From chemistry-request@server.ccl.net Wed Jul 28 00:54:48 1999 Received: from power.curtin.edu.au (root@power.curtin.edu.au [134.7.118.91]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA25314 for ; Wed, 28 Jul 1999 00:54:46 -0400 Received: from [134.7.128.122] ([134.7.128.122]) by power.curtin.edu.au (8.9.3/8.9.3) with SMTP id MAA07104; Wed, 28 Jul 1999 12:47:43 +0800 Message-Id: <199907280447.MAA07104@power.curtin.edu.au> Subject: Re: CCL:MOPAC for d-block? Date: Wed, 28 Jul 1999 12:49:53 +0800 x-mailer: Claris Emailer 2.0v3, January 22, 1998 From: Andrew Rohl To: , Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" >Also, is anyone aware of a semi-empirical code which is available which >deals with 3-D periodic systems. > havr you tried GULP? As well as atom-atom potentials, it also does semi-empirical. Contact j.gale@ic.ac.uk for more info -------------------------------------------------------------------------- Andrew Rohl Email: A.Rohl@curtin.edu.au School of Applied Chemistry Phone: +61 8 9266 7317 (Office) Curtin University of Technology +61 8 9266 3780 (Lab) PO Box U 1987 FAX: +61 8 9266 2300 Perth, 6845 WESTERN AUSTRALIA WWW: http://www.curtin.edu.au/curtin/dept/appchem/staff/alr/ -------------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Jul 28 06:16:11 1999 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA27326 for ; Wed, 28 Jul 1999 06:16:09 -0400 Message-Id: <199907281016.GAA27326@server.ccl.net> Received: from anti02 (193.6.134.181) by tigris.klte.hu (MX V5.1 VAX) with SMTP; Wed, 28 Jul 1999 12:07:39 +0200 Comments: Authenticated sender is From: "Tamas Gunda" To: cpilger@oc30.uni-paderborn.de Date: Wed, 28 Jul 1999 13:11:18 +1 MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Re: CCL:msi file format CC: chemistry@ccl.net Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) Dear Christian, > > I would like to convert SYBYL-mol2 files either into Insight-CAR format or > preferably directly into Cerius2-MSI format. > Here is what I've tried so far: > > * BABEL: neither CAR- nor MSI-Format is supported for output > * CACTVS: does not recognize the mol2-files generated by SYBYL (!) > * mol2mol: the CAR-output of this program does not contain the correct > connectivities > > Any ideas ? Did anybody face similar problems ? Can somebody provide me > with a hint where I can find a detailed description of the Cerius2-MSI > file format ? > > Any suggestions are appreciated ! > > Best wishes, > > Christian Dear Christian, Which mol2mol version do you use? The program has now been updated, with new features and several bugs hve been fixed, its Insight modul too. Could you send me your sybyl mol2 file to try it? best regards Tamas E. Gunda ************************************************************************ Dr Tamas E. Gunda phone: (+36-52) 316666-2479 Research Group of Antibiotics fax : (+36-52) 512914 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 http://dragon.klte.hu/~gundat H-4010 Debrecen Hungary ************************************************************************ From chemistry-request@server.ccl.net Wed Jul 28 13:56:59 1999 Received: from apollo.brooklyn.cuny.edu ([146.245.100.80]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA30809 for ; Wed, 28 Jul 1999 13:56:58 -0400 Received: by apollo.brooklyn.cuny.edu with Internet Mail Service (5.0.1460.8) id ; Wed, 28 Jul 1999 13:46:48 -0400 Message-ID: From: Ira Levine To: "'Comp. Chem. list (all)'" Subject: Quantum Chemistry textbook new edition Date: Wed, 28 Jul 1999 13:46:46 -0400 X-Mailer: Internet Mail Service (5.0.1460.8) The fifth edition of the textbook Quantum Chemistry by Ira Levine is now available from the publisher Prentice Hall. Ira N. Levine INLevine@brooklyn.cuny.edu From chemistry-request@server.ccl.net Tue Jul 27 15:03:19 1999 Received: from zeus.fcq.unc.edu.ar (zeus.fcq.unc.edu.ar [200.16.18.54]) by server.ccl.net (8.8.7/8.8.7) with SMTP id PAA22140 for ; Tue, 27 Jul 1999 15:02:55 -0400 Received: from localhost by zeus.fcq.unc.edu.ar; (5.65/1.1.8.2/27Feb98-1006AM) id AA00851; Tue, 27 Jul 1999 15:56:50 -0500 Sender: mariano@zeus.fcq.unc.edu.ar Message-Id: <379E1D11.167E@zeus.fcq.unc.edu.ar> Date: Tue, 27 Jul 1999 15:56:49 -0500 From: "Domingo Mariano A. Vera" X-Mailer: Mozilla 3.01Gold (X11; I; OSF1 V3.0 alpha) Mime-Version: 1.0 To: chemistry@ccl.net Subject: virtual orbitals and DFT 2 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi again As Dmitry have shown, I had an error in my original message (rather, there is an error in an example to illustrate the question): for some radical anions systems, the structure optimized at mp2/6-31+g* level and the structures optimized at corresponding b3lyp level yield similar result in the canonnical HF first virtual orbitals (ok! they're not 'MP2 orbitals'); But the question is exactly the same: What do you think about the use of coefficients and energies of the LUMOs from these kind of DFT formalisms (even when the results seem to be similar to those from other ab initio calculations)? Best regards Mariano -- D. Mariano A. Vera INFIQC / Departamento de Quimica Organica Facultad de Ciencias Quimicas - Universidad Nacional de Cordoba. Ciudad Universitaria - 5000 Cordoba - ARGENTINA. Voice: 54-351-4334170 Fax: 54-351-4333030 mariano@zeus.fcq.unc.edu.ar From chemistry-request@server.ccl.net Tue Jul 27 17:05:48 1999 Received: from celeste.INS.CWRU.Edu (root@celeste.INS.CWRU.Edu [129.22.8.214]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA22807 for ; Tue, 27 Jul 1999 17:05:48 -0400 Received: from raman2.cwru.edu (chem51374.CHEM.CWRU.Edu [129.22.200.174]) by celeste.INS.CWRU.Edu with SMTP (8.8.8+cwru/CWRU-3.6) id RAA05746; Tue, 27 Jul 1999 17:01:12 -0400 (EDT) (from hxt10@po.cwru.edu for ) Message-ID: <001201bed87b$8ddcfe00$aec81681@cwru.edu> From: "Gavin Tsai" To: Subject: degenerate eigenvalue problem Date: Tue, 27 Jul 1999 17:01:17 -0500 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_000E_01BED851.A4452CA0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 This is a multi-part message in MIME format. ------=_NextPart_000_000E_01BED851.A4452CA0 Content-Type: multipart/alternative; boundary="----=_NextPart_001_000F_01BED851.A4452CA0" ------=_NextPart_001_000F_01BED851.A4452CA0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, Everyone: Here is one problem for degenerate eigensystem... I try to diagonalize a real and symmetry matrix by using Jacobi = transformation. The program is from the book "numerical recipes". It seems does not = work for the degenerate eigensystem, the eigenvectors are the linear = combination of two degenerate eigenvectors. Is there any one can give me any suggestion or advice for the degenerate = eigensystem? Thanks! Gavin Tsai ------=_NextPart_001_000F_01BED851.A4452CA0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi, Everyone:
 
    Here is one problem for = degenerate=20 eigensystem...
 
I try to diagonalize a real and symmetry = matrix by=20 using Jacobi transformation.
The program is from the book "numerical=20 recipes".  It seems does not work for the degenerate eigensystem, = the=20 eigenvectors are the linear combination of two degenerate=20 eigenvectors.
 
Is there any one can give me any suggestion = or advice=20 for the degenerate eigensystem?
 
Thanks!
 
Gavin Tsai
------=_NextPart_001_000F_01BED851.A4452CA0-- ------=_NextPart_000_000E_01BED851.A4452CA0 Content-Type: text/x-vcard; name="Hui-Hsu (Gavin) Tsai.vcf" Content-Transfer-Encoding: quoted-printable Content-Disposition: attachment; filename="Hui-Hsu (Gavin) Tsai.vcf" BEGIN:VCARD VERSION:2.1 N:Tsai;Hui-Hsu (Gavin) FN:Hui-Hsu (Gavin) Tsai NICKNAME:Gavin ORG:CWRU, Chemistry Department TITLE:Ph.D. Candidate NOTE;ENCODING=3DQUOTED-PRINTABLE:Do molecules calculate the chemical = reaction laws before they decide=3D0D=3D0Aho=3D w to react to each others?=3D0D=3D0A TEL;HOME;VOICE:216-229-5913 ADR;HOME:;;2416 Derbyshire Road;Cleveland;OH;44106;USA LABEL;HOME;ENCODING=3DQUOTED-PRINTABLE:2416 Derbyshire = Road=3D0D=3D0ACleveland, OH 44106=3D0D=3D0AUSA X-WAB-GENDER:2 EMAIL;PREF;INTERNET:hxt10@po.cwru.edu REV:19990727T220117Z END:VCARD ------=_NextPart_000_000E_01BED851.A4452CA0-- From chemistry-request@server.ccl.net Tue Jul 27 23:04:55 1999 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA24762 for ; Tue, 27 Jul 1999 23:04:54 -0400 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.9.3/8.9.3) id XAA16004 for chemistry@ccl.net; Tue, 27 Jul 1999 23:00:14 -0400 (EDT) Date: Tue, 27 Jul 1999 23:00:14 -0400 (EDT) From: "E. Lewars" Message-Id: <199907280300.XAA16004@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: SUMMARY OF NMR SHIFTS, MP2 cf. HF 1999 July 26 REPLIES TO QUESTION ABOUT MP2- cf. HF-LEVEL NMR CHEMICAL SHIFTS THE QUESTION: > Hello, I read somewhere that NMR chemical shifts calc at the MP2 level are > somewhat better than at the HF level. Has anyone a reference to this? > Thanks. Thanks very much to all who responded. As you see, I got a lot of information. For people who wish to look at just a few of the refs, I might suggest: J. Gauss. JCP 99 3629 (1993) Cheesman et al JCP 104 5497 (1996) (I haven't yet got hold of the J. Gauss paper in Ber. Bunsenges. Phys. Chem.) The Chem Rev 1999 review is physical-theoretical rather than a presentation and analysis of calculated chemical shifts. I did a few calcs on B3LYP/6-31G* geometries, using the G94 default algorithm and the HF/6-31G* and HF/6-311+G(2d,p) wavefunctions. There was not that much difference between the two basis sets, although the latter took a lot longer. I was astonished at how accurate the chemical shifts were. ------------- THE ANSWERS: 1999 July MP2 cf. HF NMR SHIFTS #1 Matthias Hofmann > Hello, I read somewhere that NMR chemical shifts calc at the MP2 level are > somewhat better than at the HF level. Has anyone a reference to this? > Thanks. One early example is: Decisive Electron Correlation Effects on Computed 11B und 13C NMR Chemical Shifts. Application of the GIAO-MP2 Method to Boranes and Carbaboranes. M. Bue\237hl, J. Gauss, M. Hofmann, P. v. R. Schleyer, J. Am. Chem. Soc., 1993, 115, 12385-12390. For other nuclei you might search for early papers by J. Gauss, who first implemented the GIAO-MP2 methods (and higher correlated methods) in ACES2. Regards, Matthias -------------------------------------------------------------------- Dr. Matthias Hofmann | phone: 706 542-7748 Ctr. for Comp. Quantum Chem. | fax: 706 542-0406 University of Georgia | e-mail: hofmann2@zopyros.ccqc.uga.edu Athens, GA 30602-2525 | http://zopyros.ccqc.uga.edu ============----------------------------------------------------------- #2 Michael D. Bartber Jul 21 '99 at 10:42 pm Hello: You might check the references of J. Gauss; he, along with John Stanton have published a number of papers (I include references below) on the computation of checmical shifts with MBPT. Also R.J. Bartlett and coworkers have investigated shifts and coupling constants at the CC level. A lot of this is nicely summarized in a recent Chem. Rev. article by Helgaker et al., 1999, v. 99, 293-352. Other possibly useful references follow. Best regards, -Mike Bartberger UCLA +-----------------------------------------------------------------+ | Michael D. Bartberger, Ph.D. | | NIH Postdoctoral Fellow TEL: 310.206.0553 | | Department of Chemistry and Biochemistry FAX: 310.206.1843 | | University of California, Los Angeles | | Los Angeles, California 90095-1569 mdb@chem.ucla.edu | +-----------------------------------------------------------------+ Kollwitz, M; Haser, M; Gauss, J. Non-Abelian point group symmetry in direct second-order many-body perturbation theory calculations of NMR chemical shifts. JOURNAL OF CHEMICAL PHYSICS, 1998 MAY 22, V108 N20:8295-8301. Gauss, J; Stanton, JF. Electron correlation effects on the calculated C-13 NMR spectra of vinyl cations. THEOCHEM-JOURNAL OF MOLECULAR STRUCTURE, 1997 JUN 30, V398:73-80. STANTON JF; GAUSS J; SIEHL HU. CCSD(T) CALCULATION OF NMR CHEMICAL SHIFTS - CONSISTENCY OF CALCULATED AND MEASURED C-13 CHEMICAL SHIFTS IN THE 1-CYCLOPROPYLCYCLOPROPYLIDENEMETHYL CATION. CHEMICAL PHYSICS LETTERS, 1996 NOV 15, V262 N3-4:183-186. KOLLWITZ M; GAUSS J. A DIRECT IMPLEMENTATION OF THE GIAO-MBPT(2) METHOD FOR CALCULATING NMR CHEMICAL SHIFTS - APPLICATION TO THE NAPHTHALENIUM AND ANTHRACENIUM IONS. CHEMICAL PHYSICS LETTERS, 1996 OCT 4, V260 N5-6:639-646. GAUSS J. ACCURATE CALCULATION OF NMR CHEMICAL SHIFTS. BERICHTE DER BUNSEN-GESELLSCHAFT-PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 1995 AUG, V99 N8:1001-1008. BUHL M; GAUSS J; STANTON JF. ACCURATE COMPUTATIONS OF SE-77 NMR CHEMICAL SHIFTS WITH THE GIAO-CCSD METHOD. CHEMICAL PHYSICS LETTERS, 1995 JUL 21, V241 N3:248-252. SIEHL HU; MULLER T; GAUSS J; BUZEK P; and others. CYCLOPROPYLCYCLOPROPYLIDENEMETHYL CATION - A UNIQUE STABILIZED VINYL CATION CHARACTERIZED BY NMR SPECTROSCOPY AND QUANTUM CHEMICAL AB INITIO CALCULATIONS. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1994 JUL 13, V116 N14:6384-6387. BUHL M; GAUSS J; HOFMANN M; SCHLEYER PV. DECISIVE ELECTRON CORRELATION EFFECTS ON COMPUTED B-11 AND C-13 NMR CHEMICAL SHIFTS - APPLICATION OF THE GIAO-MP2 METHOD TO BORANES AND CARBABORANES. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1993 DEC 29, V115 N26:12385-12390. SCHLEYER PV; GAUSS J; BUHL M; GREATREX R; and others. EVEN MORE RELIABLE NMR CHEMICAL SHIFT COMPUTATIONS BY THE GIAO-MP2 METHOD. JOURNAL OF THE CHEMICAL SOCIETY-CHEMICAL COMMUNICATIONS, 1993 DEC 7, N23:1766-1768. SIEBER S; SCHLEYER PV; GAUSS J. THE ACCURATE C(2V) PHENONIUM AND BENZENONIUM ION STRUCTURES CONFIRMED BY CORRELATED GIAO-MP2 NMR CHEMICAL SHIFT CALCULATIONS. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1993 JUL 28, V115 N15:6987-6988. Pub type: Note. GAUSS J; SCHNEIDER U; AHLRICHS R; DOHMEIER C; and others. AL-27 NMR SPECTROSCOPIC INVESTIGATION OF ALUMINUM(I) COMPOUNDS - ABINITIO CALCULATIONS AND EXPERIMENT. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1993 MAR 24, V115 N6:2402-2408. GAUSS J. CALCULATION OF NMR CHEMICAL SHIFTS AT 2ND-ORDER MANY-BODY PERTURBATION THEORY USING GAUGE-INCLUDING ATOMIC ORBITALS. CHEMICAL PHYSICS LETTERS, 1992 APR 17, V191 N6:614-620. PERERA SA; BARTLETT RJ. STRUCTURE AND NMR SPECTRA OF THE 2-NORBORNYL CARBOCATION - PREDICTION OF (1)J((CC)-C-13-C-13) FOR THE BRIDGED, PENTACOORDINATE CARBON ATOM. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1996 AUG 21, V118 N33:7849-7850. PERERA SA; BARTLETT RJ; SCHLEYER PV. PREDICTED NMR COUPLING CONSTANTS AND SPECTRA FOR ETHYL CARBOCATION - A FINGERPRINT FOR NONCLASSICAL HYDROGEN-BRIDGED STRUCTURES. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995 AUG 16, V117 N32:8476-8477. Pub type: Note. =============== #3 MP2 NMR chemical shifts MONACO@CHEMNA.DICHI.UNINA.IT Jul 22 '99 at 9:32 am Hi although they were more concerned with MCSCF, the group of Kutzelnigg has investigated the effect of correlation on the chemical shifts. So you can look at its bibliography. As far as I remember, the effects were not amazing. Of course when the ground state and the first excited ones are very near in energy, correlation may play a role and paramagnetic contributions become more difficult to compute. Good luck Guglielmo Monaco Dip. di Chimica Universit\340 di Napoli ITALY ============= #4 schrecke@t12mail.lanl.gov Hi, while I can't find the original references in the moment, I would suggest to start with some reviews on ab initio NMR calculations: J. Gauss, Ber. Bunsenges. Phys. Chem. 1995, 99, 1001 T. Helgaker et al., Chem.Rev.1999, 99, 293 Both should have something on your question or, at least, give you further references. Besides, some limited SCF-MP2 comparison is also in B=FChl et al= . J. Phys. Chem. 1995, 99, 4000. Best regards, Georg P.S. Please summarize to the CCL. -------------------- Dr. Georg Schreckenbach Tel: (USA)-505-667 7605 Theoretical Chemistry T-12 FAX: (USA)-505-665 3909 M.S. B268, Los Alamos National E-mail: schrecke@t12.lanl.gov Laboratory, Los Alamos, New Mexico, 87545, USA Internet: http://www.t12.lanl.gov/home/schrecke/ ***new location!*** =================== #5 Doug Fox Jul 22 '99 at 12:47 (noon) Errol, Check J. Gauss, JCP vol 99 3629 (1993). We draw from this and compare it with DFT methods in Cheesman et.al. JCP vol 104, 5497 (1996). Schleyer has also made comparisons in some of his Boron work but I don't have a good reference. Douglas J. Fox Director of Technical Support help@gaussian.com ========================== From chemistry-request@server.ccl.net Wed Jul 28 01:10:08 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA25416 for ; Wed, 28 Jul 1999 01:10:03 -0400 Received: from www.censa.org (censa2.censa.org [199.232.115.57]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id BAA04954 for ; Wed, 28 Jul 1999 01:05:10 -0400 (EDT) From: rich@censa.org Subject: ACS Short Course on "Electronic Notebooks and Knowledge Management Systems in Research and Development" To: jcurrie@mainstream.net X-Mailer: Lotus Notes Release 5.0 March 30, 1999 Date: Wed, 28 Jul 1999 05:11:05 GMT Message-ID: X-Priority: 3 (Normal) X-MIMETrack: Serialize by Router on www.censa.org/Censa(Release 5.0 |March 30, 1999) at 07/28/99 01:18:56 AM MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii Dear Colleague, Attend the following exciting short course to be held in New Orleans, LA on Friday, August 20th and Saturday, August 21st. It is held two days before the start of the ACS Fall National Meeting. Please register directly with the American Chemical Society using the phone number at the end of this message. Please register right away because open slots will fill up soon. American Chemical Society (ACS) Continuing Education - Short Courses "ELECTRONIC LAB NOTEBOOK AND KNOWLEDGE MANAGEMENT SYSTEMS IN RESEARCH AND DEVELOPMENT" This exciting and fast-moving course will captivate anyone needing to know the legal, regulatory, technical, and social aspects of electronic notebooks, recordkeeping, groupware, document management, or other collaborative systems used in R&D or technical organizations. It covers advanced automation technologies and concepts leading to highly collaborative, knowledge-based R&D organizations. It explains and gives examples of the the latest concepts for electronic recordkeeping, archving, electronic books and notebooks, and project data handling systems tied into collaborative infrastructures. WHO SHOULD ATTEND Scientists, managers, engineers, MIS and computer support, librarians and notebook administrators, archivists, knowledge managers, patent attorneys, and industry regulators in the chemical, pharmaceutical, environmental, biotech, food and beverage, aerospace, automotive, and related industries, universities or government labs. HOW YOU'LL BENEFIT FROM THIS COURSE Stay current with the latest technologies, regulations, and legal imperatives for laboratory recordkeeping. Lead your company into the electronic recordkeeping age by understanding critical requirements. Quickly assess your company's infrastructure and cultural readiness to use electronic lab notebooks; learn how to prepare them if they are not. 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Dr. Richard Lysakowski is the Executive Director of the Electronic Notebook Systems Association, an international industry association dedicated to market development of electronic notebook systems and related systems for laboratory and R&D automation. Dr. James T. Currie Jr. is a laboratory automation consultant and expert who has implemented many systems automated in validated environments. He has been involved in all phases of product and system development for many LIMS, instrument interfacing, and related systems. To register or to obtain additional information, e-mail us at shortcourses@acs.org. Or, call us at 800-227-5558, ext. 4508, or 202-872-4508. From chemistry-request@server.ccl.net Wed Jul 28 01:33:06 1999 Received: from srv2.novo.dk (srv2.novo.dk [130.227.199.2]) by server.ccl.net (8.8.7/8.8.7) with SMTP id BAA25569 for ; Wed, 28 Jul 1999 01:32:52 -0400 Received: (qmail 5683 invoked from network); 28 Jul 1999 05:27:40 -0000 Received: from it6977.research.novo.dk (HELO bysse.novo.dk) (152.73.27.65) by srv2.novo.dk with SMTP; 28 Jul 1999 05:27:40 -0000 Received: (from byw@localhost) by bysse.novo.dk (980427.SGI.8.8.8/950213.SGI.AUTOCF) id HAA34742 for chemistry@ccl.net; Wed, 28 Jul 1999 07:27:39 +0200 (MEST) Date: Wed, 28 Jul 1999 07:27:39 +0200 (MEST) From: byw@novo.dk (Robert Bywater) Message-Id: <9907280727.ZM50224@bysse.novo.dk> X-Mailer: Z-Mail-SGI (3.2S.3 08feb96 MediaMail) To: chemistry@ccl.net Subject: CCL: scoring for "peptide-likeness" Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello CCLers, especially those interested in peptide mimics/analogs. We read and hear a lot about 'non-petide' or 'peptide-like' drugs or peptide mimics/analogs. But what exactly are these animals ? Who has defined what is peptide-like and not-peptide-like ? What were these definitions ? What scoring function is used by people out there to say how like or unlike a peptide your drug is ? I have seen examples of dozens of ligands that bind e.g. to proteases that are not (apparently) peptides. For example, oligosaccharides will bind very nicely to trypsin in the binding groove for the normal oligopeptide substrate. A close homolog of elastase, called heparin-binding protein (lacks the catalytic serine residue, but otherwise folds like elastase) does just that: it binds heparin, in much the same way as elastase binds its oligopeptide substrate. Doesn't that make heparin (and the other oligosaccharides mentioned above) peptide-like ? But how much like a peptide is it, quantitatively ? Of course, anthing lacking at least one peptide bond and having no natural amino acid residue-type sidechain would be classified as a "non-peptide" but it may be "peptide-like" in its behaviour. If anyone out there has any ideas on this, a scoring function maybe or even a definition of "peptide- likeness", could they share that with us ? I will summarise the replies I get and post these. Best regards Robert Bywater -- ############################################################################ from: Robert Bywater PhD Biostructure Department Novo Nordisk A/S email: byw@novo.dk tel : +45 4443 4530 fax : +45 4443 4547 GPS coordinates: N 55 deg 45.312' E 12 deg 15.021' altitude 155 ft asl snailmail: Novo Nordisk A/S Novo Nordisk Park (G8.2.76) DK-2760 MAALOEV Denmark ############################################################################ From chemistry-request@server.ccl.net Wed Jul 28 03:39:41 1999 Received: from mail.rwth-aachen.de (mail.RWTH-Aachen.DE [137.226.144.9]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA26318 for ; Wed, 28 Jul 1999 03:39:40 -0400 Received: from ac.rwth-aachen.de (kazhad-dum.ac.RWTH-Aachen.DE) by mail.rwth-aachen.de (PMDF V5.1-12 #D3869) with ESMTP id <01JE3D6QVYAW0001BS@mail.rwth-aachen.de> for CHEMISTRY@ccl.net; Wed, 28 Jul 1999 09:34:12 +0200 Date: Wed, 28 Jul 1999 09:37:37 +0200 From: Tatus Subject: Error unrecognized IType=10 in G98 Sender: krzys@mail.rwth-aachen.de To: CCL Message-id: <379EB341.9685BF88@ac.rwth-aachen.de> Organization: Inst. Inorg. Chem., RWTH Aachen, Germany MIME-version: 1.0 X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.2.5-15 i686) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Hi ccl, can somebody explain me what does it mean error "unrecognized IType=10" in g98? Below my log. ************************************************** Gaussian 98: HP-PARisc-HPUX-G98RevA.6 19-Oct-1998 28-Jul-1999 ************************************************** %MEM=100MB %CHK=scan001 %SAVE %NPROC=4 Will use up to 4 processors via shared memory. Default route: MaxDisk=800000000 ----------------------------------------------------------- #P B3LYP/6-31+G(D,P) OPT=(Z-MATRIX,TIGHT) Int=FineGrid SCAN ----------------------------------------------------------- CompJT: unrecognized IType=10. Error termination via Lnk1e in /rwthfs/rz/SW/GAUSSIAN/g98/l1.exe. Job cpu time: 0 days 0 hours 0 minutes 0.7 seconds. File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1 Regards, Krzys From chemistry-request@server.ccl.net Wed Jul 28 13:24:33 1999 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA30633 for ; Wed, 28 Jul 1999 13:24:31 -0400 Message-Id: <199907281724.NAA30633@server.ccl.net> Received: from anti02 (193.6.134.181) by tigris.klte.hu (MX V5.1 VAX) with SMTP; Wed, 28 Jul 1999 19:16:33 +0200 Comments: Authenticated sender is From: "Tamas Gunda" To: Socrates de Oliveira Dantas Date: Wed, 28 Jul 1999 20:20:12 +1 MIME-Version: 1.0 Content-Type: Multipart/Mixed; boundary=Message-Boundary-15545 Subject: Re: CCL:Hello guys... CC: chemistry@ccl.net Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) --Message-Boundary-15545 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body Socrates de Oliveira Dantas wrote: > I have the following problem i need to read a the atached > file and translate it to a zmt or pdb file. i have tried > Spartan, Babel, Hyperchem and no result at all. So do you > guys know what kind of software or visualizer could i use > to translate this file: (just after ####). Dear Sokrates, I could transform your compound with mol2mol in two steps + some manual editing into pdb and hin formats. The two files are attached. What was the creator program of the file? best regards Tamas ************************************************************************ Dr Tamas E. Gunda phone: (+36-52) 316666-2479 Research Group of Antibiotics fax : (+36-52) 512914 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 http://dragon.klte.hu/~gundat H-4010 Debrecen Hungary ************************************************************************ --Message-Boundary-15545 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Text from file 'sokrat.hin' ; ;from: GDFG.CAR Wed 28 Jul 1999 18:41:28 by Mol2Mol 3.40 forcefield mm+ sys 0 mol 1 atom 1 - S S2 - 0.000000 0.371263 3.438745 1.868961 2 7 s 19 s atom 2 - S S2 - 0.000000 -1.088674 -2.128360 -2.390549 2 26 s 27 s atom 3 - O O1 - 0.000000 1.741642 -1.722433 3.605196 1 5 a atom 4 - O O1 - 0.000000 2.974483 -3.253259 2.703207 1 5 a atom 5 - N NO - 0.000000 2.029795 -2.473436 2.674989 3 3 a 4 a 23 s atom 6 - N N2 - 0.000000 -5.432699 1.627288 -0.760997 3 30 s 33 s 34 s atom 7 - C CA - 0.000000 1.598437 2.352248 1.227876 3 1 s 8 a 16 a atom 8 - C CA - 0.000000 2.844846 2.382300 1.896473 3 7 a 9 a 35 s atom 9 - C CA - 0.000000 3.824361 1.498942 1.577305 3 8 a 10 a 36 s atom 10 - C CA - 0.000000 3.664238 0.603404 0.485338 3 9 a 11 a 15 a atom 11 - C CA - 0.000000 4.684101 -0.307010 0.115053 3 10 a 12 a 37 s atom 12 - C CA - 0.000000 4.548773 -1.095233 -0.997826 3 11 a 13 a 38 s atom 13 - C CA - 0.000000 3.390188 -0.988853 -1.792607 3 12 a 14 a 39 s atom 14 - C CA - 0.000000 2.364080 -0.161297 -1.429687 3 13 a 15 a 40 s atom 15 - C CA - 0.000000 2.452655 0.636921 -0.255479 3 10 a 14 a 16 a atom 16 - C CA - 0.000000 1.360085 1.438647 0.206110 3 7 a 15 a 17 s atom 17 - C C3 - 0.000000 -0.016387 1.348874 -0.347503 3 16 s 18 s 20 d atom 18 - C C4 - 0.000000 -0.570258 2.707491 -0.683937 4 17 s 19 s 41 s 42 s atom 19 - C C4 - 0.000000 -0.921392 3.479357 0.588479 4 1 s 18 s 43 s 44 s atom 20 - C C3 - 0.000000 -0.705137 0.188759 -0.455059 3 17 d 21 s 32 s atom 21 - C CA - 0.000000 -0.129787 -1.110304 -0.029042 3 20 s 22 a 26 a atom 22 - C CA - 0.000000 0.547413 -1.246414 1.179077 3 21 a 23 a 45 s atom 23 - C CA - 0.000000 1.219701 -2.415076 1.455033 3 5 s 22 a 24 a atom 24 - C CA - 0.000000 1.187402 -3.520353 0.610928 3 23 a 25 a 46 s atom 25 - C CA - 0.000000 0.437469 -3.426632 -0.542033 3 24 a 26 a 47 s atom 26 - C CA - 0.000000 -0.215924 -2.235486 -0.865554 3 2 s 21 a 25 a atom 27 - C CA - 0.000000 -2.339098 -0.964566 -1.942773 3 2 s 28 a 32 a atom 28 - C CA - 0.000000 -3.605652 -1.091408 -2.483309 3 27 a 29 a 48 s atom 29 - C CA - 0.000000 -4.627635 -0.227793 -2.138292 3 28 a 30 a 49 s atom 30 - C CA - 0.000000 -4.409166 0.792534 -1.191425 3 6 s 29 a 31 a atom 31 - C CA - 0.000000 -3.119348 0.905640 -0.653479 3 30 a 32 a 50 s atom 32 - C CA - 0.000000 -2.074223 0.072875 -1.029781 3 20 s 27 a 31 a atom 33 - C C4 - 0.000000 -5.065698 2.965887 -0.323657 4 6 s 51 s 52 s 53 s atom 34 - C C4 - 0.000000 -6.722735 1.533010 -1.422885 4 6 s 54 s 55 s 56 s atom 35 - H H - 0.000000 2.977306 3.058192 2.728353 1 8 s atom 36 - H H - 0.000000 4.771465 1.532418 2.095257 1 9 s atom 37 - H H - 0.000000 5.570292 -0.384885 0.727424 1 11 s atom 38 - H H - 0.000000 5.333777 -1.785467 -1.269385 1 12 s atom 39 - H H - 0.000000 3.309297 -1.589236 -2.686698 1 13 s atom 40 - H H - 0.000000 1.482397 -0.090567 -2.049390 1 14 s atom 41 - H H - 0.000000 -1.471497 2.593462 -1.286320 1 18 s atom 42 - H H - 0.000000 0.172753 3.273923 -1.245354 1 18 s atom 43 - H H - 0.000000 -1.108613 4.511939 0.293822 1 19 s atom 44 - H H - 0.000000 -1.838352 3.042397 0.983890 1 19 s atom 45 - H H - 0.000000 0.625793 -0.406260 1.853168 1 22 s atom 46 - H H - 0.000000 1.689899 -4.444752 0.854616 1 24 s atom 47 - H H - 0.000000 0.387210 -4.263361 -1.223032 1 25 s atom 48 - H H - 0.000000 -3.779857 -1.871322 -3.209799 1 28 s atom 49 - H H - 0.000000 -5.607787 -0.349095 -2.575313 1 29 s atom 50 - H H - 0.000000 -2.956379 1.676735 0.084934 1 31 s atom 51 - H H - 0.000000 -4.375864 2.896952 0.517459 1 33 s atom 52 - H H - 0.000000 -5.961143 3.505827 -0.015855 1 33 s atom 53 - H H - 0.000000 -4.585202 3.497497 -1.145006 1 33 s atom 54 - H H - 0.000000 -6.604587 1.758132 -2.482820 1 34 s atom 55 - H H - 0.000000 -7.414060 2.246679 -0.974727 1 34 s atom 56 - H H - 0.000000 -7.117313 0.523491 -1.307643 1 34 s endmol 1 --Message-Boundary-15545 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Text from file 'sokrat.pdb' HEADER from Socrates de Oliveira Dantas COMPND 9-(1,2,3,4-Tetrahydro-1-thiaphenanthren-4-ylidene)-2- COMPND dimethylamino-cis-7-nitro-10-thia-anthracene SOURCE Wed 28 Jul 1999 13:15:08 SOURCE from MOLF.CAR (X-ray) by Mol2Mol 3.40 HETATM 1 S UNK 1 0.371 3.439 1.869 1.00 0.00 S HETATM 2 S UNK 1 -1.089 -2.128 -2.391 1.00 0.00 S HETATM 3 O UNK 1 1.742 -1.722 3.605 1.00 0.00 O HETATM 4 O UNK 1 2.974 -3.253 2.703 1.00 0.00 O HETATM 5 N UNK 1 2.030 -2.473 2.675 1.00 0.00 N HETATM 6 N UNK 1 -5.433 1.627 -0.761 1.00 0.00 N HETATM 7 C UNK 1 1.598 2.352 1.228 1.00 0.00 C HETATM 8 C UNK 1 2.845 2.382 1.896 1.00 0.00 C HETATM 9 C UNK 1 3.824 1.499 1.577 1.00 0.00 C HETATM 10 C UNK 1 3.664 0.603 0.485 1.00 0.00 C HETATM 11 C UNK 1 4.684 -0.307 0.115 1.00 0.00 C HETATM 12 C UNK 1 4.549 -1.095 -0.998 1.00 0.00 C HETATM 13 C UNK 1 3.390 -0.989 -1.793 1.00 0.00 C HETATM 14 C UNK 1 2.364 -0.161 -1.430 1.00 0.00 C HETATM 15 C UNK 1 2.453 0.637 -0.255 1.00 0.00 C HETATM 16 C UNK 1 1.360 1.439 0.206 1.00 0.00 C HETATM 17 C UNK 1 -0.016 1.349 -0.348 1.00 0.00 C HETATM 18 C UNK 1 -0.570 2.707 -0.684 1.00 0.00 C HETATM 19 C UNK 1 -0.921 3.479 0.588 1.00 0.00 C HETATM 20 C UNK 1 -0.705 0.189 -0.455 1.00 0.00 C HETATM 21 C UNK 1 -0.130 -1.110 -0.029 1.00 0.00 C HETATM 22 C UNK 1 0.547 -1.246 1.179 1.00 0.00 C HETATM 23 C UNK 1 1.220 -2.415 1.455 1.00 0.00 C HETATM 24 C UNK 1 1.187 -3.520 0.611 1.00 0.00 C HETATM 25 C UNK 1 0.437 -3.427 -0.542 1.00 0.00 C HETATM 26 C UNK 1 -0.216 -2.235 -0.866 1.00 0.00 C HETATM 27 C UNK 1 -2.339 -0.965 -1.943 1.00 0.00 C HETATM 28 C UNK 1 -3.606 -1.091 -2.483 1.00 0.00 C HETATM 29 C UNK 1 -4.628 -0.228 -2.138 1.00 0.00 C HETATM 30 C UNK 1 -4.409 0.793 -1.191 1.00 0.00 C HETATM 31 C UNK 1 -3.119 0.906 -0.653 1.00 0.00 C HETATM 32 C UNK 1 -2.074 0.073 -1.030 1.00 0.00 C HETATM 33 C UNK 1 -5.066 2.966 -0.324 1.00 0.00 C HETATM 34 C UNK 1 -6.723 1.533 -1.423 1.00 0.00 C CONECT 1 7 19 CONECT 2 26 27 CONECT 3 5 CONECT 4 5 CONECT 5 3 4 23 CONECT 6 30 33 34 CONECT 7 1 8 16 CONECT 8 7 9 CONECT 9 8 10 CONECT 10 9 11 15 CONECT 11 10 12 CONECT 12 11 13 CONECT 13 12 14 CONECT 14 13 15 CONECT 15 10 14 16 CONECT 16 7 15 17 CONECT 17 16 18 20 CONECT 18 17 19 CONECT 19 1 18 CONECT 20 17 21 32 CONECT 21 20 22 26 CONECT 22 21 23 CONECT 23 5 22 24 CONECT 24 23 25 CONECT 25 24 26 CONECT 26 2 21 25 CONECT 27 2 28 32 CONECT 28 27 29 CONECT 29 28 30 CONECT 30 6 29 31 CONECT 31 30 32 CONECT 32 20 27 31 CONECT 33 6 CONECT 34 6 END --Message-Boundary-15545-- From chemistry-request@server.ccl.net Wed Jul 28 15:25:16 1999 Received: from rs5.thch.uni-bonn.de (rs5.thch.uni-bonn.de [131.220.44.15]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA31351 for ; Wed, 28 Jul 1999 15:25:15 -0400 Received: (from bernd@localhost) by rs5.thch.uni-bonn.de (8.8.8/8.8.5) id VAA14247 for chemistry@www.ccl.net; Wed, 28 Jul 1999 21:20:17 +0200 From: Bernd Engels Message-Id: <199907281920.VAA14247@rs5.thch.uni-bonn.de> Subject: symmetry breaking effect To: chemistry@server.ccl.net (Computational Chemistry List) Date: Wed, 28 Jul 1999 21:20:17 +0200 (MES) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit dear ccl'er I looking for examples of the symmetry breaking effect. As described in a paper of Davidson and Borden (JPC, 87 (1983) 3063) it is the effect that the electronic wavefunctions has a lower symmetry than the nuclear framework. An example is the allyl radical with an ROHF type wave function, where the nuclear framework has C2v symmetry but the C2v wave function corresponds to a (first order) saddle point. I am looking for more examples and some newer references. I also know a reference from Cederbaum and coworker in Mol.Phys. but I don't know the exact reference. I am not interested in the problem that ab initio programms are not able to handle the full symmetry but uses abelian subgroups. Thank you in advance and I will summarize Bernd Engels Inst. für Org. Chemie Universität Würzburg From chemistry-request@server.ccl.net Wed Jul 28 18:07:09 1999 Received: from deimos.cber.nih.gov (deimos.cber.nih.gov [128.231.52.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA00374 for ; Wed, 28 Jul 1999 18:07:08 -0400 Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA110879287; Wed, 28 Jul 1999 18:01:27 -0400 Date: Wed, 28 Jul 1999 18:01:27 -0400 (EDT) From: Rick Venable To: Gavin Tsai Cc: CHEMISTRY@ccl.net Subject: Re: CCL:degenerate eigenvalue problem In-Reply-To: <001201bed87b$8ddcfe00$aec81681@cwru.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 27 Jul 1999, Gavin Tsai wrote: > Here is one problem for degenerate eigensystem... > > I try to diagonalize a real and symmetry matrix by using Jacobi > transformation. The program is from the book "numerical recipes". It > seems does not work for the degenerate eigensystem, the eigenvectors are > the linear combination of two degenerate eigenvectors. > > Is there any one can give me any suggestion or advice for the > degenerate eigensystem? While the book "Numerical Recipes" is an excellent teaching and learning tool, not all of the routines are as robust or efficient as those found elsewhere. I recommend a visit to http://www.netlib.org where you will probably find a better routine for diagonalizing a matrix. In my own case I observed a 50-fold performance improvement for matrix inversion by changing from the Numerical Recipes routine to one I obtained from NETLIB. A final note-- the authors of Numerical Recipes have copyrighted the associated source code, and anyone who redistributes a program using their code is legally obligated to pay them some royalties. The NETLIN code is in the public domain. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or Rick_Venable@nih.gov | \ / |=| position of the FDA; for that, http://www.erols.com/rvenable \/ |=| see http://www.fda.gov )