From chemistry-request@server.ccl.net Sun Mar 19 15:07:31 2000 Received: from dns2.seanet.com (dns2.seanet.com [199.181.164.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA30181 for ; Sun, 19 Mar 2000 15:07:31 -0500 Received: from biggeek (dialup-209.245.161.233.Seattle1.Level3.net [209.245.161.233]) by dns2.seanet.com (8.9.3/8.9.0) with SMTP id MAA19954 for ; Sun, 19 Mar 2000 12:07:27 -0800 (PST) Message-ID: <000a01bf91dd$dcb19a10$01808080@biggeek> From: "Mark A. Thompson" To: Subject: UFF Date: Sun, 19 Mar 2000 12:01:05 -0800 I would like to hear from anyone who is using (or has used) the UFF force field. Mark Thompson From chemistry-request@server.ccl.net Sun Mar 19 23:53:53 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA31942 for ; Sun, 19 Mar 2000 23:53:53 -0500 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id XAA01003; Sun, 19 Mar 2000 23:53:39 -0500 (EST) Date: Sun, 19 Mar 2000 23:53:41 -0500 (EST) From: Jan Labanowski To: Ismail Badran cc: chemistry@ccl.net, Jan Labanowski Subject: Re: Ph.D. in Comp.Chem in Canada In-Reply-To: <20000319203802.23219.qmail@web117.yahoomail.com> Message-ID: On Sun, 19 Mar 2000, Ismail Badran wrote: > Hi > > Could any one help me in finding a univeristy that > offer the Ph.D in computational chemistry in canada > > best ragrards > Ismail Badran > > __________________________________________________ > Do You Yahoo!? > Talk to your friends online with Yahoo! Messenger. > http://im.yahoo.com > [I am sending a copy to the list, in case someone else has something to add] The question is sort of ill-posed. The Universities usually do not have formal Computational Chemistry Ph.D. programs/degrees. Though obviously a few have. You usually get a Ph.D. in Chemistry, rather than Ph.D. in Some Chemistry. The Universities have research groups which you can join and get your Ph.D by having your Thesis on topic in the computational chemistry field. The way to learn about who is doing what and where, is to go to your chemistry library, grab the Directory Of Graduate Research Of American Chemical Society, and look up the interests of chemistry, pharmacy, biochemistry, etc., faculty members. In addition (or if you do not access to the Am.Chem.Soc. Directory, since it is getting expensive), you can start from the general entry page for each university of interest (here Canada) www.something.ca and then look for academics/academic-departments --> chemistry --> research-interests. Then when you find a faculty member who does something which is really of interest to you, you contact him/her but you look informed and decided, rather than: "How can I do Ph.D. in comp chem?" For example: "I am interested in doing my Ph.D. in this and that. I have read the books.... I attended the following courses... I did following undergraduate projects, etc. Do you have a Ph.D. program in computational/theoretical chemistry and whom should I contact about joining? I am interested in working in your group since you do this and that which is of great interest..." And a professor will usually tell you something since you poured balsam on his ego... Again, content free questions will get you nowhere. You need to know what you want, before you can ask a useful question.. As to Canada, I did some homework for you, but did not get very far. Those are examples of general Faculty listing for Chemistry Departments, particular pages of particular faculty members, and some generic entry pages for some Canadian Universities. And if the chemistry department does not have the pertinent information about its faculty, and the faculty member (in comp. chem.) does not have his/her interest on the Web, do not bother... They do not want you, so stay away... Below is just a random (RANDOM!!! Sorry guys, I did not list you all {;-)}) example of what you can find on the net. Now is your turn to do the chores... http://www.artsci-ccwin.concordia.ca/facstaff/p-r/peslherbe/ http://www.umanitoba.ca/faculties/science/chemistry/staff/staff_de/cullen.html http://www.cerca.umontreal.ca/profs/salahub.html http://www.chem.queensu.ca/people/faculty/Research.htm http://www.uwo.ca/chem/research.html#Activities http://www.chem.utoronto.ca/people/academic.html http://www.chem.yorku.ca/grad/chemgrad.htm#faculty http://www.cobalt.chem.ucalgary.ca/group/master.html http://www.cpes.uoguelph.ca/ http://www.brocku.ca/chemistry/people/ http://www.chem.ualberta.ca/facres.htm http://www.trentu.ca/chemistry/chemfaculty.html www.dal.ca www.unb.ca www.ulaval.ca www.concordia.ca www.bc.ca www.nb.ca www.mcmaster.ca www.uottawa.ca www.ubc.ca www.uregina.ca Jan Labanowski jkl@ccl.net From chemistry-request@server.ccl.net Mon Mar 20 03:27:18 2000 Received: from denebola.ceti.etat-ge.ch (denebola.ceti.etat-ge.ch [160.53.239.115]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA00364 for ; Mon, 20 Mar 2000 03:27:18 -0500 Received: by denebola.etat-ge.ch with Internet Mail Service (5.5.2448.0) id ; Mon, 20 Mar 2000 09:24:54 +0100 Message-ID: From: "De Vito David (DIP)" To: "'chemistry@ccl.net'" Subject: Frozen optimisation in cartesian coordinates Date: Mon, 20 Mar 2000 07:55:32 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain; charset="iso-8859-1" Good Morning from Switzerland ! I'm trying to do a frozen optimisation in cartesian coordinates. I have used the keyword OPT=ModRedundant and specified at the end of my input X 7 F X 18 F X 19 F to specify that the atoms 7,18 and 19 are frozen. This works in the first optimisation cycle, but this atoms are moved in the next steps. What can I do for this ? Another little question: it is correct that PCM and CPCM models give the same cavity volume ? Thanks for the preciously help ! Best regards at all, D. De Vito. **************************************************************** D. De Vito Department of Physical Chemistry Group of Prof. Weber (Computational Chemistry) University of Geneva Office 106 - Sciences II 30, Quai Ernest-Ansermet 1211 Geneva 4 / Switzerland +4122 / 702.65.35 (Office) +4122 / 328.92.16 (Home) +4176 / 532.47.40 (Mobile) http://lcta.unige.ch/~devito (Personal Page) http://www.unige.ch/sciences/chimie (Web Master) **************************************************************** From chemistry-request@server.ccl.net Mon Mar 20 11:01:19 2000 Received: from iris.iupui.edu (iris.iupui.edu [134.68.220.32]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA03318 for ; Mon, 20 Mar 2000 11:01:18 -0500 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by iris.iupui.edu (8.9.3/8.9.3/1.2IUPUIPO) with SMTP id LAA15473; Mon, 20 Mar 2000 11:00:54 -0500 (EST) Message-ID: Date: 20 Mar 2000 11:12:47 -0500 From: "Boyd" Subject: Oh Canada To: "Labanowski, Jan" , "OSC CCL" Cc: "Boyd, Russell J." X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Hi, Regarding today's posting about computational chemistry in Canada, let me point out a very appropriate chapter in Vol. 15 of "Reviews in Computational Chemistry," which is coming out soon. Prof. Russell J. Boyd (Dalhousie) has written a chapter on "The Development of Computational Chemistry in Canada." In it, he reviews each of the research groups in Canada, what their interests are, and even discusses the academic lineage of these groups. Vol. 15 will be published later this spring. Thanks, Don Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Editor, Journal of Molecular Graphics and Modelling (publication of the ACS COMP division and MGMS) http://chem.iupui.edu/~boyd/jmgm.html E-mail boyd@chem.iupui.edu From chemistry-request@server.ccl.net Mon Mar 20 10:09:55 2000 Received: from nmr.utmb.edu (dggin1.utmb.edu [129.109.73.3]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA03115 for ; Mon, 20 Mar 2000 10:09:55 -0500 Received: from nmr.utmb.edu (morass.utmb.edu [129.109.73.39]) by nmr.utmb.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id JAA04038 for ; Mon, 20 Mar 2000 09:12:13 -0600 Sender: bruce@nmr.utmb.edu Message-ID: <38D63F94.142DA689@nmr.utmb.edu> Date: Mon, 20 Mar 2000 09:11:16 -0600 From: "Bruce A. Luxon" Reply-To: bruce@nmr.utmb.edu Organization: Sealy Center for Structural Biology X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: License Transfer Update Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Well, I took the initiative to vent my frustration and displeasure to the CCL when first trying to get my FELIX license transfered to a new box so I would like to let the list know about the outcome. MSI has been quite decent about the whole thing and after several discussions we have reached an amicable settlement of the issue. My advice to anyone in a similar fix is to keep talking with them, continue to make your case, and keep your cool. I guess this is good advice in most things. I'd like to especially thank Ms. Jennifer Glassford, MSI's midwest academic account manager, for her persistance and good will in helping me to make my case. Thanks to all for your notes of support. Bruce -- =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Bruce A. Luxon, Ph.D. Associate Professor Sealy Center for Structural Biology Dept. of Human Biological Chemistry & Genetics University of Texas Medical Branch Galveston, TX 77555-1157 (409)747-6802; Fax (409)747-6850 http://www.hbcg.utmb.edu/ http://www.nmr.utmb.edu/ mailto:bruce@nmr.utmb.edu =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Mon Mar 20 12:38:56 2000 Received: from sungod.ccs.yorku.ca (MYn1AC5qxWL6vmLSWFHl4aSw9RO02iBk@sungod.ccs.yorku.ca [130.63.236.104]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA03952 for ; Mon, 20 Mar 2000 12:38:56 -0500 Received: from sunburn.ccs.yorku.ca (sunburn.ccs.yorku.ca [130.63.236.110]) by sungod.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id MAA14117 for ; Mon, 20 Mar 2000 12:38:36 -0500 (EST) Received: from localhost (serge@localhost) by sunburn.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id MAA04046 for ; Mon, 20 Mar 2000 12:38:32 -0500 (EST) X-Authentication-Warning: sunburn.ccs.yorku.ca: serge owned process doing -bs Date: Mon, 20 Mar 2000 12:38:29 -0500 (EST) From: Sergey Gorelsky X-Sender: serge@sunburn.ccs.yorku.ca To: chemistry@ccl.net Subject: SUMMARY: DFT AND SPIN STATES Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII There was a clear interest of many people to see the results on the topic "DFT and spin states". Here is a summary of what I got from my (I am sure, not complete) library search and replies from Dmitry Khoroshun (dima@euch4e.chem.emory.edu) Klaus Stark (klaus@msi-eu.com) T. Daniel Crawford (crawdad@ne095.cm.utexas.edu) Definitely, the Hartree-Fock model with no account of correlation effects will significantly overstabilize high-spin states. Since LSD and GGA include correlation, their performance will be superior to HF. However, it looks like they (and LSD, in particular) have "too much correlation and too little exchange" and, thus, they overstabilize low-spin states. The hybrid functionals in which a fraction (around 20%) of the Hartree-Fock exchange energy is combined with the density functional exchange seems to correct this "correlation-exchange" misbalance and, as a result, they give quite accurate results for molecular energetics. For instance, for (C5H5)CrCl2(PH3)n the energy of the doublet state is going up compared to the energy of the quartet state by 5-7 kcal/mol when going from BLYP to B3LYP functionals. [Cacelli, I.; Keogh, D. W.; Poli, R.; Rizzo, A. J. Phys. Chem. A 1997, 101, 9801] So, all of this can be summarized in the following diagram: "OVERSTABILIZATION" low spin <----------------- 0 -------------------> high spin states states LSD <-------- GGA <-------hydrid functionals -----> HF There is a recent paper "Assessment of exchange correlation functionals" by A. J. Cohen and N. C. Handy [Chem. Phys. Lett., 316 (2000), 160]. However, I did not find similar reviews on the performance of DFT with respect to the energies of different spin states. It is also to be kept in mind that "LSD and GGA accounts of correlation are expected to be more trustworthy for antiparallel spins than for parallel spins, although the practical consequences of this for open-shell systems are not yet clear" (see K. Burke and J. P. Perdew, Intr. J. quant. Chem., 1995, v. 56, 199 and recent review of J. Li, L. Noodleman and D. A. Case in "Inorganic Electronic Structure and Spectroscopy, Volume I, p.661, John Wiley & Sons: 1999) ___________________________________________________________________ From: Dr. Klaus Stark DFT has a problem with high-spin states. With most functionals the low-spin state is preferred over the high-spin state even is the latter is known to be the minimum energy state. However, the bond lengths and angles are reproduced very nicely. In some cases BP86 is able to reproduce the correct minimum spin state. I heard that B3LYP should work better, however, I cannot give a reference. If your systems allows, you can check the spin state energy order with less costly methods on the DFT geometry, ZINDO works nicely, for instance. It gives the correct qualitative spin state order. However, it is not clear if the quantitative energy difference is reproduced very well. __________________________________________________ From T. Daniel Crawford, Ph.D. Institute for Theoretical Chemistry crawdad@jfs1.cm.utexas.edu Departments of Chemistry and Biochemistry http://zopyros.ccqc.uga.edu/~crawdad/ The University of Texas There have been numerous UDFT computations on transition-metal compounds, including open-shell states. See the recent review article by Siegbahn, for example: P. E. M. Siegbahn, "Electronic Structure Calculations for Molecules Containing Transition Metals", Adv. Chem. Phys., 1996, 93, 333 Many of the more recent computations for metals have included "broken symmetry" calculations for antiferromagnetically coupled singlets. These are simply the DFT analogs of the well-known UHF approach where and RHF->UHF orbital instability has been followed to obtain different alpha and beta densities. You may want to look at a reference by Noodleman for a reasonable review of this issue: L. Noodleman and D. A. Case, "Density-Functional Theory of Spin Polarization and Spin Coupling in Iron-Slufur Clusters", Adv. Inorg. Chem., 1992, 38, 423 Please feel free to send your additional comments to me. Sergey Gorelsky ________________________________________________________________ Sergey Gorelsky, M. Sc. Department of Chemistry, York University 4700 Keele St., Toronto, Ontario M3J 1P3, Canada tel.(416) 736-2100 ext#77720 and ext#70131 fax:(416) 736-5936 http://www.chem.yorku.ca/grad/SG/ ________________________________________________________________ From chemistry-request@server.ccl.net Mon Mar 20 13:42:23 2000 Received: from nucleus.harvard.edu (nucleus.harvard.edu [140.247.90.196]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA04309 for ; Mon, 20 Mar 2000 13:42:23 -0500 Received: from localhost (daizadeh@localhost) by nucleus.harvard.edu (8.9.3/8.9.3) with ESMTP id NAA15662 for ; Mon, 20 Mar 2000 13:44:57 -0500 (EST) Date: Mon, 20 Mar 2000 13:44:57 -0500 (EST) From: Iraj Daizadeh To: chemistry@ccl.net Subject: isomer enumeration. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL. I was wondering what is the general formula for generating the maximum number of structural isomers from a given empirical formula. I thought there was one; I am probably wrong. Ramberg in a recent issue of Hyle says there is not, see reference 56 in HYLE - An International Journal for the Philosophy of Chemistry, Vol. 6 (2000), No. 1... found at: http://www.uni-karlsruhe.de/~ed01/Hyle/Hyle6/ramberg.htm Thanks. Iraj Iraj Daizadeh, Ph.D. Harvard University Department of Cellular and Molecular Biology The Biological Laboratories 16 Divinity Avenue Cambridge, MA 02138 Phone: (617) 495-0783 (617) 495-0560 Fax: (617) 496-4313 Email: daizadeh@nucleus.harvard.edu WebPage: http://mcb.harvard.edu/gilbert/daizadeh From chemistry-request@server.ccl.net Mon Mar 20 19:10:23 2000 Received: from hanno.taiho.co.jp (hanno.taiho.co.jp [210.158.206.38]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA05518 for ; Mon, 20 Mar 2000 19:10:22 -0500 Received: from ishida.taiho.co.jp (dhcp127.taiho.co.jp [210.158.206.123]) by hanno.taiho.co.jp (8.9.3/3.7W) with SMTP id JAA20581 for ; Tue, 21 Mar 2000 09:16:52 +0900 Message-ID: <003601bf8ad9$ebbe0b20$7bce9ed2@taiho.co.jp> From: "Keisuke Ishida" To: Subject: HELP CHEMISTRY Date: Sat, 11 Mar 2000 06:45:15 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6600 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 HELP CHEMISTRY I want to know the information of this refrector. ************************************************** Keisuke Ishida Chemistry Laboratory, Taiho Pharmaceutical Co.,Ltd. Hanno 357-8527 Japan TEL. +81-429-72-8900 FAX. +81-429-72-8913 E-mail. ishida@taiho.co.jp ************************************************** From chemistry-request@server.ccl.net Mon Mar 20 13:05:15 2000 Received: from tahoe.orconet.com (tahoe.orconet.com [216.98.227.70]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA04152 for ; Mon, 20 Mar 2000 13:05:14 -0500 Received: from molecules.com (molecular.orconet.com [216.98.228.87]) by tahoe.orconet.com (8.9.3/8.9.3) with ESMTP id KAA26346 for ; Mon, 20 Mar 2000 10:02:42 -0800 (PST) Message-ID: <38D666F1.785402E3@molecules.com> Date: Mon, 20 Mar 2000 09:59:14 -0800 From: James Givens Reply-To: jamesg@molecules.com Organization: Molecular Arts Corp - http://www.molecules.com X-Mailer: Mozilla 4.6 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: . 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