From toukie@zui.unizh.ch Fri Jan 31 03:20:00 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id DAA06267; Fri, 31 Jan 1997 03:16:10 -0500 (EST) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA10984; Fri, 31 Jan 1997 09:21:35 +0100 Message-Id: <1.5.4.32.19970131081743.0066db90@zui.unizh.ch> X-Sender: toukie@zui.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, 31 Jan 1997 09:17:43 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: Cosmo Player version 1.0 beta 3 Dear Colleagues; I have just examined the Cosmo Player version 1.0 beta 3 version be- ing distributed by SGI for Windows 95, and I see that it is set to expire on 1 April 1997. Does anyone know with what it will be replaced, and will that replacement be distributed gratis or on a fee-basis only? Thanks in advance to all responders. Sincerely, S. Shapiro ZH toukie@zui.unizh.ch From toukie@zui.unizh.ch Fri Jan 31 03:20:30 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id DAA06263; Fri, 31 Jan 1997 03:16:01 -0500 (EST) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA11354; Fri, 31 Jan 1997 09:21:24 +0100 Message-Id: <1.5.4.32.19970131081732.0066fe2c@zui.unizh.ch> X-Sender: toukie@zui.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, 31 Jan 1997 09:17:32 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: Hammett ortho substituent constants? Dear Colleagues; It is my understanding that Hammett sigma constants are restricted to substituents at meta and para positions because steric influences on the functionality at C-1 (e.g., COOH, OH) cannot be clearly distinguished from electronic influences, whereas steric influences on the functionality at C-1 by substituents in the meta or para positions is negligible. Has anyone ever undertaken (and pubished) a detailed analysis of the influence of ortho substituents in an effort to factor the influence of ortho substituents in to electronic and steric components? I note that in the 1982 book "pKa Prediction for Organic Acids and Bases" by D. D. Perrin, B. Bempsey, and E. P. Serjeant Appendix A.5 is a small list of apparent sigma ortho values. Does anyone know of a more recent and/or extensive lists, particularly ones containing values factored into steric and electronic components for benzoic acids and phenols? Thanks in advance to all responders, S. Shapiro toukie@zui.unizh.ch From plessix@dial.oleane.com Fri Jan 31 04:20:00 1997 Received: from relay4.oleane.net for plessix@dial.oleane.com by www.ccl.net (8.8.3/950822.1) id EAA06513; Fri, 31 Jan 1997 04:14:45 -0500 (EST) Received: from plessix.dial.oleane.com (thouveni.pobox.oleane.com [194.2.6.61]) by relay4.oleane.net with SMTP id KAA07481 for ; Fri, 31 Jan 1997 10:14:57 +0100 (MET) Message-ID: Priority: Normal To: CCL MIME-Version: 1.0 From: Roger ROZOT Subject: Molecular modeling position at L'Oreal Date: Fri, 31 Jan 97 09:47:00 -0000 (WET) Content-Type: text/plain; charset=US-ASCII; X-MAPIextension=".TXT" Content-Transfer-Encoding: 7bit Molecular modeling position at L'Oreal L'Oreal is the world leader of the cosmetic industry with sales in excess of 10 billions, 40000 employees and world positions in 150 countries. L'Oreal Research has an opening for an highly motivated individual to join the molecular modeling research team. Applicants shall have a PhD in chemistry, physical chemistry or a related field, and experience in applying modeling to practical problems related to materials sciences (polymers properties, small molecule/macromolecule interaction,... ) In addition to the scientific qualifications, excellent communication and organizational skills are required to work closely with other research teams. The L'Oreal Research Center is located near Paris. Qualified individuals are invited to send a resume to: plessix@dial.oleane.com L'Oreal Research Center Human Resources 1 av Eugene-Schueller 93600 Aulnay sous Bois France From plessix@dial.oleane.com Fri Jan 31 04:20:07 1997 Received: from relay3.oleane.net for plessix@dial.oleane.com by www.ccl.net (8.8.3/950822.1) id EAA06470; Fri, 31 Jan 1997 04:06:39 -0500 (EST) Received: from plessix.dial.oleane.com (thouveni.pobox.oleane.com [194.2.6.61]) by relay3.oleane.net (8.8.Alpha.5/8.8.Alpha.5) with SMTP id KAA21054 for ; Fri, 31 Jan 1997 10:06:31 +0100 (MET) Message-ID: Read-Receipt-To: Roger ROZOT Return-Receipt-To: plessix@dial.oleane.com Priority: Normal To: CCL MIME-Version: 1.0 From: Roger ROZOT Subject: Molecular modeling position at L'Oreal Date: Fri, 31 Jan 97 09:36:27 -0000 (WET) Content-Type: text/plain; charset=US-ASCII; X-MAPIextension=".TXT" Content-Transfer-Encoding: 7bit Molecular modeling position at L'Oreal L'Oreal is the world leader of the cosmetic industry with sales in excess of 10 billions, 40000 employees and world positions in 150 countries. L'Oreal Research has an opening for an highly motivated individual to join the molecular modeling research team. Applicants shall have a PhD in chemistry, physical chemistry or a related field, and experience in applying modeling to practical problems related to materials sciences (polymers properties, small molecule/macromolecule interaction,... ) In addition to the scientific qualifications, excellent communication and organizational skills are required to work closely with other research teams. The L'Oreal Research Center is located near Paris. Qualified individuals are invited to send a resume to: plessix@dial.oleane.com L'Oreal Research Center Human Resources 1 av Eugene-Schueller 93600 Aulnay sous Bois France From smelchor@goliat.ugr.es Fri Jan 31 07:20:02 1997 Received: from goliat.ugr.es for smelchor@goliat.ugr.es by www.ccl.net (8.8.3/950822.1) id GAA07080; Fri, 31 Jan 1997 06:51:09 -0500 (EST) Received: (from smelchor@localhost) by goliat.ugr.es (8.8.0/8.7.3) id MAA18136; Fri, 31 Jan 1997 12:52:39 +0100 (MET) Date: Fri, 31 Jan 1997 12:52:39 +0100 (MET) From: Santiago Melchor Ferrer To: chemistry@www.ccl.net Subject: Subscribe Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I would like to subscribe to your services. My e-mail address is smelchor#goliat.ugr.es (# represents the "at" symbol) From ccl@www.ccl.net Fri Jan 31 13:29:39 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id MAA10191; Fri, 31 Jan 1997 12:42:17 -0500 (EST) Received: from gatekeeper.eastman.com for bewilson@eastman.com by bedrock.ccl.net (8.8.3/950822.1) id MAA28657; Fri, 31 Jan 1997 12:42:15 -0500 (EST) Received: by gatekeeper.eastman.com; id MAA26146; Fri, 31 Jan 1997 12:54:05 -0500 (EST) Received: from emngw1.eastman.com(164.89.254.2) by gatekeeper.eastman.com via smap (3.2) id xma026067; Fri, 31 Jan 97 12:53:47 -0500 Received: by eastman.com id AA24162 (5.67b/IDA-1.5 for chemistry@ccl.net); Fri, 31 Jan 1997 12:38:44 -0500 Received: from ntb150.kpt.emn.com by eastman.com with SMTP id AA19551 (5.67b/SMI-4.1 for ); Fri, 31 Jan 1997 12:38:43 -0500 Received: by ntb150.kpt.emn.com with SMTP (Microsoft Exchange Server Internet Mail Connector Version 4.0.993.5) id <01BC0F73.F812F960@ntb150.kpt.emn.com>; Fri, 31 Jan 1997 12:40:41 -0500 Message-Id: From: "Wilson, Bruce" To: "'chemistry@ccl.net'" Cc: "'bewilson@eastman.com'" Subject: Summary re term symbols Date: Fri, 31 Jan 1997 12:39:27 -0500 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.993.5 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Following is the information I received regarding references on term symbols. Thanks to Lutfur Khundkar, J. Grant, Ole Swang, and Richard Bone for their time in responding. I found both McQuarrie's book and Atkin's book in the library and have been reading through those. ----From lkhundkr@neu.edu (Lutfur Khundkar) Don McQuarrie's "Quantum Chemistry" has an excellent section on naming and deriving atomic term symbols. The molecular symmetry symbols I learned from Cotton's book "Chemical Application of Group Theory" as well as from Herzberg's bible on Molecular spectroscopy. Herzberg's books are comprehensive, but nowhere as eloquent as McQuarrie's. -------From hert0531@argon.chem.TU-Berlin.DE (Roland Hertwig) In principle, Atkins' books suit the purpose. Look for "Physical Chemistry" or even better "Molecular Quantum Mechanics" by P.W. Atkins (OXford University Press). Also a good book is "Quantum Chemistry" by I.R.A. Levine. (Prentice Hall International). --------From jeg10@po.cwru.edu (J. Grant) The Text "Spectrophotometric Identification of Organic Compounds" Fifth Edition, by Silverstein, Bassler and Morrill contains a through chapter (20 pages) with a bibliography (at chapter's end) that I have found useful. -----From Ole.Swang@si.sintef.no (Ole Swang) The following books all treat group theory for molecules: F. A. Cotton: "Chemical Application of Group Theory" P. W. Atkins: "Molecular Quantum Mechanics" F. L. Pilar: "Elementary Quantum Chemistry" Cotton's book is the classic. The two others are textbooks on quantum chemistry, with chapters on molecular symmetry. -----From rgab@easynet.co.uk (Richard Bone) I'm not sure if you'll have had a flood of replies about this yet but two books I found useful in the education system phase of my life were: P. W. Atkins, Molecular Quantum Mechanics (Oxford University Press) M. Gerloch, Orbitals, Terms and States. The first one has useful and accurate discussion in places though is not very expansive. The second book is a specialist work devoted to the entire subject in its minutiae ... Otherwise, failing that, I always found solid spectroscopy books, e.g., by G. Herzberg, to be valuable in these areas. I wouldn't settle for any undergraduate level spectroscopy text book though as it won't be precise enough or full enough for your aims. ================================================================= Bruce E. Wilson (bewilson@eastman.com) Chemical Information Services, B-150B, Lincoln Street Eastman Chemical Company Kingsport, TN 37662-5150 Voice: (423) 229-8886 FAX: (423) 229-6114 "Opinions are mine, but available free of charge." From mn1@helix.nih.gov Fri Jan 31 18:20:07 1997 Received: from helix.nih.gov for mn1@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id SAA13653; Fri, 31 Jan 1997 18:00:09 -0500 (EST) Received: (from mn1@localhost) by helix.nih.gov (8.8.4/8.8.4) id RAA20320; Fri, 31 Jan 1997 17:59:33 -0500 (EST) Date: Fri, 31 Jan 1997 17:59:33 -0500 (EST) From: "M. Nicklaus" Message-Id: <199701312259.RAA20320@helix.nih.gov> To: CHEMISTRY@www.ccl.net Subject: G94(Sum.+Q): Problem with PES Scan in DFT Cc: mn1@helix.nih.gov Dear CCL'ers, This is the, maybe preliminary, summary of the responses I got to my question concerning a problem with PES Scan in DFT in G94. A few follow-up questions are appended. @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ Question: ========= ? I seem to be having a problem with a Potential Energy Surface (PES) scan ? in G94. I am running a relaxed PES scan on a nucleoside analog, trying ? to rotate the base. I am running this job at the DFT method/basis set ? B3LYP/6-31G(d). I'm using cartesian coordinates (a newzmat-generated ? input file with a Z-matrix didn't work previously), pre-optimized at ? the same level of theory from X-ray coordinates. ? ? For the first few conformations, everything seems to have proceeded nicely; ? i.e., the energy started out some 20 kcal/mol or so above the (presumed) ? global energy minimum, and then came down, during the partial optimization, ? to a reasonable value a few kcal/mol above the global min. ? With the current conformation, however, the job seems to be stuck, since ? for nearly 20 steps now, the energy has only been oscillating in a narrow ? band. [rest omitted] @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ Responses: ========== From: Jan Labanowski Try to see, if you have very closely spaced HOMO/LUMO -- usually, due to Self Interaction problem of DFT, the SCF will oscillate in this case. I do not know how to fix it in G9X, since I do not use it for DFT, but other problems have some options, like DMIX (a portion of new density to be mixed with old density for new SCF iteration), or freezing occupances, or level shifting technique, or smear approach. If some of those are available in gaussian, use them. Going on with the run will not help, it will just keep oscillating. Of course, I may be wrong as to the cause, since I did not see your MO energies. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From: Jennie.Weston@org.chemie.uni-giessen.de (Jennie Weston) The problem is probably that the optimizer routine is taking too big steps for your pot E surface. You are apparently in the region of a very flat minimum (maybe the thing is quite rotationally flexible??). The routine must step smaller in order to find the stationary point. Kill the job at once, further comp time is just wasted. Cut out the geometry corresponding to the lowest energy in the many optimization cycles. Use it to make a new input file (so you don't loose the work already done) (so you don't loose the work already been done on the optimization). Include (For Gaussian) the option opt=tight in the key word line. If this still doesn't work, use opt=verytight. This decreases the tolerances for the optimization routine and forces it to step smaller. However, it takes more comp time. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From: d3g359@fido.pnl.gov (John Nicholas) Marc, yes I have seen it often with dft in G94. I do not know the origin of the problem. I would guess the job may never converge. However, you should check the forces, if the forces are still high, then maybe something is wrong other than g94's problem with convergence. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From: Samuel_Mikes@hmc.edu Is it possible that you entered the step in degrees while the program read it as radians? Sometimes the documentation is incomplete or just plain wrong. @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ Follow-up questions: ==================== 1. Taking up Jennie's suggestion, I realized that this conformation may indeed be in a 'difficult' region of the energy surface It is quite possible that it is very close to a local maximum relative to the scanned torsion, i.e. close to the top of the rotation barrier. With this---and only this---torsion constrained to the presribed value in the scan, I think it is very well possible that the energy surface with respect to the remaining coordinates is very flat, or otherwise 'weird looking'. Any thoughts, or experiences on this point? 2. Can one restart a PES scan job with tighter convergence for the optimization by using Opt=(Restart,Tight,AddRedundant); or will restarting the job from the checkpoint file ignore the new keyword "Tight" and proceed with the same settings as before? 3. How do I extract a specific structure from a PES scan checkpoint file; i.e., how do I tell newzmat that I want, say, the (structure of the) 17th step in the optimization of the 3rd conformation? Thanks to all who responded, and thanks in advance to future responders. Marc ------------------------------------------------------------------------ Marc C. Nicklaus Lab. of Medicinal Chemistry e-mail: mn1@helix.nih.gov National Cancer Institute, NIH Phone: (301) 402-3111 Bldg 37, Rm 5B29 Fax: (301) 496-5839 BETHESDA, MD 20892-4255 USA WWW: http://www.nci.nih.gov/intra/lmch/MCNBIO.HTM ------------------------------------------------------------------------ From ccl@www.ccl.net Fri Jan 31 19:20:07 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id SAA13802; Fri, 31 Jan 1997 18:39:29 -0500 (EST) Received: from copland.udel.edu for sbennett@wotan.duch.udel.edu by bedrock.ccl.net (8.8.3/950822.1) id SAA09280; Fri, 31 Jan 1997 18:39:27 -0500 (EST) Received: from wotan.duch.udel.edu (wotan.duch.udel.edu [128.175.54.25]) by copland.udel.edu (8.8.5/8.7.3) with SMTP id SAA22014 for <@brahms.udel.edu:chemistry@ccl.net>; Fri, 31 Jan 1997 18:38:47 -0500 (EST) Received: by wotan.duch.udel.edu (951211.SGI.8.6.12.PATCH1502/951211.SGI) id SAA05578; Fri, 31 Jan 1997 18:22:58 -0500 Date: Fri, 31 Jan 1997 18:22:57 -0500 (EST) From: Steve Bennett To: CCL Users Subject: Bond order analysis Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I have recently started using DMol to calculate bond orders between transition metals and main group elements. I am interesting in finding references concerning the Mayer implementation as in DMol and how it compares to other methodologies, such as NBO and Mulliken analyses. Any results will be compiled and summarized to the list. Thanks in advance Steven D. Bennett University of Delaware Department of Chemistry 304A Drake Hall (302) 831-8720 sbennett@wotan.duch.udel.edu (302) 737-8485 http://udel.edu/~sbennett/steves.html "Although the answer is not unknown, I'm searchin', searchin, and how I've grown; It's not all right to say goodbye, and the world on a string doesn't mean a thing" Neil Young