>From owner-chemistry@ccl.net Mon Mar 18 16:33 EST 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id QAA18487; Mon, 18 Mar 1996 16:33:30 -0500 (EST) Received: from gig.usda.gov for srheller@origin.gig.usda.gov by bedrock.ccl.net (8.7.1/950822.1) id QAA27175; Mon, 18 Mar 1996 16:33:28 -0500 (EST) Received: by gig.usda.gov (5.x/SMI-SVR4) id AA10009; Mon, 18 Mar 1996 16:21:44 -0500 Date: Mon, 18 Mar 1996 16:21:44 -0500 (EST) From: "Stephen R. Heller" To: jcicshelp , chemistry@ccl.net, chminf-l@iubvm.ucs.indiana.edu, orgchem@extreme.chem.rpi.edu Subject: Software to review Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 2239 Status: R 18 March, 1996 Subject: Computer Software for Review As the Software Review Editor for the ACS Journal of Chemical Information and Computer Science (JCICS) I often get software for review in the journal. I have one (1) new software product. I am looking for someone who is willing to review this software product. In return for the review which is published in JCICS you get to keep the software or database. The review should be completed in 1-3 months. The length of the review is 4-10 double spaced typed pages. Sample reviews can be found in most of the recent issues of JCICS. Please try to give me some (short) reason to choose you over another person. I have tried this approach for about the past four years and it is working reasonably well. (REMINDER: For those who haven't finished your reviews of software sent months and months ago, this last sentence does not apply to you!) As a result, I am continuing this new method to find reviewers using this e- mail/user group system. I reserve the right to abandon this if it is a problem, or inappropriate. I will not notify people if I have found a reviewer. If you don't hear from me within a few days I have chosen someone else to review the particular package. As I get many, many, (too many) replies to this message, please do not respond after 20 March 1996 (Wednesday), as I am sure the software will be gone by then. I can be reached on Internet (SRHELLER@GIG.USDA.GOV). PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE, and FAX NUMBER!!! (I send the software by Federal Express.) Without this information I WILL NOT consider your request. Steve Heller The package I now have is: SteamTab:Thermodynamic and Transport Properties of Steam version 1.0, from ChemicaLogic. The software comes with a set of popular steam engineering algorithms in the spreadsheet format as templates for Excel 7.0 for Windows 95 or Lotus 1-2-3 for Windows Please specify which version (Lotus or Excel) you would like to review! Steve Heller, USDA, ARS, Plant Genome Project Bldg. 005, Room 337 Beltsville, MD 20705-2350 USA Phone: 301-504-6055 FAX: 301-504-6231 E-mail: srheller@gig.usda.gov WWW; www.hellers.com/~steve >From jeg10@caleb.INS.CWRU.Edu Mon Mar 18 18:09 EST 1996 Received: from caleb.INS.CWRU.Edu for jeg10@caleb.INS.CWRU.Edu by www.ccl.net (8.7.1/950822.1) id SAA18912; Mon, 18 Mar 1996 18:09:32 -0500 (EST) Received: (jeg10@localhost) by caleb.INS.CWRU.Edu (8.6.12/CWRU-2.1-bsdi) id SAA29479; Mon, 18 Mar 1996 18:09:33 -0500 (from jeg10) Message-Id: <199603182309.SAA29479@caleb.INS.CWRU.Edu> Date: Mon, 18 Mar 1996 18:09:33 -0500 From: jeg10@po.CWRU.Edu (Jennifer E. Grant) To: CHEMISTRY@www.ccl.net Subject: Looking for NMR freeware for PC? Reply-To: jeg10@po.CWRU.Edu (Jennifer E. Grant) Content-Type: text Content-Length: 356 Status: R Cheers, to the herculean effort to develop an NMR freeware program for the MAC. Could someone please direct me to a PC analog? Nothing but 486s at my end. Jennifer Dept. Biochemistry CWRU -- "Wer denkt, schafft" Jennifer E. Grant Department of Biochemistry Phone: (216) 368-3250 Case Western Reserve University >From shenkin@still3.chem.columbia.edu Mon Mar 18 16:05 EST 1996 Received: from mailhub.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.7.1/950822.1) id QAA17821; Mon, 18 Mar 1996 16:05:56 -0500 (EST) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailhub.cc.columbia.edu (8.7.3/8.7.3) with SMTP id QAA28225; Mon, 18 Mar 1996 16:05:49 -0500 (EST) Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for @mailhub.cc.columbia.edu:toni@athe.wustl.edu id AA20301; Mon, 18 Mar 96 16:05:48 -0500 Date: Mon, 18 Mar 96 16:05:48 -0500 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <9603182105.AA20301@still3.chem.columbia.edu> To: toni@athe.wustl.edu (Toni Kazic) Subject: Re: CCL:PRONUNCIATION ON CONFORMER Cc: elewars@alchemy.chem.utoronto.ca, chemistry@www.ccl.net Content-Type: text Content-Length: 2327 Status: R > From chemistry-request@www.ccl.net Mon Mar 18 15:22:28 1996 > con FORM ME <- MF <- L ... > /con/ |for| MA tion L > > So the stress is shifting between the second and third syllable... > > > What is going on? The etymologies are sketchy so I'll guess. The verb > "conform" comes into English quite early, and then mutates into adjectives > and nouns ("conformable", "conformance", "conformer") but retains the > stress on the second syllable. > ..."conformation" is in English a straight borrowing > from Latin, and so retains its (classical? surely Vulgate) pronunciation, > allowing for compression of the last four letters into one sound. > Notice that in no case is the stress on the first syllable. Whether the > chemical sense of the term derives from "conform" or "conformation" ... > ...you can't use it to justify what I agree > may be the most common pronunciation. I suspect CONformer comes by analogy > to ISOmer. ... "Conformation" has the primary stress on the third syllable, but a secondary stress on the first. This is why I think that "CON-for-mer" is derived from the pronounciation of "conformation". If you remove the last two syllables of the latter, you're left with "CON-for". The "ICE-o-mer" analogy only strengthens the argument in favor of CON-for-mer, in my opinion, though I'm less convinced this is it's origin. Be all this as it may, I've had a lot of fun with this, and hope you all have also. I promise to shut up on this topic starting now. :-) On a far more clear-cut and embarrassing subject, Benzion Fuchs, , pointed out that the "In memorium" in my signature should have read "In memoriam". I consulted Fowler's "Modern English Usage" before making the "data" / "agenda" analogy, and if I had consulted a mere dictionary before typing "In memorium", I'd not have made the error. Who was it who said that great discoveries are to be found in front of our very noses? Thanks, Benzion. I've now made the change. -P. **************** In Memoriam, Minnie Pearl, 1913-1996, RIP ***************** *** Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ., *** *** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *** MacroModel home page: www.cc.columbia.edu/cu/chemistry/mmod/mmod.html*** From MCDI3CMW@fs1.ch.umist.ac.uk Tue Mar 19 08:17:24 1996 Received: from ursa.cns.umist.ac.uk for MCDI3CMW@fs1.ch.umist.ac.uk by www.ccl.net (8.7.1/950822.1) id HAA27857; Tue, 19 Mar 1996 07:53:16 -0500 (EST) Received: from fs1.ch.umist.ac.uk by ursa.cns.umist.ac.uk with SMTP (PP); Tue, 19 Mar 1996 12:37:17 +0000 Received: from UMIST-CH-FS1/MAILQUEUE by fs1.ch.umist.ac.uk (Mercury 1.20); 19 Mar 96 12:37:19 GMT Received: from MAILQUEUE by UMIST-CH-FS1 (Mercury 1.20); 19 Mar 96 12:36:13 GMT From: "C.M.Windsor" To: CHEMISTRY@www.ccl.net Date: Tue, 19 Mar 1996 12:36:04 gmt Subject: MO Coefficients X-Confirm-Reading-To: "C.M.Windsor" X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail v3.22 Message-ID: <477306FD3@fs1.ch.umist.ac.uk> I have calculated the MO coefficients for formaldimine using Gaussian's POP=full command. I now want to calculate the HOMO and LUMO coefficients for the molecule but do not understand the format of the output. ------------------------------------------------------------------- Molecular Orbital Coefficients 1 2 3 4 ...... 8 O O O O O EIGENVALUES -- H 1S 2S N 1S etc.... ------------------------------------------------------------------- What I need to know is the meaning of the different O(real) orbitals 1- 8 and which one (or ones) do I use in the LCAO summation? As an aside, are there any programs (preferably free) that can visualise atomic orbitals from the Gaussian output? Thanks in advance! Carl -------------------------------------------------------------- Brought to you by the letters Q & S and the number 7 -------------------------------------------------------------- From Carl Mark Windsor University of Manchester Institute of Science and Technology. (U.M.I.S.T.) Chemistry Department. -------------------------------------------------------------- From KGRAFTON@aardvark.ucs.uoknor.edu Tue Mar 19 11:17:25 1996 Received: from aardvark.ucs.uoknor.edu for KGRAFTON@aardvark.ucs.uoknor.edu by www.ccl.net (8.7.1/950822.1) id LAA01249; Tue, 19 Mar 1996 11:06:36 -0500 (EST) From: Received: from aardvark.ucs.uoknor.edu by aardvark.ucs.uoknor.edu (PMDF V4.3-13 #7521) id <01I2IOY5TX8W0019AA@aardvark.ucs.uoknor.edu>; Tue, 19 Mar 1996 10:06:25 -0600 (CST) Date: Tue, 19 Mar 1996 10:06:25 -0600 (CST) Subject: G: Cube option in G94... To: CHEMISTRY@www.ccl.net Message-id: <01I2IOY5W2EQ0019AA@aardvark.ucs.uoknor.edu> X-Envelope-to: CHEMISTRY@www.ccl.net X-VMS-To: IN%"CHEMISTRY@www.ccl.net" X-VMS-Cc: KGRAFTON MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT I have tried for some time now to get the Cube option to work in Gaussian94. If someone out there has gotten it to work, I would very much like to see a sample input file. If there is interest, I'll repost here, but please email responses to me directly at kurt@osric.chem.uoknor.edu Thanks, Kurt Grafton Department of Chemistry University of Oklahoma From rochus@felix.anorg.chemie.tu-muenchen.de Tue Mar 19 12:16:14 1996 Received: from felix.anorg.chemie.tu-muenchen.de for rochus@felix.anorg.chemie.tu-muenchen.de by www.ccl.net (8.7.1/950822.1) id KAA00856; Tue, 19 Mar 1996 10:32:31 -0500 (EST) Received: by felix.anorg.chemie.tu-muenchen.de (940816.SGI.8.6.9/930416.SGI) for chemistry@www.ccl.net id QAA16725; Tue, 19 Mar 1996 16:26:58 +0100 From: "Rochus Schmid" Message-Id: <9603191626.ZM16723@felix> Date: Tue, 19 Mar 1996 16:26:57 +0100 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: SUMMARY: CH4/CH4 potential Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear netters, My request was: On Mar 12, 1:57pm, Rochus Schmid wrote: > Subject: CCL:CH4/CH4 potential > Dear netters, > > Can someone point me to references concerning the calculation of the potential > between two methan molecules (calculated by any theoretical method)? > I would also be interested in experimental results. > > I will summarize to the list. > Thanks in advance. > > Greetings from Munich, > > Rochus > > > >-- End of excerpt from Rochus Schmid Thanks to an anonymous person , D. E. Williams , and Heinz Schiffer . J. Phys. Chem. 1996, 100, 2588-2596 J. Phys. Chem. 1987, 91, 6365 J. Chem. Phys. 81(3) (1984) 1389-1395 I have a further interesting reference, which was cited in the publications: J. Phys. Chem. 1994, 98, 1830-1833. Greetings, Rochus -- ******************************************************************************** Rochus Schmid Technische Universitaet Muenchen Tel. ++49 89 3209 3140 Anorganisch Chemisches Institut 1 Fax. ++49 89 3209 3473 Prof. W. A. Herrmann E-mail: Lichtenbergstrasse 4 rochus@felix.anorg.chemie.tu-muenchen.de 85747 Garching ******************************************************************************** From boyd@chem.iupui.edu Tue Mar 19 12:17:37 1996 Received: from indyvax.iupui.edu for boyd@chem.iupui.edu by www.ccl.net (8.7.1/950822.1) id LAA01646; Tue, 19 Mar 1996 11:47:55 -0500 (EST) Return-receipt-to: Boyd Received: from macgw.chem.iupui.edu by INDYVAX.IUPUI.EDU (PMDF V5.0-5 #5862) id <01I2ISEJDU0000CC3B@INDYVAX.IUPUI.EDU> for chemistry@www.ccl.net; Tue, 19 Mar 1996 11:42:40 -0500 Date: Tue, 19 Mar 1996 11:36:16 -0500 From: Boyd Subject: RCC: books To: OSC CCL Message-id: X-Mailer: Mail*Link SMTP-MS 3.0.2 Content-transfer-encoding: 7BIT Did you cite some chapters of REVIEWS IN COMPUTATIONAL CHEMISTRY in your publications in 1995? If so, we would like to hear about it. You may be in for a pleasant surprise. Details are given at http://chem.iupui.edu/~boyd/rcc.html Don Boyd From uli@smaug.physics.mun.ca Tue Mar 19 12:24:17 1996 Received: from smaug.physics.mun.ca for uli@smaug.physics.mun.ca by www.ccl.net (8.7.1/950822.1) id LAA01678; Tue, 19 Mar 1996 11:51:23 -0500 (EST) Received: by smaug.physics.mun.ca (940816.SGI.8.6.9/911001.SGI) id NAA11150; Tue, 19 Mar 1996 13:22:13 -0330 Date: Tue, 19 Mar 1996 13:22:13 -0330 (NST) From: Uli Salzner To: ccl Subject: Meaning of eigenvalues in density functional theory Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, Callaway and March (Sol. State Phys. 38, 135 (1984)) discuss the meaning or better "non-meaning" of eigenvalues in density functional methods. It seems that the band gap of a sufficiently large system can be calculated by taking the energy difference between the valence and the conduction band but that the difference between HOMO and LUMO in molecules can not be used in connection with Koopman's theorem. I am wondering whether this is the end of the story or whether it is possible for practical purposes to use HOMO and LUMO levels. Would that be a crude approximation or total garbage? I am especially interested in density functional methods as implemnented in GAUSSIAN 94, which lists the HOMO and LUMO levels in DFT just as for HF. It is quite tempting to use them and as far as I tried the results seem to be reasonable. What I would like to do is to compare solid state calculations (with Cerius2) and calculations for oligomers of increasing size and try to extrapolate towards the solid. I am only interested in systems at 0 temperature where the occupation of the one-electron functions is either 0 or 1. I would be very thankful for any comments or related references. A summary of the answers will be posted. Thanks in advance, Uli uli@smaug.physics.mun.ca From boyd@chem.iupui.edu Tue Mar 19 12:31:22 1996 Received: from indyvax.iupui.edu for boyd@chem.iupui.edu by www.ccl.net (8.7.1/950822.1) id LAA01553; Tue, 19 Mar 1996 11:40:34 -0500 (EST) Return-receipt-to: Boyd Received: from macgw.chem.iupui.edu by INDYVAX.IUPUI.EDU (PMDF V5.0-5 #5862) id <01I2IS6OCD0G00D5LM@INDYVAX.IUPUI.EDU>; Tue, 19 Mar 1996 11:36:21 -0500 Date: Tue, 19 Mar 1996 11:33:08 -0500 From: Boyd Subject: Reviews in Computational Chemistry To: Cache list , CHMINF-L , OSC CCL Message-id: X-Mailer: Mail*Link SMTP-MS 3.0.2 Content-transfer-encoding: 7BIT We wish to announce the publication of Volume 8 of REVIEWS IN COMPUTATIONAL CHEMISTRY. The emphasis of this volume is on quantum mechanics, especially as applied to large assemblies and heavy atoms. The authors and chapters are: 1. Zdenek Slanina, Shyi-Long Lee, and Chin-hui Yu, Computations in Treating Fullerenes and Carbon Aggregates. 2. Gernot Frenking, Iris Antes, Marlis Boehme, Stefan Dapprich, Andreas W. Ehlers, Volker Jonas, Arndt Neuhaus, Michael Otto, Ralf Stegmann, Achim Veldkamp, and Sergei F. Vyboishchikov, Pseudopotential Calculations of Transition Metal Compounds - Scope and Limitations. 3. Thomas R. Cundari, Michael T. Benson, M. L. Lutz, and Shaun O. Sommerer, Effective Core Potential Approaches to the Chemistry of the Heavier Elements. 4. Jan Almlof and Odd Gropen, Relativistic Effects in Chemistry. 5. D. B. Chesnut, The Ab Initio Computation of Nuclear Magnetic Resonance Chemical Shielding. A copy of the book will be available for your perusal at the VCH Publishers booth at the New Orleans ACS meeting next week. Volume 8 (xxi + 324 pp) ISBN 1-56081-929-4, 1996. Kenny B. Lipkowitz and Donald B. Boyd Co-editors, REVIEWS IN COMPUTATIONAL CHEMISTRY Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. http://chem.iupui.edu/ From stevensa@dax.biol.port.ac.uk Tue Mar 19 14:17:26 1996 Received: from dax.biol.port.ac.uk for stevensa@dax.biol.port.ac.uk by www.ccl.net (8.7.1/950822.1) id KAA00835; Tue, 19 Mar 1996 10:30:01 -0500 (EST) Received: by dax.biol.port.ac.uk (940816.SGI.8.6.9/940415.SGI.SS) id PAA20456; Tue, 19 Mar 1996 15:28:59 GMT From: "Adrian Stevens" Message-Id: <9603191528.ZM20454@dax.sci.port.ac.uk> Date: Tue, 19 Mar 1996 15:28:54 +0000 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Summary of responses Re: Vibrational query Cc: D.Tilbrook@surrey.ac.uk, aldert@chemde4.leidenuniv.nl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear all, I'd like to thank everyone who responded to my original query concerning the accuracy of calculated normal modes of vibration and also appologise for the length of time that it has taken to post the summary of responses back to the CCL. The replies have proved most helpful towards the current research, which is focused on the use of normal modes as the basis for a structural descriptor that can be applied in QSAR-type applications. For anyone that is interested in finding out further details of this research, a paper by Prof. Laurie Phillips and PhD thesis by Dave Turner should be published in the near future and provide the most detailed accounts. Alter- natively, I'm hoping to eventually put a web page onto the net, that should give a general introduction and overview of the concepts applied. I must add that it is currently in the early stages of development and may take some time to be completed - my own PhD thesis currently occupies all spare time. If interested parties could mail me directly, then I'll get in touch at the appropriate time. Thanks to: Attila Berces Jon Erickson Alan Shusterman David A. Tilbrook Edgardo Garcia Aldert Westra Hoekzema Cheers, Adrian. ========================= Original message follows: I have a query with regard to the accuracy of calculated normal modes of vibration (as for example, determined via semi-empirical methods) A while back, there was some discussion on the list, of the calculation of normal modes of vibration. In particular, David Young (at Michigan State University, young@slater.cem.msu.edu) posted a short introduction to the subject, titled 'Computational Modeling of Molecular Vibrations' (see Sun, 13 Aug 1995 in the CCL archive for the full posting). In it, he highlighted that vibrational frequencies from semi-empirical calculations tend to be qualitative in that bond stretches have high frequencies, bond angle bending lower frequencies, torsions even lower, etc. However, he also pointed out that the actual values are often erratic. When compared with experiment, some values come close while others are either too low or too high. He also made mention that density-functional theory methods give frequencies with this same erratic behavior, albeit, with a somewhat smaller deviation from the experimental results. I have certainly experienced such erratic behaviour in my current work. I started off initially, deciding to do a calibration test of the MOPAC software against the experimentally observed values for benzene - a reasonable starting point for any study is to check the accuracy of the model being applied. Taking the whole task of actually trying to figure out which eigenvalue corresponded to the c-c mode of 1485 cm-1 for an unsubstituted ring (in a substituted ring, eg tolualdehyde, this is the ~1600 cm-1 peak), there was no value to my mind, within an acceptable margin (it was pointed out to me, that a value returned within *5%* of the experimental result is acceptable!). It has been suggested to me, that the main reason for the deviation from experiment is attributable (and this I'm told applies also to ab initio Hartree Fock calculations) mainly to the intrinsic over-estimation of the electron- electron repulsion terms in the Hartree-Fock approach (an electron correlation effect?). What I would really appreciate primarily, would be confirmation or rejection of this statement, but idealy, an explanation of the underlying reason, with possible work-arounds, corrections, etc. It certainly puzzles me, that DFT also returns this error, when it treats the electrons in such a different fashion to Hartree-Fock? ============================ Summary of responses follow: 1) From: Attila Berces Date: Fri Mar 1, 3:44pm -0500 To: Stevensa@chem.port.ac.uk Cc: Subject: vibrations Hello Adrian, For the E2u mode of benzene, which is 1494 cm-1 experimentally, the simplest local density funtional method gives 1462 cm-1. Close enough? As far as benzene goes, the B2u mode of 1150 cm-1 is the worst by theoretical method, because this is the dissociation coordinates into 2 HCCH units. Even that is within the magic 5%, you are expecting. A detailed study on benzene: Berces and Ziegler, J. Chem. Phys. 98, 1993, p4793 Berces and Ziegler, J. Phys. Chem. 98, 1995, p11417. For transition metal complexes: J. Phys. Chem. 98, 1994, 1584 J. Phys. Chem. 98, 1994, 13233 > It has been suggested to me, that the main reason for the deviation from > experiment is attributable (and this I'm told applies also to ab initio Hartree > Fock calculations) mainly to the intrinsic over-estimation of the electron- > electron repulsion terms in the Hartree-Fock approach (an electron correlation> effect?). What I would really appreciate primarily, would be confirmation > or rejection of this statement, but idealy, an explanation of the underlying > reason, with possible work-arounds, corrections, etc. Any error in quantum chemistry comes either from the model ( i.e. harmonic approximation) or the correlation effect. It looks like harmonic approximation works pretty well except for high frequency stretches. Therefore, only correlation effect is left to blame. The problem in frequency calculations comes from the fact that error in stretches and bendings is not the same. Therefore, the order between stretches and bends of similar frequency may be switched or they mix too much or too little. Look at the first reference for such examples. Pulay and cowork worked out a scheme for correcting force constant systematically by different scaling factors for stretches, bends etc. These scaling factors are transferable to a certain extent and give not only very good eigenvalues but also good eigenvectors. Lately in Chem. Phys Letters there was a paper on frequencies of porphyrine. Attila 2) From: JERICKSON@dowelanco.com Date: Fri Mar 1, 4:04pm -0500 To: STEVENSA@chem.port.ac.uk Cc: Subject: semi-empirical vibrational frequencies Adrian, I did some work comparing AM1 vibrational frequencies with experimental values (JOC, 1995, 60, 1626) and they appeared to be ~18% off for C=O stretching. Stewart found this to be the case, as well (J. Comp. Chem. 1991, 12, 948). Not much better for HF/6-31G*, off by ~10% (In Hehre, An Initio Molecular Orbital Theory, 1986, Wiley). Jon Erickson DowElanco CAMD jerickson@dowelanco.com 3) From: Alan.Shusterman@directory.Reed.EDU (Alan Shusterman) Date: 01 Mar 96 11:54:15 PST To: stevensa@chem.port.ac.uk Cc: Subject: Re: CCL:M:Errors in Vibrational mode calcs... --- You wrote: It has been suggested to me, that the main reason for the deviation from experiment is attributable (and this I'm told applies also to ab initio Hartree Fock calculations) mainly to the intrinsic over-estimation of the electron- electron repulsion terms in the Hartree-Fock approach (an electron correlation effect?). What I would really appreciate primarily, would be confirmation or rejection of this statement, but idealy, an explanation of the underlying reason, with possible work-arounds, corrections, etc. --- end of quoted material --- Confirm! The HF wavefunction dissociates incorrectly, i.e., it keeps electrons paired up and delocalized in the bond that is being stretched. The electrons in this bond really want to localize on each atom, i.e., correlate their motions. Therefore, the HF energy surface rises too rapidly as the bond is stretched, and this steep surface yields stretching frequencies that are too high. The simplest workaround is to scale ab initio HF frequencies, i.e., multiply them by 0.89. This is not a perfect fix because not all vibrations are equally affected by correlation, but the resulting numbers are usually pretty good. Alan Shusterman Department of Chemistry Reed College Portland, OR 97202 4) From: D.Tilbrook@surrey.ac.uk (David A. Tilbrook) Date: Sun, 03 Mar 1996 01:12:11 +0000 To: Adrian Stevens Cc: Subject: Re: CCL:M:Errors in Vibrational mode calcs... >I have certainly experienced such erratic behaviour in my current work. I >started off initially, deciding to do a calibration test of the MOPAC software >against the experimentally observed values for benzene - a reasonable starting >point for any study is to check the accuracy of the model being applied. >Taking the whole task of actually trying to figure out which eigenvalue >corresponded to the c-c mode of 1485 cm-1 for an unsubstituted ring (in a >substituted ring, eg tolualdehyde, this is the ~1600 cm-1 peak), there was >no value to my mind, within an acceptable margin (it was pointed out to me, >that a value returned within *5%* of the experimental result is acceptable!). I'll run the calculation myself Adrian and will try and see what I get. Are you 'scaling' for frequencies by say 0.9 to give correction for the harmonic approximation? >It has been suggested to me, that the main reason for the deviation from >experiment is attributable (and this I'm told applies also to ab initio Hartree >Fock calculations) mainly to the intrinsic over-estimation of the electron- >electron repulsion terms in the Hartree-Fock approach (an electron correlation >effect?). What I would really appreciate primarily, would be confirmation >or rejection of this statement, but idealy, an explanation of the underlying >reason, with possible work-arounds, corrections, etc. It certainly puzzles >me, that DFT also returns this error, when it treats the electrons in such a >different fashion to Hartree-Fock? Keep in touch about your work Regards David Tilbrook 5) From: edgardo garcia Date: Mon, 4 Mar 1996 14:39:58 -0300 (GRNLNDST) To: Adrian Stevens Cc: Subject: Re: CCL:M:Errors in Vibrational mode calcs... Hi Adrian, I also experienced errors of +/- 50cm-1 with AM1 freq. calc. on organic molecules with up to 100 atoms. I would say that: 1. In general the accuracy of freq. predicctions go down in the direction : bonds > angles > torsions Also for torsions you will have populations of conformers that will show different freq. 2. Semiempirical methods are not parametrized for freq. so you can't really expect them to be good, they can be erratic. 3. In any HF method the curvatures on the hyperenergy surface are sharpper than if elec. correlation is included leading to higger freq. for bonds. 4. In most methods a harmonic oscilator approximation is used to get the freq. from the energy results, the anharmonicity shoud lower the frequencies. 5. Maybe taking in account the 0th point virbrational energy will also lower the frequencies ? Points 3 to 5 are the ones responsible for the general correction factor of 0.8 - 0.95 usually found. About DFM I don't have a clue. They certaily shoud result in higer freq. because of points 4 & 5, also they don't include all electron correlations. But, why they show erratic results relative to experiment ? Best regards, Dr. Edgardo Garcia Universidade de Brasilia Brasilia DF Brazil 6) From: aldert@chemde4.leidenuniv.nl (Aldert Westra Hoekzema) Date: Wed, 6 Mar 96 11:28:03 +0100 To: "Adrian Stevens" Cc: Subject: Re: CCL:M:Errors in Vibrational mode calcs... Hi Adrian, First of all I am not familiar with benzene frequencies, but have done a lot of frequency calculations on normal alkanes, including HF, MPx, CISD and DFT (B3PW91) levels of theory (6-31g** basis set). Roughly speaking, there are two main sources of error in the calculated as compared to experimental frequencies: a. the efffect that you suggested, namely the lack of correlation. As a result the curvature (and force contstant) in the well is too large and frequency will be too high. Improving the correlation treatment reduces this error, in my calculations DFT turned out to be the "best" (indeed, frequencies within the 5% you mentioned). b. the use of the harmonic approximation. There is not much one can do about this error (I do not know about programs that calculate anharmonic frequencies). In general stretching modes suffer mostly >from the use of the harmonic approximation. Perhaps experimental information from overtones can help to estimate this error. Hope this is clear and helpfull. Please send me a summary of the responses you get. Bye, Aldert -- ------------------------------------------------------ Adrian Stevens Research Associate Centre for Molecular Design, University of Portsmouth, c/o SSRIU, Halpern House, 1/2 Hampshire Terrace, Portsmouth, Hampshire, UK, PO1 2QF. Voice: +44 (0) 1705 843623 Fax: +44 (0) 1705 843722 ------------------------------------------------------ Stevensa@chem.port.ac.uk http://rooster.sci.port.ac.uk/chemistry/stevensa/ ------------------------------------------------------ From owner-chemistry@ccl.net Tue Mar 19 21:17:29 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id UAA08971; Tue, 19 Mar 1996 20:32:00 -0500 (EST) Received: from auric.chem.csiro.au for D.Winkler@chem.csiro.au by bedrock.ccl.net (8.7.1/950822.1) id UAA15196; Tue, 19 Mar 1996 20:31:54 -0500 (EST) Received: from [138.194.40.190] (mac-40190.chem.csiro.au) by auric.chem.csiro.au with SMTP id AA27419 (5.67b/IDA-1.5 for chemistry@ccl.net); Wed, 20 Mar 1996 12:25:53 +1000 X-Sender: win097@auric.chem.csiro.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 20 Mar 1996 12:26:35 +1000 To: listserv@cc.utas.edu.au, aschin-list@nuscc.nus.sg, chminf-l@iubvm.ucs.indiana.edu, chemistry@ccl.net From: D.Winkler@chem.csiro.au (Dr. Dave Winkler) Subject: Preliminary conference announcement. RACI/Melbourne/Dec 96 Please excuse any cross posts. RACI MEDICINAL & AGRICULTURAL DIVISION 13TH NATIONAL CONFERENCE "UP AND COMING RESEARCH IN AUSTRALIA" 8-11 DECEMBER, 1996, Monash University, Clayton 3168, Victoria, Australia The conference will cover all aspects of medicinal and agricultural chemistry. Papers are invited for both lecture and poster sessions. The meeting will be held in conjunction with the ASCEPT pharmacology conference and some joint sessions will be organized. The conference will focus on students and new researchers, emerging research areas in medicinal and agricultural chemistry, and the interaction of medicinal chemists and pharmacologists. There will also be a symposium on research funding and the research/industry interface. Preliminary session topics include: o agrochemistry; o toxins; o anti-infectives; o enzyme inhibitors; o automated methods of synthesis and screening; o glycobiology and glycochemistry; o DNA and drugs; o QSAR methods and o medicinal chemistry teaching. Registration forms and details will be published later to this list and on our Web page. Enquiries to: Dr. Margaret Wong, Department of Applied Chemistry, Swinburne University of Technology, Hawthorn 3122 Victoria Ph: (03)9214-8542 Fax: (03)9819-0834 email: marg@chem1.chem.swin.edu.au or me. Cheers, Dave Dr. David A. Winkler Voice: 61-3-9542-2244 Principal Research Scientist Fax: 61-3-9543-8160 CSIRO Division of Chemicals and Polymers CSIRO: http://www.csiro.au Private Bag 10,Rosebank MDC, Clayton, Australia http://www.wark.csiro.au