From portmann@cscs.ch Tue Sep 9 05:23:03 1997 Received: from pobox.cscs.ch for portmann@cscs.ch by www.ccl.net (8.8.3/950822.1) id FAA06053; Tue, 9 Sep 1997 05:17:09 -0400 (EDT) Received: from oncidium.cscs.ch (oncidium.cscs.ch [148.187.1.141]) by pobox.cscs.ch (8.8.5/8.7.3) with ESMTP id LAA14672 for ; Tue, 9 Sep 1997 11:17:04 +0200 (MET DST) Received: from chysis (chysis [148.187.140.16]) by oncidium.cscs.ch (8.6.10/8.6.10) with ESMTP id JAA01965; Tue, 9 Sep 1997 09:17:03 GMT From: Stefan Portmann Received: by chysis (950413.SGI.8.6.12) id JAA26884; Tue, 9 Sep 1997 09:17:03 GMT Date: Tue, 9 Sep 1997 09:17:03 GMT Message-Id: <9709091117.ZM26882@www.vis.cscs.ch> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: G2 test set Cc: portmann@cscs.ch Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL members, I'm looking for properties available for molecules of the G2 test set (calculated or measured). In particular I'm interested in force constants. Does a data base exist? Any hints are welcome. Thanks for you help Stefan -- Dr. Stefan Portmann CSCS/SCSC Centro Svizzero di Calcolo Scientifico Via Cantonale CH-6928 Manno, Switzerland Phone (Manno): +41 (91) 610 82 65 Phone (Zurich): +41 (1) 632 57 82 Fax (Manno): +41 (91) 610 82 82 Fax (Zurich): +41 (1) 632 11 04 e-mail: portmann@cscs.ch From sanja@indigo.irb.hr Tue Sep 9 07:23:05 1997 Received: from indigo.irb.hr for sanja@indigo.irb.hr by www.ccl.net (8.8.3/950822.1) id GAA06367; Tue, 9 Sep 1997 06:48:33 -0400 (EDT) Received: from indigo by indigo.irb.hr via SMTP (940816.SGI.8.6.9/930416.SGI.AUTO) for id MAA01633; Tue, 9 Sep 1997 12:41:28 +0200 Sender: sanja@indigo.irb.hr Message-ID: <341527D7.41C6@indigo.irb.hr> Date: Tue, 09 Sep 1997 12:41:27 +0200 From: sanja X-Mailer: Mozilla 3.01 (X11; I; IRIX 5.3 IP20) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: OH+HF PES Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I wonder if potential energy surface for the OH+HF reaction has been calculated. I made a search for the last few years but haven't find any reference on it. Thanks, sanja -- *~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* Sanja Sekusak, Ph.D e-mail: sanja@indigo.irb.hr Rudjer Boskovic Institute phone: (385-1) 456 10 89 HR-10001 Zagreb, CROATIA fax: (385-1) 42 54 97 *~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* From grzesb@asp.biogeo.uw.edu.pl Tue Sep 9 10:23:06 1997 Received: from asp.biogeo.uw.edu.pl for grzesb@asp.biogeo.uw.edu.pl by www.ccl.net (8.8.3/950822.1) id JAA07199; Tue, 9 Sep 1997 09:58:49 -0400 (EDT) Received: by asp.biogeo.uw.edu.pl (5.61/1.34) id AA20342; Tue, 9 Sep 97 15:57:22 +0200 From: grzesb@asp.biogeo.uw.edu.pl (Grzegorz Bakalarski) Message-Id: <9709091357.AA20342@asp.biogeo.uw.edu.pl> Subject: line width in InsightII To: CHEMISTRY@www.ccl.net X-Mailer: ELM [version 2.4 PL22] Content-Type: text Dear CCL I have problem regarding line width in insightII (ver. 95.5)(from MSI). I make a picture (potential map) with use GRID/SLICE utility. I want to use contour map because it is more precise than color map (mapplane). And the program gives nice isolines in specified plane. But this isolines are very thin, so when I take a picture from screen they are almoust invisible on photo. I've tried to change linewidth using OBJECT/LineWidth command applied to grid object but It did not help (no change). Have you any suggestion ? Thanks in advance. G.Bakalarski From elewars@alchemy.chem.utoronto.ca Tue Sep 9 11:23:06 1997 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.8.3/950822.1) id LAA07644; Tue, 9 Sep 1997 11:01:16 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id LAA07595 for chemistry@www.ccl.net; Tue, 9 Sep 1997 11:01:16 -0400 (EDT) Date: Tue, 9 Sep 1997 11:01:16 -0400 (EDT) From: "E. Lewars" Message-Id: <199709091501.LAA07595@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: RELATIVITY IN COMP CHEM 1997 Sept 9 Hello, Concerning the importance of the theory of relativity in computational chemistry: 1) Are there cases where the Dirac-Fock equation, rather than the Schroedinger equation, should be used? 2) To what extent are the effective core potentials of ab initio calculations derived empirically, to fit experiment, rather than theoretically? 3) Where should you start using effective core potentials to simulate relativistic effects --at which element does the error start becoming significant (somewhere around element 33 to 37, I suspect--As, Se, Br, Kr, Rb)? Thanks E. Lewars ===== From govindan@chet.medc.umn.edu Tue Sep 9 13:23:06 1997 Received: from chet.medc.umn.edu for govindan@chet.medc.umn.edu by www.ccl.net (8.8.3/950822.1) id MAA08303; Tue, 9 Sep 1997 12:26:28 -0400 (EDT) Received: (from govindan@localhost) by chet.medc.umn.edu (8.8.5/8.8.5) id LAA03117 for CHEMISTRY@www.ccl.net; Tue, 9 Sep 1997 11:26:27 -0500 (CDT) From: Govindan Subramanian Message-Id: <199709091626.LAA03117@chet.medc.umn.edu> Subject: NCS AMBER parameters To: CHEMISTRY@www.ccl.net Date: Tue, 9 Sep 1997 11:26:26 -0500 (CDT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hai CCLers, I would appreciate receiving any information on the stretching, bending, torsion, improper, van der Waals parameters for the NCS moeity in benzene iso- -thiocyanate (C6H5NCS) that can be incorporated into AMBER parameter file. Also of interest to me is the parameter set for sulfur (sp2) in thiophene, benzothio- -phene. Will summarize the infos I receive. Thanks in advance. -subramanian.g From brian@bert.chem.wsu.edu Tue Sep 9 13:35:41 1997 Received: from cheetah.it.wsu.edu for brian@bert.chem.wsu.edu by www.ccl.net (8.8.3/950822.1) id NAA08440; Tue, 9 Sep 1997 13:12:36 -0400 (EDT) Received: from bert.chem.wsu.edu (bert.chem.wsu.edu [134.121.43.22]) by cheetah.it.wsu.edu (8.8.5/8.8.5) with SMTP id KAA02288 for ; Tue, 9 Sep 1997 10:12:36 -0700 (PDT) Received: by bert.chem.wsu.edu (AIX 3.2/UCB 5.64/4.03) id AA20473; Tue, 9 Sep 1997 10:12:42 -0700 From: brian@bert.chem.wsu.edu (Brian W. Beck) Message-Id: <9709091712.AA20473@bert.chem.wsu.edu> Subject: Metalloproteins To: CHEMISTRY@www.ccl.net (Computational Chemistry List) Date: Tue, 9 Sep 1997 10:12:42 -0700 (PDT) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit In various talks and lectures, I have several times heard the quote that roughly 70% of all known proteins are metalloproteins (ie. have specific metal binding sites). 1) Does anyone have a reference for this statement? 2) Can anyone give me a reference for the number of proteins in the PDB which have metals in them? -Brian -- ============================================================================= | .---------.| Brian W. Beck | E-mail Addresses: | |/\ | || Biochem/Biophysics | brian@bert.chem.wsu.edu | || \\ WSU || Washington St. Univ| brian_beck@wsu.edu | |\ - *|| 639 Fulmer | URL http://elmo.chem.wsu.edu/~brian | | | || Pullman, WA, USA | VOICE (509) 335-4083 | | \___________|| 99164-4660 | FAX (509) 335-9688 | ============================================================================= From turnerm@CRHSC.UMontreal.CA Tue Sep 9 14:23:08 1997 Received: from condor.CC.UMontreal.CA for turnerm@CRHSC.UMontreal.CA by www.ccl.net (8.8.3/950822.1) id OAA08874; Tue, 9 Sep 1997 14:00:13 -0400 (EDT) Received: from slinky (slinky.CRHSC.UMontreal.CA [132.204.82.50]) by condor.CC.UMontreal.CA with SMTP id NAA26508 (8.6.11/IDA-1.6 for ); Tue, 9 Sep 1997 13:58:57 -0400 Received: from calvin by slinky (920330.SGI/5.17) id AA13848; Tue, 9 Sep 97 14:16:41 -0700 Sender: turnerm@CRHSC.UMontreal.CA Message-Id: <3415AF3A.41C6@crhsc.umontreal.ca> Date: Tue, 09 Sep 1997 13:19:06 -0700 From: Maria Turner X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) Mime-Version: 1.0 To: ccl Subject: standard colours? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello! Can anyone tell me whether it is standard to publish images of molecular models on a black background? Most of the figures I have seen have a black background even when another colour might show things more clearly. I'd like to know whether this is a standardized thing, or just a matter of choice. Thanks for the help! (Sorry for the trivial question) Maria -- Maria Turner Centre de Recherche, Hopital du Sacre-Coeur email: turnerm@crhsc.umontreal.ca From kellogg@h178078.nist.gov Tue Sep 9 15:04:46 1997 Received: from h178078.nist.gov for kellogg@h178078.nist.gov by www.ccl.net (8.8.3/950822.1) id NAA08545; Tue, 9 Sep 1997 13:34:56 -0400 (EDT) Received: (from kellogg@localhost) by h178078.nist.gov (8.6.12/8.6.9) id NAA15502 for chemistry@www.ccl.net; Tue, 9 Sep 1997 13:36:56 -0400 From: "C. Brian Kellogg" Message-Id: <199709091736.NAA15502@h178078.nist.gov> Subject: RE: CCL:RELATIVITY IN COMP CHEM To: chemistry@www.ccl.net Date: Tue, 9 Sep 1997 13:36:56 -0400 (EDT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear Dr. Lewars- In reference to your questions about relativity in quantum chemistry > 1) Are there cases where the Dirac-Fock equation, rather than the > Schroedinger equation, should be used? > Any molecular system which has heavy elements or exhibits large spin-orbit or spin-spin interactions should be more adequately described by Dirac-Fock based methods. Because of the significantly larger basis set requirements of the Dirac-Fock method, however, effective core potential methods are typically employed to estimate relativistic effects. > 2) To what extent are the effective core potentials of ab initio > calculations derived empirically, to fit experiment, rather than > theoretically? Effective core potentials are constructed solely with reference to the theoretically derived atomic structure. In brief, the core potentials are derived such that when they are employed in the atomic case, they provide the best possible reproduction of the valence atomic wavefunction obtained for the all-electron case. > 3) Where should you start using effective core potentials to simulate > relativistic effects --at which element does the error start becoming > significant (somewhere around element 33 to 37, I suspect--As, Se, Br, > Kr, Rb)? Small errors in equilibrium properties can even show up in the third row, and spin-orbit effects may be found throughout the periodic table. Generally, ECP based methods are thought to be effective for the estimation of relativistic effects on most molecular properties for Z = 19-36, and even up through Z=54, but that for heavier elements, the agreement between Dirac-Fock predictions and ECP predictions is often poor. If you would like to see a more lengthy discussion of these topics, I have an on-line introduction to relativistic quantum chemistry which should provide you with more in-depth answers as well as some references. It can be found at: http://zopyros.ccqc.uga.edu/~kellogg/docs/rltvt/rltvt.html In particular, you may find the final section of that web page, "Relativistic Effects in Atoms", more helpful. That section presents some graphs of the magnitude of relativistic effects for main group elements and discusses the major trends of relativity across the periodic table. I hope this helps. -Brian Kellogg -- C. Brian Kellogg Physics Building (221), office A367 phone: (301)975-2526 National Institute of Standards and Technology fax: (301)975-3670 Gaithersburg, MD 20899 From rochus@felix.anorg.chemie.tu-muenchen.de Mon Sep 8 14:22:55 1997 Received: from felix.anorg.chemie.tu-muenchen.de for rochus@felix.anorg.chemie.tu-muenchen.de by www.ccl.net (8.8.3/950822.1) id NAA02809; Mon, 8 Sep 1997 13:40:53 -0400 (EDT) Received: by felix.anorg.chemie.tu-muenchen.de (940816.SGI.8.6.9/930416.SGI) for chemistry@www.ccl.net id TAA07841; Mon, 8 Sep 1997 19:40:36 +0200 From: "Rochus Schmid" Message-Id: <9709081940.ZM7839@felix> Date: Mon, 8 Sep 1997 19:40:36 -0600 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Summary: dispersion interactions Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear netters: My original question was: ******* from my poor textbook knowledge I rmemeber, that the dispersion interaction between e.g. rare gas atoms is something like a "induced dipole- induced dipole" interaction and it follows -1/r^6. Right? It is a "correlation" effect, thus, it doesn't appear in HF-calcs. can someone point me to a ref. or explain me the origin in more detail? And are there any methods to somehow extract the amount of dispersion interaction energy from post-HF calcs.? (or is this a stupid idea?) ******* Thanks to Jon Erickson, Guido Germano, Heinz Schiffer, Hayes Williams, Martin Kaupp and Bernd Kallies. Here a list of references (from H. Schiffer) ********* A. D. Buckingham Basic theory of intermolecular forces: Applications to small molecules in: B. Pullmann (ed.), Intermolecular Interactions, From Diatomics to Biopolymers, Wiley, New York 1978, Chp.1, pp 1-67 P. Claverie Elaboration of approximate formulas for the interaction between large molecules: Applications in organic chemistry in: B. Pullmann (ed.), Intermolecular Interactions, From Diatomics to Biopolymers, Wiley, New York 1978, Chp. 2, pp. 69-305 Bogumil Jeziorski, Robert Moszynski, Krzysztof Szalewicz Perturbation Theory Approach to Intermolecular Potential Energy Surfaces of van der Waals Complexes Chem. Rev. 94 (1994) 1887-1930 Sandor Kristyan, Peter Pulay Can (semi)local density functional theory account for the London dispersion forces ? Chem. Phys. Lett. 229 (1994) 175-180 Jose M. Perez-Jorda, A. D. Becke A density-functional study of van der Waals forces: rare gas diatomics Chem. Phys. Lett. 233 (1995) 134-137 Evert Jan Meijer, Michiel Sprik A density-functional study of the intermolcular interactions of benzene J. Chem. Phys. 105(19) (1996) 8684-8689 Michiel Sprik Ab intio molecular dynamics simulation of liquids and solutions J. Phys.: Condens. Matter 8 (1996) 9405-9409 Daxu Yin, Alexander D. MacKerell, Jr. Ab initio Calculations on the Use of Helium and Neon as Probes of the van der Waals Surfaces of Molecules J. Phys. Chem. 100 (1996) 2588-2596 Joerg-R. Hill Use of Test Particle Calculations for the Derivation of van der Waals Parameters Used in Force Fields J. Comput. Chem. 18(2) (1007) 211-220 ********* Additionally from H. Williams: *********** Symmetry-Adapted Perturbation Theory (SAPT) is a method for finding the interaction energy between two closed-shell ground state atoms or molecules directly (as a post-HF computation). This interaction energy includes the dispersion energy as one of its components. The major reference to this work is: B. Jeziorski, R. Moszynski, and K. Szalewicz, Chem. Rev. v94, p1887 (1994). I haven't seen the printed version yet, but the next major review article will be: K. Szalewicz and B. Jeziorski, in {\em Molecular Interactions -- From van der Waals to Strongly Bound Complexes}, edited by S. Scheiner, Wiley 1996. One of my first applications of this work was to the Ar-H_2 system in: J. Chem. Phys., v98, p1279 (1993). SAPT has been used to investigate He_2, Ar-HF, He-HF, He-CO, He-C_2H_2 and a few others which I don't have at my fingertips at the moment. Also, there is a large body of theoretical work on the subject as well. The SAPT codes are freely available from Dr. Szalewicz (email: szalewic@udel.edu), but they are research level quality and may require some tinkering on your part. **************** Thanks to all who replied. Cheers Rochus -- ******************************************************************************** Dr. Rochus Schmid Technische Universitaet Muenchen Tel. ++49 89 2891 3385 Lehrstuhl f. Anorganische Chemie 1 Fax. ++49 89 2891 3473 Prof. W. A. Herrmann E-mail: Lichtenbergstrasse 4 rochus@felix.anorg.chemie.tu-muenchen.de 85747 Garching ******************************************************************************** From mn1@helix.nih.gov Tue Sep 9 19:23:10 1997 Received: from helix.nih.gov for mn1@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id TAA10678; Tue, 9 Sep 1997 19:12:24 -0400 (EDT) Received: (from mn1@localhost) by helix.nih.gov (8.8.5/8.8.5) id TAA15185; Tue, 9 Sep 1997 19:12:17 -0400 (EDT) Date: Tue, 9 Sep 1997 19:12:17 -0400 (EDT) From: "M. Nicklaus" Message-Id: <199709092312.TAA15185@helix.nih.gov> To: CHEMISTRY@www.ccl.net Subject: NCI SMILES Database Cc: mn1@helix.nih.gov The promised SMILES version of the open part of the NCI database is up on http://epnws1.ncifcrf.gov:2345/dis3d/3ddatabase/nci_smil.html and ready for download. (Thanks to Dan Zaharevitz for his help with this.) In fact, two versions of the SMILES database are available. Thanks to Wolf-Dietrich Ihlenfeldt, we re-converted the NCI database with the program CACTVS v. 3.2, using conversion scripts provided by Wolf- Dietrich that handle formal charge problems and took care of other 'weird stuff' in the NCI database. The other conversion program used is Babel, v. 1.6. The formal charge problem regarding nitro groups was fixed by simple string substitution in the Babel output; none of the other potential problems was addressed. We found that the output of the two programs differ substantially if one just does a simple string comparison. For the first 1000 NSC numbers, 64% of the SMILES strings showed differences between Babel and CACTVS. This does not mean, however, that either one of the differing SMILES strings for the same compound need be wrong, since neither conversion program claims to generate Unique SMILES (to our knowledge). For this reason, we decided to make both versions available. If you compare them to each other, we'd be interested to know which one you find better, more correct, more useful for a certain purpose etc. No further evaluation was conducted on either database, so please PERFORM YOUR OWN CHECKS before you use the SMILES strings for any given purpose. Both versions contain SMILES strings for the same set of 237,771 structures. The files are just over 4 MB compressed, and uncompress to about 15 MB each. Marc C. Nicklaus & Bruno Bienfait ------------------------------------------------------------------------ Marc C. Nicklaus, Ph.D. National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 37, Rm 5B29 Phone: (301) 402-3111 BETHESDA, MD 20892-4255 USA Fax: (301) 496-5839 http://www.nci.nih.gov/intra/lmch/MCNBIO.HTM Laboratory of Medicinal Chemistry, National Cancer Institute, & Lab. of Structural Biology, Div. of Computer Research and Technology ------------------------------------------------------------------------