From chemistry-request@www.ccl.net Sun Aug 30 15:19:52 1998 Received: from mailrelay1.cc.columbia.edu (cu41754@mailrelay1.cc.columbia.edu [128.59.35.143]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA22066 Sun, 30 Aug 1998 15:19:51 -0400 (EDT) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id PAA13918 for <@smtp.columbia.edu:chemistry@www.ccl.net>; Sun, 30 Aug 1998 15:19:53 -0400 (EDT) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) for chemistry@www.ccl.net id PAA00478; Sun, 30 Aug 1998 15:19:52 -0400 Date: Sun, 30 Aug 1998 15:19:52 -0400 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <199808301919.PAA00478@still3.chem.columbia.edu> To: chemistry@www.ccl.net Subject: Re: CCL:Quantitative normal mode analysis Hi, > From chemistry-request@www.ccl.net Fri Aug 28 20:11:19 1998 > From: Yar Tikhiy > A lot of good software for visualizing IR vibrations exists today. > However, movies seem insufficient in case of complex systems > like cluster models with "adsorbed" molecules on them. I'd like > to find out if there are any methods or software allowing assignment > (approximate, of course) of normal modes to this or that group of > atoms when given normal vibration forms. Thank you. MacroModel allows specified atoms in a system to be "frozen". the remaining atoms can still be handled at the level of second derivatives; these "feel" the effect of the frozen atoms as an external, immutable field. We can make a movie of the normal modes of the system; if this is done on a system with frozen atoms, only the ones that are unfrozen will actually move. There are ways to color the system so that all the frozen atoms are, say, white. I doubt that we're unique in this regard; I should think that any program that allows atoms to be frozen and also allows the visualization of normal modes whould be able to accomplish this. -P. **************** "Cultured people are the scum that floats **************** *************** on the deep river of production" (Churchill) ************** *Peter Shenkin; Chemistry, Columbia U.; shenkin@columbia.edu (212)854-5143* *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * From chemistry-request@www.ccl.net Sun Aug 30 23:34:33 1998 Received: from NPD1.NPD.UFPE.BR ([150.161.6.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id XAA23840 Sun, 30 Aug 1998 23:34:32 -0400 (EDT) Received: from danon (Danon.DQF.UFPE.BR) by NPD.UFPE.BR (PMDF V5.1-4 #20469) with SMTP id <01J18FQ3DQWG000B9A@NPD.UFPE.BR> for chemistry@www.ccl.net; Mon, 31 Aug 1998 00:30:18 GMT-3 Date: Mon, 31 Aug 1998 00:47:23 -0300 From: Gustavo de Miranda Seabra Subject: overlap integrals on GAMESS To: chemistry@www.ccl.net Reply-to: Gustavo de Miranda Seabra Message-id: <004701bdd492$10674900$7d05a196@danon.dqf.ufpe.br> MIME-version: 1.0 X-Mailer: Microsoft Outlook Express 4.72.2106.4 Content-type: multipart/alternative; boundary="----=_NextPart_000_0044_01BDD478.EAAC0CF0" X-Priority: 3 X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Dear all, Does anyone know how can I print the overlap integrals on GAMESS - = US? Thanks very much. Gustavo de Miranda Seabra MSc Student in Chemistry seabra@npd.ufpe.br Federal University of Pernambuco Brazil From chemistry-request@www.ccl.net Mon Aug 31 02:59:31 1998 Received: from hera.wku.edu (root@hera.wku.edu [161.6.20.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id CAA25295 Mon, 31 Aug 1998 02:59:30 -0400 (EDT) Received: from adler by hera.wku.edu with local (Exim 1.82 #1) id 0zDNw1-0005P1-00; Mon, 31 Aug 1998 01:59:29 -0500 From: Allen Adler To: chemistry@www.ccl.net, adler@hera.wku.edu Subject: Aufbau irregularities Message-Id: Date: Mon, 31 Aug 1998 01:59:29 -0500 As one progresses through the elements by atomic number, the pattern by which the electronic shells get filled is fairly regular, but there are a few elements displaying irregularities, e.g. those marked by an asterisk in the table on p.B-1 of my issue of the CRC Handbook of Chemistry and Physics. I imagine that these irregularities have been the object of a lot of study, particularly in computational chemistry. So what I would like to know is: (1) have these irregularities been independently confirmed by ab initio computations? (2) Apart from a brute force computation, have heuristic reasons been given why the Schrodinger (or whatever) equation should give rise to these anomalies? (3) I know that different isotopes of an element are supposed to have the same chemical properties; but the atomic mass does appear in the Schrodinger equation, so it is conveivable that by choosing a suitable isotope for each element, one can obtain a table of electronic configurations in which no irregularities appear. Has this been observed or calculated? (4) Assuming the premise of (3) is correct, is there a table of the electronic configurations of all of the isotopes? Naively, Allan Adler adler@hera.wku.edu From chemistry-request@www.ccl.net Mon Aug 31 05:10:33 1998 Received: from gate2.akzonobel.nl (gate2.oss.akzonobel.nl [192.87.3.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA25736 Mon, 31 Aug 1998 05:10:32 -0400 (EDT) Received: (from fwmaster@localhost) by gate2.akzonobel.nl (8.8.4/8.6.12) id LAA04207 for ; Mon, 31 Aug 1998 11:10:33 +0200 (MET DST) Received: by gate2.oss.akzonobel.nl via smap (V1.3) id sma004161; Mon, 31 Aug 98 11:10:20 +0200 Received: by apou01.akzonobel.nl id LAA00727; Mon, 31 Aug 1998 11:19:30 +0200 (MET DST) Received: from organon.oss.akzonobel.nl (orchid.oss.akzonobel.nl) by vesta.oss.akzonobel.nl (PMDF V5.1-7 #22904) with SMTP id <01J1924U7PPS93EDWI@vesta.oss.akzonobel.nl> for chemistry@www.ccl.net; Mon, 31 Aug 1998 11:11:21 +0100 Received: (from knegtel@localhost) by organon.oss.akzonobel.nl (950413.SGI.8.6.12/8.6.12) id JAA29776 for chemistry@www.ccl.net; Mon, 31 Aug 1998 09:10:30 +0000 (GMT) Date: Mon, 31 Aug 1998 11:10:30 +0200 (WDT) From: Knegtel Ronald Subject: Summary cavities in protein-ligand complexes To: chemistry@www.ccl.net Message-id: <199808310910.JAA29776@organon.oss.akzonobel.nl> MIME-version: 1.0 X-Mailer: ELM [version 2.4 PL24 ME8b] Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit Dear all, below follows a summary of the replies I received on my question about measuring cavities in protein-ligand complexes. Thanks to everybody for sending me information! Ronald Knegtel ------------------------------------------------------------------------ You might look at Craig Taverner's steric program (ftp://hobbes.gh.wits.ac.za/pub/steric/) based on solid angles. The solid angle corresponds to a projection onto an enclosing sphere. The program also has the complementary ability to measure cavities (like those in zeolites). It will also calculate the molecular volume and radial extent, so from that, the solid angle data and the volume of a sphere, you can probably calculate just about anything you're looking for. > - Jack > > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- > Jack A. Smith || > Union Carbide || Phone: (304) 747-5797 > Catalyst Skill Center || FAX: (304) 747-4672 > P.O. Box 8361 || > S. Charleston, WV 25303 || smithja@ucarb.com > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- -------------------------------------------------------------------------- Hi Ronald, SURFNET from Janet Thornton's group will do what you want. It's available at: http://www.biochem.ucl.ac.uk/bsm/biocomp/index.html Cheers Michael -- ################################################################# Dr Michael Dooley Centre for Drug Design and Development The University of Queensland St Lucia, Qld, 4072 Australia Brisbane Molecular Modeling Group http://www.uq.edu.au/~ddmdoole/ ---------------------------------------------------------------------------- Hi, The grasp package calculates volumes/surfaces of molecules and also cavities. All the functions are available through a graphical interface(http://honiglab.cpmc.columbia.edu/). Another interesting package is O. One of the programs (VOIDOO) calculates 3 different cavities (probe acccessible, probe center accessible and Van der Waals ) (http://alpha2.bmc.uu.se/~alwyn/). -- WURTZ Jean-Marie ________________________________________________________________________ IGBMC E-mail : wurtz@igbmc.u-strasbg.fr Laboratoire de Biologie Structurale Phone : (33) 3 88 65 35 29 Parc d'Innovation Fax : (33) 3 88 65 32 01 1, rue Laurent Fries, BP 163 67404 ILLKIRCH, CU STRASBOURG France ________________________________________________________________________ -------------------------------------------------------------------------- Try VOIDOO from Uppsala Software Factory. http://alpha2.bmc.uu.se/~gerard/manuals/gerard_manuals.html Mirek ******************************************************************************* Jaromir MAREK e-mail:marek@chemi.muni.cz tel. ++ 420-5-411-29-411 fax. ++ 420-5-412-11-214 X-ray Laboratory of Dept. of Inorganic Chemistry http://www.sci.muni.cz/~dusan/inorg.html & Laboratory of Biomolecular http://www.chemi.muni.cz/lbsd/lbsd.html Structure and Dynamics Faculty of Science http://www.sci.muni.cz/ Masaryk University http://www.muni.cz/ Kotlarska (street) 2 BRNO CZ 611 37 Czech Republic ----------------------------------------------------------------------------- From cbystrom@darkwing.uoregon.edu Tue Aug 25 18:23:14 1998 Greetings, Two software packages you might be most interested in: Surfnet: http://bsmcha1.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html MSRoll http://www.biohedron.com/msp.html Hope this helps, Cory Bystrom --------------------------------------------------------------------------- From abdallah@mpiz-koeln.mpg.de Tue Aug 25 18:00:43 1998 Dear Ronald, you could try surfnet http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html that comes free for academic users (as far as i remember) or, icm, http://www.molsoft.com a (very good) commercial solution for your problem. best Regards, Fuad Fuad Abdallah Max-Planck-Institut fuer Zuechtungsforschung / ZWDV Tel.: 0221/5062-739 / Priv: 0221/584563 -------------------------------------------------------------- From leboeuf@CERCA.UMontreal.CA Tue Aug 25 17:22:34 1998 Hi ! I'm not sure exactly what kind of cavity you're talking about, but if it is defined through a polygonal surface, the marching cube algorithm will give you both surface and volume. The original article is Lorensen & Cline, Comp. Graph., vol.21, no. 4, '87, p163 bye, Martin. ------------------------------------------------------------------------------- Dr. Ronald M. A. Knegtel Research Scientist Dept. of Molecular Design and Informatics Phone : +31-412-661469 N.V. Organon, RK2340 Fax : +31-412-662539 P.O. Box 20 5340 BH Oss http://www.organon.com/ The Netherlands E-Mail : r.knegtel@organon.oss.akzonobel.nl ------------------------------------------------------------------------------- From chemistry-request@www.ccl.net Mon Aug 31 06:24:23 1998 Received: from palladium.enscm.fr (palladium.enscm.fr [193.52.207.107]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA25956 Mon, 31 Aug 1998 06:24:21 -0400 (EDT) Received: from localhost (alexei@localhost) by palladium.enscm.fr (8.8.7/8.8.7) with SMTP id MAA10740; Mon, 31 Aug 1998 12:18:29 +0200 (MDT) Date: Mon, 31 Aug 1998 12:18:29 +0200 (MDT) From: Arbouznikov Alexei X-Sender: alexei@palladium Reply-To: Arbouznikov Alexei To: Wolfram Koch cc: chemistry@www.ccl.net Subject: Re: CCL:DFT questions In-Reply-To: <9808211425.AA42693@argon.chem.tu-berlin.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Wolfram, I am also interested in the topics you are discussing, especially in the MULTIDETERMINANTAL extension of DFT. I could propose you some references on this subject: - from the classical ones with general discussion on the application of the DFT to open-shell systems: P.S.Bagus, B.I.Bennet, Int. J. Quantum Chem., 9, 143-148 (1975) and T.Ziegler, A.Rauk, Theor. Chim. Acta, 43, 261-271 (1977) - to more recent discussions: A.Savin, Beyond the Kohn-Sham determinant, in: Recent Advances in Density Functional Methods/ Ed. by D.P.Chong, World Scientific, Singapore, 1996 A.D.Becke, A.Savin, H.Stoll, Theor. Chim. Acta, 91, 147-156 (1995) A.Savin, On degeneracy, near-degeneracy and Density Functional Theory, in: Recent Developments and Applications of Modern Density Functional Theory/ Ed. by J.M.Seminario, Elsevier, 1996, p.327. F.Moscardo, E.San-Fabian, Phys. Rev.A, 44(3), 1549-1553(1991) Concerning your first question (excited states), you can find very useful discussions in: E.K.U.Gross, L.N.Oliveira, W.Kohn, Phys.Rev.A,37(8),2805-2808 (1988) E.K.U.Gross, L.N.Oliveira, W.Kohn, Phys.Rev.A,37(8),2809-2810 (1988) E.K.U.Gross, L.N.Oliveira, W.Kohn, Phys.Rev.A,37(8),2821-2833(1988) C.Daul, Int. J. Quantum Chem., 52, 867-877 (1994) A.Nagy, Int.J.Quantum Chem., Quantum Chem.Symp 29, 297-301 (1995) Since you are also interested in the discussion of symmetry problems in DFT, I can propose you also a rewiev: A.Gorling, Phys. Rev.A, 47(4), 2783-2799 (1993) Of course, I propose you only the papers which I know, - you can find more references elsewhere. Best regards, Alexei -------------------------------------------------------------------- Dr. Alexei Arbouznikov Ecole Nationale Superieure de Chimie, Laboratoire de Materiaux Catalytiques et Catalyse en Chimie Organique, UMR 5618 CNRS-ENSCM - Prof. F.Fajula, 8, rue de l'Ecole Normale 34296 Montpellier, Cedex 5 FRANCE Telephone: (33) 4-67-14-72-68 Fax: (33) 4-67-14-43-49 E-mail: alexei@palladium.enscm.fr --------------------------------------------------------------------- From chemistry-request@www.ccl.net Mon Aug 31 08:26:26 1998 Received: from zzmkgtw.zzmk.unizh.ch (zzmkgtw.unizh.ch [130.60.67.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id IAA26398 Mon, 31 Aug 1998 08:26:22 -0400 (EDT) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA06917; Mon, 31 Aug 1998 14:26:20 +0200 Message-Id: <3.0.3.32.19980831143028.0068a3f0@highdent> X-Sender: toukie@highdent (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Mon, 31 Aug 1998 14:30:28 +0200 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: Boltzamnn-weighted conformations Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleagues; Does anyone have/know of a DOS or Windows programme that will take sets of coordinates corresponding to different conformations of a given molecule plus their Boltzmann weightings or proportions and generate a "Boltzmann-weighted" conformation? Kindly provide details. Thanks, S. Shapiro toukie@zui.unizh.ch From chemistry-request@www.ccl.net Mon Aug 31 11:13:36 1998 Received: from mailrelay1.cc.columbia.edu (cu41754@mailrelay1.cc.columbia.edu [128.59.35.143]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA28254 Mon, 31 Aug 1998 11:13:35 -0400 (EDT) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id LAA16090 for <@smtp.columbia.edu:chemistry@www.ccl.net>; Mon, 31 Aug 1998 11:13:34 -0400 (EDT) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) for chemistry@www.ccl.net id LAA02299; Mon, 31 Aug 1998 11:13:33 -0400 From: "Peter Shenkin" Message-Id: <9808311113.ZM2297@still3.chem.columbia.edu> Date: Mon, 31 Aug 1998 11:13:33 -0400 In-Reply-To: patrick "CCL:Frequency calculation of transition state" (Aug 28, 10:57pm) References: X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Re: CCL:Frequency calculation of transition state Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Aug 28, 10:57pm, patrick wrote: > Subject: CCL:Frequency calculation of transition state > > > > Hi! How are you? During computation of frequency of molecules at > transition state, one of frequencies is negative. Why? Is it a rule for > identification of transition state? Is it possible if two or more > frequencies are negative when molecules are at transition state? > > Thank you for your attention. As others will no doubt tell you, this has to do with the definition of a transition-state as a saddle-point on the potential-energy surface, and to the mathematical definition of a saddle point. This goes back to Henry Eyring (at least) and his theory of the activated complex. Certainly extrema with two or more negative "frequencies" are geometrically possible; I don't know exactly what their chemical significance, if any, would be, or how many, if any, have actually been identified. I know people have thought about this and even looked into it, and perhaps some who know will respond here. -P. -- **************** "Cultured people are the scum that floats **************** *************** on the deep river of production" (Churchill) ************** *Peter Shenkin; Chemistry, Columbia U.; shenkin@columbia.edu (212)854-5143* *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * From chemistry-request@www.ccl.net Mon Aug 31 14:37:58 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA00080 Mon, 31 Aug 1998 14:37:57 -0400 (EDT) Received: from helix.nih.gov (helix.nih.gov [128.231.2.3]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id OAA11288 for ; Mon, 31 Aug 1998 14:37:53 -0400 (EDT) Received: (from mn1@localhost) by helix.nih.gov (8.8.5/8.8.5) id OAA09198; Mon, 31 Aug 1998 14:37:22 -0400 (EDT) Date: Mon, 31 Aug 1998 14:37:22 -0400 (EDT) From: "Marc N." To: Victoria Buch cc: CHEMISTRY@ccl.net Subject: Re: CCL:Linux on Alpha, math library In-Reply-To: <199808290928.MAA06442@poodle.fh.huji.ac.il> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sat, 29 Aug 1998, Victoria Buch wrote: > >>>>>>>>>>>> > >>>>>>>>> > > Igor J. Barani writes: > > > Dear CCL Readers, > > > > > > I have just recently installed Linux on a DEC Alpha and when I compile > > > several programs in fortran on it, they seem to compile to twice the > > > size and require 9 times as long to run than on DEC UNIX. Do you have > > > any idea why this may be so and how I may be able to speed up the > > > processes? Any suggestions would be greatly appreciated. Thank you. > >>>>>>>>>>>>>> > > We have just been there. You have the latest Red Hat Linux, dont you? > So: the latest math library libm version 2.0.7 from gnu is messed up. > Our system menager installed old version 2.0.1 - works faster by a factor 2. > More generally our sexperience suggests that > Alpha / Linux for FP operations is good only > for simple operations + - * / . My simulation > programs are still 40% below > the performance of Alpha-DEC, and only 10% faster than Petium II (400MHz) > which is more than 2 times cheaper. Disappointing. Well, this seems to be somewhat of an oversimplification. Indeed, the libraries are very important, and so one can probably say that the standard libraries that come with [Red Hat] Linux/Alpha are good only for "simple operations + - * /". However, with the right, i.e., optimized libraries, we've found, e.g., Gaussian 94 on a 500MHz Alpha/Linux box to be 2.5 times as fast as on a 400MHz Pentium II Linux system. Marc ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 37, Rm 5B29 Phone: (301) 402-3111 37 Convent Dr, MSC 4255 Fax: (301) 496-5839 BETHESDA, MD 20892-4255 USA http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm Laboratory of Medicinal Chemistry, National Cancer Institute ------------------------------------------------------------------------ From chemistry-request@www.ccl.net Mon Aug 31 17:13:55 1998 Received: from swan2.uspnet.usp.br (swan2.uspnet.usp.br [143.107.253.69]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id RAA05105 Mon, 31 Aug 1998 17:13:40 -0400 (EDT) Received: from Sergio by swan2.uspnet.usp.br (SMI-8.6/SMI-SVR4) id SAA22834; Mon, 31 Aug 1998 18:10:54 -0300 Message-ID: <005201bdd523$b26b73c0$6e72fea9@Sergio.lammol.ffclrp.usp.br> From: "Sergio Emanuel Galembeck" To: , Subject: Re: CCL:uhf and biradicals: summary Date: Mon, 31 Aug 1998 18:06:33 -0300 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Dear Frederique, Recently it is published a very interestig paper of E. Davidson (Int. J. Quantum Chem., 69, 241-245) that analyse the pitfails of calculations of diradicals using DFT methods. Hope this help you, Sergio From chemistry-request@www.ccl.net Mon Aug 31 17:36:30 1998 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA05209 Mon, 31 Aug 1998 17:36:28 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id RAA01951 for chemistry@www.ccl.net; Mon, 31 Aug 1998 17:36:25 -0400 (EDT) Date: Mon, 31 Aug 1998 17:36:25 -0400 (EDT) From: "E. Lewars" Message-Id: <199808312136.RAA01951@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: RESPONSE TO QUESTION ABOUT NEG FREQS 1998 August 31 Re the question: > 31-AUG-1998 15:30:49.21 >From: IN%"pang@dft.chem.cuhk.edu.hk" "patrick" >To: IN%"chemistry@www.ccl.net" >CC: >Subj: CCL:Frequency calculation of transition state > > >Hi! How are you? During computation of frequency of molecules at >transition state, one of frequencies is negative. Why? Is it a rule for >identification of transition state? Is it possible if two or more >frequencies are negative when molecules are at transition state? > >Thank you for your attention. > >Patrick Pang ===================== The number of "negative" (actually, imaginary) frequencies that an optimized structure has is a basic feature of its nature, i.e. it tells whether you have a minimum (no imag. freqs), a transition state or first-order saddle point (1 imag freq), or a hilltop i.e. a second or higher-order saddle point (two or more imag freqs). The imaginary number arises because along the reaction path the second derivative of E with respect to geometry is negative at the stationary point (draw it), i.e the force constant for this vibrational mode is negative. To calculate the normal-mode freqs we need the square root of the force constant (and the masses of the atoms) [look up the simple equation for a diatomic molecule], and the square root of a negative number is what mathematicians call imaginary (printed as a negative number in most outputs). For good introductions see "Exploring Chemistry with Electronic Structure Methods", J. B. Foresman and A. Frisch, 1st or 2nd Ed. "Ab Initio Molecular Orbital Theory", W. J. Hehre, L. Radom, P. v.R. Schleyer, J. A. Pople E. Lewars =============== From chemistry-request@www.ccl.net Mon Aug 31 17:56:05 1998 Received: from faui45.informatik.uni-erlangen.de (root@faui45.informatik.uni-erlangen.de [131.188.2.45]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA05455 Mon, 31 Aug 1998 17:56:03 -0400 (EDT) Received: from as1200.organik.uni-erlangen.de (as1200-1.organik.uni-erlangen.de [131.188.128.6]) by faui45.informatik.uni-erlangen.de (8.9.1/8.1.49-FAU) with ESMTP id XAA04283 for ; Mon, 31 Aug 1998 23:55:55 +0200 (MET DST) Received: (from dransfld@localhost) by as1200.organik.uni-erlangen.de (8.8.7/8.1.11-FAU) id XAA06243; Mon, 31 Aug 1998 23:55:55 +0200 (MET DST) From: Alk Dransfeld Message-Id: <199808312155.XAA06243@as1200.organik.uni-erlangen.de> Subject: NMR:MacSHARCIVAR.beta.Version To: CHEMISTRY@www.ccl.net Date: Mon, 31 Aug 1998 23:55:54 +0200 (MET DST) Cc: Alk.Dransfeld@chem.kuleuven.ac.be (A. Alk at KULeuven) X-Mailer: ELM [version 2.4 PL25] Content-Type: text Dear Netters, If you are computing NMR properties then you may be interested in THE freeware tool to evaluate your results, MacSHARCIVAR. MacSHARCIVAR is a PERL script developed under MacPerl 5.3.1 MacSHARCIVAR is platform independent [1] and small (0.3 MB) MacSHARCIVAR features: - handles data from GAUSSIAN, ACESII, DeMon-NMR, ... - data files may be in local folders OR on external discs - informs cooperating groups about your work without giving results - searches formula conditions (e.g. more than 4 carbons) The MacSHARCIVAR system is based on A) the archiving format, NMR-SHARC, which has been tested and refined for three years (about 9ooo entities) in CCC Erlangen,[2] B) the sharcid, which allows to identify entities inambiguously without a central archive assigning entry numbers. Nevertheless, your help is need. WHAT's to be done? I need some .beta.-Tester to finish this tool. Therefore, I would like to send you the 0.3 MB PERL skript by mail and expect your comments and suggestions for refinements. ThanX in advance and Best regards A. Dransfeld (dransfld@ccc.uni-erlangen.de AND Alk.Dransfeld@chem.kulleuven.ac.be) [1] platform specific features are automatically considered (e.g. UNIX /;MacOS :) [2] Acknowledgements to all research groups and scientific stuff of CCC Erlangen for help. Scripts to transform GAUSSIAN, ACES II, DeMon-NMR or IGLO outputs into the NMR-SHARC format are available at http://www.ccc.uni-erlangen.de/sharc/ .