From msj@fskru5.hre.hydro.com Mon Jul 7 04:50:34 1997 Received: from fskru5.hre.hydro.com for msj@fskru5.hre.hydro.com by www.ccl.net (8.8.3/950822.1) id EAA07521; Mon, 7 Jul 1997 04:45:51 -0400 (EDT) Received: by fskru5.hre.hydro.com (950413.SGI.8.6.12/930416.SGI.AUTO) for chemistry@www.ccl.net id KAA13402; Mon, 7 Jul 1997 10:44:57 +0200 From: "Merethe Sjovoll" Message-Id: <9707071044.ZM13400@fskru5.hre.hydro.com> Date: Mon, 7 Jul 1997 10:44:56 -0600 Reply-To: Merethe.Sjovoll@hre.hydro.com X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Summary on organic/inorganic interfaces Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Here is finally the summary of the responses I got on available litterature relating to forcefields used for organic/inorganic interfaces. Thanks to those who responded. Hello everyone, I would appreciate very much any reference to publications on molecular mechanics simulations of organic/inorganic interfaces, particularly in the field of scale and corrosion inhibition. I know of the article by Catlow et al. on barium sulfate. Does anybody know of any other references? Best wishes Merethe Sjovoll I've seen papers by Michael Sennet and others on silanes adhering to aluminum, a topic that I'm about to publish on. Out of interest, why are you interested in molecular mechanics in particular? I would have thought that most of the published work on adsorption onto various surfaces has been done using QM methods. Anyway, I'm generally interested in the whole area of molecular mechanics modelling of adsorption so please let me know what replies you get. I found this in some old mail I saved off the CCL @ARTICLE{Hill94, author = {J{\"o}rg-R. Hill and Joachim Sauer}, title = {Molecular Mechanics Potential for Silica and Zeolite Catalysts Based on ab Initio Calculations. 1. {D}ense and Microporous Silica}, journal = {Journal of Physical Chemistry}, volume = 98, year = 1994, pages = "1238--1244" } @article{Hill95, author = {Hill, J. R. and Sauer, J. }, title = {Molecular mechanics potential for silica and zeolite catalysts based on ab initio calculations. 2. Aluminosilicates}, journal = {Journal of Physical Chemistry}, year = 1995, month = "8~" # jun, volume = "99", number = "23", pages = "9536--9550", abstract = {A consistent force field for the simulation of protonated aluminosilicates is presented. It has been developed on the basis of ab initio calculations on molecular models following a method proposed in a previous paper (J. Phys. Chem. 1994, 98, 1238). The molecular models consist of SiO4 and protonated AlO4 tetrahedra connected to chains, rings, and cages. The ab initio calculations used a ''double-zeta plus polarization'' basis set on the Si, Al, and H atoms and a ''triple-zeta plus polarization'' one on the O atoms. The calculated structures of the finite models yield a structural model of Bornsted acidic sites which is consistent with observed data but more complete than models derived from experiments. Compared with these ab initio results the derived force field predicts reasonable structures for aluminosilicates, but the errors are larger than the errors that our all-silica potential yielded for all-silica polymorphs. A new method is proposed for calculating the atomic charges as a function of the structure, and the corresponding potential results in better structure predictions. The force field is applied to the calculation of the local structures of different bridging hydroxyl groups in faujasite, and it is shown that results of the same accuracy as with a shell model potential are obtained. The predictions for a H-faujasite (Si/Al = 2.43) are consistent with mean bond distances and angles deduced from neutron diffraction data.} } And this on Langmuir layers For details of this work, see: J. Perlstein, "Molecular Self-Assemblies 4..." J. Am. Chem. Soc 116, 11420 (1994) and references therein. For applications of these ideas see: H. Chen et. al. "Aggregation of Surfactant Squaraine in LB Films...", J. Phys. Chem. 98, 5138 (1994) as well as the internet page below. Software for doing monolayer packing called PACK is available as an interface to the CHEMX/CHEMLIB modeling program on SGI workstations from Chemical Design, Inc. in Mahwah, N.J.(tel. 201-529-3323). Hope that is some help Dr. Ross Underhill Royal Military College of Canada Kingston, Ontario K7K 5L0 (I have looked at clay-organic and clay-water interfaces, though not related to scale inhibition. An example of the clay work is in J. Phys. Chem. B 101:1579-1587 (1997). I have done some unpublished work on barite using the MSI Insight/Discover programs. Best wishes, Brian J. Teppen teppen@srel.edu Advanced Analytical Center for Environmental Sciences Savannah River Ecology Laboratory University of Georgia Drawer E Aiken, SC 29802 phone:803-725-8157 fax:803-725-3309 613) 541-6000 X6175 Molecular Simulations has a case study of scale inhibitor design via comp. chem.. I believe you can find it on their web site (www.msi.com). Good luck, brian peterson petersbk@apci.com -- ******************************************************** Merethe Sjovoll, Ph.D. * * Research Scientist * * Norsk Hydro a.s Research Center * * * * P.O.Box 2560 * HYDRO * N-3901 Porsgrunn, * RESEARCH * Norway * * * ((( * email: Merethe.Sjovoll@hre.hydro.com * (=====) * Phone:+47 35 56 48 97 * * Fax :+47 35 56 36 86 * * ******************************************************** From msj@fskru5.hre.hydro.com Mon Jul 7 05:50:24 1997 Received: from fskru5.hre.hydro.com for msj@fskru5.hre.hydro.com by www.ccl.net (8.8.3/950822.1) id FAA07622; Mon, 7 Jul 1997 05:07:50 -0400 (EDT) Received: by fskru5.hre.hydro.com (950413.SGI.8.6.12/930416.SGI.AUTO) for chemistry@www.ccl.net id LAA13423; Mon, 7 Jul 1997 11:07:39 +0200 From: "Merethe Sjovoll" Message-Id: <9707071107.ZM13421@fskru5.hre.hydro.com> Date: Mon, 7 Jul 1997 11:07:38 -0600 Reply-To: Merethe.Sjovoll@hre.hydro.com X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Summary of extended Hueckel programs Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Here is the summary of the responses I got regarding the QCPE extended Hueckel program (No. 571). Thanks to those who responded and especially to the author of YAeHMOP, Greg Landrum, who offers his code for free. It seems to be more easy to use and the graphics work wonderfully, Greg! There is one response from S. Shapiro who wonders whether I have any experience in porting fortran 77 programs to Windows 95 or DOS executables. Unfortunately, I haven't, and I therefore send it on to the CC list. Well, here is the summary: Hello everyone, I was wondering whether anybody have experience with the QCPE program no. 571 which is an extended Hueckel program. I have certain problems when trying to run the test examples that follow the code. It appears that there is something wrong with the file that the EH code passes on to the property code (fort.1), although the EH calculation seem to run nicely. The program starts to read read the file, but the numbers are totally crazy. The other thing is the plotting program which follows, compiles with a lot of errors on an IBM 590. The README file that follows says the code is not debugged for SGI computers. It appears not to be for IBM either. Has anybody experienced the problems that I describe? Has anybody debugged the plotting program, and is it a big job? I would also be interested in having the programs run on an SGI machine. Please send eventual responses directly to me, as this subject is possibly of limited interest to most of the CClist members. Best wishes Merethe Dear Merethe if you are interested in EH calculation on solid state, you should look at : http://overlap.chem.cornell.edu:8080/yaehmop.html for a verion related to qcpe 571 (always a hoffmann program) if you are interested at molecules you should try CACAO you can download cacao from : ftp: ftp.area.fi.cnr.it login: anonymous password: your e-mail address. the contents of the cacao ftp-anonymous are in the directy: /pub/issecc and its subdirectories. In particular the package CACAO40.exe is in: /pub/issecc/cacao please let me know if you have any trouble downloading or using cacao. The two file are the text and one figure. best regards Davide Dear Dr. Sjovoll; Sorry that I can't help you our with your CCL query. But maybe you can help me: If you or any of your colleagues have some experience porting FORTRAN77 source codes to Windows 95 or DOS executables, I'd be most grateful if you'd contact me at your earliest convenience. Yours most respectfully, S. Shapiro toukie@zui.unizh.ch Dear Merethe, If you are looking for an extended Hueckel program with graphics that will run on IBMs or SGIs (or any Unix machine), you may want to consider YAeHMOP (Yet Another extended Hueckel Molecular Orbital Package). This program is freely available in both source code and pre-compiled form for some Unix machines (IBMs, SGIs, and HPs) via anonymous ftp to: overlap.chem.cornell.edu it's in the directory: dist/yaehmop The program is described on the YAeHMOP home page at URL: http://overlap.chem.cornell.edu:8080/yaehmop.html I hope you find the program useful. Regards, -greg Landrum ----- Greg Landrum (GL19@cornell.edu) Graduate Student Hoffmann Group Cornell Chemistry http://overlap.chem.cornell.edu:8080/~landrum Hallo Merethe, I adapted the programs to run on a HP730 machine. (basically changed all upper case letters to lower case exept for the DATA statements and commented the lines calling the vax time routine.) The good news: I was able to obtain the DOS and its projections but I cheeted with the plot routine. I changed the interactive routine to only give me tables of numbers. I then used gnuplot to do the plots. Unfortunately this was three years ago during my diplom thesis. When I tried to run my "plot" routine a few month ago it didn't work anymore. I could send you my ehpp version if you are intrested. Carola ---------------------------------------------- Carola Begemann email: carola@tc1.chemie.uni-bielefeld.de adress: Leuchte 21a, 32657 Lemgo, Germany ---------------------------------------------- -- ******************************************************** Merethe Sjovoll, Ph.D. * * Research Scientist * * Norsk Hydro a.s Research Center * * * * P.O.Box 2560 * HYDRO * N-3901 Porsgrunn, * RESEARCH * Norway * * * ((( * email: Merethe.Sjovoll@hre.hydro.com * (=====) * Phone:+47 35 56 48 97 * * Fax :+47 35 56 36 86 * * ******************************************************** From jan@TORVS.CCC.Uni-Erlangen.DE Mon Jul 7 06:50:30 1997 Received: from enar.organik.uni-erlangen.de for jan@TORVS.CCC.Uni-Erlangen.DE by www.ccl.net (8.8.3/950822.1) id GAA08006; Mon, 7 Jul 1997 06:47:38 -0400 (EDT) Received: from izar.erosnet (izar.organik.uni-erlangen.de) by enar.organik.uni-erlangen.de with SMTP id AA07061 for chemistry@www.ccl.net (5.65c/IDA-1.4.4/bs-02); Mon, 7 Jul 1997 12:47:35 +0200 Date: Mon, 7 Jul 1997 12:47:35 +0200 From: Jan Schuur Message-Id: <199707071047.AA07061@enar.organik.uni-erlangen.de> To: yubofan@guomai.sh.cn Subject: Re: CCL:Want a program to control CPU time. Cc: chemistry@www.ccl.net, jan@TORVS.CCC.Uni-Erlangen.DE Dear YAN, I think you have two possibilities first upgrade your Gaussian Version to a 32-bit Version, second switch e.g. to Spartan for Windows 95. This program cooperates very smothley with the environment, and lets you work very well with other programs. For my knowledge there is no mechanism in Windows 95 to specify the amount of CPU usage for a specific program. But windows 95 knows priorities for 32-bit programs and uses time slices for each 32-bit program. Greetings, Jan Schuur -------------------------------------------------------------------------- Jan H. Schuur Ph.D. Student Computer-Chemie-Centrum Institut f. Org. Chemie Universitaet Erlangen-Nuernberg Naegelsbachstr. 25 D-91052 Erlangen, Germany Tel. ++49 (0)9181 658577 ------------------------------------------------------------------------- From cwm@proteus.co.uk Mon Jul 7 08:50:31 1997 Received: from petersgate.proteus.co.uk for cwm@proteus.co.uk by www.ccl.net (8.8.3/950822.1) id HAA08167; Mon, 7 Jul 1997 07:51:04 -0400 (EDT) Received: from Icthus.proteus.co.uk (Icthus [193.115.24.114]) by petersgate.proteus.co.uk (8.6.12/8.6.6) with ESMTP id MAA13816 for ; Mon, 7 Jul 1997 12:15:40 GMT From: "Chris Murray" Message-Id: <9707071240.ZM9694@Sangria> Date: Mon, 7 Jul 1997 12:40:30 +0100 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Computational Chemists Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear all, Proteus Molecular Design Ltd, UK. is looking to recruit a computational chemist to work on the development and maintenance of CAMD software. Requirements are strong C programming skills and a PhD degree or equivalent experience in computational chemistry, computer sciences or a related field. Advantageous would be experience in CAMD software development/application or in programming language development. A good working knowledge of chemistry would be helpful. Anyone interested in knowing more should email me directly or mail their CV to me. Thank you for your patience, Chris Murray -- Chris Murray | Proteus Molecular Design Ltd., | Tel: 01625-500555 Lyme Green Business Park, | Fax: 01625-500666 Macclesfield, Cheshire, | Email: C.W.Murray@proteus.co.uk SK11 0JL, UK | From magan@aec.co.za Mon Jul 7 09:50:26 1997 Received: from firewall.aec.co.za for magan@aec.co.za by www.ccl.net (8.8.3/950822.1) id JAA08671; Mon, 7 Jul 1997 09:24:13 -0400 (EDT) Received: by firewall.aec.co.za; id PAA21066; Mon, 7 Jul 1997 15:24:05 +0200 (SAT) Received: from aec.co.za(168.206.10.91) by firewall.aec.co.za via smap (3.2) id xma021062; Mon, 7 Jul 97 15:24:02 +0200 Received: from UNIXBACK/SpoolDir by aec.co.za (Mercury 1.21); 7 Jul 97 15:25:51 +0200 Received: from SpoolDir by UNIXBACK (Mercury 1.30); 7 Jul 97 15:25:22 +0200 Received: from MoosaS.aec.co.za by aec.co.za (Mercury 1.30); 7 Jul 97 15:25:13 +0200 Received: by MoosaS.aec.co.za with Microsoft Mail id <01BC8AEA.240F63E0@MoosaS.aec.co.za>; Mon, 7 Jul 1997 15:26:29 +0200 Message-ID: <01BC8AEA.240F63E0@MoosaS.aec.co.za> From: Magan Govender To: "'chemistry@www.ccl.net'" Subject: RE: Relaxation Measurements Date: Mon, 7 Jul 1997 15:26:23 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear netters I am interested in measuring Vibrational relaxation times using Time-Resolved Spectroscopy. Can anyone suggest possible theoretical methods or papers therein that canbe used? Many Thanks Magan From clemendot@pegase.total.fr Mon Jul 7 09:52:48 1997 Received: from pegase.total.fr for clemendot@pegase.total.fr by www.ccl.net (8.8.3/950822.1) id JAA08666; Mon, 7 Jul 1997 09:23:54 -0400 (EDT) Received: (from clemendot@localhost) by pegase.total.fr (8.6.8/8.6.6) id PAA03156; Mon, 7 Jul 1997 15:23:55 +0200 From: "clemendot au CERT/TRD tel: +33 (0)2.35551482" Message-Id: <199707071323.PAA03156@pegase.total.fr> Subject: critical constants calculations for hydrocarbons To: chemistry@www.ccl.net Date: Mon, 7 Jul 97 15:23:54 METDST Cc: sylvain.clemendot@total.com Mailer: Elm [revision: 70.85] Dear all, I'm wondering if someone has experience or informations about softwares that can predict critical constants (Tc, Pc) and asymetric factors of heteroatoms containing hydrocarbons. I'll summarise. Very best regard Sylvain Clemendot ----------------------------------------------------------- Sylvain CLEMENDOT TOTAL RESEARCH CENTRE Molecular Modelling BP 27 76700 HARFLEUR FRANCE Tel. +33 2.35.55.14.82 Fax. +33 2.35.55.12.99 ----------------------------------------------------------- From panc@isc.kyushu-u.ac.jp Mon Jul 7 12:50:29 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 MAA09851; Mon, 7 Jul 1997 12:05:33 -0400 (EDT) Received: from [133.5.200.108] ([133.5.200.108]) by ryugaku.isc.kyushu-u.ac.jp (8.7.5/3.4W4) with SMTP id BAA02172 for ; Tue, 8 Jul 1997 01:07:34 +0900 (JST) Message-Id: <199707071607.BAA02172@ryugaku.isc.kyushu-u.ac.jp> X-Mailer: Macintosh Eudora Pro Version 2.1.4-J Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-2022-JP" Date: Tue, 8 Jul 1997 01:09:13 +0900 To: chemistry@www.ccl.net From: panc@isc.kyushu-u.ac.jp (Canping Pan) Subject: G: autodock2.4 on MKlinux Hi there, Did anyone there compile the Autodock 2.4 on a MKlinux? (http://www.scripps.edu/olson/) Could someone experienced it help me with the compile problem? As the readme file there comments little info about Linux. Or if you could offer a binary package? Thanks in advance. Yours, -- Canping Pan Department of Agric. Chemistry Faculty of Agriculture Kyushu University 46-02 Japan 812 http://133.5.200.42/pan.html email: panc@isc.kyushu-u.ac.jp ---------------------------- From boyd@chem.iupui.edu Mon Jul 7 13:04:10 1997 Received: from indyvax.iupui.edu for boyd@chem.iupui.edu by www.ccl.net (8.8.3/950822.1) id MAA09918; Mon, 7 Jul 1997 12:14:35 -0400 (EDT) Return-receipt-to: Boyd Received: from macgw.chem.iupui.edu (134.68.137.71) by INDYVAX.IUPUI.EDU (PMDF V5.0-5 #5862) id <01IKYBTPD1GW00ELOG@INDYVAX.IUPUI.EDU> for chemistry@www.ccl.net; Mon, 07 Jul 1997 11:14:29 -0500 Date: Mon, 07 Jul 1997 11:13:53 -0500 From: Boyd Subject: molecular modeling definitions To: OSC CCL Message-id: X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.0.0 Content-transfer-encoding: 7BIT CCLers: Regarding the recent flurry of interest in what constitutes molecular modeling, several definitions have been suggested over the last 15+ years. I have seen definitions as narrow as: "Molecular mechanics combined with computer graphics" to as broad as: "Virtually anything which is done to depict, describe, or evaluate any aspect of the properties or structure of a molecule that requires the use of a computer". As I have pointed out in the prefaces and appendices of several volumes of "Reviews in Computational Chemistry", the terms computational chemistry and molecular modeling continue to be used interchangeably by many people, although others like to make a distinction. I would be interested in literature references where other definitions of molecular modeling and computational chemistry have been offered. Thanks, Don Donald B. Boyd, Ph.D. Research Professor of Chemistry Editor, REVIEWS IN COMPUTATIONAL CHEMISTRY Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Telephone 317-274-6891 Facsimile 317-274-4701 Internet boyd@chem.iupui.edu REVIEWS IN COMPUTATIONAL CHEMISTRY Home Page on the World Wide Web URL http://chem.iupui.edu/~boyd/rcc.html