From CHEMA@vms.huji.ac.il Tue Jan 17 08:37:19 1995 Received: from VMS.HUJI.AC.IL for CHEMA@vms.huji.ac.il by www.ccl.net (8.6.9/930601.1506) id IAA19582; Tue, 17 Jan 1995 08:12:10 -0500 Date: Tue, 17 Jan 1995 08:12:10 -0500 Message-Id: <199501171312.IAA19582@www.ccl.net> Received: by HUJIVMS (HUyMail-V7a); Tue, 17 Jan 95 15:12:10 +0200 From: CHEMA@HUJIVMS To: CHEMISTRY@ccl.net Subject: Email file (LOOKING_.) Date: Tue, 17 Jan 95 14:48 +0200 Message-id: <17010095144806@HUJIVMS> From: To: ccl@ccl.net MIME-version: 1.0 Content-type: Text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: membranes data does anyone know where I can get crystalography data (coordinates) of membranes? thanks doron chema e mail:chema@vms.huji.ac.il From delaney@jh01sg.demon.co.uk Tue Jan 17 08:48:16 1995 Received: from gate.demon.co.uk for delaney@jh01sg.demon.co.uk by www.ccl.net (8.6.9/930601.1506) id IAA19575; Tue, 17 Jan 1995 08:08:48 -0500 Received: from post.demon.co.uk by gate.demon.co.uk id ab09688; 17 Jan 95 12:58 GMT Received: from jh01sg.demon.co.uk by post.demon.co.uk id ab01640; 17 Jan 95 12:57 GMT Received: by JH01SG (931110.SGI/zeneca.jf.gwm.3Nov94) for @gate.demon.co.uk:chemistry@ccl.net id AA10104; Tue, 17 Jan 95 12:03:29 GMT From: john delaney Message-Id: <9501171203.AA10104@JH01SG> Subject: re: chemical diversity To: chemistry@ccl.net Date: Tue, 17 Jan 1995 12:03:27 +0000 (GMT) X-Mailer: ELM [version 2.4 PL21] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 2937 Thanks to Minhhuy Ho for this reply to the query - Can anyone tell me what the Shannon-Weaver diversity is ? Are there any recognised methods for measuring chemical diversity ? I get the impression that diversity is relative rather than absolute. ------------------------------------------------------------------------------- From @qucdn.queensu.ca:homh@chem.queensu.ca Fri Jan 13 08:46:03 1995 Received: from punt.demon.co.uk by JH01SG via SMTP (931110.SGI/zeneca.jf.gwm.3Nov94) for delaney id AA26234; Fri, 13 Jan 95 08:46:03 GMT Received: from punt.demon.co.uk via puntmail for delaney@jh01sg.demon.co.uk; Thu, 12 Jan 95 18:25:26 GMT Received: from qucdn.queensu.ca by punt.demon.co.uk id aa07552; 12 Jan 95 18:23 GMT Received: from quchem.chem.QueensU.CA by QUCDN.QueensU.CA (IBM VM SMTP V2R2) with TCP; Thu, 12 Jan 95 13:21:31 EST Received: by quchem.chem.QueensU.CA (4.1/SMI-4.0) id AA17448; Thu, 12 Jan 95 13:30:50 EST Date: Thu, 12 Jan 95 13:30:50 EST From: Minhhuy Ho Message-Id: <9501121830.AA17448@quchem.chem.QueensU.CA> To: delaney Subject: Shannon-Weaver entropy Status: RO Dear Dr. Delaney, The Shannon-Weaver information entropy measures the uncertainty of 'information' of a system with continuous probability distribution rho(x) by the relationship / S = | rho(x) ln rho(x) d(x) / There have been several attempts to apply the Shannon entropy to elucidate chemical and physical properties of atomic and molecular systems by our group and others. The Kullback information entropy distance which is based on the Shannon-Weaver entropy is calculated as / / Id(AB) = | rho_A ln (rho_A/rho_B) d(x) + | rho_B ln (rho_B/rho_A) d(x) / / We have investigated the applicability of this distance as a measure of chemical 'diversity'. Note that rho_A and rho_B in the above equation indicates that the distance is a relative quantity, as you mentioned in your post. Following are some articles could be of interested to you: C. E. Shannon Bell Syst. Tech. J. v27, pp379 (1948) S. Kullback, Information Theory and Staticstics, Wiley, New York (1959) S. R. Gadre et al. Phys. Rev. vA 32, pp2602 (1985) V. H. Smith, Jr. et al. J. Phys. B, v27, pp5149 (1994) ibid Chem. Phys. Lett., v219, pp15 (1994) ibid Int. J. Quant. Chem., to be appeared in (1995) If we can be of any further help, please do not hestitate to contact us. Regards, Minhhuy Ho Dept. of Chemistry Queen's University Kingston, ON. Canada email: HOMH@QUCDN.QueensU.CA ------------------------------------------------------------------------------- A good source of information on diversity is any under-graduate book on ecology. Ecologists have a great deal of experience in studying species diversity and seem to have developed many methods for quantifying it. John Delaney Zeneca Agrochem delaney@jh01sg.demon.co.uk From usdccz73@ibmmail.com Tue Jan 17 10:38:45 1995 Received: from ibmmail.COM for usdccz73@ibmmail.com by www.ccl.net (8.6.9/930601.1506) id KAA21657; Tue, 17 Jan 1995 10:10:30 -0500 From: Message-Id: <199501171510.KAA21657@www.ccl.net> Received: from IBMMAIL.COM by ibmmail.COM (IBM VM SMTP V2R3) with BSMTP id 0348; Tue, 17 Jan 95 10:09:55 EST Date: Tue, 17 Jan 1995 10:09:42 EST To: chemistry@ccl.net, internet@ibmmail.com MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Subject: Platinum parameters NOTE FROM: C. Qian usdccz73@ibmmail.com NITC EXPR CTR CO41B1 Tel. (517)496-6938, Fax (517)496-5121 SUBJECT: Platinum parameters Dear all: Is anyone aware of a basis set for Platinum which might be used with Gaussian 90? We are interested to get some optimized structures of Pt - C=C complexes. Thank you in advance. C. Peter Qian NITC EXPR CTR, CO41B1, Dow Corning Corp. Midland, MI 48686-0994 From chpajt@bath.ac.uk Tue Jan 17 10:49:01 1995 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.6.9/930601.1506) id KAA21848; Tue, 17 Jan 1995 10:20:47 -0500 Received: from bath.ac.uk (actually mary.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Tue, 17 Jan 1995 14:49:29 +0100 Date: Tue, 17 Jan 1995 14:48:59 +0000 (GMT) From: A J Turner To: chpajt@bath.ac.uk cc: chemistry@ccl.net Subject: Charmm force field Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! I am just starting on some work involving the Charmm force field. Unfortunateley, none around hear had a copy of the mathematical description of the Charmm force field. Can anyone point me in the right direction. Best to you all Alex J Turner +--------------------------------------------------+ |Alternate E-mail A.J.Turner@Bath.ac.uk | |www home @ http://www.bath.ac.uk/~chpajt/home.html| +--------------------------------------------------+ From claudio@hal.unimo.it Tue Jan 17 12:37:32 1995 Received: from hal.unimo.it for claudio@hal.unimo.it by www.ccl.net (8.6.9/930601.1506) id MAA23832; Tue, 17 Jan 1995 12:09:44 -0500 From: Received: by hal.unimo.it (AIX 3.2/UCB 5.64/4.03) id AA16077; Tue, 17 Jan 1995 18:09:35 +0100 Date: Tue, 17 Jan 1995 18:09:35 +0100 Message-Id: <9501171709.AA16077@hal.unimo.it> To: chemistry@ccl.net Subject: Schools in Quantum Chemistry Dear netters I will be grateful to receive information about schools in Quantum Chemistry during 1995. Please mail direct to me and I'll summarize for the list. Thanks in advance Claudio Bertarini E-Mail: claudio@hal.unimo.it From heelisp@delta.newi.ac.uk Tue Jan 17 13:37:34 1995 Received: from delta for heelisp@delta.newi.ac.uk by www.ccl.net (8.6.9/930601.1506) id MAA24463; Tue, 17 Jan 1995 12:37:23 -0500 From: Date: Tue, 17 Jan 1995 17:36:14 +0100 Message-Id: <95011717361405@delta.newi.ac.uk> To: chemistry@ccl.net Subject: Spectroscopy software X-VMS-To: SMTP%"chemistry@ccl.net" Dear Netters, I would appreciate receiving advice on softare to calculate spectra of organic compounds in different simualated solvents, preferably PC or windows based. All help appreciated Paul Heelis Heelisp@newi.ac.uk From R29CLOSE@ETSU.EAST-TENN-ST.EDU Tue Jan 17 14:37:27 1995 Received: from phem3 for R29CLOSE@ETSU.EAST-TENN-ST.EDU by www.ccl.net (8.6.9/930601.1506) id OAA26904; Tue, 17 Jan 1995 14:30:03 -0500 Received: from ETSU.EAST-TENN-ST.EDU (MAILER@ETSU) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HLYFSCIU808Y5YZO@phem3.acs.ohio-state.edu>; Tue, 17 Jan 1995 14:29:48 EDT Received: from ETSU.EAST-TENN-ST.EDU (NJE origin R29CLOSE@ETSU) by ETSU.EAST-TENN-ST.EDU (LMail V1.2a/1.8a) with BSMTP id 4134; Tue, 17 Jan 1995 14:29:34 -0500 Date: Tue, 17 Jan 1995 14:17:04 -0500 (EST) From: David Close Subject: MOPAC7 Problems? To: chemistry@ccl.net Message-id: <01HLYFSCIU828Y5YZO@phem3.acs.ohio-state.edu> Organization: East Tennessee State University Content-transfer-encoding: 7BIT Dear Netters: In December I wrote this group about problems with MOPAC7 on a PC. Some of the discussion (Summarized on Dec. 6, 1994) involved DOS vs. LINUX etc. But the bottom line is that Rainer Koch convinced me that my errors were very small, and that for the test case I was considering, MOPAC7 appeared to be working. Further tests have indicated new problems. On Nov. 25, 1993 Mike Peterson submitted a test example "MOPAC6 under LINUX" involving a carboxyl radical with the correct answer 3.19 Kcal. I get 4.19 Kcal. On Oct. 2, 1993 Wojiech Galazka sent in an example of C.I. = 2 on water. The result was 58.99497 Kcal. I get 59.40290. I feel that these are significant differences, and that maybe I have some problems with my version of MOPAC7. Can anyone tell me if I should be concerned? It would be most helpful to have some more good test examples. I would like to run these tests, and perhaps request further output with DEBUG keywords inserted so that I can track down any errors that may be ocrurring. Regards, DAve Close. From itsigeln@chem.UCSD.EDU Tue Jan 17 15:37:32 1995 Received: from ucsd.edu for itsigeln@chem.UCSD.EDU by www.ccl.net (8.6.9/930601.1506) id PAA27965; Tue, 17 Jan 1995 15:10:34 -0500 Received: from chem.chem.ucsd.edu by ucsd.edu; id MAA11316 sendmail 8.6.9/UCSD-2.2-sun via SMTP Tue, 17 Jan 1995 12:10:33 -0800 for Received: by chem.chem.ucsd.edu (5.51) id AA20148; Tue, 17 Jan 95 12:09:10 PST Received: by chemod0.ucsd.edu (931110.SGI) id AA03316; Tue, 17 Jan 95 12:12:41 -0800 Date: Tue, 17 Jan 95 12:12:41 -0800 From: itsigeln@chem.UCSD.EDU (Igor Tsyguelnyi) Message-Id: <9501172012.AA03316@chemod0.ucsd.edu> To: CHEMISTRY@ccl.net Subject: Euler Gromos I try to find out where to get an academic license for parallel version of Euler Gromos. All answers are highly appreciated. ------------------------------------------------ IGOR TSIGELNY itsigeln@ucsd.edu From seniuk@muhammad.usask.ca Tue Jan 17 16:37:27 1995 Received: from ishmael.USask.ca for seniuk@muhammad.usask.ca by www.ccl.net (8.6.9/930601.1506) id QAA29926; Tue, 17 Jan 1995 16:11:56 -0500 Received: (from seniuk@localhost) by ishmael.USask.ca (8.6.9/8.6.9) id PAA11849 for chemistry@ccl.net; Tue, 17 Jan 1995 15:11:53 -0600 Date: Tue, 17 Jan 1995 15:11:53 -0600 From: Andrew Seniuk Message-Id: <199501172111.PAA11849@ishmael.USask.ca> To: chemistry@ccl.net Subject: RE: funny question Dear Dr. Agrafiotis, I am a Master's student in Theoretical Chemistry. These are my suggestions, which may be more-or-less fragmentary (I haven't formed them just yet). - if there is a 1-1 correspondence between valence electron pairs and edges, with a loop for a lone-pair, and multiple edges for general bonding, and if only a single "resonance structure" (hereafter unquoted) is considered to represent a molecule, then my hypotheses are established. - the total number of arcs in this graph is then easily established by the stoichiometry (and the molecular charge). Unpaired electrons are not being treated here now, so no free radicals or odd-electron systems. - if the vertex set (distinguished by nuclear charge, lets suppose) is given (I mean we choose some fixed stoichiometry), then not only the number of edges, but moreover the DEGREE of each vertex is established simply - it should be the "valence" of the atom, eg) deg(H) = 1, deg(O) = deg(N) = deg(C) = 4, etc.. - Note that the above includes lone pairs. It is convenient that a loop (lone pair) contributes +2 to the degree of the vertex on which it resides, since then formal charge calculations, which offer other useful restrictions to guide us in the solution of this problem, are trivial. (Nuclear charge minus the vertice's degree.) - in fact, you are interested in the total number of connected graphs over some fixed stoichiometry, subject the the above constraints. - since different resonance structures of the same molecule will be ennumerated this way, and I see this as occurring in a subtle way, this approach may be frustrated. I hope you will let me know if this is of some use for you. Andy seniuk@ishmael.usask.ca From y_zheng@ccmail.pnl.gov Tue Jan 17 17:37:25 1995 Received: from pnl.gov for y_zheng@ccmail.pnl.gov by www.ccl.net (8.6.9/930601.1506) id QAA00633; Tue, 17 Jan 1995 16:49:15 -0500 From: Received: from ccmail.pnl.gov by pnl.gov (PMDF V4.3-13 #6012) id <01HLYEDY69SG00004U@pnl.gov>; Tue, 17 Jan 1995 13:49:10 -0800 (PST) Date: Tue, 17 Jan 1995 13:44 -0800 (PST) Subject: Summary of G-matrix To: chemistry@ccl.net Message-id: <01HLYEDY8HUA00004U@pnl.gov> MIME-version: 1.0 Content-transfer-encoding: 7BIT Hi, all, First, I would like to thank all of you who responded to my original posting about G-matrix programs. Many of you wanted a summary, so here is a brief summary. Prof. Diem at CUNY, Hunter College has a program. The reference is J. Chem. Educ. 1991, vol. 68, p.35-39. Hedberg and Mills have a program called ASYM20, which is available from QCPE. The most recent version is ASYM40. The reference is J. Mol. Spectroscopy, 1993, vol. 160, p.117-142. Prof. Thomas Bally of the University of Fribourg, Switzerland, has a very nice program which is able to extract force constants from ab initio calculations. The program is going to be distributed by Gaussian. I do not know the date. I also find two recent papers related to G-matrix programs. Vijay, A. and Sathyanarayana, D. N. J. Mol. Struct. 1994, 328, 269-276. Durig et al. J. Mol. Struct. 1994, 327, 55-69. Thanks. Yajun From jmbriggs@chemcca10.ucsd.edu Tue Jan 17 18:37:25 1995 Received: from chemcca10.ucsd.edu for jmbriggs@chemcca10.ucsd.edu by www.ccl.net (8.6.9/930601.1506) id SAA01667; Tue, 17 Jan 1995 18:08:00 -0500 Received: by chemcca10.ucsd.edu (931110.SGI/931108.SGI.ANONFTP) for CHEMISTRY@ccl.net id AA04593; Tue, 17 Jan 95 15:08:01 -0800 From: jmbriggs@chemcca10.ucsd.edu (Jim Briggs) Message-Id: <9501172308.AA04593@chemcca10.ucsd.edu> Subject: Re: CCL:Euler Gromos To: itsigeln@chem.ucsd.edu (Igor Tsyguelnyi) Date: Tue, 17 Jan 1995 15:08:01 -0800 (PST) Cc: CHEMISTRY@ccl.net, tclark@Kacha.chem.uh.edu In-Reply-To: <9501172012.AA03316@chemod0.ucsd.edu> from "Igor Tsyguelnyi" at Jan 17, 95 12:12:41 pm X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 856 Igor, Contact Terry Clark at the University of Houston. His e-mail address is: tclark@kacha.chem.uh.edu Jim Briggs UCSD - Chem > > > I try to find out where to get an academic license for parallel > version of Euler Gromos. All answers are highly appreciated. > ------------------------------------------------ > IGOR TSIGELNY > itsigeln@ucsd.edu > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: itsigeln@chem.UCSD.EDU > -- Original Sender From: Address: itsigeln@chem.UCSD.EDU > CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator > MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 > Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search > http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV >