ac.jp> Date: Mon, 11 Mar 1996 11:21:13 +0900 To: chemistry@www.ccl.net From: panc@isc.kyushu-u.ac.jp (Canping Pan) Subject: Re: CCL:QSAR Cc: "Miller, Susan [PRI]" MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) At 3:56 PM 97.3.10 -0500, Miller, Susan [PRI] wrote: Susan>Dear CCL'ers' Susan> Susan> I am about to start doing some QSAR on a set of 120 compounds. How Susan>long should I expect it to take to overlay all 120 compounds and adjust Susan>their Susan>conformations, to achieve maximal overlap? A range of times or an Susan>approximate number of hours will make a fine answer. Thanks alot. Susan> Susan> Hi there, It depends on the machine power, qsar software, compound size, parameter selecting .....Generally, as I am doing now for about 100 compounds(MW. 300) using a PowerMac8100 with CAChe Project leader, one month or 500 hrs around is the common expense. Maybe I am lazy. Any QSAR topic I am interesting in. Yours, Canping Pan --------------------------------- E-mail: pan_canp@agr.kyushu-u.ac.jp Tel: 092-611-7122(H) 092-642-2858(O) Fax: 092-642-2864 http://133.5.200.42/pan.html Department of Agricultural Chemistry Faculty of Agriculture Kyushu University　46-02 Fukuoka 812 Japan ---------------------------------- From arthur_j@chem.usyd.edu.au Mon Mar 10 22:28:29 1997 Received: from lars.chem.su.oz.au for arthur_j@chem.usyd.edu.au by www.ccl.net (8.8.3/950822.1) id WAA19110; Mon, 10 Mar 1997 22:27:46 -0500 (EST) Received: (from arthur_j@localhost) by lars.chem.su.oz.au (8.6.9/8.6.9) id OAA04506; Tue, 11 Mar 1997 14:27:38 +1100 Date: Tue, 11 Mar 1997 14:27:36 +1100 (EDT) From: Jonathan Arthur Sender: Jonathan Arthur Reply-To: Jonathan Arthur Subject: Thermodynamic integration To: Computational chemistry list Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Hello all, I am trying to perform a molecular dynamics calculation of the free energy for the mutation of a water molecule into a methane molecule in solution. I am using the thermodynamic integration technique. Although I have been trying for quite a while, gradually finding the bugs in my code, I have still not been able to reproduce the literature values for this reaction. I am starting to suspect that I may not have a correct understanding of how this technique is used. While the many references I have consulted talk of 'accumulating the partial derivative dU/dlambda' they do not describe exactly what this partial derviative is in terms of the positions, velocites etc that can be accumulated each time step. Could someone please give me some advice and/or point me in the direction of a good paper, some code or another source which deals with the 'nuts and bolts' of writing code to perform a thermodynamic integration in molecular dynamics? Thanks for your help. Jonathan _______________________________________________________________ Jonathan Arthur Theoretical Chemistry e-mail: arthur_j@chem.usyd.edu.au School of Chemistry (F11) telephone: +61-2-9351-2733 The University of Sydney fax: +61-2-9351-3329 NSW 2006 AUSTRALIA _______________________________________________________________