From lma@univ-orleans.fr Tue Mar 14 04:12:19 1995 Received: from centre.univ-orleans.fr for lma@univ-orleans.fr by www.ccl.net (8.6.10/930601.1506) id DAA03312; Tue, 14 Mar 1995 03:25:05 -0500 Received: from mailhost.univ-orleans.fr ([193.49.81.10]) by centre.univ-orleans.fr (8.6.9/8.6.9) with SMTP id JAA24130 for ; Tue, 14 Mar 1995 09:30:26 +0100 LD?Resent-Date: Tue, 14 Mar 1995 09:30:26 +0100 Date: Tue, 14 Mar 1995 09:30:26 +0100 Message-Id: <199503140830.JAA24130@centre.univ-orleans.fr> X-Sender: lma@mailhost.univ-orleans.fr X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: lma@univ-orleans.fr (Luc Morin-Allory) Subject: Semi empirical parameters for Platinum Dear netters, I am looking for the parameters of platinum for use in MOPAC ( any method) , I am wondering if anyone can help me with these values . Thanks in advance for any help **************************************************************************** ********* Luc Morin-Allory Modelisation- Chemometrics Group Laboratoire de Chimie Bioorganique et Analytique ( LCBA) ICOA, URA CNRS 499 University of Orleans B.P. 6759 45067 Orleans Cedex 2 France Tel (33) 38 41 70 42 Fax: (33) 38 41 72 81 e.Mail: lma@univ-orleans.fr **************************************************************************** ********* From dsg@hartree.quantchem.kuleuven.ac.be Tue Mar 14 06:12:15 1995 Received: from hartree.quantchem.kuleuven.ac.b for dsg@hartree.quantchem.kuleuven.ac.be by www.ccl.net (8.6.10/930601.1506) id GAA04684; Tue, 14 Mar 1995 06:09:47 -0500 From: Received: by hartree.quantchem.kuleuven.ac.be id AA19532 (5.67a/IDA-1.5 for CHEMISTRY@ccl.net); Tue, 14 Mar 1995 12:04:28 +0100 Date: Tue, 14 Mar 1995 12:04:28 +0100 Message-Id: <199503141104.AA19532@hartree.quantchem.kuleuven.ac.be> To: CHEMISTRY@ccl.net Subject: Info needed Hi Netters, Is there any list like CCL in the field of Photochemisrty, Photophysics, time resolved fluorescence spectroscopy and microscopy? Debasis dsg@hartree.quantchem.kuleuven.ac.be From shenkin@still3.chem.columbia.edu Tue Mar 14 11:13:53 1995 Received: from mailhub.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.10/930601.1506) id KAA08582; Tue, 14 Mar 1995 10:20:16 -0500 Received: from still3.chem.columbia.edu by mailhub.cc.columbia.edu with SMTP id AA07408 (5.65c+CU/IDA-1.4.4/HLK for <@mailhub.cc.columbia.edu:CHEMISTRY@ccl.net>); Tue, 14 Mar 1995 10:20:15 -0500 Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for @mailhub.cc.columbia.edu:CHEMISTRY@ccl.net id AA09048; Tue, 14 Mar 95 10:20:14 -0500 From: "Peter Shenkin" Message-Id: <9503141020.ZM9046@still3.chem.columbia.edu> Date: Tue, 14 Mar 1995 10:20:11 -0500 In-Reply-To: nauss@ucmod2.che.uc.EDU (Jeffrey L. Nauss) "CCL:Spelling question" (Mar 13, 2:10pm) References: <9503131910.AA14030@ucmod2.che.uc.edu> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: nauss@ucmod2.che.uc.EDU, CHEMISTRY@ccl.net Subject: Re: CCL:Spelling question Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Mar 13, 2:10pm, Jeffrey L. Nauss wrote: > Subject: CCL:Spelling question > > Sorry about the rather mundane question but... > > We have a minor controversy here. What is the correct spelling > for van der Waals parameters or forces? ... > c. van der Waals parameters (lower case v and no apostrophy) His name was "van der Waals". If one wanted to use the possessive, one would refer to "van der Waals' parameters", or, in England, "van der Waals's parameters", but certainly not "van der Waal's parameters". Should the possessive be used? Probably not. Looking through the index of Levine's "Physical Chemistry", I see "van der Waals equation", "van der Waals force", etc., etc. However, we also have "Stokes' law" and "Trouton's rule", so a case can be made for the possessive, I suppose. A case can also be made for "van-der-Waals parameters" (by analogy to "The New-York Historical Society", (complex noun serving as an adjective) but this would probably be deemed pedantic. Then again, you do have a .edu address.... -P. -- ************************ The secret of life: ************************* *Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ.,* * New York, NY 10027; shenkin@columbia.edu; (212) 854-5143 * ************* If you find a loose thread, don't pull it. ************* From aiba@ir.phys.chem.ethz.ch Tue Mar 14 11:32:05 1995 Received: from bernina.ethz.ch for aiba@ir.phys.chem.ethz.ch by www.ccl.net (8.6.10/930601.1506) id LAA09731; Tue, 14 Mar 1995 11:31:57 -0500 Received: from volta (actually volta.ethz.ch) by bernina.ethz.ch with SMTP inbound; Tue, 14 Mar 1995 17:31:29 +0100 Date: Tue, 14 Mar 1995 17:31:20 +0200 Message-Id: <95031417311981@ir.phys.chem.ethz.ch> From: aiba@ir.phys.chem.ethz.ch (Ayaz Bakasov, Phys. Chem., ETH Zurich) To: chemistry@ccl.net Subject: QUERY - MOLECULAR GRAPHICS X-VMS-To: SMTP%"chemistry@ccl.net" X-VMS-Cc: AIBA Status: R Dear Netters, could someone advise me please on a molecular graphics software which: a) is ftp-able or commercial, for a workstation like IBM/RS or Alpha DEC; b) is for not too large molecules (atoms < 20-30); c) draws bonds and can mark them (length); d) draws bond angles and dihedral angles and can mark them; c) draws selected planes for pairs of bonds; e) puts (desirable) different colours on atoms and marks atoms (for slides); e) any other useful features on top of above-specified ones will be welcome (e.g. animation). Tried RASMOL and found that it is for VERY large molecules, while I need to draw molecules ranging from hydrogen peroxide to some first aminoacids. Also, RASMOL doesn't take care of small details I am interested in (like specification of bond angles and dihedral angles on the graph, or drawing planes of pairs of bonds) Perhaps, Mathematica or Maple have already some supplementary packages ?! Thank you. It will be my pleasure to summarize on the net the suggestions. Ayaz Bakasov. From stoutepf@chemsci1.dmpc.com Tue Mar 14 15:13:56 1995 Received: from gatekeeper.es.dupont.com for stoutepf@chemsci1.dmpc.com by www.ccl.net (8.6.10/930601.1506) id OAA13430; Tue, 14 Mar 1995 14:21:58 -0500 Received: by gatekeeper.es.dupont.com; id AA01153; Tue, 14 Mar 95 14:21:50 -0500 Received: from [158.117.153.76] (esm153076.dmpc.com) by chemsci1.dmpc.com (4.1/SMI-4.1) id AA20865; Tue, 14 Mar 95 14:20:21 EST Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Organization: The DuPont Merck Pharmaceutical Company X-Mailer: Eudora 1.5.1 for Macintosh Date: Tue, 14 Mar 1995 14:22:56 -0500 To: chemistry@ccl.net From: stoutepf@chemsci1.dmpc.com (Pieter Stouten) Subject: Re: CCL:Spelling question Cc: shenkin@still3.chem.columbia.edu Peter Shenkin wrote: >His name was "van der Waals". > True, BUT when used standalone (e.g. without a first name) the "v" in "van" gets capitalized. So "Van der Waals" is correct. Cheers, Pieter. -- DuPont Merck is getting its own computer network (physically separated -- from Du Pont) and we are having intermittent e-mail problems. If mail to -- me bounces, please try again some hours later. Sorry for any inconvenience. Pieter Stouten, Senior Research Scientist Computer Aided Drug Design Group The DuPont Merck Pharmaceutical Company P.O. Box 80353, Wilmington, DE 19880-0353 Phone: +1 (302) 695 3515 Fax: +1 (302) 695 2813 Internet: stoutepf@chemsci1.dmpc.com CompuServe: 73172,2004 WWW: http://www.halcyon.com/stouten/stouten.html From shenkin@still3.chem.columbia.edu Tue Mar 14 16:12:27 1995 Received: from mailhub.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.10/930601.1506) id PAA14257; Tue, 14 Mar 1995 15:13:36 -0500 Received: from still3.chem.columbia.edu by mailhub.cc.columbia.edu with SMTP id AA14688 (5.65c+CU/IDA-1.4.4/HLK for <@mailhub.cc.columbia.edu:chemistry@ccl.net>); Tue, 14 Mar 1995 15:13:31 -0500 Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for @mailhub.cc.columbia.edu:chemistry@ccl.net id AA14908; Tue, 14 Mar 95 15:13:30 -0500 From: "Peter Shenkin" Message-Id: <9503141513.ZM14906@still3.chem.columbia.edu> Date: Tue, 14 Mar 1995 15:13:28 -0500 In-Reply-To: stoutepf@chemsci1.dmpc.com (Pieter Stouten) "Re: CCL:Spelling question" (Mar 14, 2:22pm) References: X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: stoutepf@chemsci1.dmpc.com (Pieter Stouten), chemistry@ccl.net Subject: Re: CCL:Spelling question Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Mar 14, 2:22pm, Pieter Stouten wrote: > Subject: Re: CCL:Spelling question > Peter Shenkin wrote: > > >His name was "van der Waals". > > > True, BUT when used standalone (e.g. without a first name) the "v" in "van" > gets capitalized. So "Van der Waals" is correct. > > Cheers, Pieter. Clearly, I must yield in the face of superior authority.... Chiers, -P. -- ************************ The secret of life: ************************* *Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ.,* * New York, NY 10027; shenkin@columbia.edu; (212) 854-5143 * ************* If you find a loose thread, don't pull it. ************* From bishop@london.ks.uiuc.edu Tue Mar 14 16:19:49 1995 Received: from london.ks.uiuc.edu for bishop@london.ks.uiuc.edu by www.ccl.net (8.6.10/930601.1506) id PAA15096; Tue, 14 Mar 1995 15:58:21 -0500 Received: from riga.ks.uiuc.edu by london.ks.uiuc.edu with SMTP (1.37.109.15/16.2) id AA240684699; Tue, 14 Mar 1995 14:58:20 -0600 From: Tom Connor Bishop Message-Id: <199503142058.AA240684699@london.ks.uiuc.edu> Received: by riga.ks.uiuc.edu (NX5.67d/NX3.0X) id AA07970; Tue, 14 Mar 95 14:58:19 -0600 Date: Tue, 14 Mar 95 14:58:19 -0600 Received: by NeXT.Mailer (1.100) Received: by NeXT Mailer (1.100) To: chemistry@ccl.net Subject: H-bond analysis of MD Reply-To: bishop@london.ks.uiuc.edu dear netters, I am looking for a program which takes an x-plor format molecular dynamics trajectory file (a DCD file), determines the hydrogen bonds and formats the output in a suitable fashion for reporting. (This information can be extracted from x-plor but it's no simple matter to accumulate the data in a reportable format, as far as I know) The system we wish to analyze contains DNA and excess water and we would like to analyze only the h-bonding of the water to the DNA, and not DNA-DNA h-bonds or water-water hbonds. Any suggestions would be very much appreciated. Thanks tom bishop --- +------------------------------------------------- |Theoretical Biophysics bishop@ks.uiuc.edu |Beckman Institute Tel: (217)-244-1851 |University of Illinois fax: (217)-244-6078 |405 N Mathews, Urbana, IL61801 NeXTmail Ok | | I don't suffer from insanity; I'm enjoying | every minute of it. +-------------------------------------------------- From toms@watcom.on.ca Tue Mar 14 17:12:29 1995 Received: from gateway.watcom.on.ca for toms@watcom.on.ca by www.ccl.net (8.6.10/930601.1506) id QAA15931; Tue, 14 Mar 1995 16:45:09 -0500 Received: from msmail.watcom.on.ca by gateway.watcom.on.ca (5.67/1.38) id AA26258; Tue, 14 Mar 95 16:44:59 -0500 Received: by gateway with Microsoft Mail id <2F660DE9@gateway>; Tue, 14 Mar 95 16:43:05 EST From: "Slee,Tom" To: "'chemistry list'" Subject: RE: CCL:Spelling question Date: Tue, 14 Mar 95 16:41:00 EST Message-Id: <2F660DE9@gateway> Encoding: 22 TEXT X-Mailer: Microsoft Mail V3.0 | | >His name was "van der Waals". | > | True, BUT when used standalone (e.g. without a first name) the "v" in "van" | gets capitalized. So "Van der Waals" is correct. | | Cheers, Pieter. | Pieter Stouten, Senior Research Scientist I am glad to hear this, as Bob LeRoy, with whom I did a postdoc and who knows his intermolecular forces very well, always uses "Van der Waals interactions" (capital V) for just this reason. In the intermolecular forces literature, however, "van der Waals interactions" (lower case v) is ubiquitous. Assuming Dr. Stouten is correct, most of the intermolecular forces literature is wrong in this. Tom Slee toms@watcom.on.ca From matt@synthesis.chem.arizona.edu Tue Mar 14 20:12:25 1995 Received: from synthesis.chem.arizona.edu for matt@synthesis.chem.arizona.edu by www.ccl.net (8.6.10/930601.1506) id TAA18030; Tue, 14 Mar 1995 19:39:47 -0500 Received: by synthesis.chem.arizona.edu (5.65/DEC-Ultrix/4.3) id AA13455; Tue, 14 Mar 1995 17:35:57 -0700 Date: Tue, 14 Mar 1995 17:35:56 -0700 (MST) From: Matt Stahl To: chemistry@ccl.net Subject: peptide data needed Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Netters, I'm interested in testing a method of rapid generation of peptide conformations from distance constraints and primary sequence. I need data to validate the method. Does anyone have a structure of a peptide which has been accurately determined by the combination of NMR and constrained MD? I need both the coordinates for the structure and the table of distance constraints generated from NOESY and/or COSY data. thanks, matt ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Mr. Matthew Stahl | Department of Chemistry | I'd rather be right half of the University of Arizona | time than half right all the Tucson, AZ 85721 | time. matt@synthesis.chem.arizona.edu | -Malcom S. Forbes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From mercie@mail.med.cornell.edu Tue Mar 14 20:17:02 1995 Received: from mail.med.cornell.edu for mercie@mail.med.cornell.edu by www.ccl.net (8.6.10/930601.1506) id TAA18259; Tue, 14 Mar 1995 19:55:48 -0500 Received: (from mercie@localhost) by mail.med.cornell.edu (8.6.11/ech1.75) id TAA23367; Tue, 14 Mar 1995 19:55:46 -0500 Date: Tue, 14 Mar 1995 19:55:45 -0500 (EST) From: Gustavo Mercier To: CCL Subject: 3D complex to complex FFT routine, Car-Parrinelo Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! The CP program fhi93cp uses several ESSL library routines not available at our site. One of these is a 3 - dimensional, single precision, complex to complex FFT routine called SCFT3. Checking through netlib I have not come across an equivalent subroutine, although I can probably combine some 1D routines to obtain the necessary results. Before I do so, I wonder if somebody has a routine equivalent to SCFT3 and is willing to make it available through the net. Finally, is there a WWW site or kind soul that may have online ESSL documentation on this routine that could be made available through the net? Some WebCrawler searches were not very productive. Documentaion on a second routine used to get eigenvectors (called CHPSV) would also be useful since I have to replace this one by eispack routines. Thanks! Cheers! Gustavo A. Mercier, Jr. mercie@mail.med.cornell.edu From marvin@iris131.biosym.com Tue Mar 14 23:12:27 1995 Received: from bioc1.biosym.com for marvin@iris131.biosym.com by www.ccl.net (8.6.10/930601.1506) id WAA20164; Tue, 14 Mar 1995 22:56:21 -0500 Received: from iris131.biosym.com by bioc1.biosym.com (5.64/0.0) id AA25805; Tue, 14 Mar 95 19:56:40 -0800 Received: by iris131.biosym.com (940816.SGI.8.6.9/930416.SGI) for CHEMISTRY@ccl.net id TAA21139; Tue, 14 Mar 1995 19:55:47 -0800 Date: Tue, 14 Mar 1995 19:55:47 -0800 From: marvin@biosym.com (Marvin Waldman) Message-Id: <199503150355.TAA21139@iris131.biosym.com> To: CHEMISTRY@ccl.net Subject: Spelling of v(V?)an der Waals('?) I found it somewhat amusing that my copy of Physical Chemistry by Moore, Third Edition, (Copyright 1962) - that's not the year I used it (not even close), so don't try to guess my age from that date - has the following usages of van der Waals in the same book(!) : Page 18: Caption for Table 1.2: Critical Point Data and van der Waals Constants Page 19, second line from bottom: The van der Waals equation provides ... Page 20, third line from top: ... the van der Waals' equation. ^^^^^^ Emphasis added by me. Page 21: Title for Section 16: 16. THE VAN DER WAALS EQUATION AND LIQUEFACTION OF GASES Page 21, next line(!): Van der Waals' equation provides ... ^^^^^^ Conclusion: Usage or non-usage of the apostrophe (or even being consistent about it) does not constitute grounds for rejection of your article, book, user manual, or any other document from which you hope to achieve fame and fortune. The same apparently applies to using a small or capital "v". ------------------------------------------------------------------------ Addtional Historical Background By the way, it appears that there are several van der Waals' involved in the theory of intermolecular forces. The most famous one (associated with the van der Waals equation of state) is J.D. van der Waals Sr. as referenced on page 131 of Molecular Theory of Gases and Liquids by Hirschfelder, Curtiss, and Bird (Copyright 1954 - with notes and corrections added in March, 1964) as follows: "The experimentally observed deviations from the ideal gas law were interpreted qualitatively by van der Waals (Ref 1) ..." Ref 1: J.D. van der Waals Sr., Doctoral Dissertation (Leiden 1873). It is the same van der Waals to whom credit is generally given for intermolecular attractive forces as described on page 206 of Theoretical Inorganic Chemistry by Day and Selbin (Second Edition, Copyright 1969) as follows: "The existence of such weak attractive forces was first recognized by van der Waals as early as 1813 (this is clearly a typo!). At that time, he introduced the a/V**2 term in his equation of state to allow for such interactions. It is for this reason that these forces are referred to as van der Waals forces." In Moore's Physical Chemistry text, van der Waals (in the context of the person discovering the Equation of State) is referenced in the index on page vii of the Index of Names as van der Waals, J.C. This again appears to be a typo since the same van der Waals is listed on page 221 as having discovered the Equation of State for gases in 1873. However, there are two more van der Waals(!) mentioned in Theory of Intermolecular Forces by Margenau and Kestner (Second Edition, Copyright 1971). On page 8, they describe: "J.H. van der Waals (1908, Part I, pp. 207 et seq) returns to Laplace's problem of capillarity, but with special concern for the nature and mathematical form of the forces. Ignoring previous specific formulations he invokes what is now called the Yukawa potential, V = -A/r x exp(-r/a), A and a being empirical constants." And, on page 10, they write: "The idea of electronic dipoles was elaborated in Reinganum's second paper which appeared after van der Waals (J.D. van der Waals Jr. (1909)) had treated the interaction of rotating dipoles statistically, but in a manner not wholly convincing to Reinganum." Apparently, this latter van der Waals is the son of van der Waals Sr. The references for the latter two van der Waals' are given in the Bibiliography as: van der Waals, J. D. Jr. (1909) Amst.Acad.Proc., pp. 132, 315. van der Waals, J. H. (1908) Lehrbuch der Thermodynamik, Mass and Van Suchtelen, Leipzig, Part 1. Regards, Marvin Waldman, Ph.D. Manager, Rational Drug Design Biosym Technologies, Inc. e-mail: marvin@biosym.com